Multiplex Detection of Clinically Relevant Mutations in Liquid Biopsies of Cancer Patients Using a Hybridization-Based Platform

Giménez‐Capitán, Ana; Bracht, Jillian Wilhelmina Paulina; Garcı́a, Juan José; Jordana‐Ariza, Núria; García, Beatriz; Garzón, Mónica; Mayo‐de‐las‐Casas, Clara; Viteri-Ramírez, S.; Martínez‐Bueno, Alejandro; Aguilar, Andrés; Sullivan, Ivana-Gabriela; Johnson, Eric; Huang, Chung‐Ying; Gerlach, Jay; Warren, Sarah; Beechem, Joseph M.; Teixidó, Cristina; Rosell, Rafael; Reguart, Noemı́; Molina-Vila, Miguel Ángel

doi:10.1093/clinchem/hvaa248

Cited by 12 publications

(7 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Clinical tests have been developed employing nCounter technology, including the FDA-approved nCounter Prosigna test, which stratifies breast cancer subtypes and predicts recurrence risk in post-menopausal women [27,28], and the tumor inflammation signature (TIS) assay, which forecasts PD-1 checkpoint blockade and clinical response across several tumor types [29]. This platform has also been employed for the discovery of potential biomarker signatures in various types of LB biosources, including cfDNA, cell-free RNA (cfRNA), EVs (including DNA, micro RNA (miRNA) and mRNA), as well as CTCs [30][31][32][33][34][35][36]. However, the platelet transcriptome has not been explored yet through this technology for LB purposes.…”

Section: Introductionmentioning

confidence: 99%

Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection

D’Ambrosi

Giannoukakos

Antunes-Ferreira

et al. 2023

IJMS

Self Cite

View full text Add to dashboard Cite

Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results in insufficient sensitivity and specificity necessary to reach diagnostic utility. Combinatorial biomarker approaches may offer a more reliable diagnosis. Here, we investigated the synergistic contributions of circRNA and mRNA signatures derived from blood platelets as biomarkers for lung cancer detection. We developed a comprehensive bioinformatics pipeline permitting an analysis of platelet-circRNA and mRNA derived from non-cancer individuals and lung cancer patients. An optimal selected signature is then used to generate the predictive classification model using machine learning algorithm. Using an individual signature of 21 circRNA and 28 mRNA, the predictive models reached an area under the curve (AUC) of 0.88 and 0.81, respectively. Importantly, combinatorial analysis including both types of RNAs resulted in an 8-target signature (6 mRNA and 2 circRNA), enhancing the differentiation of lung cancer from controls (AUC of 0.92). Additionally, we identified five biomarkers potentially specific for early-stage detection of lung cancer. Our proof-of-concept study presents the first multi-analyte-based approach for the analysis of platelets-derived biomarkers, providing a potential combinatorial diagnostic signature for lung cancer detection.

show abstract

Section: Introductionmentioning

confidence: 99%

Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection

D’Ambrosi

Giannoukakos

Antunes-Ferreira

et al. 2023

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…This technology has been embraced in translational research, including the development and validation of liquid biopsies, due to its capability of working with a low quantity of highly degraded samples [ 15 , 16 ]. Recent studies reported the use of nCounter for the study of several categories of circulating biomarkers [ 17 , 18 , 19 , 20 , 21 ], including EV-derived DNA [ 22 ], miRNA [ 23 , 24 ], mRNA [ 25 ] and circRNA [ 26 ]. However, nCounter analysis of EV-circRNAs has not been investigated for early detection of lung cancer.…”

Section: Introductionmentioning

confidence: 99%

Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer

et al. 2022

View full text Add to dashboard Cite

Background: The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. However, standardized and robust protocols need to be developed to boost their potential in the clinical setting. Although nCounter has been used for the analysis of other liquid biopsy substrates and biomarkers, it has never been employed for EV-circRNA analysis of LC patients. Methods: EVs were isolated from early-stage LC patients (n = 36) and controls (n = 30). Different volumes of plasma, together with different number of pre-amplification cycles, were tested to reach the best nCounter outcome. Differential expression analysis of circRNAs was performed, along with the testing of different machine learning (ML) methods for the development of a prognostic signature for LC. Results: A combination of 500 μL of plasma input with 10 cycles of pre-amplification was selected for the rest of the study. Eight circRNAs were found upregulated in LC. Further ML analysis selected a 10-circRNA signature able to discriminate LC from controls with AUC ROC of 0.86. Conclusions: This study validates the use of the nCounter platform for multiplexed EV-circRNA expression studies in LC patient samples, allowing the development of prognostic signatures.

show abstract

“…Samples previously evaluated for cyto-molecular NGS testing include FFPE cell blocks, ascites/ peritoneal washing supernatants, cell pellets, direct smears, cells scraped from slides, and additional aspirated samples (14)(15)(16). NGS analysis of FFPE cell blocks from two pancreatic cancer patients and supernatants of ascitic fluid from three gastric and one colon cancer patients showed concordant results with tissue samples (14,17). Other studies evaluated cell free DNA (cfNDA) from ascitic fluid and detected TP53, EGFR, ALK, BRAF from ovary and lung cancer patients using duplex sequencing or PNA-Q-PCR (18)(19)(20).…”

Section: Discussionmentioning

confidence: 92%

Targeted Sequencing of Ascites and Peritoneal Washing Fluid of Patients With Gastrointestinal Cancers and Their Clinical Applications and Limitations

et al. 2021

View full text Add to dashboard Cite

Cytology from gastrointestinal (GI) cancers is frequently obtained from ascites and peritoneal washing fluids. Examination of ascites and peritoneal washing fluids from patients with GI cancers can help in the tumor staging and prognosis. Tumor-derived DNA in these cytology samples can be a target for next generation sequencing (NGS). Targeted NGS was evaluated in ascites and peritoneal washing samples obtained from 33 patients with GI cancers. These sequences were compared with those from tumor tissue samples, and correlated with cytopathologic findings of the ascites and peritoneal fluid samples. The correlation between fluid and tissue genotyping results was 25%, with a sensitivity of 21.43%. The volume of tumor contained within the fluid samples was low, ranging from ~0 to 10%. Importantly, the sensitivity of detection of somatic mutations in the fluid samples could be increased to 69.2% by assessing samples containing >2% tumor volume. Evaluation of cells from ascitic fluid showed the presence of KRAS, TP53, and CDH1 mutations in 33, 13, and 7%, respectively, of patients with pancreatic cancer, and the presence of KRAS, TP53, and APC mutations in 25, 12, and 13%, respectively, of patients with gastric cancer. Ascites of one of the latter patients acquired KRAS mutation, which was a novel mutation during metastasis. Targeted NGS of ascites and peritoneal washing fluid have clinical implications, as well as limitations, in patients with GI cancers. NGS-based cytology examination may expand cytomolecular practices in GI cancer patients.

show abstract

Multiplex Detection of Clinically Relevant Mutations in Liquid Biopsies of Cancer Patients Using a Hybridization-Based Platform

Cited by 12 publications

References 30 publications

Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection

Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection

Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer

Targeted Sequencing of Ascites and Peritoneal Washing Fluid of Patients With Gastrointestinal Cancers and Their Clinical Applications and Limitations

Contact Info

Product

Resources

About