Long Non-Coding RNAs as Molecular Signatures for Canine B-Cell Lymphoma Characterization
| Autor: | Sara Napoli, Francesco Bertoni, Luca Aresu, Luca Giudice, Rosalba Giugno, Diana Giannuzzi, Luciano Cascione, Serena Ferraresso, Laura Marconato |
|---|---|
| Přispěvatelé: | Cascione, Luciano, Giudice, Luca, Ferraresso, Serena, Marconato, Laura, Giannuzzi, Diana, Napoli, Sara, Bertoni, Francesco, Giugno, Rosalba, Aresu, Luca |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Treatment response Future studies lcsh:QH426-470 Follicular lymphoma bioinformatics omics analysis lymphoma Computational biology Biology Biochemistry Article High performance system Transcriptome 03 medical and health sciences 0302 clinical medicine immune system diseases hemic and lymphatic diseases Genetics medicine Analysis pipeline Long non-coding RNA Lymphoma Prognostic signature prognostic signature B-cell lymphoma Molecular Biology long non-coding RNA analysis pipeline bioinformatics medicine.disease lcsh:Genetics 030104 developmental biology 030220 oncology & carcinogenesis omics analysis |
| Zdroj: | Non-Coding RNA Non-Coding RNA, Vol 5, Iss 3, p 47 (2019) Volume 5 Issue 3 |
| ISSN: | 2311-553X |
| Popis: | Background: Diffuse large B-cell lymphoma (DLBCL), marginal zone lymphoma (MZL) and follicular lymphoma (FL) are the most common B-cell lymphomas (BCL) in dogs. Recent investigations have demonstrated overlaps of these histotypes with the human counterparts, including clinical presentation, biologic behavior, tumor genetics, and treatment response. The molecular mechanisms that underlie canine BCL are still unknown and new studies to improve diagnosis, therapy, and the utilization of canine species as spontaneous animal tumor models are undeniably needed. Recent work using human DLBCL transcriptomes has suggested that long non-coding RNAs (lncRNAs) play a key role in lymphoma pathogenesis and pinpointed a restricted number of lncRNAs as potential targets for further studies. Results: To expand the knowledge of non-coding molecules involved in canine BCL, we used transcriptomes obtained from a cohort of 62 dogs with newly-diagnosed multicentric DLBCL, MZL and FL that had undergone complete staging work-up and were treated with chemotherapy or chemo-immunotherapy. We developed a customized R pipeline performing a transcriptome assembly by multiple algorithms to uncover novel lncRNAs, and delineate genome-wide expression of unannotated and annotated lncRNAs. Our pipeline also included a new package for high performance system biology analysis, which detects high-scoring network biological neighborhoods to identify functional modules. Moreover, our customized pipeline quantified the expression of novel and annotated lncRNAs, allowing us to subtype DLBCLs into two main groups. The DLBCL subtypes showed statistically different survivals, indicating the potential use of lncRNAs as prognostic biomarkers in future studies. Conclusions: In this manuscript, we describe the methodology used to identify lncRNAs that differentiate B-cell lymphoma subtypes and we interpreted the biological and clinical values of the results. We inferred the potential functions of lncRNAs to obtain a comprehensive and integrative insight that highlights their impact in this neoplasm. |
| Databáze: | OpenAIRE |
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