Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods
In acute stroke, timely diagnosis is essential to prevent extensive neuronal damage and improve patient outcomes. However, differentiating between ischemic stroke, intracerebral hemorrhage, and stroke mimics remains challenging. Transfer RNA-derived fragments (tRFs) have emerged as potential biomark...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-06-01
|
| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253125001076 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849322634460790784 |
|---|---|
| author | Tamar Woudenberg M. Leontien van der Bent Daphne A.L. van den Homberg T. Truc My Nguyen Marieke J.H. Wermer Ido R. van den Wijngaard Paul H.A. Quax A. Yaël Nossent Nyika D. Kruyt |
| author_facet | Tamar Woudenberg M. Leontien van der Bent Daphne A.L. van den Homberg T. Truc My Nguyen Marieke J.H. Wermer Ido R. van den Wijngaard Paul H.A. Quax A. Yaël Nossent Nyika D. Kruyt |
| author_sort | Tamar Woudenberg |
| collection | DOAJ |
| description | In acute stroke, timely diagnosis is essential to prevent extensive neuronal damage and improve patient outcomes. However, differentiating between ischemic stroke, intracerebral hemorrhage, and stroke mimics remains challenging. Transfer RNA-derived fragments (tRFs) have emerged as potential biomarkers for distinguishing between these stroke subtypes. Here we used reverse transcription-quantitative PCR (RT-qPCR) to investigate the expression of specific tRFs that we previously identified in small RNA sequencing data as potential biomarkers. Out of 12 measured tRFs, only the fragments ArgTCG53–67 and TyrGTA1–19 showed a trend for differential expression between stroke subtypes, but with insufficient predictive value to be of use in clinical practice. Combining expression data of specific tRFs into a joint model did not improve the predictive ability. Technical and computational challenges may compromise the reliability of tRF expression data from RNA sequencing, possibly explaining our inability to validate the specific tRFs as potential stroke biomarkers. Moreover, the limitations of RT-qPCR challenge a reliable quantification of these fragments even further. Our findings highlight the need for improved quantitative methods for tRF analysis to fully exploit their potential as clinically meaningful biomarkers. Addressing these technical barriers could unlock the diagnostic potential of tRFs, facilitating faster, more accurate stroke subtype identification in an acute setting. |
| format | Article |
| id | doaj-art-cd46f00da08941e092c727283b45a73c |
| institution | Kabale University |
| issn | 2162-2531 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj-art-cd46f00da08941e092c727283b45a73c2025-08-20T03:49:17ZengElsevierMolecular Therapy: Nucleic Acids2162-25312025-06-0136210255310.1016/j.omtn.2025.102553Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methodsTamar Woudenberg0M. Leontien van der Bent1Daphne A.L. van den Homberg2T. Truc My Nguyen3Marieke J.H. Wermer4Ido R. van den Wijngaard5Paul H.A. Quax6A. Yaël Nossent7Nyika D. Kruyt8Department of Vascular Surgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 RC Leiden, the NetherlandsDepartment of Vascular Surgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 RC Leiden, the NetherlandsDepartment of Vascular Surgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 RC Leiden, the NetherlandsDepartment of Neurology, Leiden University Medical Center, 2300 RC Leiden, the NetherlandsDepartment of Neurology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Neurology, University Medical Center Groningen, 9700 RB Groningen, the NetherlandsDepartment of Neurology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; University Neurovascular Center Leiden-The Hague, 2300 RC Leiden, the Netherlands; Neurology, Haaglanden Medical Center, 2501 CK The Hague, the NetherlandsDepartment of Vascular Surgery, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2300 RC Leiden, the NetherlandsDepartment of Nutrition, Exercise and Sports, University of Copenhagen, 2200 Copenhagen, Denmark; Corresponding author: A. Yaël Nossent, Department of Nutrition, Exercise and Sports, University of Copenhagen, 2200 Copenhagen, Denmark.Department of Neurology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; University Neurovascular Center Leiden-The Hague, 2300 RC Leiden, the Netherlands; Corresponding author: Nyika D. Kruyt, Department of Neurology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands.In acute stroke, timely diagnosis is essential to prevent extensive neuronal damage and improve patient outcomes. However, differentiating between ischemic stroke, intracerebral hemorrhage, and stroke mimics remains challenging. Transfer RNA-derived fragments (tRFs) have emerged as potential biomarkers for distinguishing between these stroke subtypes. Here we used reverse transcription-quantitative PCR (RT-qPCR) to investigate the expression of specific tRFs that we previously identified in small RNA sequencing data as potential biomarkers. Out of 12 measured tRFs, only the fragments ArgTCG53–67 and TyrGTA1–19 showed a trend for differential expression between stroke subtypes, but with insufficient predictive value to be of use in clinical practice. Combining expression data of specific tRFs into a joint model did not improve the predictive ability. Technical and computational challenges may compromise the reliability of tRF expression data from RNA sequencing, possibly explaining our inability to validate the specific tRFs as potential stroke biomarkers. Moreover, the limitations of RT-qPCR challenge a reliable quantification of these fragments even further. Our findings highlight the need for improved quantitative methods for tRF analysis to fully exploit their potential as clinically meaningful biomarkers. Addressing these technical barriers could unlock the diagnostic potential of tRFs, facilitating faster, more accurate stroke subtype identification in an acute setting.http://www.sciencedirect.com/science/article/pii/S2162253125001076MT: Non-coding RNAstRNA-derived fragmentsdiagnostic biomarkerischemic strokeintracerebral hemorrhagestroke mimic |
| spellingShingle | Tamar Woudenberg M. Leontien van der Bent Daphne A.L. van den Homberg T. Truc My Nguyen Marieke J.H. Wermer Ido R. van den Wijngaard Paul H.A. Quax A. Yaël Nossent Nyika D. Kruyt Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods Molecular Therapy: Nucleic Acids MT: Non-coding RNAs tRNA-derived fragments diagnostic biomarker ischemic stroke intracerebral hemorrhage stroke mimic |
| title | Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods |
| title_full | Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods |
| title_fullStr | Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods |
| title_full_unstemmed | Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods |
| title_short | Validation of tRNA-derived fragments as diagnostic biomarkers in suspected acute stroke; limitations in analysis and quantification methods |
| title_sort | validation of trna derived fragments as diagnostic biomarkers in suspected acute stroke limitations in analysis and quantification methods |
| topic | MT: Non-coding RNAs tRNA-derived fragments diagnostic biomarker ischemic stroke intracerebral hemorrhage stroke mimic |
| url | http://www.sciencedirect.com/science/article/pii/S2162253125001076 |
| work_keys_str_mv | AT tamarwoudenberg validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT mleontienvanderbent validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT daphnealvandenhomberg validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT ttrucmynguyen validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT mariekejhwermer validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT idorvandenwijngaard validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT paulhaquax validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT ayaelnossent validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods AT nyikadkruyt validationoftrnaderivedfragmentsasdiagnosticbiomarkersinsuspectedacutestrokelimitationsinanalysisandquantificationmethods |