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Original research
Gene expression profiles of ischemic stroke clots retrieved by mechanical thrombectomy are associated with disease etiology
  1. Vincent M Tutino1,2,3,4,5,
  2. Sarah Fricano1,2,
  3. Aichi Chien6,
  4. Tatsat R Patel1,4,
  5. Andre Monteiro1,3,
  6. Hamid H Rai1,3,
  7. Adam A Dmytriw7,8,
  8. Lee D Chaves1,3,
  9. Muhammad Waqas1,3,
  10. Elad I Levy1,3,
  11. Kerry E Poppenberg1,3,
  12. Adnan H Siddiqui1,3
  1. 1Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
  2. 2Department of Pathology and Anatomical Sciences, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
  3. 3Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
  4. 4Department of Mechanical and Aerospace Engineering, University at Buffalo School of Engineering and Applied Sciences, Buffalo, New York, USA
  5. 5Department of Biomedical Engineering, University at Buffalo School of Engineering and Applied Sciences, Buffalo, New York, USA
  6. 6Department of Radiological Sciences, UCLA, Los Angeles, California, USA
  7. 7Neuroendovascular Program, Massachusetts General Hospital, Boston, Massachusetts, USA
  8. 8Department of Neuroradiology and Neurointervention, Brigham and Women's Hospital, Boston, Massachusetts, USA
  1. Correspondence to Dr Vincent M Tutino, Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA; vincentt{at}buffalo.edu

Abstract

Background Determining stroke etiology is crucial for secondary prevention, but intensive workups fail to classify ~30% of strokes that are cryptogenic.

Objective To examine the hypothesis that the transcriptomic profiles of clots retrieved during mechanical thrombectomy are unique to strokes of different subtypes.

Methods We isolated RNA from the clots of 73 patients undergoing mechanical thrombectomy. Samples of sufficient quality were subjected to 100-cycle, paired-end RNAseq, and transcriptomes with less than 10 million unique reads were excluded from analysis. Significant differentially expressed genes (DEGs) between subtypes (defined by the Trial of Org 10 172 in Acute Stroke Treatment) were identified by expression analysis in edgeR. Gene ontology enrichment analysis was used to study the biologic differences between stroke etiologies.

Results In all, 38 clot transcriptomes were analyzed; 6 from large artery atherosclerosis (LAA), 21 from cardioembolism (CE), 5 from strokes of other determined origin, and 6 from cryptogenic strokes. Among all comparisons, there were 816 unique DEGs, 174 of which were shared by at least two comparisons, and 20 of which were shared by all three. Gene ontology analysis showed that CE clots reflected high levels of inflammation, LAA clots had greater oxidoreduction and T-cell processes, and clots of other determined origin were enriched for aberrant platelet and hemoglobin-related processes. Principal component analysis indicated separation between these subtypes and showed cryptogenic samples clustered among several different groups.

Conclusions Expression profiles of stroke clots were identified between stroke etiologies and reflected different biologic responses. Cryptogenic thrombi may be related to multiple etiologies.

  • Stroke
  • Thrombectomy
  • Genetic
  • Inflammation

Data availability statement

Data are available upon reasonable request. We have provided a full list of differentially expressed genes in the Supplementary Data. Raw gene expression data is available from the corresponding author upon reasonable request.

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Data availability statement

Data are available upon reasonable request. We have provided a full list of differentially expressed genes in the Supplementary Data. Raw gene expression data is available from the corresponding author upon reasonable request.

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Footnotes

  • Twitter @andremonteiromd, @AdamDmytriw

  • Contributors VMT conceptualized and designed the study, analyzed the study results, drafted the manuscript, and provided funding. VMT is the guarantor. SF analyzed gene expression data and drafted the manuscript. AC critically revised the manuscript. TRP, AM, and HHR assisted with data curation. AAD assisted with study conceptualization and critically revised the manuscript. LDC performed qPCR experiments. MW assisted in sample collection and interpretation of results. EIL oversaw sample collection. KEP designed the study, performed gene expression analysis, interpreted the results, and drafted the manuscript. AHS conceptualized the study, oversaw the clinical project, collected samples, and provided funding.

  • Funding This work was funded by the Cummings Foundation (VMT, AHS) and by the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH) under award number UL1TR001412 to the University at Buffalo (VMT, AHS). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

  • Competing interests VMT: Financial Interest/Investor/Stock Options/Ownership: Neurovascular Diagnostics, Inc., QAS.ai, Inc. Grant Support: National Center for Advancing Translational Sciences of the National Institutes of Health under award number UL1TR001412 through the University at Buffalo, Cummings Foundation. SF: None. AC: None. TRP: None. AM: None. HHR: None. AAD: None. LDC: None. MW: None. EIL: None. KEP: None. AHS: Financial Interest/Investor/Stock Options/Ownership: Neurovascular Diagnostics, Inc., QAS.ai, Inc. Consultant/Advisory Board: Cerenovus, Penumbra, Q’Apel Medical, Inc., Stryker Neurovascular. National PI/Steering Committees: Cerenovus EXCELLENT and ARISE II Trial; Medtronic SWIFT PRIME, VANTAGE, EMBOLISE and SWIFT DIRECT Trials; MicroVention FRED Trial & CONFIDENCE Study; MUSC POSITIVE Trial; Penumbra 3D Separator Trial, COMPASS Trial; MIVI neuroscience EVAQ Trial. Board membership: Secretary, Society of NeuroInterventional Surgery (SNIS) Board of Directors. Grant Support: National Center for Advancing Translational Sciences of the National Institutes of Health under award number UL1TR001412 through the University at Buffalo. Cummings Foundation.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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