1
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Niu C, Zhang J, Fang Y, Wang X, Tang Y, Dong L. Development of a nine-variant reference material panel to standardize cell-free DNA detection. Anal Bioanal Chem 2024:10.1007/s00216-024-05336-3. [PMID: 38782781 DOI: 10.1007/s00216-024-05336-3] [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: 03/26/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Detection of specific gene mutations in cell-free DNA (cfDNA) serves as a valuable cancer biomarker and is increasingly being explored as an appealing alternative to tissue-based methods. However, the lack of available reference materials poses challenges in accurately evaluating the performance of different assays. In this study, we present the development of a comprehensive reference material panel for cfDNA detection, encompassing nine hotspot mutations in KRAS/BRAF/EGFR/PIK3CA at three variant allele frequencies (VAFs), ranging from 0.33 to 23.9%. To mimic cfDNA, these reference materials were generated by enzymatically digesting cell-line DNA into approximately 154-bp to 173-bp fragments using a laboratory-developed reaction system. The VAFs for each variation were precisely determined through validated digital PCR assays with high accuracy. Furthermore, the reliability and applicability of this panel were confirmed through two independent NGS assays, yielding concordant results. Collectively, our findings suggest that this novel reference material panel holds great potential for validation, evaluation, and quality control processes associated with liquid biopsy assays.
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Affiliation(s)
- Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Jiejie Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yan Fang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yanru Tang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China.
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2
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Sorbini M, Carradori T, Togliatto GM, Vaisitti T, Deaglio S. Technical Advances in Circulating Cell-Free DNA Detection and Analysis for Personalized Medicine in Patients' Care. Biomolecules 2024; 14:498. [PMID: 38672514 PMCID: PMC11048502 DOI: 10.3390/biom14040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) refers to small fragments of DNA molecules released after programmed cell death and necrosis in several body fluids such as blood, saliva, urine, and cerebrospinal fluid. The discovery of cfDNA has revolutionized the field of non-invasive diagnostics in the oncologic field, in prenatal testing, and in organ transplantation. Despite the potential of cfDNA and the solid results published in the recent literature, several challenges remain, represented by a low abundance, a need for highly sensitive assays, and analytical issues. In this review, the main technical advances in cfDNA analysis are presented and discussed, with a comprehensive examination of the current available methodologies applied in each field. Considering the potential advantages of cfDNA, this biomarker is increasing its consensus among clinicians, as it allows us to monitor patients' conditions in an easy and non-invasive way, offering a more personalized care. Nevertheless, cfDNA analysis is still considered a diagnostic marker to be further validated, and very few centers are implementing its analysis in routine diagnostics. As technical improvements are enhancing the performances of cfDNA analysis, its application will transversally improve patients' quality of life.
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Affiliation(s)
- Monica Sorbini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
| | - Tullia Carradori
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
| | - Gabriele Maria Togliatto
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
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3
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Jain M, Atayan D, Rakhmatullin T, Dakhtler T, Popov P, Kim P, Viborniy M, Gontareva I, Samokhodskaya L, Egorov V. Cell-Free Tumor DNA Detection-Based Liquid Biopsy of Plasma and Bile in Patients with Various Pancreatic Neoplasms. Biomedicines 2024; 12:220. [PMID: 38255325 PMCID: PMC10813046 DOI: 10.3390/biomedicines12010220] [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: 12/25/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The key challenge of cell-free tumor DNA (cftDNA) analysis in pancreatic ductal adenocarcinoma (PDAC) is overcoming its low detection rate, which is mainly explained by the overall scarcity of this biomarker in plasma. Obstructive jaundice is a frequent event in PDAC, which enables bile collection as a part of routine treatment. The aim of this study was to evaluate the performance of KRAS-mutated cftDNA detection-based liquid biopsy of plasma and bile in patients with pancreatic neoplasms using digital droplet PCR. The study included healthy volunteers (n = 38), patients with PDAC (n = 95, of which 20 had obstructive jaundice) and other pancreatic neoplasms (OPN) (n = 18). The sensitivity and specificity compared to the control group were 61% and 100% (AUC-ROC-0.805), and compared to the OPN group, they were 61% and 94% (AUC-ROC-0.794), respectively. Bile exhibited higher cftDNA levels than plasma (248.6 [6.743; 1068] vs. 3.26 [0; 19.225] copies/mL) and a two-fold higher detection rate (p < 0.01). Plasma cftDNA levels were associated with distant metastases, tumor size, and CA 19-9 (p < 0.05). The probability of survival was worse in patients with higher levels of cftDNA in plasma (hazard ratio-2.4; 95% CI: 1.3-4.6; p = 0.005) but not in bile (p > 0.05). Bile is a promising alternative to plasma in patients with obstructive jaundice, at least for the diagnostic purposes of liquid biopsy.
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Affiliation(s)
- Mark Jain
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - David Atayan
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Tagir Rakhmatullin
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Tatyana Dakhtler
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Popov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Kim
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Mikhail Viborniy
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Iuliia Gontareva
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Larisa Samokhodskaya
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Vyacheslav Egorov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
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4
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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5
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Burr R, Leshchiner I, Costantino CL, Blohmer M, Sundaresan T, Cha J, Seeger K, Guay S, Danysh BP, Gore I, Jacobs RA, Slowik K, Utro F, Rhrissorrakrai K, Levovitz C, Barth JL, Dubash T, Chirn B, Parida L, Sequist LV, Lennerz JK, Mino-Kenudson M, Maheswaran S, Naxerova K, Getz G, Haber DA. Germline mutations and developmental mosaicism underlying EGFR-mutant lung cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296274. [PMID: 37808694 PMCID: PMC10557804 DOI: 10.1101/2023.09.28.23296274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
While the development of multiple primary tumors in smokers with lung cancer can be attributed to carcinogen-induced field cancerization, the occurrence of multiple primary tumors in individuals with EGFR-mutant lung cancer who lack known environmental exposures remains unexplained. We identified ten patients with early-stage, resectable non-small cell lung cancer who presented with multiple anatomically distinct EGFR-mutant tumors. We analyzed the phylogenetic relationships among multiple tumors from each patient using whole exome sequencing (WES) and hypermutable poly-guanine (poly-G) repeat genotyping, as orthogonal methods for lineage tracing. In two patients, we identified germline EGFR variants, which confer moderately enhanced signaling when modeled in vitro. In four other patients, developmental mosaicism is supported by the poly-G lineage tracing and WES, indicating a common non-germline cell-of-origin. Thus, developmental mosaicism and germline variants define two distinct mechanisms of genetic predisposition to multiple EGFR-mutant primary tumors, with implications for understanding their etiology and clinical management.
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Affiliation(s)
- Risa Burr
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ignaty Leshchiner
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Blohmer
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karsen Seeger
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sara Guay
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian P Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ira Gore
- St Vincent’s Hospital, Birmingham, AL, USA
| | - Raquel A Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Taronish Dubash
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Brian Chirn
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | | | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamila Naxerova
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
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6
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Verlicchi A, Canale M, Chiadini E, Cravero P, Urbini M, Andrikou K, Pasini L, Flospergher M, Burgio MA, Crinò L, Ulivi P, Delmonte A. The Clinical Significance of Circulating Tumor DNA for Minimal Residual Disease Identification in Early-Stage Non-Small Cell Lung Cancer. Life (Basel) 2023; 13:1915. [PMID: 37763318 PMCID: PMC10532754 DOI: 10.3390/life13091915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/18/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Lung cancer (LC) is the deadliest malignancy worldwide. In an operable stage I-III patient setting, the detection of minimal residual disease (MRD) after curative treatment could identify patients at higher risk of relapse. In this context, the study of circulating tumor DNA (ctDNA) is emerging as a useful tool to identify patients who could benefit from an adjuvant treatment, and patients who could avoid adverse events related to a more aggressive clinical management. On the other hand, ctDNA profiling presents technical, biological and standardization challenges before entering clinical practice as a decisional tool. In this paper, we review the latest advances regarding the role of ctDNA in identifying MRD and in predicting patients' prognosis, with a particular focus on clinical trials investigating the potential of ctDNA, the technical challenges to address and the biological parameters that influence the MRD detection.
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Affiliation(s)
- Alberto Verlicchi
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Paola Cravero
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Kalliopi Andrikou
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Luigi Pasini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Michele Flospergher
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Marco Angelo Burgio
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Angelo Delmonte
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
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7
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Zhu L, Xu R, Yang L, Shi W, Zhang Y, Liu J, Li X, Zhou J, Bing P. Minimal residual disease (MRD) detection in solid tumors using circulating tumor DNA: a systematic review. Front Genet 2023; 14:1172108. [PMID: 37636270 PMCID: PMC10448395 DOI: 10.3389/fgene.2023.1172108] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 08/29/2023] Open
Abstract
Minimal residual disease (MRD) refers to a very small number of residual tumor cells in the body during or after treatment, representing the persistence of the tumor and the possibility of clinical progress. Circulating tumor DNA (ctDNA) is a DNA fragment actively secreted by tumor cells or released into the circulatory system during the process of apoptosis or necrosis of tumor cells, which emerging as a non-invasive biomarker to dynamically monitor the therapeutic effect and prediction of recurrence. The feasibility of ctDNA as MRD detection and the revolution in ctDNA-based liquid biopsies provides a potential method for cancer monitoring. In this review, we summarized the main methods of ctDNA detection (PCR-based Sequencing and Next-Generation Sequencing) and their advantages and disadvantages. Additionally, we reviewed the significance of ctDNA analysis to guide the adjuvant therapy and predict the relapse of lung, breast and colon cancer et al. Finally, there are still many challenges of MRD detection, such as lack of standardization, false-negatives or false-positives results make misleading, and the requirement of validation using large independent cohorts to improve clinical outcomes.
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Affiliation(s)
- Lemei Zhu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Ran Xu
- Geneis Beijing Co., Ltd., Beijing, China
| | | | - Wei Shi
- Geneis Beijing Co., Ltd., Beijing, China
| | - Yuan Zhang
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Juan Liu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Xi Li
- Department of Orthopedics, Xiangya Hospital Central South University, Changsha, China
| | - Jun Zhou
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Pingping Bing
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
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8
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Tortajada-Genaro LA, Lazaro A, Martorell S, Maquieira A. Nucleotide-selective amplification and array-based detection for identifying multiple somatic mutations. Anal Chim Acta 2023; 1265:341343. [PMID: 37230582 DOI: 10.1016/j.aca.2023.341343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
In the context of personalized and cost-effective treatment, knowledge of the mutational status of specific genes is advantageous to predict which patients are responsive to therapies. As an alternative to one-by-one detection or massive sequencing, the presented genotyping tool determines multiple polymorphic sequences that vary a single nucleotide. The biosensing method includes an effective enrichment of mutant variants and selective recognition by colorimetric DNA arrays. The proposed approach is the hybridization between sequence-tailored probes and products from PCR with SuperSelective primers to discriminate specific variants in a single locus. A fluorescence scanner, a documental scanner, or a smartphone captured the chip images to obtain spot intensities. Hence, specific recognition patterns identified any single-nucleotide change in the wild-type sequence overcoming qPCR methods and other array-based approaches. Studied mutational analyses applied to human cell lines provided high discrimination factors, the precision was 95%, and the sensitivity was 1% mutant of total DNA. Also, the methods showed a selective genotyping of the KRAS gene from tumorous samples (tissue and liquid biopsy), corroborating results by NGS. The developed technology supported on low-cost robust chips and optical reading provides an attractive pathway toward implementing fast, cheap, reproducible discrimination of oncological patients.
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Affiliation(s)
- Luis A Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Valencia, Spain.
| | - Ana Lazaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Sara Martorell
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Angel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Valencia, Spain
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9
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Lou X, Yan H, Su L, Sun Y, Wang X, Gong L, Chen Y, Li Z, Fang Z, Mao H, Chen K, Zhang Y. Detecting the Neuraminidase R294K Mutation in Avian Influenza A (H7N9) Virus Using Reverse Transcription Droplet Digital PCR Method. Viruses 2023; 15:v15040983. [PMID: 37112963 PMCID: PMC10146270 DOI: 10.3390/v15040983] [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: 03/09/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The R294K mutation in neuraminidase (NA) causes resistance to oseltamivir in the avian influenza virus H7N9. Reverse transcription droplet digital polymerase chain reaction (RT-dd PCR) is a novel technique for detecting single-nucleotide polymorphisms. This study aimed to develop an RT-dd PCR method for detecting the R294K mutation in H7N9. Primers and dual probes were designed using the H7N9 NA gene and the annealing temperature was optimized at 58.0 °C. The sensitivity of our RT-dd PCR method was not significantly different from that of RT-qPCR (p = 0.625), but it could specifically detect R294 and 294K in H7N9. Among 89 clinical samples, 2 showed the R294K mutation. These two strains were evaluated using a neuraminidase inhibition test, which revealed that their sensitivity to oseltamivir was greatly reduced. The sensitivity and specificity of RT-dd PCR were similar to those of RT-qPCR and its accuracy was comparable to that of NGS. The RT-dd PCR method had the advantages of absolute quantitation, eliminating the need for a calibration standard curve, and being simpler in both experimental operation and result interpretation than NGS. Therefore, this RT-dd PCR method can be used to quantitatively detect the R294K mutation in H7N9.
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Affiliation(s)
- Xiuyu Lou
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Hao Yan
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Lingxuan Su
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Yi Sun
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Xinyin Wang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Liming Gong
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Yin Chen
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Zhen Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Haiyan Mao
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Yanjun Zhang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
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10
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Sasu BJ, Opiteck GJ, Gopalakrishnan S, Kaimal V, Furmanak T, Huang D, Goswami A, He Y, Chen J, Nguyen A, Balakumaran A, Shah NN, Hamadani M, Bone KM, Prashad S, Bowen MA, Pertel T, Embree HD, Gidwani SG, Chang D, Moore A, Leonard M, Amado RG. Detection of chromosomal alteration after infusion of gene-edited allogeneic CAR T cells. Mol Ther 2023; 31:676-685. [PMID: 36518079 PMCID: PMC10014221 DOI: 10.1016/j.ymthe.2022.12.004] [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: 09/13/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
A chromosome 14 inversion was found in a patient who developed bone marrow aplasia following treatment with allogeneic chimeric antigen receptor (CAR) Tcells containing gene edits made with transcription activator-like effector nucleases (TALEN). TALEN editing sites were not involved at either breakpoint. Recombination signal sequences (RSSs) were found suggesting recombination-activating gene (RAG)-mediated activity. The inversion represented a dominant clone detected in the context of decreasing absolute CAR Tcell and overall lymphocyte counts. The inversion was not associated with clinical consequences and wasnot detected in the drug product administered to this patient or in any drug product used in this or other trials using the same manufacturing processes. Neither was the inversion detected in this patient at earlier time points or in any other patient enrolled in this or other trials treated with this or other product lots. This case illustrates that spontaneous, possibly RAG-mediated, recombination events unrelated to gene editing can occur in adoptive cell therapy studies, emphasizes the need for ruling out off-target gene editing sites, and illustrates that other processes, such as spontaneous V(D)J recombination, can lead to chromosomal alterations in infused cells independent of gene editing.
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Affiliation(s)
- Barbra J Sasu
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | | | | | - Vivek Kaimal
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Tom Furmanak
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - David Huang
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | | | - Ying He
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Jiamin Chen
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Anh Nguyen
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | | | - Nirav N Shah
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mehdi Hamadani
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kathleen M Bone
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sacha Prashad
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | | | - Thomas Pertel
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | | | | | - David Chang
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Alison Moore
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Mark Leonard
- Allogene Therapeutics, South San Francisco, CA 94080, USA
| | - Rafael G Amado
- Allogene Therapeutics, South San Francisco, CA 94080, USA.
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11
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Aran V, Zogbi VM, Miranda RL, Andreiuolo F, Silva Canedo NH, Nazaré CV, Niemeyer Filho P, Neto VM. The Use of Liquid Biopsy in the Molecular Analysis of Plasma Compared to the Tumour Tissue from a Patient with Brain Metastasis: A Case Report. Medicina (B Aires) 2023; 59:medicina59030459. [PMID: 36984460 PMCID: PMC10055748 DOI: 10.3390/medicina59030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Different cancers have multiple genetic mutations, which vary depending on the affected tumour tissue. Small biopsies may not always represent all the genetic landscape of the tumour. To improve the chances of identifying mutations at different disease stages (early, during the disease course, and refractory stage), liquid biopsies offer an advantage to traditional tissue biopsy. In addition, it is possible to detect mutations related to metastatic events depending on the cancer types analysed as will be discussed in this case report, which describes a patient with brain metastasis and lung cancer that harboured K-RAS mutations both in the brain tumour and in the ctDNA present in the bloodstream.
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Affiliation(s)
- Veronica Aran
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
- Correspondence: ; Tel.: +55-2-19-7208-8811
| | - Vinicius Mansur Zogbi
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual Do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Felipe Andreiuolo
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual Do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Nathalie Henriques Silva Canedo
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual Do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Carolina Victor Nazaré
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Paulo Niemeyer Filho
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
| | - Vivaldo Moura Neto
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro 20231-092, Brazil
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12
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Development of a Sensitive Digital Droplet PCR Screening Assay for the Detection of GPR126 Non-Coding Mutations in Bladder Cancer Urine Liquid Biopsies. Biomedicines 2023; 11:biomedicines11020495. [PMID: 36831030 PMCID: PMC9953558 DOI: 10.3390/biomedicines11020495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Recent whole-genome sequencing studies identified two novel recurrent mutations in the enhancer region of GPR126 in urothelial bladder cancer (UBC) tumor samples. This mutational hotspot is the second most common after the TERT promoter in UBC. The aim of the study was to develop a digital droplet PCR screening assay for the simultaneous detection of GPR126 mutations in a single tube. Its performance combined with TERT promoter mutation analysis was evaluated in urine of healthy volunteers (n = 50) and patients with cystitis (n = 22) and UBC (n = 70). The developed assay was validated using DNA constructs carrying the studied variants. None of the mutations were detected in control and cystitis group samples. GPR126 mutations were observed in the urine of 25/70 UBC patients (area under the ROC curve (AUC) of 0.679; mutant allele fraction (MAF) of 21.61 [8.30-44.52] %); TERT mutations-in 40/70 (AUC of 0.786; MAF = 28.29 [19.03-38.08] %); ≥1 mutation-in 47/70 (AUC of 0.836)). The simultaneous presence of GPR126 and TERT mutations was observed in 18/70 cases, with no difference in MAFs for the paired samples (31.96 [14.78-47.49] % vs. 27.13 [17.00-37.62] %, p = 0.349, respectively). The combined analysis of these common non-coding mutations in urine allows the sensitive and non-invasive detection of UBC.
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13
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Yang H, Hou Y, Liang T, Lan Y, He J, Lu J, Wei L. Quantification of Postoperative Graft-Derived Cell-Free DNA to Evaluate the Risks of Impaired Allograft Function at Early Stage of Kidney Transplantation. Transplant Proc 2022; 54:2159-2164. [DOI: 10.1016/j.transproceed.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/19/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022]
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14
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Kao EY, Wakeman KM, Wu Y, Gross JM, Chen EY, Ricciotti RW, Liu YJ, Mantilla JG. Prevalence and detection of actionable BRAF V600 and NRAS Q61 mutations in malignant peripheral nerve sheath tumor by droplet digital PCR. Hum Pathol 2022; 129:90-97. [PMID: 36067829 DOI: 10.1016/j.humpath.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
Malignant peripheral nerve sheath tumors ( MPNSTs) are aggressive tumors with poor prognosis that do not typically respond well to standard chemotherapy. Recently, point mutations involving BRAF V600E have been demonstrated in a subset of MPNST, offering the possibility of targeted treatment. However, the reported prevalence of these alterations is variable. Mutations involving NRAS, which is also involved in the MAPK/ERK pathway and amenable to targeted inhibitors, have not been well characterized in MPNST. In this study, we validated droplet digital polymerase chain reaction for the detection of BRAF V600E and NRAS Q61 mutations and evaluate the prevalence of BRAF V600E and NRAS Q61 mutations in 79 cases of MPNST, including 45 sporadic, 27 NF-1 associated, and 7 radiation-associated tumors. We detected actionable BRAF or NRAS mutations in 3 of 44 sporadic MPNSTs (6.8%), including 2 BRAF V600 and 1 NRAS Q61 mutations, as well as 1 NRAS Q61 mutation in a tumor that was ultimately considered to represent melanoma. These 3 cases with positive mutations were exclusively in sporadic, high-grade MPNST (FNCLCC grade 3 of 3), with a prevalence of 11.5% in this group (3.8% NRAS Q61 mutations and 7.7% BRAF V600 mutations). None of the tumors associated with NF-1 or prior radiation had detectable mutations in the genes tested. Overall, the prevalence of these alterations offers the possibility of targeted therapy in this aggressive type of sarcoma and suggests the potential benefit of routine clinical testing.
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Affiliation(s)
- Erica Y Kao
- Department of Pathology, Brooke Army Medical Center, San Antonio, TX 78234, USA
| | - Kristina M Wakeman
- Department of Pathology, University of Louisville, Louisville, KY, 40202, USA
| | - Yu Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - John M Gross
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Eleanor Y Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Robert W Ricciotti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Jose G Mantilla
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
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15
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He Q, Liu Z, Wang J. Targeting KRAS in PDAC: A New Way to Cure It? Cancers (Basel) 2022; 14:cancers14204982. [PMID: 36291766 PMCID: PMC9599866 DOI: 10.3390/cancers14204982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic cancer is one of the most intractable malignant tumors worldwide, and is known for its refractory nature and poor prognosis. The fatality rate of pancreatic cancer can reach over 90%. In pancreatic ductal carcinoma (PDAC), the most common subtype of pancreatic cancer, KRAS is the most predominant mutated gene (more than 80%). In recent decades, KRAS proteins have maintained the reputation of being “undruggable” due to their special molecular structures and biological characteristics, making therapy targeting downstream genes challenging. Fortunately, the heavy rampart formed by KRAS has been broken down in recent years by the advent of KRASG12C inhibitors; the covalent inhibitors bond to the switch-II pocket of the KRASG12C protein. The KRASG12C inhibitor sotorasib has been received by the FDA for the treatment of patients suffering from KRASG12C-driven cancers. Meanwhile, researchers have paid close attention to the development of inhibitors for other KRAS mutations. Due to the high incidence of PDAC, developing KRASG12D/V inhibitors has become the focus of attention. Here, we review the clinical status of PDAC and recent research progress in targeting KRASG12D/V and discuss the potential applications.
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Affiliation(s)
- Qianyu He
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Correspondence: (Z.L.); (J.W.)
| | - Jin Wang
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Correspondence: (Z.L.); (J.W.)
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16
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Xie T, Luo Y, Wang P, Wu L, Cui X, Sun B, Li G. Controlled Rehydration of Dried Reagents for Robust Multiplex Digital PCR. Anal Chem 2022; 94:13223-13232. [DOI: 10.1021/acs.analchem.2c02920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tengbao Xie
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Yu Luo
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Ping Wang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang 471000, China
| | - Lei Wu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Xu Cui
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Bangyong Sun
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Gang Li
- Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Chongqing University, Chongqing 400044, China
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17
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Strati A, Zavridou M, Paraskevis D, Magiorkinis G, Sapounas S, Lagiou P, Thomaidis NS, Lianidou ES. Development and Analytical Validation of a One-Step Five-Plex RT-ddPCR Assay for the Quantification of SARS-CoV-2 Transcripts in Clinical Samples. Anal Chem 2022; 94:12314-12322. [PMID: 35960711 PMCID: PMC9397566 DOI: 10.1021/acs.analchem.2c00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
Highly sensitive methodologies for SARS-CoV-2 detection are essential for the control of COVID-19 pandemic. We developed and analytically validated a highly sensitive and specific five-plex one-step RT-ddPCR assay for SARS-CoV-2. We first designed in-silico novel primers and probes for the simultaneous absolute quantification of three different regions of the nucleoprotein (N) gene of SARS-CoV-2 (N1, N2, N3), a synthetic RNA as an external control (RNA-EC), and Beta-2-Microglobulin (B2M) as an endogenous RNA internal control (RNA-IC). The developed assay was analytically validated using synthetic DNA and RNA calibrator standards and then was applied to 100 clinical specimens previously analyzed with a commercially available CE-IVD RT-qPCR assay. The analytical validation of the developed assay resulted in very good performance characteristics in terms of analytical sensitivity, linearity, analytical specificity, and reproducibility and recovery rates even at very low viral concentrations. The simultaneous absolute quantification of the RNA-EC and RNA-IC provides the necessary metrics for quality control assessment. Direct comparison of the developed one-step five-plex RT-ddPCR assay with a CE-IVD RT-qPCR kit revealed a very high concordance and a higher sensitivity [concordance: 99/100 (99.0%, Spearman's correlation coefficient: -0.850, p < 0.001)]. The developed assay is highly sensitive, specific, and reproducible and has a broad linear dynamic range, providing absolute quantification of SARS-COV-2 transcripts. The inclusion of two RNA quality controls, an external and an internal, is highly important for standardization of SARS-COV-2 molecular testing in clinical and wastewater samples.
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Affiliation(s)
- Areti Strati
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Martha Zavridou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | | | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Nikolaos S. Thomaidis
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Evi S. Lianidou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
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18
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Hot-Spot-Specific Probe (HSSP) for Rapid and Accurate Detection of KRAS Mutations in Colorectal Cancer. BIOSENSORS 2022; 12:bios12080597. [PMID: 36004993 PMCID: PMC9406089 DOI: 10.3390/bios12080597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022]
Abstract
Detection of oncogene mutations has significance for early diagnosis, customized treatment, treatment progression, and drug resistance monitoring. Here, we introduce a rapid, sensitive, and specific mutation detection assay based on the hot-spot-specific probe (HSSP), with improved clinical utility compared to conventional technologies. We designed HSSP to recognize KRAS mutations in the DNA of colorectal cancer tissues (HSSP-G12D (GGT→GAT) and HSSP-G13D (GGC→GAC)) by integration with real-time PCR. During the PCR analysis, HSSP attaches to the target mutation sequence for interference with the amplification. Then, we determine the mutation detection efficiency by calculating the difference in the cycle threshold (Ct) values between HSSP-G12D and HSSP-G13D. The limit of detection to detect KRAS mutations (G12D and G13D) was 5–10% of the mutant allele in wild-type populations. This is superior to the conventional methods (≥30% mutant allele). In addition, this technology takes a short time (less than 1.5 h), and the cost of one sample is as low as USD 2. We verified clinical utility using 69 tissue samples from colorectal cancer patients. The clinical sensitivity and specificity of the HSSP assay were higher (84% for G12D and 92% for G13D) compared to the direct sequencing assay (80%). Therefore, HSSP, in combination with real-time PCR, provides a rapid, highly sensitive, specific, and low-cost assay for detecting cancer-related mutations. Compared to the gold standard methods such as NGS, this technique shows the possibility of the field application of rapid mutation detection and may be useful in a variety of applications, such as customized treatment and cancer monitoring.
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19
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Nauheim D, Moskal D, Renslo B, Chadwick M, Jiang W, Yeo CJ, Nevler A, Bowne W, Lavu H. KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer. J Surg Oncol 2022; 126:314-321. [PMID: 35333412 DOI: 10.1002/jso.26860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/05/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) provides information on genetic mutations and mutant allele frequency in tumor specimens. We investigated the prognostic significance of KRAS mutant allele frequency in patients with right-sided pancreatic ductal adenocarcinoma (PDAC) treated with surgical resection. METHODS A retrospective study reviewed patients who underwent surgical resection for PDAC and analyzed tumors with an in-house mutational panel. Microdissected samples were studied using an NGS-based assay to detect over 200 hotspot mutations in 42 genes (Pan42) commonly involved in PDAC. RESULTS A total of 144 PDAC right-sided surgical patients with a Pan42 panel were evaluated between 2015 and 2020; 121 patients (84%) harbored a KRAS mutation. Detected mutant allele frequencies were categorized as less than 20% (low mKRAS, n = 92) or greater than or equal to 20% (high mKRAS, n = 29). High mKRAS (KRAS ≥ 20%) patients were noted to have shorter disease-free survival after surgery (11.5 ± 2.1 vs. 19.5 ± 3.5 months, p = 0.03), more advanced tumor stage (p = 0.02), larger tumors (3.6 vs. 2.7 cm, p = 0.001), greater tumor cellularity (26% vs. 18%, p = 0.001), and higher rate of distant recurrence (p = 0.03) than low mKRAS patients. CONCLUSION This study demonstrates the importance of KRAS mutant allele frequency on pathological characteristics and prognosis in right-sided PDAC treated with surgery.
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Affiliation(s)
- David Nauheim
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Moskal
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Bryan Renslo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matthew Chadwick
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wei Jiang
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles J Yeo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Avinoam Nevler
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wilbur Bowne
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Harish Lavu
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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Satomi K, Yoshida A, Matsushita Y, Sugino H, Fujimoto K, Honda-Kitahara M, Takahashi M, Ohno M, Miyakita Y, Narita Y, Yatabe Y, Shibahara J, Ichimura K. Clinical application of a highly sensitive digital PCR assay to detect a small fraction of IDH1 R132H-mutant alleles in diffuse gliomas. Brain Tumor Pathol 2022; 39:210-217. [PMID: 35902443 DOI: 10.1007/s10014-022-00442-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
The current World Health Organization classification of diffuse astrocytic and oligodendroglial tumors requires the examination of isocitrate dehydrogenase 1 (IDH1) or IDH2 mutations. Conventional analysis tools, including Sanger DNA sequencing or pyrosequencing, fail in detecting these variants of low frequency owing to their limited sensitivity. Digital polymerase chain reaction (dPCR) is a recently developed, highly sensitive, and precise quantitative rare variant assay. This study aimed to establish a robust limit of quantitation of the dPCR assay to detect a small fraction of IDH1 R132H mutation. The dPCR assays with serially diluted IDH1 R132H constructs detected 0.05% or more of mutant IDH1 R132H in samples containing mutant DNA. The measured target/total value of the experiments was proportional to the dilution factors and was almost equal to the actual frequencies of the mutant alleles. Based on the average target/total values, together with a twofold standard deviation of the normal DNA, a limit of quantitation of 0.25% was set to secure a safe margin to judge the mutation status of the IDH1 R132H dPCR assay. In clinical settings, detecting IDH1 R132H using dPCR assays can validate ambiguous immunohistochemistry results even when conventional DNA sequencing cannot detect the mutation and assure diagnostic quality.
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Affiliation(s)
- Kaishi Satomi
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan. .,Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan. .,Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo, 181-8611, Japan.
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yuko Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Brain Disease Translational Research, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kenji Fujimoto
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto-shi, Kumamoto, 860-8555, Japan
| | - Mai Honda-Kitahara
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Makoto Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasuji Miyakita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo, 181-8611, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Brain Disease Translational Research, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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21
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International co-validation on absolute quantification of single nucleotide variants of KRAS by digital PCR. Anal Bioanal Chem 2022; 414:5899-5906. [DOI: 10.1007/s00216-022-04155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/01/2022]
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22
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Igari F, Tanaka H, Giuliano AE. The applications of plasma cell-free DNA in cancer detection: Implications in the management of breast cancer patients. Crit Rev Oncol Hematol 2022; 175:103725. [PMID: 35618229 DOI: 10.1016/j.critrevonc.2022.103725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Liquid biopsy probes DNA, RNA, and proteins in body fluids for cancer detection and is one of the most rapidly developing areas in oncology. Tumor-derived DNA (circulating tumor DNA, ctDNA) in the context of cell-free DNA (cfDNA) in blood has been the main target for its potential utilities in cancer detection. Liquid biopsy can report tumor burden in real-time without invasive interventions, and would be feasible for screening tumor types that lack standard-of-care screening approaches. Two major approaches to interrogating ctDNA are genetic mutation and DNA methylation profiling. Mutation profiling can identify tumor driver mutations and guide precision therapy. Targeted genomic profiling of DNA methylation has become the main approach for cancer screening in the general population. Here we review the recent technological development and ongoing efforts in clinical applications. For clinical applications, we focus on breast cancer, in which subtype-specific biology demarcates the applications of ctDNA.
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Affiliation(s)
- Fumie Igari
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Breast Oncology, Juntendo University, Tokyo, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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23
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Multivariate Risk Analysis of RAS, BRAF and EGFR Mutations Allelic Frequency and Coexistence as Colorectal Cancer Predictive Biomarkers. Cancers (Basel) 2022; 14:cancers14112792. [PMID: 35681771 PMCID: PMC9179415 DOI: 10.3390/cancers14112792] [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: 05/02/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The colorectal cancer (CRC) stage and evolution should be described by biomarker profiles. In 60 CRC cases, KRAS, NRAS, BRAF, and EGFR mutations were analyzed by droplet digital PCR (ddPCR). KRAS G12/G13 mutation was present in all patients with variable allelic frequencies. KRAS Q61 mutation was correlated with tumor invasion beyond the subserosa and poor differentiation, both associated with worst prognosis. Tumors with NRAS and BRAF mutations were prevalently localized on the right segment colon. The discovery of the KRAS Q61 role in tumor phenotypes provides the foundation for new therapeutic strategies and perspectives on molecular subtypes classification of CRC. Abstract Background: Biomarker profiles should represent a coherent description of the colorectal cancer (CRC) stage and its predicted evolution. Methods: Using droplet digital PCR, we detected the allelic frequencies (AF) of KRAS, NRAS, BRAF, and EGFR mutations from 60 tumors. We employed a pair-wise association approach to estimate the risk involving AF mutations as outcome variables for clinical data and as predicting variables for tumor-staging. We evaluated correlations between mutations of AFs and also between the mutations and histopathology features (tumor staging, inflammation, differentiation, and invasiveness). Results: KRAS G12/G13 mutations were present in all patients. KRAS Q61 was significantly associated with poor differentiation, high desmoplastic reaction, invasiveness (ypT4), and metastasis (ypM1). NRAS and BRAF were associated with the right-side localization of tumors. Diabetic patients had a higher risk to exhibit NRAS G12/G13 mutations. BRAF and NRAS G12/G13 mutations co-existed in tumors with invasiveness limited to the submucosa. Conclusions: The associations we found and the mutational AF we reported may help to understand disease processes and may be considered as potential CCR biomarker candidates. In addition, we propose representative mutation panels associated with specific clinical and histopathological features of CRC, as a unique opportunity to refine the degree of personalization of CRC treatment.
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Cheng YH, Wang CH, Hsu KF, Lee GB. Integrated Microfluidic System for Cell-Free DNA Extraction from Plasma for Mutant Gene Detection and Quantification. Anal Chem 2022; 94:4311-4318. [PMID: 35235296 DOI: 10.1021/acs.analchem.1c04988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ovarian cancer (OvCa) is among the most severe gynecologic cancers, yet individuals may be asymptomatic during its early stages. Routine, early screening for genetic abnormalities associated with OvCa could improve prognoses, and this can be achieved by detecting mutant genes in cell-free DNA (cfDNA). Herein, we developed an integrated microfluidic chip (IMC) that could extract cfDNA from plasma and automatically detect and quantify mutations in the OvCa biomarker BRCA1. The cfDNA extraction module relied on a vortex-type micromixer to mix cfDNA with magnetic beads surface-coated with cfDNA probes and could isolate 76% of molecules from a 200 μL plasma sample in 45 min. The cfDNA quantification module, which comprised a micropump that evenly distributed 4.5 μL of purified cfDNA into the on-chip, allele-specific quantitative polymerase chain reaction (qPCR) zones, was capable of quantifying mutant genes within 90 min. By automating the cfDNA extraction and qPCR processes, this IMC could be used for clinical screening for OvCa-associated mutations.
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Affiliation(s)
- Yu-Hung Cheng
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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25
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Sorokina A, Artyuhov A, Goltsova A, Dashinimaev E. Detection of CCR5Δ32 Mutant Alleles in Heterogeneous Cell Mixtures Using Droplet Digital PCR. Front Mol Biosci 2022; 9:805931. [PMID: 35265670 PMCID: PMC8898955 DOI: 10.3389/fmolb.2022.805931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/10/2022] [Indexed: 01/05/2023] Open
Abstract
The C-C chemokine receptor type 5 (CCR5 or CD195) is one of the co-receptor binding sites of the human immunodeficiency virus (HIV). Transplantations of hematopoietic stem cells with the CCR5Δ32 knockout mutation could represent an effective tool for the complete cure of HIV; these methods having passed the stage of proof-of-principle. At the same time, using the modern CRISPR/Cas9 genome editing method, we can effectively reproduce the CCR5Δ32 mutation in any wild-type cells. Thus, the task of searching for and accurately quantifying the content of mutant CCR5Δ32 alleles in heterogeneous cell mixtures becomes relevant. In this study, we describe the generation of an artificial CCR5Δ32 mutation using CRISPR/Cas9 followed by multiplex droplet digital polymerase chain reaction (ddPCR) to quantify its content in cell mixtures. The system we have developed allows us to quickly and accurately measure the content of cells with the CCR5Δ32 mutation, down to 0.8%.
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Affiliation(s)
- Alyona Sorokina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexander Artyuhov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Erdem Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
- *Correspondence: Erdem Dashinimaev,
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26
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Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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27
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Choi MH, Tjora E, Forthun RB, Engjom T, Ræder H, Hovland R, Molven A. KRAS mutation analysis by droplet digital PCR of duodenal juice from patients with MODY8 and other pancreatic diseases. Pancreatology 2021; 21:1460-1465. [PMID: 34580018 DOI: 10.1016/j.pan.2021.09.010] [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: 08/28/2021] [Accepted: 09/19/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Maturity-onset diabetes of the young type 8 (MODY8 or CEL-MODY) is an inherited pancreatic disease characterized by chronic inflammation of the pancreas and diabetes. It is not known whether MODY8 patients have increased risk for developing pancreatic cancer. We investigated KRAS mutation load in duodenal juice from MODY8 patients, comparing with other groups of pancreatic disease. METHODS Droplet digital PCR (ddPCR) was used to detect KRAS codon 12/13/61 mutations in duodenal juice sampled from 11 MODY8 patients, nine healthy subjects and 100 patients clinically investigated due to suspected pancreatic disease. RESULTS KRAS mutations were detected in 4/11 patients with MODY8 (36%), 1/9 healthy subjects (11%), 15/44 patients with chronic pancreatitis (CP, 34%), 3/5 patients with pancreatic ductal adenocarcinoma (PDAC, 60%), 3/20 patients with acute pancreatitis (15%), 0/13 patients with other pancreatic disorders and 2/18 patients with nonpancreatic gastrointestinal disease (11%). Of the 28 positive juice samples, 25 (89%) had low-abundance mutations in codons 12/13, with a variant allele frequency (VAF) less than 1%. KRAS-positive patients with MODY8 or CP had significantly lower VAFs than patients with PDAC (Mann-Whitney U test; p = 0.041). Although the overall mutation detection rate was higher for subjects ≥50 years old (26%) than for younger subjects (15%), the difference was not statistically significant. CONCLUSIONS KRAS mutations were detectable in duodenal juice from MODY8 patients, but with low abundance and at the same frequency as in CP patients. The discriminative value of the analysis with regard to other pancreatic disease was limited.
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Affiliation(s)
- Man Hung Choi
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Erling Tjora
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Trond Engjom
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Helge Ræder
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Randi Hovland
- Section for Tumor Genomics, Haukeland University Hospital, Bergen, Norway; Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway.
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28
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Moding EJ, Nabet BY, Alizadeh AA, Diehn M. Detecting Liquid Remnants of Solid Tumors: Circulating Tumor DNA Minimal Residual Disease. Cancer Discov 2021; 11:2968-2986. [PMID: 34785539 PMCID: PMC8976700 DOI: 10.1158/2159-8290.cd-21-0634] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Growing evidence demonstrates that circulating tumor DNA (ctDNA) minimal residual disease (MRD) following treatment for solid tumors predicts relapse. These results suggest that ctDNA MRD could identify candidates for adjuvant therapy and measure response to such treatment. Importantly, factors such as assay type, amount of ctDNA release, and technical and biological background can affect ctDNA MRD results. Furthermore, the clinical utility of ctDNA MRD for treatment personalization remains to be fully established. Here, we review the evidence supporting the value of ctDNA MRD in solid cancers and highlight key considerations in the application of this potentially transformative biomarker. SIGNIFICANCE ctDNA analysis enables detection of MRD and predicts relapse after definitive treatment for solid cancers, thereby promising to revolutionize personalization of adjuvant and consolidation therapies.
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Affiliation(s)
- Everett J. Moding
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barzin Y. Nabet
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Current address: Department of Oncology Biomarker Development, Genentech, South San Francisco, CA 94080, USA
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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29
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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30
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Five novel copy number variations detected in patients with familial exudative vitreoretinopathy. Mol Vis 2021; 27:632-642. [PMID: 34924743 PMCID: PMC8645187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/18/2021] [Indexed: 11/05/2022] Open
Abstract
Purpose Familial exudative vitreoretinopathy (FEVR) is an inherited retinal vascular disease genetically heterogeneous with multiple causative genes. The aim of this study is to report five novel copy number variation (CNV) regions in FEVR patients and to investigate the possible contributions of novel CNVs to FEVR. Methods In this study, 824 FEVR families were collected. All cases were performed using the targeted next generation sequencing (NGS) assay, and families with no definite pathogenic mutations in FEVR genes were screened for CNVs according to the NGS results. Droplet digital polymerase chain reaction (ddPCR) testing was introduced to validate the screened CNV regions. We also reviewed the clinical presentations of the probands and affected family members associated with the novel CNVs and conducted segregation analysis. Results Five CNVs in five patients were detected in this study: heterozygous deletions of kinesin family member 11 (KIF11) exons 2-4, KIF11 exon 11, KIF11 exons 1-10, tetraspanin-12 (TSPAN12) exons 1-3, and low-density lipoprotein receptor-related protein 5 (LRP5) exons 19-21. Among the five affected families, TSPAN12 exons 1-3 heterozygous deletion and LRP5 exons 19-21 heterozygous deletion originate from the mother and the father of the proband, respectively. No other family members manifested as FEVR except for the probands. The correlation between disease severity and CNV loci seems uncertain. Conclusions Five novel CNV loci in FEVR patients were uncovered in this study, including one maternally-inherited and one paternally-inherited CNV region. Though there is no evidence of co-segregation between these CNVs and FEVR, our findings suggest novel genetic risk factors for FEVR.
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31
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Ott A, Quintela-Baluja M, Zealand AM, O'Donnell G, Haniffah MRM, Graham DW. Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance. ENVIRONMENTAL MICROBIOME 2021; 16:21. [PMID: 34794510 PMCID: PMC8600772 DOI: 10.1186/s40793-021-00391-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Understanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks. RESULTS Here we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation. CONCLUSIONS Methods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.
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Affiliation(s)
- Amelie Ott
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew M Zealand
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | | | - David W Graham
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK.
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Maggi R, Breitschwerdt EB, Qurollo B, Miller JC. Development of a Multiplex Droplet Digital PCR Assay for the Detection of Babesia, Bartonella, and Borrelia Species. Pathogens 2021; 10:pathogens10111462. [PMID: 34832618 PMCID: PMC8620149 DOI: 10.3390/pathogens10111462] [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: 10/25/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
We describe the development, optimization, and validation of a multiplex droplet digital PCR (ddPCR) assay for the simultaneous detection of Babesia, Bartonella, and Borrelia spp. DNA from several sample matrices, including clinical blood samples from animals and humans, vectors, in-vitro infected human and animal cell lines, and tissues obtained from animal models (infected with Bartonella and/or B. burgdorferi). The multiplex ddPCR assay was able to detect 31 Bartonella, 13 Borrelia, and 24 Babesia species, including Theileria equi, T. cervi, and Cytauxzoon felis. No amplification of Treponema or Leptospira spp. was observed. Sensitivity of 0.2-5 genome equivalent DNA copies per microliter was achieved for different members of the Bartonella and Borrelia genus, depending on the species or matrix type (water or spiked blood DNA) tested. The ddPCR assay facilitated the simultaneous detection of co-infections with two and three vector-borne pathogens comprising four different genera (Babesia, Bartonella, Borrelia, and Theileria) from clinical and other sample sources.
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Affiliation(s)
- Ricardo Maggi
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
- Correspondence:
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
| | - Barbara Qurollo
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
| | - Jennifer C. Miller
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
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Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. NANO LETTERS 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Role of oncogenic KRAS in the prognosis, diagnosis and treatment of colorectal cancer. Mol Cancer 2021; 20:143. [PMID: 34742312 PMCID: PMC8571891 DOI: 10.1186/s12943-021-01441-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease at the cellular and molecular levels. Kirsten rat sarcoma (KRAS) is a commonly mutated oncogene in CRC, with mutations in approximately 40% of all CRC cases; its mutations result in constitutive activation of the KRAS protein, which acts as a molecular switch to persistently stimulate downstream signaling pathways, including cell proliferation and survival, thereby leading to tumorigenesis. Patients whose CRC harbors KRAS mutations have a dismal prognosis. Currently, KRAS mutation testing is a routine clinical practice before treating metastatic cases, and the approaches developed to detect KRAS mutations have exhibited favorable sensitivity and accuracy. Due to the presence of KRAS mutations, this group of CRC patients requires more precise therapies. However, KRAS was historically thought to be an undruggable target until the development of KRASG12C allele-specific inhibitors. These promising inhibitors may provide novel strategies to treat KRAS-mutant CRC. Here, we provide an overview of the role of KRAS in the prognosis, diagnosis and treatment of CRC.
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Milavec M, Cleveland MH, Bae YK, Wielgosz RI, Vonsky M, Huggett JF. Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements. Anal Bioanal Chem 2021; 414:791-806. [PMID: 34738220 PMCID: PMC8568362 DOI: 10.1007/s00216-021-03712-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Megan H Cleveland
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Robert I Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Maxim Vonsky
- D.I. Mendeleev Institute for Metrology, Moskovsky pr., 19, Saint-Petersburg, 190005, Russian Federation
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK.,School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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Jun E, Koo B, Kim EJ, Hwang DW, Lee JH, Song KB, Lee W, Park Y, Hong S, Shin Y, Kim SC. Analysis of KRAS Mutation Subtype in Tissue DNA and Cell-Free DNA Using Droplet Digital PCR and the Function of Cell-Free DNA as a Recurrence Predictive Marker in Pancreatic Cancer. Biomedicines 2021; 9:biomedicines9111599. [PMID: 34829828 PMCID: PMC8615414 DOI: 10.3390/biomedicines9111599] [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: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
KRAS mutation is a major regulator in the tumor progression of pancreatic cancer. Here, we compared the frequency and mutation burden of KRAS mutation subtypes with paired tumor tissue and blood in patients and examined their clinical significance. DNA from tumor tissues and cell-free DNA (cfDNA) from preoperative blood were obtained from 70 patients with pancreatic cancer. Subtypes and mutation burdens of KRAS G12D and G12V mutations were evaluated using droplet digital PCR. Comparing the presence of mutations in tissue, accumulative and simultaneous mutations of G12D or G12V were identified of 67 (95.7%), and 48 patients (68.6%). Conversely, in blood, they were only identified in 18 (25.7%) and four (5.7%) patients; respectively. Next, comparing the mutation burden in tissue, the mutation burden varied from less than 0.1 to more than five, whereas that of cfDNA in blood was mostly between one and five, as cases with a mutation burden lower than 0.1 and higher than five were rare. Finally, the presence of the G12V mutation alone in cfDNA and the combination of the G12V mutation with elevated CA 19-9 levels were associated with poor recurrence-free survival. These fundamental data on the KRAS mutation subtypes and their clinical significance could support their potential as predictive markers for postoperative recurrence.
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Affiliation(s)
- Eunsung Jun
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea;
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Eo Jin Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea;
| | - Dae Wook Hwang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Jae Hoon Lee
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Ki Byung Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Woohyung Lee
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Yejong Park
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Sarang Hong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
| | - Song Cheol Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
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Aran V, Heringer M, da Mata PJ, Kasuki L, Miranda RL, Andreiuolo F, Chimelli L, Filho PN, Gadelha MR, Neto VM. Identification of mutant K-RAS in pituitary macroadenoma. Pituitary 2021; 24:746-753. [PMID: 33954928 DOI: 10.1007/s11102-021-01151-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE RAS genes are among the most frequently mutated genes in cancer, where their mutation frequency varies according to the distinct RAS isoforms and tumour types. Despite occurring more prevalent in malignant tumours, RAS mutations were also observed in few benign tumours. Pituitary adenomas are examples of benign tumours which vary in size and aggressiveness. The present study was performed to investigate, via liquid biopsy and tissue analysis, the presence of K-RAS mutations in a pituitary macroadenoma. METHODS Molecular analysis was performed to investigate K-RAS mutations using the droplet digital PCR (ddPCR) method by evaluating both plasma (liquid biopsy) and the solid tumour of a patient diagnosed with a giant clinically non-functioning pituitary tumour. RESULTS The patient underwent surgical resection due to visual loss, and the histopathological analysis showed a gonadotrophic pituitary macroadenoma. The molecular analysis revealed the presence of mutant K-RAS both in the plasma and in the tumour tissue which, to our knowledge, has not been previously reported in the literature. CONCLUSION Our findings highlight the exceptional capacity of the digital PCR in detecting low frequency mutations (below 1%), since we detected, for the first time, K-RAS mutations in pituitary macroadenoma. The potential impact of K-RAS mutations in these tumours should be further investigated.
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Affiliation(s)
- Veronica Aran
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil.
| | - Manoela Heringer
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil
| | - Paulo Jose da Mata
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Leandro Kasuki
- Neuroendocrine Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Endocrine Unit and Neuroendocrinology Research Center, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Felipe Andreiuolo
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Leila Chimelli
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Paulo Niemeyer Filho
- Neurosurgery Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
| | - Monica Roberto Gadelha
- Neuroendocrine Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, Brazil
- Endocrine Unit and Neuroendocrinology Research Center, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivaldo Moura Neto
- Laboratório de Biomedicina do Cérebro, Instituto Estadual do Cérebro Paulo Niemeyer, Rua do Rezende156-Centro, Rio de Janeiro, 20231-092, Brazil
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Label-free enrichment of rare unconventional circulating neoplastic cells using a microfluidic dielectrophoretic sorting device. Commun Biol 2021; 4:1130. [PMID: 34561533 PMCID: PMC8463600 DOI: 10.1038/s42003-021-02651-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Cellular circulating biomarkers from the primary tumor such as circulating tumor cells (CTCs) and circulating hybrid cells (CHCs) have been described to harbor tumor-like phenotype and genotype. CHCs are present in higher numbers than CTCs supporting their translational potential. Methods for isolation of CHCs do not exist and are restricted to low-throughput, time consuming, and biased methodologies. We report the development of a label-free dielectrophoretic microfluidic platform facilitating enrichment of CHCs in a high-throughput and rapid fashion by depleting healthy peripheral blood mononuclear cells (PBMCs). We demonstrated up to 96.5% depletion of PBMCs resulting in 18.6-fold enrichment of cancer cells. In PBMCs from pancreatic adenocarcinoma patients, the platform enriched neoplastic cells identified by their KRAS mutant status using droplet digital PCR with one hour of processing. Enrichment was achieved in 75% of the clinical samples analyzed, establishing this approach as a promising way to non-invasively analyze tumor cells from patients.
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Chen X, Liu F, Xue Q, Weng X, Xu F. Metastatic pancreatic cancer: Mechanisms and detection (Review). Oncol Rep 2021; 46:231. [PMID: 34498718 PMCID: PMC8444192 DOI: 10.3892/or.2021.8182] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer (PC) is a lethal malignancy. Its prevalence rate remains low but continues to grow each year. Among all stages of PC, metastatic PC is defined as late-stage (stage IV) PC and has an even higher fatality rate. Patients with PC do not have any specific clinical manifestations. Most cases are inoperable at the time-point of diagnosis. Prognosis is also poor even with curative-intent surgery. Complications during surgery, postoperative pancreatic fistula and recurrence with metastatic foci make the management of metastatic PC difficult. While extensive efforts were made to improve survival outcomes, further elucidation of the molecular mechanisms of metastasis poses a formidable challenge. The present review provided an overview of the mechanisms of metastatic PC, summarizing currently known signaling pathways (e.g. epithelial-mesenchymal transition, NF-κB and KRAS), imaging that may be utilized for early detection and biomarkers (e.g. carbohydrate antigen 19-9, prostate cancer-associated transcript-1, F-box/LRR-repeat protein 7 and tumor stroma), giving insight into promising therapeutic targets.
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Affiliation(s)
- Xiangling Chen
- Department of Public Health, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Fangfang Liu
- Department of Art, Art College, Southwest Minzu University, Chengdu, Sichuan 610041, P.R. China
| | - Qingping Xue
- Department of Public Health, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Xiechuan Weng
- Department of Neuroscience, Beijing Institute of Basic Medical Sciences, Beijing 100850, P.R. China
| | - Fan Xu
- Department of Public Health, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
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40
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Liquid Biopsy for Biomarker Testing in Non-Small Cell Lung Cancer: A European Perspective. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2030022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The development of targeted therapies has improved survival rates for patients with advanced non-small cell lung cancer (NSCLC). However, tissue biopsy is unfeasible or inadequate in many patients, limiting biomarker testing and access to targeted therapies. The increasing numbers of established and emerging biomarkers with available targeted treatments highlights the challenges associated with sequential single-gene testing and limited tissue availability. Multiplex next-generation sequencing (NGS) offers an attractive alternative and represents a logical next step, and in cases where the tumour is inaccessible, tissue biopsy yields insufficient tumour content, or when the patient’s performance status does not allow a tissue biopsy, liquid biopsy can provide valuable material for molecular diagnosis. Here, we explore the role of liquid biopsy (i.e., circulating cell-free DNA analysis) in Europe. Liquid biopsies could be used as a complementary approach to increase rates of molecular diagnosis, with the ultimate aim of improving patient access to appropriate targeted therapies. Expert opinion is also provided on potential future applications of liquid biopsy in NSCLC, including for cancer prevention, detection of early stage and minimum residual disease, monitoring of response to therapy, selection of patients for immunotherapy, and monitoring of tumour evolution to enable optimal adaptation/combination of drug therapies.
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Di W, Ran Q, Yang H, Lu J, Hou Y, Wang X, He J, Wei L. Use of graft-derived cell-free DNA as a novel biomarker to predict allograft function after kidney transplantation. Int J Urol 2021; 28:1019-1025. [PMID: 34229363 DOI: 10.1111/iju.14638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To investigate the association between graft-derived cell-free DNA and pretransplantation clinical variables, and to determine whether the former could be used as a novel biomarker to predict renal function. METHODS A total of 87 recipients who underwent primary kidney transplantation were recruited to the study. For each recipient, 10 mL peripheral blood was collected on days 1, 7, 14-20, and 30-45 after transplantation. The fractional abundance of graft-derived cell-free DNA was determined using droplet digital polymerase chain reaction. RESULTS For most recipients, graft-derived cell-free DNA fraction values were significantly elevated on the first day after transplantation, followed by a rapid decline, and reaching baseline values of graft-derived cell-free DNA fraction in the range of <1% at 7 days. Statistical analysis showed that longer cold ischemia time was significantly associated with higher graft-derived cell-free DNA fraction values (P = 0.02). Moreover, we also found that graft-derived cell-free DNA fraction values among recipients with delayed graft function were significantly higher than those of recipients without delayed graft function on the first day after transplantation. Kaplan-Meier analysis showed that recipients who had a graft-derived cell-free DNA fraction value of <1% at 7 days had a significantly lower probability of an estimated glomerular filtration rate ≤60 mL/min/1.73 m2 at 90 days. Using a random forest regression model, the predicted values of estimated glomerular filtration rate at 90 days were almost the same as the actual values. CONCLUSIONS Our findings suggest that graft-derived cell-free DNA might be used as a novel biomarker to predict delayed graft function and renal function.
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Affiliation(s)
- Wenjia Di
- Organ Transplantation Center, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Qing Ran
- Organ Transplantation Center, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Hongji Yang
- Organ Transplantation Center, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, School of Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jun Lu
- S&KM Biotechnology Co., Ltd, Chengdu, Sichuan, China
| | - Yifu Hou
- Organ Transplantation Center, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Xiaoxiao Wang
- Organ Transplantation Center, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jiayang He
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, School of Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Liang Wei
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, School of Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid. Mol Cell Probes 2021; 58:101746. [PMID: 34102255 DOI: 10.1016/j.mcp.2021.101746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, Republic of Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea.
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Wang X, Zhang Y, Niu C, Wang S, Li L, Guo Y, Zhu L, Jin X, Gao H, Xu W, Zhu P, Lan Q, Du M, Cheng X, Gao Y, Dong L. Establishment of primary reference measurement procedures and reference materials for EGFR variant detection in non-small cell lung cancer. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2114-2123. [PMID: 33870958 DOI: 10.1039/d1ay00328c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circulating tumor DNA (ctDNA)-based mutation detection is promising to change the clinical practice of genotype-directed therapy for cancer. A growing number of non-invasive tests for cancer screening and monitoring that involve the detection of ctDNA have been commercialized. Primary reference measurement procedures (PRMPs) and reference materials (RMs) are urgently needed to assess the non-invasive tests. In this study, a PRMP based on digital PCR (dPCR) and ctDNA RMs for quantification of the frequently occurring variant in epidermal growth factor receptor (EGFR L858R, T790M, and 19Del) in non-small cell lung cancer (NSCLC) were established. The candidate dPCR PRMP showed high specificity (false positive rate 0-0.003%), good repeatability (coefficient of variance (CV), 2-3% for 104 copies/reaction), and high interlaboratory reproducibility (3-10%). A good linearity (0.97 < slope < 1.03, R2 ≥ 0.9999) between the measured mutant (MU) value and prepared value was observed for all assays over the fractional abundance (FA) range, between 25% and 0.05%. The limit of quantification (LoQ) was determined to be 34 L858R, 23 T790M, and 34 19Del copies/reaction, corresponding to a FA of 0.2%. An inter-laboratory study of using the EGFR ctDNA RMs and dPCR assays demonstrated that the participating laboratories produced consistent concentrations of MU and wild-type (WT), as well as FA. This study demonstrates that dPCR can act as a potential PRMP for EGFR mutation for validation of NSCLC genotyping tests and ctDNA quantitative tests. The PRMP and RMs established here could improve interlaboratory repeatability and reproducibility, which supports rapid translation and application of non-invasive tests into clinical practice.
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Affiliation(s)
- Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing 210049, People's Republic of China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Xiaohua Jin
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, People's Republic of China
| | - Qingkuo Lan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Xiaoyan Cheng
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
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Cazacu IM, Semaan A, Stephens B, Swartzlander DB, Guerrero PA, Singh BS, Lungulescu CV, Danciulescu MM, Cherciu Harbiyeli IF, Streata I, Popescu C, Saftoiu A, Roy-Chowdhuri S, Maitra A, Bhutani MS. Diagnostic value of digital droplet polymerase chain reaction and digital multiplexed detection of single-nucleotide variants in pancreatic cytology specimens collected by EUS-guided FNA. Gastrointest Endosc 2021; 93:1142-1151.e2. [PMID: 33058885 DOI: 10.1016/j.gie.2020.09.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/29/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS EUS-guided FNA is recommended as a first-line procedure for the histopathologic diagnosis of pancreatic cancer. Molecular analysis of EUS-FNA samples might be used as an auxiliary tool to strengthen the diagnosis. The current study aimed to evaluate the diagnostic performances of K-ras testing using droplet digital polymerase chain reaction (ddPCR) and a novel single-nucleotide variant (SNV) assay performed on pancreatic EUS-FNA samples. METHODS EUS-FNA specimens from 31 patients with pancreatic masses (22 pancreatic ductal adenocarcinomas, 7 chronic pancreatitis, and 2 pancreatic neuroendocrine tumors) were included in the study. K-ras testing was initially performed by ddPCR. In addition, mutational status was evaluated using an SNV assay by NanoString technology, using digital enumeration of unique barcoded probes to detect 97 SNVs from 24 genes of clinical significance. RESULTS The overall specificity and sensitivity of cytologic examination were 100% and 63%, respectively. K-ras mutation testing was performed using ddPCR, and the sensitivity increased to 87% with specificity 90%. The SNV assay detected at least 1 variant in 90% of pancreatic ductal adenocarcinoma samples; the test was able to detect 2 K-ras codon 61 mutations in 2 cases of pancreatic ductal adenocarcinoma, which were missed by ddPCR. The overall diagnostic accuracy of the cytologic examination alone was 74%, and it increased to 91% when the results of both molecular tests were considered for the cases with negative and inconclusive results. CONCLUSIONS The current study illustrated that integration of K-ras analysis with cytologic evaluation, especially in inconclusive cases, can enhance the diagnostic accuracy of EUS-FNA for pancreatic lesions.
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Affiliation(s)
- Irina M Cazacu
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA; Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Alexander Semaan
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Bret Stephens
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel B Swartzlander
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Paola A Guerrero
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Ben S Singh
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | - Ioana Streata
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Carmen Popescu
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Adrian Saftoiu
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anirban Maitra
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Manoop S Bhutani
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
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Wahl SGF, Dai HY, Emdal EF, Ottestad AL, Dale VG, Richardsen E, Halvorsen TO, Grønberg BH. Prognostic value of absolute quantification of mutated KRAS in circulating tumour DNA in lung adenocarcinoma patients prior to therapy. J Pathol Clin Res 2021; 7:209-219. [PMID: 33502820 PMCID: PMC8073004 DOI: 10.1002/cjp2.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a highly sensitive and accurate method for quantification of nucleic acid sequences. We used absolute quantification of mutated v-Ki-ras2 Kirsten rat sarcoma viral oncogene homology gene (KRAS) by ddPCR to investigate the prognostic role of mutated KRAS in patients with KRAS-mutated lung adenocarcinomas. Pre-treatment plasma samples from 60 patients with stages I-IV KRAS-mutated lung adenocarcinomas were analysed for KRAS mutations. The associations between survival, detectable KRAS mutations in plasma, and the plasma concentration of mutated KRAS were assessed. Overall, 23 of 60 (38%) patients had detectable KRAS mutation in plasma. The percentage of patients with detectable mutation was 8% in stage I, 30% in stage II, 71% in stage III, and 73% in stage IV. Estimated overall median progression-free survival (PFS) and overall survival (OS) were 26.2 months [95% confidence interval (CI) 12.5-39.9] and 50.8 months (95% CI 0-107.3), respectively. Patients with detectable mutations in plasma had significantly worse median PFS compared to patients with undetectable mutation (13.1 versus 70.1 months) and shorter median OS (20.7 versus not reached). High circulating tumour DNA (ctDNA) concentrations of mutated KRAS were significantly associated with shorter PFS [hazard ratio (HR) 1.008, 95% CI 1.004-1.012] and OS (HR 1.007, 95% CI 1.003-1.011). All associations remained statistically significant in multivariable analyses. In conclusion, ddPCR is an accurate and easily feasible technique for quantification of KRAS mutations in ctDNA. The presence of detectable KRAS mutation in plasma at baseline was associated with worse PFS and OS. High concentration of mutated KRAS in ctDNA was an independent negative prognostic factor for both PFS and OS.
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Affiliation(s)
- Sissel Gyrid Freim Wahl
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Hong Yan Dai
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Elisabeth F Emdal
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Anine L Ottestad
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
| | - Vibeke G Dale
- Department of PathologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Elin Richardsen
- Department of Medical BiologyUiT, The Arctic University of NorwayTromsøNorway
- Department of Clinical PathologyUniversity Hospital of North NorwayTromsøNorway
| | - Tarje O Halvorsen
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular MedicineNTNU, Norwegian University of Technology and ScienceTrondheimNorway
- Department of OncologySt. Olavs Hospital, Trondheim University HospitalTrondheimNorway
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Yang Z, Chen W, Wang J, Shi M, Zhang R, Dai S, Wu T, Zhao M. Programmable One-Pot Enzymatic Reaction for Direct Fluorescence Detection of Ultralow-Abundance Mutations in the DNA Duplex. Anal Chem 2021; 93:7086-7093. [PMID: 33901400 DOI: 10.1021/acs.analchem.1c00564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sensitive detection of low-abundance driver mutations may provide valuable information for precise clinical treatment. Compared to next-generation sequencing and droplet digital PCR methods, fluorescent probes show great flexibility in rapid detection of specific mutations with high sensitivity and easily accessible instruments. However, existing approaches with fluorescent probes need an additional step to convert duplex DNA to single-stranded DNA (ssDNA) before the detection step, which increases the time, cost, and risk of loss of low-input target strands. In this work, we attempt to integrate the ssDNA-generation step with the subsequent detection into a programable one-pot reaction by employing lambda exonuclease (λ exo), a versatile nanopore nuclease which exercises different functions on different substrates. The capability of λ exo in discrimination of mismatched bases in 5'- FAM-ended 2 nt-unpaired DNA duplexes was first demonstrated. Specific fluorescent probes were developed for EGFR exon 19 E746-A750del and PIK3CA E545K mutations with discrimination factors as high as 8470 and 884, respectively. By mixing the probes and λ exo with the PCR products of cell-free circulating DNA extracted from plasma samples, the reaction was immediately initiated, which allowed sensitive detection of the two types of mutations at an abundance as low as 0.01% within less than 2 h. Compared to existing approaches, the new method has distinct advantages in simplicity, low cost, and rapidity. It provides a convenient tool for companion diagnostic tests and other routine analysis targeting genetic mutations in clinical samples.
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Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Minghe Shi
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ruilan Zhang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shenbin Dai
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Osteosarcoma, chondrosarcoma and Ewing sarcoma: Clinical aspects, biomarker discovery and liquid biopsy. Crit Rev Oncol Hematol 2021; 162:103340. [PMID: 33894338 DOI: 10.1016/j.critrevonc.2021.103340] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
Bone sarcomas, although rare, are associated with significant morbidity and mortality. The most frequent primary bone cancers include osteosarcoma, chondrosarcoma and Ewing sarcoma. The treatment approaches are heterogeneous and mainly chosen based on precise tumour staging. Unfortunately, clinical outcome has not changed significantly in over 30 years and tumour grade is still the best prognosticator of metastatic disease and survival. An option to improve this scenario is to identify molecular biomarkers in the early stage of the disease, or even before the disease onset. Blood-based liquid biopsies are a promising, non-invasive way to achieve this goal and there are an increasing number of studies which investigate their potential application in bone cancer diagnosis, prognosis and personalised therapy. This review summarises the interplay between clinical and molecular aspects of the three main bone sarcomas, alongside biomarker discovery and promising applications of liquid biopsy in each tumour context.
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Lund-Andersen C, Torgunrud A, Fleten KG, Flatmark K. Omics analyses in peritoneal metastasis-utility in the management of peritoneal metastases from colorectal cancer and pseudomyxoma peritonei: a narrative review. J Gastrointest Oncol 2021; 12:S191-S203. [PMID: 33968437 DOI: 10.21037/jgo-20-136] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
High-throughput "-omics" analysis may provide a broader and deeper understanding of cancer biology to define prognostic and predictive biomarkers and identify novel therapy targets. In this review we provide an overview of studies where the peritoneal tumor component of peritoneal metastases from colorectal cancer (PM-CRC) and pseudomyxoma peritonei (PMP) were analyzed. Most of the available data was derived from DNA mutation analysis, but a brief review of findings from transcriptomic and protein expression analysis was also performed. Studies reporting genomic analysis of peritoneal tumor samples from 1,779 PM-CRC and 623 PMP cases were identified. The most frequently mutated genes in PM-CRC were KRAS, APC, SMAD4, BRAF, and PIK3CA, while in PMP KRAS, GNAS, FAT4, TGFBR1, TP53 and SMAD3/4 mutations were most commonly identified. Analyses were performed by single-gene analyses and to some extent targeted next-generation sequencing, and a very limited amount of broad explorative data exists. The investigated cohorts were typically small and heterogeneous with respect to the methods used and to the reporting of clinical data. This was even more apparent regarding transcriptomic and protein data, as the low number of cases examined and quality of clinical data would not support firm conclusions. Even for the most frequently mutated genes, the results varied greatly; for instance, KRAS mutations were reported at frequencies between 20-57% in PM-CRC and 38-100% in PMP. Such variation could be caused by random effects in small cohorts, heterogeneity in patient selection, or sensitivity of applied technology. Although a large number of samples have been subjected to analysis, cross-study comparisons are difficult to perform, and combined with small cohorts and varying quality and detail of clinical information, the observed variation precludes useful interpretation in a clinical context. Although omics data in theory could answer questions to aid management decisions in PM-CRC and PMP, the existing data does not presently support clinical implementation. With the necessary technologies being generally available, the main challenge will be to obtain sufficiently large, representative cohorts with adequate clinical data and standardized reporting of results. Importantly, studies where the focus is specifically on peritoneal disease are needed, where the study designs are aligned with clearly defined research questions to allow robust conclusions. Such studies are highly warranted if patients with PM-CRC and PMP are to derive benefit from recent advances in precision cancer medicine.
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Affiliation(s)
- Christin Lund-Andersen
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Annette Torgunrud
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Karianne Giller Fleten
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterological Surgery, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis. PLoS One 2021; 16:e0248775. [PMID: 33770081 PMCID: PMC7997033 DOI: 10.1371/journal.pone.0248775] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Methods Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. Results A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74–0.79), 0.87 (95%CI: 0.85–0.89), and 23.96 (95%CI: 13.72–41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76–8.19) and 0.29 (95%CI: 0.21–0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Conclusion Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. Trial registration PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Yuanyuan Wei
- Department of Physiology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
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50
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Romanelli K, Wells J, Patel A, Mendonca Torres M, Costello J, Jensen K, Vasko V. Clinical and molecular characterization of thyroid cancer when seen as a second malignant neoplasm. Ther Adv Endocrinol Metab 2021; 12:20420188211058327. [PMID: 35154635 PMCID: PMC8832328 DOI: 10.1177/20420188211058327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Second malignant neoplasms (SMN) are among the most serious long-term adverse health conditions in cancer survivors. The aim of this study was to characterize clinical findings of patients who developed thyroid cancers as SMN, and to examine genomic alterations in thyroid cancer tissue. METHODS Retrospective analysis of medical records from patients seen for management of thyroid cancer over 10-year period was performed. Clinical and pathologic data were retrieved from their medical charts. Tumor DNA and RNA were extracted from formalin-fixed, paraffin-embedded tissue and subjected to next-generation sequencing (NGS) using Ion Torrent Oncomine Focus Assay. Microfluidic digital polymerase chain reactions (PCRs) were performed using QIAcuity Digital PCR System to identify BRAF V600E mutations and RET/PTC fusions. RESULTS Sixteen of 620 patients operated for thyroid cancer had history of previously diagnosed malignancy. Eight patients were male and eight patients were female, with a median age at diagnosis of 58.5 years (range, 4-78). Four patients had history of pediatric malignancy (PedCa), and 12 patients had a history of prior malignancy as an adult (AdCa). The latency periods for development of SMN in PedCa and AdCa patients were 10.8 (±5.2) years and 9.5 (±5.2) years, respectively. Histopathology revealed papillary thyroid cancers in 15 cases, and follicular thyroid cancer in 1 case. All tumors were classified as T1 or T2, and there were no patients presenting with metastases at the time of surgery. Genomic alterations were detected in 13/16 (81.2%) tumors including eight gene mutations (BRAF V600E (N = 4), RAS (N = 2), PI3CA (N = 2) and five gene fusions (RET/PTC1 (N = 4) and STRN/ALK (N = 1). In patients with PedCa and AdCa, mutations were detected in 1/4 (25%) and 7/12 (58.3%), respectively, p = 0.56; and fusions were detected in 3/4 (75%) and 2/12 (16.6%), respectively, p = 0.06. In patients with and without history of therapeutic irradiation, mutations were detected with the same frequencies (5/10 (50%), and 3/6 (50%), respectively, p = 1.0). Gene fusions were detected in patients with and without history of irradiation in 5/10 (55.5%) and 0/6 (0%), respectively, p = 0.09. CONCLUSIONS Monitoring of cancer survivors for thyroid disorders allowed diagnosis of second thyroid cancers at early stages. Second thyroid cancers harbor genomic alterations that are typical for sporadic as well as for radio-induced thyroid cancers.
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Affiliation(s)
- Kristen Romanelli
- Department of Pediatric, Hematology/Oncology,
Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Justin Wells
- Department of Pathology, Walter Reed National
Military Medical Center, Bethesda, MD, USA
| | - Aneeta Patel
- Department of Pediatrics, Uniformed Services
University of Health Sciences, Bethesda, MD, USA
| | - Maria Mendonca Torres
- Department of Pediatrics, Uniformed Services
University of Health Sciences, Bethesda, MD, USA
| | - John Costello
- Department of Pediatrics, Uniformed Services
University of Health Sciences, Bethesda, MD, USA
| | - Kirk Jensen
- Department of Pediatrics, Uniformed Services
University of Health Sciences, Bethesda, MD, USA
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