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Chen J, Liu X, Zhang Z, Su R, Geng Y, Guo Y, Zhang Y, Su M. Early Diagnostic Markers for Esophageal Squamous Cell Carcinoma: CNA Gene Identification and cfDNA Detection. J Transl Med 2024:102127. [PMID: 39182610 DOI: 10.1016/j.labinv.2024.102127] [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: 05/25/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
The high mortality rate of esophageal squamous cell carcinoma (ESCC) is exacerbated by the absence of early diagnostic markers. The pronounced heterogeneity of mutations in ESCC renders copy number alterations (CNAs) more prevalent among patients. The identification of CNA genes within esophageal squamous dysplasia (ESD), a precancerous stage of ESCC, is crucial for advancing early detection efforts. Utilization of liquid biopsies via droplet-based digital PCR (ddPCR) offers a novel strategy for detecting incipient tumor traces. This study undertook a thorough investigation of CNA profiles across ESCC development stages, integrating data from existing databases and prior investigations to pinpoint and confirm CNA markers conducive to early detection of ESCC. Targeted sequencing was employed to select potential early detection genes, followed by the establishment of prediction models for ESCC early detection using ddPCR. Our analysis reveals widespread CNAs during the ESD stage, mirroring the CNA landscape observed in ESCC. A total of 40 CNA genes were identified as highly frequent in both ESCC and ESD lesions, through a comprehensive gene-level CNA analysis encompassing ESD and ESCC tissues, ESCC cell lines, and pan-cancer datasets. Subsequent validation of five candidate markers via ddPCR underscored the efficacy of combined predictive models-encompassing PIK3CA, SOX2, EGFR, MYC, and CCND1-in early ESCC screening, as evidenced by the area under the curve (AUC) values exceeding 0.92 (p<0.0001) across various detection contexts. The findings highlight the significant utility of CNA genes in the early screening of ESCC, presenting robust models that could facilitate early detection, broad-scale population screening, and adjunctive diagnosis.
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Affiliation(s)
- Jiamin Chen
- Institute of Clinical Pathology& Department of Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Xi Liu
- Institute of Clinical Pathology& Department of Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Zhihua Zhang
- Institute of Clinical Pathology& Department of Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Ruibing Su
- Institute of Clinical Pathology& Department of Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China; Department of Cardiology, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Yiqun Geng
- Guangdong Provincial International Collaborative Center of Molecular Medicine, Laboratory of Molecular Pathology, Shantou University Medical College, Shantou 515041, China
| | - Yi Guo
- Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Yimin Zhang
- Clinical research center, Shantou Central Hospital, Guangdong Province, Shantou 515041, China
| | - Min Su
- Institute of Clinical Pathology& Department of Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, Guangdong, China.
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Henriksen TV, Demuth C, Frydendahl A, Nors J, Nesic M, Rasmussen MH, Reinert T, Larsen OH, Jaensch C, Løve US, Andersen PV, Kolbro T, Thorlacius-Ussing O, Monti A, Gögenur M, Kildsig J, Bondeven P, Schlesinger NH, Iversen LH, Gotschalck KA, Andersen CL. Unraveling the potential clinical utility of circulating tumor DNA detection in colorectal cancer-evaluation in a nationwide Danish cohort. Ann Oncol 2024; 35:229-239. [PMID: 37992872 DOI: 10.1016/j.annonc.2023.11.009] [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: 06/19/2023] [Revised: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment. Digital PCR (dPCR) offers low analysis costs and turnaround times of less than a day, making it ripe for clinical implementation. Here, we used tumor-informed dPCR for ctDNA detection in a large colorectal cancer (CRC) cohort to evaluate the potential for post-operative risk assessment and serial monitoring, and how the metastatic site may impact ctDNA detection. Additionally, we assessed how altering the ctDNA-calling algorithm could customize performance for different clinical settings. PATIENTS AND METHODS Stage II-III CRC patients (N = 851) treated with a curative intent were recruited. Based on whole-exome sequencing on matched tumor and germline DNA, a mutational target was selected for dPCR analysis. Plasma samples (8 ml) were collected within 60 days after operation and-for a patient subset (n = 246)-every 3-4 months for up to 36 months. Single-target dPCR was used for ctDNA detection. RESULTS Both post-operative and serial ctDNA detection were prognostic of recurrence [hazard ratio (HR) = 11.3, 95% confidence interval (CI) 7.8-16.4, P < 0.001; HR = 30.7, 95% CI 20.2-46.7, P < 0.001], with a cumulative ctDNA detection rate of 87% at the end of sample collection in recurrence patients. The ctDNA growth rate was prognostic of survival (HR = 2.6, 95% CI 1.5-4.4, P = 0.001). In recurrence patients, post-operative ctDNA detection was challenging for lung metastases (4/21 detected) and peritoneal metastases (2/10 detected). By modifying the cut-off for calling a sample ctDNA positive, we were able to adjust the sensitivity and specificity of our test for different clinical contexts. CONCLUSIONS The presented results from 851 stage II-III CRC patients demonstrate that our personalized dPCR approach effectively detects MRD after operation and shows promise for serial ctDNA detection for recurrence surveillance. The ability to adjust sensitivity and specificity shows exciting potential to customize the ctDNA caller for specific clinical settings.
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Affiliation(s)
- T V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - A Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - J Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M Nesic
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - M H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - T Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - O H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus
| | - C Jaensch
- Department of Surgery, Regional Hospital Gødstrup, Herning
| | - U S Løve
- Department of Surgery, Regional Hospital Viborg, Viborg
| | - P V Andersen
- Department of Surgery, Odense University Hospital, Odense
| | - T Kolbro
- Department of Surgery, Odense University Hospital, Svendborg
| | | | - A Monti
- Department of Surgery, North Denmark Regional Hospital Hjørring, Hjørring
| | - M Gögenur
- Center for Surgical Sciences, Zealand University Hospital, Køge
| | - J Kildsig
- Department of Surgery, Copenhagen University Hospital, Herlev
| | - P Bondeven
- Department of Surgery, Regional Hospital Randers, Randers
| | - N H Schlesinger
- Department of Surgery, Copenhagen University Hospital, Bispebjerg
| | - L H Iversen
- Department of Surgery, Aarhus University Hospital, Aarhus
| | - K A Gotschalck
- Department of Surgery, Regional Hospital Horsens, Horsens, Denmark
| | - C L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus; Department of Clinical Medicine, Aarhus University, Aarhus.
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3
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Rozeman EA, Versluis JM, Sikorska K, Hoefsmit EP, Dimitriadis P, Rao D, Lacroix R, Grijpink-Ongering LG, Lopez-Yurda M, Heeres BC, van de Wiel BA, Flohil C, Sari A, Heijmink SWTPJ, van den Broek D, Broeks A, de Groot JWB, Vollebergh MA, Wilgenhof S, van Thienen JV, Haanen JBAG, Blank CU. IMPemBra: a phase 2 study comparing pembrolizumab with intermittent/short-term dual MAPK pathway inhibition plus pembrolizumab in patients with melanoma harboring the BRAFV600 mutation. J Immunother Cancer 2023; 11:e006821. [PMID: 37479483 PMCID: PMC10364170 DOI: 10.1136/jitc-2023-006821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Continuous combination of MAPK pathway inhibition (MAPKi) and anti-programmed death-(ligand) 1 (PD-(L)1) showed high response rates, but only limited improvement in progression-free survival (PFS) at the cost of a high frequency of treatment-related adverse events (TRAE) in patients with BRAFV600-mutated melanoma. Short-term MAPKi induces T-cell infiltration in patients and is synergistic with anti-programmed death-1 (PD-1) in a preclinical melanoma mouse model. The aim of this phase 2b trial was to identify an optimal regimen of short-term MAPKi with dabrafenib plus trametinib in combination with pembrolizumab. METHODS Patients with treatment-naïve BRAFV600E/K-mutant advanced melanoma started pembrolizumab 200 mg every 3 weeks. In week 6, patients were randomized to continue pembrolizumab only (cohort 1), or to receive, in addition, intermittent dabrafenib 150 mg two times per day plus trametinib 2 mg one time per day for two cycles of 1 week (cohort 2), two cycles of 2 weeks (cohort 3), or continuously for 6 weeks (cohort 4). All cohorts continued pembrolizumab for up to 2 years. Primary endpoints were safety and treatment-adherence. Secondary endpoints were objective response rate (ORR) at week 6, 12, 18 and PFS. RESULTS Between June 2016 and August 2018, 33 patients with advanced melanoma have been included and 32 were randomized. Grade 3-4 TRAE were observed in 12%, 12%, 50%, and 63% of patients in cohort 1, 2, 3, and 4, respectively. All planned targeted therapy was given in 88%, 63%, and 38% of patients in cohort 2, 3, and 4. ORR at week 6, 12, and 18 were 38%, 63%, and 63% in cohort 1; 25%, 63%, and 75% in cohort 2; 25%, 50%, and 75% in cohort 3; and 0%, 63%, and 50% in cohort 4. After a median follow-up of 43.5 months, median PFS was 10.6 months for pembrolizumab monotherapy and not reached for patients treated with pembrolizumab and intermittent dabrafenib and trametinib (p=0.17). The 2-year and 3-year landmark PFS were both 25% for cohort 1, both 63% for cohort 2, 50% and 38% for cohort 3 and 75% and 60% for cohort 4. CONCLUSIONS The combination of pembrolizumab plus intermittent dabrafenib and trametinib seems more feasible and tolerable than continuous triple therapy. The efficacy is promising and appears to be favorable over pembrolizumab monotherapy. TRIAL REGISTRATION NUMBER NCT02625337.
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Affiliation(s)
- Elisa A Rozeman
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Judith M Versluis
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karolina Sikorska
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esmée P Hoefsmit
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petros Dimitriadis
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Disha Rao
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben Lacroix
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marta Lopez-Yurda
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Birthe C Heeres
- Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart A van de Wiel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Claudie Flohil
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aysegul Sari
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marieke A Vollebergh
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sofie Wilgenhof
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Johannes V van Thienen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - John B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian U Blank
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical center, Leiden, The Netherlands
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Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies. Int J Mol Sci 2023; 24:ijms24020923. [PMID: 36674433 PMCID: PMC9865676 DOI: 10.3390/ijms24020923] [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: 11/27/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Low-level tumor somatic DNA mutations in tissue and liquid biopsies obtained from cancer patients can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up, or early cancer detection. Unless detected, such low-frequency DNA alterations can misinform patient management decisions or become missed opportunities for personalized medicine. Next-generation sequencing technologies and digital-PCR can resolve low-level mutations but require access to specialized instrumentation, time, and resources. Enzymatic-based approaches to detection of low-level mutations provide a simple, straightforward, and affordable alternative to enrich and detect such alterations and is broadly available to low-resource laboratory settings. This review summarizes the traditional uses of enzymatic mutation detection and describes the latest exciting developments, potential, and applications with specific reference to the field of liquid biopsy in cancer.
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Henriksen TV, Reinert T, Rasmussen MH, Demuth C, Løve US, Madsen AH, Gotschalck KA, Iversen LH, Andersen CL. Comparing single-target and multi-target approaches for postoperative circulating tumor DNA detection in stage II-III colorectal cancer patients. Mol Oncol 2022; 16:3654-3665. [PMID: 35895438 PMCID: PMC9580876 DOI: 10.1002/1878-0261.13294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Circulating tumour DNA (ctDNA) detection for postoperative risk stratification in cancer patients has great clinical potential. However, low ctDNA abundances complicates detection. Multitarget (MT) detection strategies have been developed to increase sensitivity. Yet, empirical evidence supporting performance gains of MT vs. single‐target (ST) strategies in a postoperative setting is limited. We compared ctDNA detection in 379 paired plasma samples from 112 stage II–III colorectal cancer patients by ST digital PCR and MT sequencing of 16 patient‐specific variants. The strategies exhibited good concordance (90%, Cohen's Kappa 0.79), with highly correlated ctDNA quantifications (Pearson r = 0.985). A difference was observed in ctDNA detection preoperatively (ST 72/92, MT 88/92). However, no difference was observed immediately after surgery in recurrence (ST 11/22, MT 10/22) or nonrecurrence (both 2/34) patients. In serial samples, detection was similar within recurrence (ST 13/16, MT 14/16) and nonrecurrence (ST 3/49, MT 1/49) patients. Both approaches yielded similar lead times to standard‐of‐care radiology (ST 4.0 months, MT 4.1 months). Our findings do not support significant performance gains of the MT strategy over the ST strategy for postoperative ctDNA detection.
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Affiliation(s)
- Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Uffe Schou Løve
- Department of Surgery, Regional Hospital Viborg, Banevejen 7C, DK-8800, Viborg, Denmark
| | - Anders Husted Madsen
- Department of Surgery, Regional Hospital Herning, Hospitalsparken 15, DK-7400, Herning, Denmark
| | | | - Lene Hjerrild Iversen
- Department of Surgery, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 35, DK-8200, Aarhus N, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
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Henriksen TV, Drue SO, Frydendahl A, Demuth C, Rasmussen MH, Reinert T, Pedersen JS, Andersen CL. Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR. Clin Chem 2022; 68:657-667. [PMID: 35030248 DOI: 10.1093/clinchem/hvab274] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller. METHODS We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods. RESULTS For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty. CONCLUSIONS Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.
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Affiliation(s)
- Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Simon O Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jakob S Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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8
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Oranger A, Manzari C, Chiara M, Notario E, Fosso B, Parisi A, Bianco A, Iacobellis M, d'Avenia M, D'Erchia AM, Pesole G. Accurate detection and quantification of SARS-CoV-2 genomic and subgenomic mRNAs by ddPCR and meta-transcriptomics analysis. Commun Biol 2021; 4:1215. [PMID: 34686777 PMCID: PMC8536764 DOI: 10.1038/s42003-021-02748-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/16/2021] [Indexed: 01/04/2023] Open
Abstract
SARS-CoV-2 replication requires the synthesis of a set of structural proteins expressed through discontinuous transcription of ten subgenomic mRNAs (sgmRNAs). Here, we have fine-tuned droplet digital PCR (ddPCR) assays to accurately detect and quantify SARS-CoV-2 genomic ORF1ab and sgmRNAs for the nucleocapsid (N) and spike (S) proteins. We analyzed 166 RNA samples from anonymized SARS-CoV-2 positive subjects and we observed a recurrent and characteristic pattern of sgmRNAs expression in relation to the total viral RNA content. Additionally, expression profiles of sgmRNAs, as determined by meta-transcriptomics sequencing of a subset of 110 RNA samples, were highly correlated with those obtained by ddPCR. By providing a comprehensive and dynamic snapshot of the levels of SARS-CoV-2 sgmRNAs in infected individuals, our results may contribute a better understanding of the dynamics of transcription and expression of the genome of SARS-CoV-2 and facilitate the development of more accurate molecular diagnostic tools for the stratification of COVID-19 patients. Oranger et al use digital droplet PCR to develop an assay that provides a dynamic snapshot of the levels of SARS-CoV-2 sub-genomic messanger RNA in infected individuals. This has the potential to improve diagnostic accuracy for COVID-19
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Affiliation(s)
- Annarita Oranger
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Matteo Chiara
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126, Bari, Italy.,Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Elisabetta Notario
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, 70017, Putignano (Bari), Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, 70017, Putignano (Bari), Italy
| | - Michela Iacobellis
- Servizio Centralizzato Aziendale di Citopatologia e Screening- PO "Di Venere" - ASL, 70131, Bari, Italy
| | - Morena d'Avenia
- Servizio Centralizzato Aziendale di Citopatologia e Screening- PO "Di Venere" - ASL, 70131, Bari, Italy
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy. .,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126, Bari, Italy. .,Consorzio Interuniversitario Biotecnologie, 34100, Trieste, Italy.
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy. .,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126, Bari, Italy. .,Consorzio Interuniversitario Biotecnologie, 34100, Trieste, Italy.
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