Impact of soft tissue homogenization methods on RNA quality.

IF 2.6 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Biology Reports Pub Date : 2025-04-25 DOI:10.1007/s11033-025-10508-0

Julia Ostapowicz, Bartosz Maćkowiak, Kamila Ostrowska, Barbara Kaczmarek, Natalia Pietras, Dawid Frąckowiak, Magdalena Fundowicz, Katarzyna Kulcenty, Wojciech Golusiński, Wiktoria Suchorska

{"title":"Impact of soft tissue homogenization methods on RNA quality.","authors":"Julia Ostapowicz, Bartosz Maćkowiak, Kamila Ostrowska, Barbara Kaczmarek, Natalia Pietras, Dawid Frąckowiak, Magdalena Fundowicz, Katarzyna Kulcenty, Wojciech Golusiński, Wiktoria Suchorska","doi":"10.1007/s11033-025-10508-0","DOIUrl":null,"url":null,"abstract":"Background: High-quality RNA isolation from tissues is crucial for transcriptomic analysis. The tissue disruption influences the RNA quality. The aim of this study was to compare different methods of tissue homogenization.Methods: Three homogenization methods were used (mortar and pestle, ball mill, and tissue homogenizer) to disrupt head and neck cancerous tissues, healthy tissues from free margin of head and neck cancer patients, and breast skin from breast cancer patients. The comparison of isolated RNA quantity and quality by measuring the concentration and absorbance, RIN, and Ct values of reference genes were performed.Results: RNA isolated after tissue homogenizer usage has the highest 260/230 ratio (p = 0.02) and concentration (p = 0.02) also RIN values tend to be highest across all studied tissues. There are no significant differences between Ct values across all tissues processed with different homogenization methods; however, the Ct values of GAPDH and S18 are negatively correlated with RIN number (p = 0.002, p = 0.003).Conclusion: The tissue homogenizer is the most suitable for obtaining high-quality RNA across all examined tissues, which is essential in various RNA-based analyses. GAPDH and S18 Ct can indicate the RNA quality measured by RIN values.","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"52 1","pages":"425"},"PeriodicalIF":2.6000,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12031802/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Biology Reports","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s11033-025-10508-0","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background: High-quality RNA isolation from tissues is crucial for transcriptomic analysis. The tissue disruption influences the RNA quality. The aim of this study was to compare different methods of tissue homogenization.

Methods: Three homogenization methods were used (mortar and pestle, ball mill, and tissue homogenizer) to disrupt head and neck cancerous tissues, healthy tissues from free margin of head and neck cancer patients, and breast skin from breast cancer patients. The comparison of isolated RNA quantity and quality by measuring the concentration and absorbance, RIN, and Ct values of reference genes were performed.

Results: RNA isolated after tissue homogenizer usage has the highest 260/230 ratio (p = 0.02) and concentration (p = 0.02) also RIN values tend to be highest across all studied tissues. There are no significant differences between Ct values across all tissues processed with different homogenization methods; however, the Ct values of GAPDH and S18 are negatively correlated with RIN number (p = 0.002, p = 0.003).

Conclusion: The tissue homogenizer is the most suitable for obtaining high-quality RNA across all examined tissues, which is essential in various RNA-based analyses. GAPDH and S18 Ct can indicate the RNA quality measured by RIN values.

查看原文本刊更多论文

软组织匀浆方法对RNA质量的影响。

背景：从组织中分离高质量的RNA对转录组学分析至关重要。组织破坏影响RNA的质量。本研究的目的是比较不同的组织匀浆方法。方法：采用研钵、球磨机、组织均质机三种均质方法对头颈部癌组织、头颈部癌游离缘健康组织、乳腺癌患者乳腺皮肤进行均质破坏。通过测定内参基因的浓度和吸光度、RIN和Ct值，比较分离RNA的数量和质量。结果：组织匀浆器使用后分离的RNA具有最高的260/230比（p = 0.02）和浓度（p = 0.02），并且在所有研究组织中RIN值趋于最高。采用不同均质方法处理的所有组织的Ct值无显著差异；而GAPDH和S18的Ct值与RIN数呈负相关（p = 0.002, p = 0.003）。结论：组织匀浆器最适合在所有被检测组织中获得高质量的RNA，这在各种基于RNA的分析中是必不可少的。GAPDH和S18 Ct可以指示以RIN值测量的RNA质量。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Molecular Biology Reports 生物-生化与分子生物学

CiteScore

5.00

自引率

0.00%

发文量

1048

审稿时长

5.6 months

期刊介绍： Molecular Biology Reports publishes original research papers and review articles that demonstrate novel molecular and cellular findings in both eukaryotes (animals, plants, algae, funghi) and prokaryotes (bacteria and archaea).The journal publishes results of both fundamental and translational research as well as new techniques that advance experimental progress in the field and presents original research papers, short communications and (mini-) reviews.