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Characterization of Long Non-coding RNA Signatures of Intracranial Aneurysm in Circulating Whole Blood

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Abstract

Background and Objective

Long non-coding RNAs (lncRNAs) may serve as biomarkers for complex disease states, such as intracranial aneurysms. In this study, we investigated lncRNA expression differences in the whole blood of patients with unruptured aneurysms.

Methods

Whole blood RNA from 67 subjects (34 with aneurysm, 33 without) was used for next-generation RNA sequencing. Differential expression analysis was used to define a signature of intracranial aneurysm-associated lncRNAs. To estimate the signature’s ability to classify aneurysms and to identify the most predictive lncRNAs, we implemented a nested cross-validation pipeline to train classifiers using linear discriminant analysis. Ingenuity pathway analysis was used to study potential biological roles of differentially expressed lncRNAs, and lncRNA ontology was used to investigate ontologies enriched in signature lncRNAs. Co-expression correlation analysis was performed to investigate associated differential protein-coding messenger RNA expression.

Results

Of 4639 detected lncRNAs, 263 were significantly different (p < 0.05) between the two groups, and 84 of those had an absolute fold-change ≥ 1.5. An eight-lncRNA signature (q < 0.35, fold-change ≥ 1.5) was able to separate patients with and without aneurysms on principal component analysis, and had an estimated accuracy of 70.9% in nested cross-validation. Bioinformatics analyses showed that networks of differentially expressed lncRNAs (p < 0.05) were enriched for cell death and survival, connective tissue disorders, carbohydrate metabolism, and cardiovascular disease. Signature lncRNAs shared ontologies that reflected regulation of gene expression, signaling, ubiquitin processing, and p53 signaling. Co-expression analysis showed correlations with messenger RNAs related to inflammatory responses.

Conclusions

Differential expression in whole blood lncRNAs is detectable in patients harboring aneurysms, and reflects expression/signaling regulation, and ubiquitin and p53 pathways. Following validation in larger cohorts, these lncRNAs may be potential diagnostic targets for aneurysm detection by blood testing.

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Acknowledgements

We thank the patients who participated in this study. We acknowledge Jonathan Bard, MA and Brandon Marzullo, MS for RNA sequencing data analysis assistance, and Jennifer L. Gay, CCRP for study protocol management. This work was performed in part at the New York State Center of Excellence in Bioinformatics and Life Sciences’ Genomics and Bioinformatics Core.

Author information

Authors and Affiliations

  1. Canon Stroke and Vascular Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA

    Vincent M. Tutino, Kerry E. Poppenberg, Robert J. Damiano, Tatsat R. Patel, Muhammad Waqas, Kenneth V. Snyder & Adnan H. Siddiqui

  2. Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA

    Vincent M. Tutino, Kerry E. Poppenberg, Muhammad Waqas, Kenneth V. Snyder & Adnan H. Siddiqui

  3. Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, USA

    Vincent M. Tutino

  4. Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA

    Vincent M. Tutino

  5. Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY, USA

    Vincent M. Tutino, Robert J. Damiano & Tatsat R. Patel

  6. Department of Radiology, University at Buffalo, Buffalo, NY, USA

    Adnan H. Siddiqui

  7. Department of Pediatrics, University at Buffalo, Buffalo, NY, USA

    James N. Jarvis

  8. Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY, USA

    James N. Jarvis

  9. Department of Medical Imaging, University of Toronto, Toronto, ON, Canada

    Adam A. Dmytriw

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  1. Vincent M. Tutino
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Corresponding author

Correspondence to Vincent M. Tutino.

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Funding

This work was funded by the Brain Aneurysm Foundation (VMT), the New York State Center for Advanced Technology in Big Data and Health Sciences (VMT), and the Cummings Foundation (VMT).

Conflict of interest

Vincent M. Tutino is the principal investigator for National Science Foundation Award No. 1746694 and NIH NINDS award R43 NS115314-0, awardee of the abovementioned Brain Aneurysm Foundation grant, Center for Advanced Technology grant, and Cummings Foundation grant, and a co-founder of Neurovascular Diagnostics, Inc. Kerry E. Poppenberg, Robert J. Damiano, Tatsat R. Patel, Muhammad Waqas, and Adam A. Dmytriw have no conflicts of interest that are directly relevant to the content of this article. Kenneth V. Snyder is a consultant and teacher for Canon Medical Systems Corporation, Penumbra Inc., Medtronic, and Jacobs Institute and a co-founder of Neurovascular Diagnostics, Inc. Adnan H. Siddiqui has a financial interest/stock options/ownership/investment in Adona Medical, Inc., Amnis Therapeutics, BlinkTBI, Inc, Boston Scientific Corp (for purchase of Claret Medical), Buffalo Technology Partners, Inc., Cardinal Consultants, LLC, Cerebrotech Medical Systems, Inc, Cognition Medical, Endostream Medical, Ltd, Imperative Care, Inc., International Medical Distribution Partners, Neurovascular Diagnostics, Inc., Q’Apel Medical, Inc., Radical Catheter Technologies, Inc., Rebound Therapeutics Corp. (purchased 2019 by Integra Lifesciences, Corp), Rist Neurovascular, Inc., Sense Diagnostics, Inc., Serenity Medical, Inc., Silk Road Medical, Spinnaker Medical, Inc., StimMed, Synchron, Three Rivers Medical, Inc., Vastrax, LLC, VICIS, Inc., and Viseon, Inc.; is a consultant/advisory board member for Amnis Therapeutics, Boston Scientific, Canon Medical Systems USA, Inc., Cerebrotech Medical Systems, Inc., Cerenovus, Corindus, Inc., Endostream Medical, Ltd, Imperative Care, Inc., Integra LifeSciences Corp., Medtronic, MicroVention, Minnetronix Neuro, Inc., Northwest University – DSMB Chair for HEAT Trial, Penumbra, Q’Apel Medical, Inc., Rapid Medical, Rebound Therapeutics Corp., Serenity Medical, Inc., Silk Road Medical, StimMed, Stryker, Three Rivers Medical, Inc., VasSol, and W.L. Gore & Associates; is a national principal investigator/steering committee member for Cerenovus LARGE Trial and ARISE II Trial, Medtronic SWIFT PRIME and SWIFT DIRECT Trials, MicroVention FRED Trial & CONFIDENCE Study, MUSC POSITIVE Trial, Penumbra 3D Separator Trial, COMPASS Trial, and INVEST Trial; has received research grants/co-investigator for NIH/NINDS 1R01NS091075 Virtual Intervention of Intracranial Aneurysms; and is a co-principal investigator for NIH-NINDS R21 NS109575-01 Optimizing Approaches to Endovascular Therapy of Acute Ischemic Stroke. James N. Jarvis is the principal investigator for NIH Grant R01-AR-060604.

Ethics approval

This study was approved by the University at Buffalo Institutional Review Board (no. 030-474433).

Consent to participate

All subjects provided written informed consent before participating in this study, as described in the approved protocol.

Consent for publication

Not applicable.

Availability of data and material

Raw data are available upon reasonable request to the corresponding author.

Code availability

Not applicable.

Author contributions

VMT and KEP conceived and designed the research. VMT, KEP, MW, KVS, and AHS collected and reviewed the data. VMT, KEP, RJD, and TRP analyzed the data and performed the statistical analysis. VMT handled the funding and supervision of the research. VMT, KEP, RJD, and JNJ drafted the manuscript. VMT, KEP, RJD, TRP, MW, AAD, KVS, AHS, and JNJ revised the manuscript and reviewed the final version.

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Tutino, V.M., Poppenberg, K.E., Damiano, R.J. et al. Characterization of Long Non-coding RNA Signatures of Intracranial Aneurysm in Circulating Whole Blood. Mol Diagn Ther 24, 723–736 (2020). https://doi.org/10.1007/s40291-020-00494-3

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