Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer
Early detection of cancer holds high promise for reducing cancer-related mortality. Detection of circulating tumor-specific nucleic acids holds promise, but sensitivity and specificity issues remain with current technology. We studied cell-free RNA (cfRNA) in patients with non-small cell lung cancer...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-02-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/12/2/353 |
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| author | Martin Metzenmacher Renáta Váraljai Balazs Hegedüs Igor Cima Jan Forster Alexander Schramm Björn Scheffler Peter A. Horn Christoph A. Klein Tibor Szarvas Hennig Reis Nicola Bielefeld Alexander Roesch Clemens Aigner Volker Kunzmann Marcel Wiesweg Jens T. Siveke Martin Schuler Smiths S. Lueong |
| author_facet | Martin Metzenmacher Renáta Váraljai Balazs Hegedüs Igor Cima Jan Forster Alexander Schramm Björn Scheffler Peter A. Horn Christoph A. Klein Tibor Szarvas Hennig Reis Nicola Bielefeld Alexander Roesch Clemens Aigner Volker Kunzmann Marcel Wiesweg Jens T. Siveke Martin Schuler Smiths S. Lueong |
| author_sort | Martin Metzenmacher |
| collection | DOAJ |
| description | Early detection of cancer holds high promise for reducing cancer-related mortality. Detection of circulating tumor-specific nucleic acids holds promise, but sensitivity and specificity issues remain with current technology. We studied cell-free RNA (cfRNA) in patients with non-small cell lung cancer (NSCLC; <i>n</i> = 56 stage IV, <i>n</i> = 39 stages I-III), pancreatic cancer (PDAC, <i>n</i> = 20 stage III), malignant melanoma (MM, <i>n</i> = 12 stage III-IV), urothelial bladder cancer (UBC, <i>n</i> = 22 stage II and IV), and 65 healthy controls by means of next generation sequencing (NGS) and real-time droplet digital PCR (RT-ddPCR). We identified 192 overlapping upregulated transcripts in NSCLC and PDAC by NGS, more than 90% of which were noncoding. Previously reported transcripts (e.g., HOTAIRM1) were identified. Plasma cfRNA transcript levels of POU6F2-AS2 discriminated NSCLC from healthy donors (AUC = 0.82 and 0.76 for stages IV and I−III, respectively) and significantly associated (<i>p</i> = 0.017) with the established tumor marker Cyfra 21-1. cfRNA yield and POU6F2-AS transcript abundance discriminated PDAC patients from healthy donors (AUC = 1.0). POU6F2-AS2 transcript was significantly higher in MM (<i>p</i> = 0.044). In summary, our findings support further validation of cfRNA detection by RT-ddPCR as a biomarker for early detection of solid cancers. |
| first_indexed | 2024-03-12T08:26:39Z |
| format | Article |
| id | doaj.art-4874d5a973c148d09a6666de21c39766 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-12T08:26:39Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-4874d5a973c148d09a6666de21c397662023-09-02T18:01:15ZengMDPI AGCancers2072-66942020-02-0112235310.3390/cancers12020353cancers12020353Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of CancerMartin Metzenmacher0Renáta Váraljai1Balazs Hegedüs2Igor Cima3Jan Forster4Alexander Schramm5Björn Scheffler6Peter A. Horn7Christoph A. Klein8Tibor Szarvas9Hennig Reis10Nicola Bielefeld11Alexander Roesch12Clemens Aigner13Volker Kunzmann14Marcel Wiesweg15Jens T. Siveke16Martin Schuler17Smiths S. Lueong18Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, GermanyDepartment of Dermatology, University Hospital Essen, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, GermanyDepartment of Thoracic Surgery, Ruhrlandklinik, University Duisburg-Essen, D-45239 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyLaboratory for Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyInstitute for Transfusion Medicine, University Hospital Essen, 45122 Essen, GermanyExperimental Medicine and Therapy Research, University of Regensburg, 93053 Regensburg, GermanyDepartment of Urology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45122 Essen, GermanyInstitute of Pathology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyDepartment of Dermatology, University Hospital Essen, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, GermanyDepartment of Thoracic Surgery, Ruhrlandklinik, University Duisburg-Essen, D-45239 Essen, GermanyDepartment of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, GermanyDepartment of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyDepartment of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, GermanyGerman Cancer Consortium (DKTK), Partner site University Hospital Essen, Hufelandstrasse 55, 45122 Essen, GermanyEarly detection of cancer holds high promise for reducing cancer-related mortality. Detection of circulating tumor-specific nucleic acids holds promise, but sensitivity and specificity issues remain with current technology. We studied cell-free RNA (cfRNA) in patients with non-small cell lung cancer (NSCLC; <i>n</i> = 56 stage IV, <i>n</i> = 39 stages I-III), pancreatic cancer (PDAC, <i>n</i> = 20 stage III), malignant melanoma (MM, <i>n</i> = 12 stage III-IV), urothelial bladder cancer (UBC, <i>n</i> = 22 stage II and IV), and 65 healthy controls by means of next generation sequencing (NGS) and real-time droplet digital PCR (RT-ddPCR). We identified 192 overlapping upregulated transcripts in NSCLC and PDAC by NGS, more than 90% of which were noncoding. Previously reported transcripts (e.g., HOTAIRM1) were identified. Plasma cfRNA transcript levels of POU6F2-AS2 discriminated NSCLC from healthy donors (AUC = 0.82 and 0.76 for stages IV and I−III, respectively) and significantly associated (<i>p</i> = 0.017) with the established tumor marker Cyfra 21-1. cfRNA yield and POU6F2-AS transcript abundance discriminated PDAC patients from healthy donors (AUC = 1.0). POU6F2-AS2 transcript was significantly higher in MM (<i>p</i> = 0.044). In summary, our findings support further validation of cfRNA detection by RT-ddPCR as a biomarker for early detection of solid cancers.https://www.mdpi.com/2072-6694/12/2/353liquid biopsycfrnacancerddpcrngspou6f2-as2early detection |
| spellingShingle | Martin Metzenmacher Renáta Váraljai Balazs Hegedüs Igor Cima Jan Forster Alexander Schramm Björn Scheffler Peter A. Horn Christoph A. Klein Tibor Szarvas Hennig Reis Nicola Bielefeld Alexander Roesch Clemens Aigner Volker Kunzmann Marcel Wiesweg Jens T. Siveke Martin Schuler Smiths S. Lueong Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer Cancers liquid biopsy cfrna cancer ddpcr ngs pou6f2-as2 early detection |
| title | Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer |
| title_full | Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer |
| title_fullStr | Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer |
| title_full_unstemmed | Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer |
| title_short | Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer |
| title_sort | plasma next generation sequencing and droplet digital qpcr based quantification of circulating cell free rna for noninvasive early detection of cancer |
| topic | liquid biopsy cfrna cancer ddpcr ngs pou6f2-as2 early detection |
| url | https://www.mdpi.com/2072-6694/12/2/353 |
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