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Zungsontiporn N, Ouwongprayoon P, Boonsirikamchai P, Leelayuwatanakul N, Vinayanuwattikun C, Moonai K, Khongkhaduead E, Thorner PS, Shuangshoti S, Teerapakpinyo C. Detection of EGFR T790M mutation using liquid biopsy for non-small cell lung cancer: Utility of droplet digital polymerase chain reaction vs. cobas real-time polymerase chain reaction. Pathol Res Pract 2024; 255:155213. [PMID: 38394807 DOI: 10.1016/j.prp.2024.155213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/03/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Digital platforms for mutation detection yield higher sensitivity than non-digital platforms but lack universal positive cut-off values that correlate with the outcome of osimertinib treatment. This study determined compared droplet digital polymerase chain reaction (ddPCR) to the standard cobas assay for epithelial growth factor receptor (EGFR) T790M mutation detection in patients with non-small cell lung cancer. METHODS Study patients had EGFR-mutant tumours with disease progression on first/second generation EGFR tyrosine kinase inhibitors, and osimertinib treatment after T790M mutation detection. T790M status was tested by cobas assay using liquid biopsy, and only by ddPCR if an EGFR mutation was identified but T790M was negative. Clinical efficacy of osimertinib was compared between patients with T790M detected by cobas vs. only by ddPCR. A positive cut-off value for ddPCR was determined by assessing efficacy with osimertinib. RESULTS 61 patients had tumors with an acquired T790M mutation, 38 detected by cobas and an additional 23 only by ddPCR. The median progression-free survival (PFS) for the cobas- and ddPCR-positive groups was 9.5 and 7.8 months, respectively (p=0.43). For ddPCR, a fractional abundance (FA) of 0.1% was used as a cut-off value. The median PFS of patients with FA ≥0.1% and <0.1% was 8.3 and 4.6 months, respectively (p=0.08). FA ≥0.1% was independently associated with a longer PFS. CONCLUSION Using ddPCR to follow up the cobas assay yielded more cases (38% of total) with a T790M mutation. A cut-off value of FA ≥0.1% identified patients who responded as well to osimertinib as those identified by cobas assay. This sequential approach should detect additional patients who might benefit from osimertinib treatment.
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Affiliation(s)
- Nicha Zungsontiporn
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Pongsakorn Ouwongprayoon
- Department of Radiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Piyaporn Boonsirikamchai
- Department of Radiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nophol Leelayuwatanakul
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Chanida Vinayanuwattikun
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Kantika Moonai
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Ekkachai Khongkhaduead
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Paul Scott Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Shanop Shuangshoti
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand; Department of Pathology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Chinachote Teerapakpinyo
- Chula GenePRO Center, Research Affairs, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand.
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Nel I, Münch C, Shamkeeva S, Heinemann ML, Isermann B, Aktas B. The Challenge to Stabilize, Extract and Analyze Urinary Cell-Free DNA (ucfDNA) during Clinical Routine. Diagnostics (Basel) 2023; 13:3670. [PMID: 38132253 PMCID: PMC10743081 DOI: 10.3390/diagnostics13243670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The "Liquid Biopsy" has become a powerful tool for cancer research during the last decade. Circulating cell-free DNA (cfDNA) that originates from tumors has emerged as one of the most promising analytes. In contrast to plasma-derived cfDNA, only a few studies have investigated urinary cfDNA. One reason might be rapid degradation and hence inadequate concentrations for downstream analysis. In this study, we examined the stability of cfDNA in urine using different methods of preservation under various storage conditions. METHODOLOGY To mimic patient samples, a pool of healthy male and female urine donors was spiked with a synthetic cfDNA reference standard (fragment size 170 bp) containing the T790M mutation in the EGFR gene. Spiked samples were preserved with three different buffers and with no buffer over four different storage periods (0 h; 4 h; 12 h; 24 h) at room temperature vs. 4 °C. The preservatives used were Urinary Analyte Stabilizer (UAS, Novosanis, Wijnegem, Belgium), Urine Conditioning Buffer (UCB, Zymo, Freiburg, Germany) and a self-prepared buffer called "AlloU". CfDNA was extracted using the QIAamp MinElute ccfDNA Mini Kit (Qiagen, Hilden, Germany). CfDNA concentration was measured using the Qubit™ 4 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Droplet digital PCR (ddPCR) was used for detection and quantification of the T790M mutation. RESULTS Almost no spiked cfDNA was recoverable from samples with no preservation buffer and the T790M variant was not detectable in these samples. These findings indicate that cfDNA was degraded below the detection limit by urinary nucleases. Stabilizing buffers showed varying efficiency in preventing this degradation. The most effective stabilizing buffer under all storage conditions was the UAS, enabling adequate recovery of the T790M variant using ddPCR. CONCLUSION From a technical point of view, stabilizing buffers and adequate storage conditions are a prerequisite for translation of urinary cfDNA diagnostics into clinical routine.
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Affiliation(s)
- Ivonne Nel
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Carolin Münch
- Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Saikal Shamkeeva
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Mitja L. Heinemann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University Hospital, 04103 Leipzig, Germany
| | - Bahriye Aktas
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
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Jafri HSMO, Mushtaq S, Baig S, Bhatty A, Siraj S. Comparison of KRAS gene in circulating tumor DNA levels vs histological grading of colorectal cancer patients through liquid biopsy. Saudi J Gastroenterol 2023; 29:371-375. [PMID: 37602638 PMCID: PMC10754382 DOI: 10.4103/sjg.sjg_85_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Background To determine KRAS gene in circulating tumor DNA in comparison with histological grading through liquid biopsy in colorectal cancer patients. Methods This dual-centered cross-sectional study included 73 diagnosed patients of colorectal cancer at different grading levels [Grade I, well differentiated (n = 7, 9.5%); Grade II, moderately differentiated (n = 14,18.9%); and Grade III, poorly differentiated (n = 52, 70%)]. Blood was collected, and plasma was separated. ctDNA was extracted, using magnetic bead-based technique (MagMAX Cell-Free DNA kit). KRAS gene was quantified through qPCR. STRING database was used to find KRAS interactomes. Results Mean threshold cycle (CT value) of KRAS gene in Grade III samples showed significantly higher (P = 0.001) levels of ctDNA (2.7 ± 1.14) compared with Grade II and Grade I (3.1 ± 0.68, 2.3 ± 0.60), respectively. Grading characterization showed that rectal cancer (n = 22, 42.3%) with Grade III (68.8%) was more prevalent than colon and sigmoid cancer (n = 19, 36.5%, n = 11, 21%, respectively). STRING database showed 10 functional genes interacting with KRAS expressed as gene/proteins. Conclusion Liquid biopsy can be used to detect ctDNA in plasma of CRC patients and enabled to detect the KRAS gene by qPCR. The technique being less invasive and cost-effective is convenient for multiple biopsies in different cancers.
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Affiliation(s)
| | - Shamim Mushtaq
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Saeeda Baig
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Afreen Bhatty
- Department of Biochemistry, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
| | - Sabra Siraj
- Department of Pharmacology, Basic Health Sciences, Ziauddin University, Karachi, Pakistan
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Mugoni V, Ciani Y, Quaini O, Tomasini S, Notarangelo M, Vannuccini F, Marinelli A, Leonardi E, Pontalti S, Martinelli A, Rossetto D, Pesce I, Mansy SS, Barbareschi M, Ferro A, Caffo O, Attard G, Di Vizio D, D'Agostino VG, Nardella C, Demichelis F. Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients. J Extracell Biol 2023; 2:e108. [PMID: 38046436 PMCID: PMC10688391 DOI: 10.1002/jex2.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on n = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Yari Ciani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Simone Tomasini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Federico Vannuccini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Alessia Marinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Elena Leonardi
- Unit of Surgical Pathology, Santa Chiara Hospital, APSSTrentoItaly
| | - Stefano Pontalti
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Angela Martinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Isabella Pesce
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Sheref S. Mansy
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | | | - Antonella Ferro
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Orazio Caffo
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
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Huang CT, Lin CA, Su TJ, Yang CY, Tsai TH, Hsu CL, Liao WY, Chen KY, Ho CC, Yu CJ. Monitoring of T790M in plasma ctDNA of advanced EGFR-mutant NSCLC patients on first- or second-generation tyrosine kinase inhibitors. BMC Cancer 2023; 23:234. [PMID: 36915101 PMCID: PMC10010021 DOI: 10.1186/s12885-023-10698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The T790M mutation is the major resistance mechanism to first- and second-generation TKIs in EGFR-mutant NSCLC. This study aimed to investigate the utility of droplet digital PCR (ddPCR) for detection of T790M in plasma circulating tumor DNA (ctDNA), and explore its impact on prognosis. METHODS This prospective study enrolled 80 advanced lung adenocarcinoma patients treated with gefitinib, erlotinib, or afatinib for TKI-sensitizing mutations between 2015 and 2019. Plasma samples were collected before TKI therapy and at tri-monthly intervals thereafter. Genotyping of ctDNA for T790M was performed using a ddPCR EGFR Mutation Assay. Patients were followed up until the date of death or to the end of 2021. RESULTS Seventy-five of 80 patients experienced progressive disease. Fifty-three (71%) of 75 patients underwent rebiopsy, and T790M mutation was identified in 53% (28/53) of samples. Meanwhile, plasma ddPCR detected T790M mutation in 23 (43%) of 53 patients. The concordance rate of T790M between ddPCR and rebiopsy was 76%, and ddPCR identified 4 additional T790M-positive patients. Ten (45%) of 22 patients who did not receive rebiopsy tested positive for T790M by ddPCR. Serial ddPCR analysis showed the time interval from detection of plasma T790M to objective progression was 1.1 (0-4.1) months. Compared to 28 patients with rebiopsy showing T790M, the overall survival of 14 patients with T790M detected solely by ddPCR was shorter(41.3 [95% CI, 36.6-46.0] vs. 26.6 months [95% CI, 9.9-43.3], respectively). CONCLUSION Plasma ddPCR-based genotyping is a useful technology for detection and monitoring of the key actionable genomic alteration, namely, T790M, in patients treated with gefitinib, erlotinib, or afatinib for activating mutations, to achieve better patient care and outcome.
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Affiliation(s)
- Chun-Ta Huang
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-An Lin
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Te-Jen Su
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Yao Yang
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Tzu-Hsiu Tsai
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Chia-Lin Hsu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Wei-Yu Liao
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan.
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
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Wang W, Han Q, Xu X, Wen C. miR-146 Relieves Acute Asthma via Decreasing Epidermal Growth Factor Receptor/Toll-Like Receptor 4 (EGFR/TLR4) and Enhancing Autophagy. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
There is a close relationship between acute asthma and autophagy. In addition, some studies claim that miR-146 can regulate autophagy and participate in acute asthma. This study further explores the role of miR-146 in acute asthma and underlying mechanism. Twenty BALB/c mice were selected
and randomly divided into two groups, the model group and the control group, each with 10 mice. Lung tissues, peripheral blood, alveolar lavage fluid, and primary lymphocytes were separated into miR-146 over expression group (miR-146 mimic), miR-146 low expression group (miR-146 inhibitor),
negative control group (NC), blank group, or SBI-0206965 group. Acute asthma was established and the expression levels of miR-146, EGFR, TLR4, LC3, beclin1, and ATG5 in each group was measured. The targeting relationship and correlation between miR-146 and EGFR were also investigated. The
expression of IL-4 in model group was increased compared to control arm while the expression of IFN-γ was opposite (P < 0.05). The expressions of miR-146, LC3, beclin1, and the expression of ATG5 were decreased (P < 0.05). The expressions of miR-146 gene and
LC3, beclin1, ATG5 mRNA and protein in the miR-146 mimic group were the highest, while the expressions of EGFR and TLR4 were the lowest. The SBI-0206965 group and the miR-146 inhibitor group are opposite to the miR-146 mimic group, the SBI-0206965 group and the miR-146 inhibitor group have
significant differences (P < 0.05). miR-146 has a directly targeted EGFR and TLR4, and both showed a negative correlation (rEGFR=−0.397, P = 0.013; rTLR4=−0.402, P = 0.021). During the onset of asthma, miR-146 was abnormally decreased. miR-146 directly targets
and negatively regulates EGFR. In addition, miR-146 down-regulates TLR4 gene to increase CD4+ lymphocytes’ aphagocytosis-related markers (LC3, beclin1, ATG5) which further promotes the autophagy process and ultimately alleviates the degree of acute asthma. Its main mechanism is related
to the down-regulation of the EGFR/TLR4 through regulated the expression of autophagy. Our study provided a scientific reference for further understanding of acute pathogenesis of asthma.
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Affiliation(s)
- Wei Wang
- Department of Pediatrics, Daqing Oilfield General Hospital, Daqing, Heilongjiang, 163000, China
| | - Qiuguo Han
- Department of Pediatrics, Daqing Oilfield General Hospital, Daqing, Heilongjiang, 163000, China
| | - Xin Xu
- Department of Vascular Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang, 163000, China
| | - Chen Wen
- Department of Pharmaceutical Laboratory Science, Daqing Medical College, Daqing, Heilongjiang, 163000, China
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Dal Maso A, Del Bianco P, Cortiula F, Nardo G, Zulato E, Bonanno L, Follador A, De Maglio G, Pasello G, Indraccolo S. EGFR T790M testing through repeated liquid biopsy over time: a real-world multicentric retrospective experience. J Thorac Dis 2022; 14:3364-3375. [PMID: 36245580 PMCID: PMC9562526 DOI: 10.21037/jtd-22-745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023]
Abstract
Background About 15% of non-small cell lung cancers (NSCLCs) harbor epidermal growth factor receptor (EGFR) mutations. Upfront treatment with first and second generation EGFR tyrosine kinase inhibitors (1-2gen TKIs) is superior to chemotherapy. The most frequent resistance mechanism to 1-2gen TKIs is EGFR T790M mutation, which is targeted by osimertinib. T790M mutation can be revealed by liquid biopsy (LB) or by tissue rebiopsy (TB). LB is easily feasible but less sensitive than TB. We focused on repeated LBs and analyzed clinical features associated with EGFR T790M detection. Methods This is a retrospective multicenter observational study including EGFR-mutant NSCLC consecutive patients with disease progression (PD) after 1-2gen TKIs and with a first EGFR LB negative for T790M mutation, referred between 2016 and 2019. Aims of the study were to determine the prevalence of T790M mutation using LB in a real-life setting and the prevalence of T790M mutation by repeated LBs. We explored the association of T790M with clinical-pathological features and, through a survey, we evaluated the decision-making process behind LB request. Data on TBs were also collected. Results One hundred and ten patients were included in the study, for a total of 326 LBs. Median number of LB per patient was 3.0. The T790M prevalence through LB was 34.5%. Over time, significantly more LBs were requested "at clinical and radiological PD" and "at radiological PD" compared to "arbitrarily". The probability of finding the T790M mutation for a patient across each subsequent LB did not significantly change. Liver and lymph node PD were significantly correlated to T790M positivity. Notably, "at PD" compared to "arbitrarily" LB request and liver, bone or lymph node PD were correlated to the detection of any EGFR mutation in cfDNA. TB was performed in 59.7% of patients with a T790M negative LB and 18.8% of them were T790M positive. In most cases, TB was not feasible due to anatomical reasons. In our study population, the overall T790M prevalence-detected with both LB and TB-was 42.7%. Conclusions Repeated LB testing can be useful in a real-life scenario to detect EGFR T790M mutation.
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Affiliation(s)
- Alessandro Dal Maso
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy;,Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Paola Del Bianco
- Clinical Research Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Francesco Cortiula
- Department of Oncology, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giorgia Nardo
- Basic Experimental and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Elisabetta Zulato
- Basic Experimental and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Laura Bonanno
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Alessandro Follador
- Department of Oncology, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giovanna De Maglio
- Department of Pathology, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giulia Pasello
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy;,Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Stefano Indraccolo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy;,Basic Experimental and Translational Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
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Li YQ, Tan GJ, Zhou YQ. Digital PCR and its applications in noninvasive prenatal testing. Brief Funct Genomics 2022; 21:376-386. [PMID: 35923115 DOI: 10.1093/bfgp/elac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
In the past decade, digital PCR (dPCR), as a new nucleic acid absolute quantification technology, has been widely used in clinical research. dPCR does not rely on the standard curve and has a higher tolerance to inhibitors. Therefore, it is more accurate than quantitative real-time PCR (qPCR) for the absolute quantification of target sequences. In this article, we aim to review the application of dPCR in noninvasive prenatal testing (NIPT). We focused on the progress of dPCR in screening and identifying fetal chromosome aneuploidies and monogenic mutations. We introduced some common strategies for dPCR in NIPT and analyzed the advantages and disadvantages of different methods. In addition, we compared dPCR with qPCR and next-generation sequencing, respectively, and described their superiority and shortcomings in clinical applications. Finally, we envisaged what the future of dPCR might be in NIPT. Although dPCR can provide reproducible results with improved accuracy due to the digital detection system, it is essential to combine the merits of dPCR and other molecular techniques to achieve more effective and accurate prenatal diagnostic strategies.
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Affiliation(s)
- Yue-Qi Li
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Gong-Jun Tan
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Yu-Qiu Zhou
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
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Zhao Z, Wu T, Wang M, Chen X, Liu T, Si Y, Zhou Y, Ying B. A new droplet digital PCR assay: improving detection of paucibacillary smear-negative pulmonary tuberculosis. Int J Infect Dis 2022; 122:820-828. [PMID: 35870796 DOI: 10.1016/j.ijid.2022.07.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Smear-negative pulmonary tuberculosis (PTB) is difficult to diagnose. Current diagnosis and treatment monitoring methods have inherent limitations. Droplet digital PCR (ddPCR) is a new technique with high sensitivity. This study presents a novel ddPCR for rapid and sensitive identification of Mycobacterium tuberculosis (MTB). METHODS MTB DNA was detected in respiratory specimens from suspected PTB cases using ddPCR assay, which was directed at two different locations within IS6110. We, for the first time, evaluated the clinical diagnostic ability of this ddPCR for paucibacillary smear-negative PTB. RESULTS A total of 605 PTB suspects were recruited, including 263 confirmed PTB patients (84.03% from smear-negative PTB) and 342 non-PTB. The sensitivity and specificity of IS6110 ddPCR were 61.22% (95% confidence interval (CI), 55.00%-67.10%) and 95.03% (95% CI, 92.20%-97.10%) for total PTB, and 57.92% (95% CI, 51.10%-64.50%) and 94.57% (95% CI, 91.20%-96.90%) for smear-negative PTB. ddPCR assay outperformed Xpert MTB/RIF (53.08% vs. 28.46%, p = 0.020) in smear-negative PTB detection. Furthermore, effective anti-tuberculosis treatment was linked to significantly lower IS6110 copies detected by ddPCR. CONCLUSIONS Herein, we developed and validated a highly sensitive and robust ddPCR assay for MTB quantification in respiratory specimens, which improve diagnosis and therapeutic effect evaluation of smear-negative PTB.
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Affiliation(s)
- Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Tao Wu
- Department of Clinical Laboratory Medicine, People's Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest Minzu University), Yinchuan, Ningxia Hui Autonomous Region, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaojuan Chen
- Department of Laboratory Medicine, The People's Hospital of Leshan, Leshan, Sichuan, China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanjun Si
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Xia L, Zhuang J, Zou Z, Yin J, Mu Y. Direct digital polymerase chain reaction chip for the detection of EGFR T790M mutation in plasma. Talanta 2022; 237:122977. [PMID: 34736699 DOI: 10.1016/j.talanta.2021.122977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/02/2023]
Abstract
Nucleic acid extraction and purification before amplification is considered an essential step for nucleic acid amplification testing. However, this may cause losses or introduce errors that can lead to inaccurate results, especially when using samples with a small nucleic acid concentration. Here, we developed a direct digital chip that enabled us to detect nucleic acid without DNA extraction and purification. We have developed a self-priming liquid-dispensing digital PCR chip that does not require any external power. This is a robust anti-evaporation digital PCR chip with fast sampling and accurate quantification performance. Using this chip, we have established an on-chip direct nucleic acid amplification method that does not require nucleic acid extraction and purification for liquid biopsy samples. In order to verify the feasibility of this chip for clinical samples, we detected the EGFR T790M mutation from plasma. Results showed that EGFR T790M mutation could be detected with an accuracy of 100% and a sensitivity of 0.01%. Without nucleic acid extraction and purification, the assay avoids complex pre-processing, thus saving time and achieving precise quantification. We expect our direct digital PCR chip to have practical applications in diagnosis, screening, and research, especially in resource-deprived regions.
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Palacín-Aliana I, García-Romero N, Asensi-Puig A, Carrión-Navarro J, González-Rumayor V, Ayuso-Sacido Á. Clinical Utility of Liquid Biopsy-Based Actionable Mutations Detected via ddPCR. Biomedicines 2021; 9:906. [PMID: 34440110 PMCID: PMC8389639 DOI: 10.3390/biomedicines9080906] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and remains a major public health challenge. The introduction of more sensitive and powerful technologies has permitted the appearance of new tumor-specific molecular aberrations with a significant cancer management improvement. Therefore, molecular pathology profiling has become fundamental not only to guide tumor diagnosis and prognosis but also to assist with therapeutic decisions in daily practice. Although tumor biopsies continue to be mandatory in cancer diagnosis and classification, several studies have demonstrated that liquid biopsies could be used as a potential tool for the detection of cancer-specific biomarkers. One of the main advantages is that circulating free DNA (cfDNA) provides information about intra-tumoral heterogeneity, reflecting dynamic changes in tumor burden. This minimally invasive tool has become an accurate and reliable instrument for monitoring cancer genetics. However, implementing liquid biopsies across the clinical practice is still ongoing. The main challenge is to detect genomic alterations at low allele fractions. Droplet digital PCR (ddPCR) is a powerful approach that can overcome this issue due to its high sensitivity and specificity. Here we explore the real-world clinical utility of the liquid biopsy ddPCR assays in the most diagnosed cancer subtypes.
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Affiliation(s)
- Irina Palacín-Aliana
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain
- Faculty of Science, Universidad de Alcalá, 28801 Madrid, Spain
| | - Noemí García-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | - Adrià Asensi-Puig
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
| | - Josefa Carrión-Navarro
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | | | - Ángel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
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