Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue
Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from va...
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MDPI AG
2023-08-01
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| Series: | Journal of Clinical Medicine |
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| Online Access: | https://www.mdpi.com/2077-0383/12/15/5109 |
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| author | Jaroslav Pelisek Yankey Yundung Benedikt Reutersberg Lorenz Meuli Fabian Rössler Laetitia Rabin Reinhard Kopp Alexander Zimmermann |
| author_facet | Jaroslav Pelisek Yankey Yundung Benedikt Reutersberg Lorenz Meuli Fabian Rössler Laetitia Rabin Reinhard Kopp Alexander Zimmermann |
| author_sort | Jaroslav Pelisek |
| collection | DOAJ |
| description | Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (<i>ACTB, GAPDH</i>), ribosomal genes (<i>18S</i>, <i>28S</i>), and long non-coding RNAs (<i>MALAT1</i>, <i>H19</i>). Our results show that RINs from diseased vascular tissue are low (2–4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA’s disintegration state, is a better decision-making aid in choosing samples for omics analyses. |
| first_indexed | 2024-03-11T00:23:54Z |
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| institution | Directory Open Access Journal |
| issn | 2077-0383 |
| language | English |
| last_indexed | 2024-03-11T00:23:54Z |
| publishDate | 2023-08-01 |
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| series | Journal of Clinical Medicine |
| spelling | doaj.art-e22abad7fd73430491d8737d273e1f4a2023-11-18T23:09:33ZengMDPI AGJournal of Clinical Medicine2077-03832023-08-011215510910.3390/jcm12155109Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular TissueJaroslav Pelisek0Yankey Yundung1Benedikt Reutersberg2Lorenz Meuli3Fabian Rössler4Laetitia Rabin5Reinhard Kopp6Alexander Zimmermann7Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Surgery and Transplantation, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandDepartment of Vascular Surgery, University Hospital Zurich, 8091 Zurich, SwitzerlandProper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (<i>ACTB, GAPDH</i>), ribosomal genes (<i>18S</i>, <i>28S</i>), and long non-coding RNAs (<i>MALAT1</i>, <i>H19</i>). Our results show that RINs from diseased vascular tissue are low (2–4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA’s disintegration state, is a better decision-making aid in choosing samples for omics analyses.https://www.mdpi.com/2077-0383/12/15/5109biobankingSwiss Vascular Biobankvascular tissuecardiovascular diseasesatherosclerosisRNA integrity number (RIN) |
| spellingShingle | Jaroslav Pelisek Yankey Yundung Benedikt Reutersberg Lorenz Meuli Fabian Rössler Laetitia Rabin Reinhard Kopp Alexander Zimmermann Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue Journal of Clinical Medicine biobanking Swiss Vascular Biobank vascular tissue cardiovascular diseases atherosclerosis RNA integrity number (RIN) |
| title | Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue |
| title_full | Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue |
| title_fullStr | Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue |
| title_full_unstemmed | Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue |
| title_short | Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue |
| title_sort | swiss vascular biobank evaluation of optimal extraction method and admission solution for preserving rna from human vascular tissue |
| topic | biobanking Swiss Vascular Biobank vascular tissue cardiovascular diseases atherosclerosis RNA integrity number (RIN) |
| url | https://www.mdpi.com/2077-0383/12/15/5109 |
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