학술논문
Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies.
Document Type
Academic Journal
Author
Decruyenaere P; Department of Hematology, Ghent University Hospital, Ghent, Belgium.; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Giuili E; Interuniversity Institute of Bioinformatics in Brussels (IB2), Free University of Brussels, Brussels, Belgium.; Department of Biotechnology and Pharmacy, University of Bologna, Bologna, Italy.; Verniers K; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; Anckaert J; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.; De Grove K; Department of Hematology, Ghent University Hospital, Ghent, Belgium.; Van der Linden M; Department of Pathology, Ghent University Hospital, Ghent, Belgium.; Deeren D; Department of Hematology, Algemeen Ziekenhuis (AZ) Delta Roeselare-Menen, Roeselare, Belgium.; Van Dorpe J; Department of Pathology, Ghent University Hospital, Ghent, Belgium.; Offner F; Department of Hematology, Ghent University Hospital, Ghent, Belgium.; Vandesompele J; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
Source
Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101568867 Publication Model: eCollection Cited Medium: Print ISSN: 2234-943X (Print) Linking ISSN: 2234943X NLM ISO Abbreviation: Front Oncol Subsets: PubMed not MEDLINE
Subject
Language
English
ISSN
2234-943X
Abstract
Introduction: Diffuse large B-cell lymphoma (DLBCL) and primary mediastinal B-cell lymphoma (PMBCL) are aggressive histological subtypes of non-Hodgkin's lymphoma. Improved understanding of the underlying molecular pathogenesis has led to new classification and risk stratification tools, including the development of cell-free biomarkers through liquid biopsies. The goal of this study was to investigate cell-free RNA (cfRNA) biomarkers in DLBCL and PMBCL patients.
Materials and Methods: Blood plasma samples (n=168) and matched diagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples (n=69) of DLBCL patients, PMBCL patients and healthy controls were collected between 2016-2021. Plasma samples were collected at diagnosis, at interim evaluation, after treatment, and in case of refractory or relapsed disease. RNA was extracted from 200 µl plasma using the miRNeasy serum/plasma kit and from FFPE tissue using the miRNeasy FFPE kit. RNA was subsequently sequenced on a NovaSeq 6000 instrument using the SMARTer Stranded Total RNA-seq pico v3 library preparation kit.
Results: Higher cfRNA concentrations were demonstrated in lymphoma patients compared to healthy controls. A large number of differentially abundant genes were identified between the cell-free transcriptomes of DLBCL patients, PMBCL patients, and healthy controls. Overlap analyses with matched FFPE samples showed that blood plasma has a unique transcriptomic profile that significantly differs from that of the tumor tissue. As a good concordance between tissue-derived gene expression and the immunohistochemistry Hans algorithm for cell-of-origin (COO) classification was demonstrated in the FFPE samples, but not in the plasma samples, a 64-gene cfRNA classifier was developed that can accurately determine COO in plasma. High plasma levels of a 9-gene signature ( BECN1 , PRKCB , COPA , TSC22D3 , MAP2K3 , UQCRHL , PTMAP4 , EHD1 , NAP1L1 pseudogene) and a 5-gene signature ( FTH1P7 , PTMAP4 , ATF4 , FTH1P8 , ARMC7 ) were significantly associated with inferior progression-free and overall survival in DLBCL patients, respectively, independent of the NCCN-IPI score.
Conclusion: Total RNA sequencing of blood plasma samples allows the analysis of the cell-free transcriptome in DLBCL and PMBCL patients and demonstrates its unexplored potential in identifying diagnostic, cell-of-origin, and prognostic cfRNA biomarkers.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Decruyenaere, Giuili, Verniers, Anckaert, De Grove, Van der Linden, Deeren, Van Dorpe, Offner and Vandesompele.)
Materials and Methods: Blood plasma samples (n=168) and matched diagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples (n=69) of DLBCL patients, PMBCL patients and healthy controls were collected between 2016-2021. Plasma samples were collected at diagnosis, at interim evaluation, after treatment, and in case of refractory or relapsed disease. RNA was extracted from 200 µl plasma using the miRNeasy serum/plasma kit and from FFPE tissue using the miRNeasy FFPE kit. RNA was subsequently sequenced on a NovaSeq 6000 instrument using the SMARTer Stranded Total RNA-seq pico v3 library preparation kit.
Results: Higher cfRNA concentrations were demonstrated in lymphoma patients compared to healthy controls. A large number of differentially abundant genes were identified between the cell-free transcriptomes of DLBCL patients, PMBCL patients, and healthy controls. Overlap analyses with matched FFPE samples showed that blood plasma has a unique transcriptomic profile that significantly differs from that of the tumor tissue. As a good concordance between tissue-derived gene expression and the immunohistochemistry Hans algorithm for cell-of-origin (COO) classification was demonstrated in the FFPE samples, but not in the plasma samples, a 64-gene cfRNA classifier was developed that can accurately determine COO in plasma. High plasma levels of a 9-gene signature ( BECN1 , PRKCB , COPA , TSC22D3 , MAP2K3 , UQCRHL , PTMAP4 , EHD1 , NAP1L1 pseudogene) and a 5-gene signature ( FTH1P7 , PTMAP4 , ATF4 , FTH1P8 , ARMC7 ) were significantly associated with inferior progression-free and overall survival in DLBCL patients, respectively, independent of the NCCN-IPI score.
Conclusion: Total RNA sequencing of blood plasma samples allows the analysis of the cell-free transcriptome in DLBCL and PMBCL patients and demonstrates its unexplored potential in identifying diagnostic, cell-of-origin, and prognostic cfRNA biomarkers.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Decruyenaere, Giuili, Verniers, Anckaert, De Grove, Van der Linden, Deeren, Van Dorpe, Offner and Vandesompele.)