The Analysis of Platelet-Derived circRNA Repertoire as Potential Diagnostic Biomarker for Non-Small Cell Lung Cancer
by
, ,
Silvia D’Ambrosi
1, 
Allerdien Visser
2,†,
Mafalda Antunes-Ferreira
1,†,
Ankie Poutsma
2,
Stavros Giannoukakos
3,4, 
Nik Sol
5,6,
Siamack Sabrkhany
7,
Idris Bahce
8,
Marijke J. E. Kuijpers
9
,
Mirjam G. A. Oude Egbrink
7,
Arjan W. Griffioen
10,
Myron G. Best
1,5,
Danijela Koppers-Lalic
1,5
,
Cees Oudejans
2 and
Thomas Würdinger
1,5,* 1
Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
2
Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
3
Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
4
Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, 18100 Granada, Spain
5
Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
6
Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
7
Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands
8
Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
9
Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, 6229 ER Maastricht, The Netherlands
10
Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this study.
Cancers 2021, 13(18), 4644; https://doi.org/10.3390/cancers13184644
Submission received: 28 July 2021
/
Revised: 6 September 2021
/
Accepted: 13 September 2021
/
Published: 16 September 2021
(This article belongs to the Special Issue Circular RNAs: New Insights into the Molecular Biology of Cancer)
Simple Summary
Interaction between blood platelets and cancer cells play an important role in various steps of cancer development and progression. These interactions lead to changes in the platelets’ RNA content, resulting in tumor-mediated “education” of platelets. Tumor-educated platelets (TEPs) can be used as a non-invasive biomarker source for cancer detection and progression monitoring. Our lab has previously identified that spliced mRNA TEP signatures provide specific information on the presence, location, and molecular features of cancers. Next to mRNA, other RNA types are present in platelets, and their repertoire can potentially be subjected to cancer-mediated alterations. Despite the evidence that circRNA could be a promising cancer biomarker, they have not yet been analyzed in blood platelets of cancer patients. In this proof-of-concept study, we aim to evaluate whether platelets’ circRNA signature could be used as a biomarker for cancer detection and progression.
Abstract
Tumor-educated Platelets (TEPs) have emerged as rich biosources of cancer-related RNA profiles in liquid biopsies applicable for cancer detection. Although human blood platelets have been found to be enriched in circular RNA (circRNA), no studies have investigated the potential of circRNA as platelet-derived biomarkers for cancer. In this proof-of-concept study, we examine whether the circRNA signature of blood platelets can be used as a liquid biopsy biomarker for the detection of non-small cell lung cancer (NSCLC). We analyzed the total RNA, extracted from the platelet samples collected from NSCLC patients and asymptomatic individuals, using RNA sequencing (RNA-Seq). Identification and quantification of known and novel circRNAs were performed using the accurate CircRNA finder suite (ACFS), followed by the differential transcript expression analysis using a modified version of our thromboSeq software. Out of 4732 detected circRNAs, we identified 411 circRNAs that are significantly (p-value < 0.05) differentially expressed between asymptomatic individuals and NSCLC patients. Using the false discovery rate (FDR) of 0.05 as cutoff, we selected the nuclear receptor-interacting protein 1 (NRIP1) circRNA (circNRIP1) as a potential biomarker candidate for further validation by reverse transcription–quantitative PCR (RT-qPCR). This analysis was performed on an independent cohort of platelet samples. The RT-qPCR results confirmed the RNA-Seq data analysis, with significant downregulation of circNRIP1 in platelets derived from NSCLC patients. Our findings suggest that circRNAs found in blood platelets may hold diagnostic biomarkers potential for the detection of NSCLC using liquid biopsies.
Keywords:
circular RNA; non-small cell lung cancer; platelets; liquid biopsy; biomarkers
