Immuno-laser capture microdissection of perfusion-fixed mouse brain tissue coupled to RNA-seq.

IF 2.3 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS
Journal of Neuroscience Methods Pub Date : 2025-11-01 Epub Date: 2025-08-06 DOI:10.1016/j.jneumeth.2025.110548
Shujun Ge, Wenqi Gan, Keaton Karlinsey, Beiyan Zhou, Joel S Pachter
{"title":"Immuno-laser capture microdissection of perfusion-fixed mouse brain tissue coupled to RNA-seq.","authors":"Shujun Ge, Wenqi Gan, Keaton Karlinsey, Beiyan Zhou, Joel S Pachter","doi":"10.1016/j.jneumeth.2025.110548","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Laser capture microdissection (LCM), when combined with immunostaining (immuno-LCM) and coupled to RNA profiling, provides a means for in situ transcriptomic interrogation of complex tissues. However, preserving RNA integrity through the multiple harsh steps of immuno-LCM has proved challenging, greatly limiting the potential for high-resolution spatial analysis of global gene expression.</p><p><strong>New method: </strong>Here, we describe a protocol whereby perfusion fixation and subsequent ex vivo post-fixation of mouse brain with paraformaldehyde, followed by protease digestion of immuno-LCM-acquired material from brain sections, allows for isolation of RNA of relatively high integrity that is amenable to RNA-seq with minimal technical variability.</p><p><strong>Results: </strong>The individual steps of the fixation/immuno-LCM protocol were evaluated for their respective effects on RNA integrity and found not to produce significant compromise, as judged by RIN values determined using a Bioanalyzer or Tape Station. Utilizing the fixation/immuno-LCM protocol to assess gene expression from targeted brain microvascular tissue further showed high reproducibility in both qRT-PCR and RNA-seq analysis, as determined by interpolation and Pearson Correlation, respectively, with the latter detecting ∼ 22,000 genes, including those in the established blood-brain barrier transcriptome.</p><p><strong>Comparison with existing methods: </strong>To date, there has been no detailed analysis of how fixation combined with immuno-LCM impacts RNA integrity and transcriptomic analysis.</p><p><strong>Conclusions: </strong>The rigorous analyses performed demonstrate that paraformaldehyde fixation - which covalently cross-links RNA and protein - can be reversed without significant damage to RNA integrity, and can be combined with immuno-LCM to enable high-resolution spatial analysis of global gene expression.</p>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":" ","pages":"110548"},"PeriodicalIF":2.3000,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12377190/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Neuroscience Methods","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1016/j.jneumeth.2025.110548","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/8/6 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

Abstract

Background: Laser capture microdissection (LCM), when combined with immunostaining (immuno-LCM) and coupled to RNA profiling, provides a means for in situ transcriptomic interrogation of complex tissues. However, preserving RNA integrity through the multiple harsh steps of immuno-LCM has proved challenging, greatly limiting the potential for high-resolution spatial analysis of global gene expression.

New method: Here, we describe a protocol whereby perfusion fixation and subsequent ex vivo post-fixation of mouse brain with paraformaldehyde, followed by protease digestion of immuno-LCM-acquired material from brain sections, allows for isolation of RNA of relatively high integrity that is amenable to RNA-seq with minimal technical variability.

Results: The individual steps of the fixation/immuno-LCM protocol were evaluated for their respective effects on RNA integrity and found not to produce significant compromise, as judged by RIN values determined using a Bioanalyzer or Tape Station. Utilizing the fixation/immuno-LCM protocol to assess gene expression from targeted brain microvascular tissue further showed high reproducibility in both qRT-PCR and RNA-seq analysis, as determined by interpolation and Pearson Correlation, respectively, with the latter detecting ∼ 22,000 genes, including those in the established blood-brain barrier transcriptome.

Comparison with existing methods: To date, there has been no detailed analysis of how fixation combined with immuno-LCM impacts RNA integrity and transcriptomic analysis.

Conclusions: The rigorous analyses performed demonstrate that paraformaldehyde fixation - which covalently cross-links RNA and protein - can be reversed without significant damage to RNA integrity, and can be combined with immuno-LCM to enable high-resolution spatial analysis of global gene expression.

结合RNA-seq的免疫激光捕获灌注固定小鼠脑组织显微解剖。
背景:激光捕获显微解剖(LCM),当与免疫染色(免疫-LCM)结合并与RNA分析相结合时,为复杂组织的原位转录组学研究提供了一种手段。然而,通过免疫- lcm的多个苛刻步骤来保持RNA的完整性被证明是具有挑战性的,这极大地限制了对全球基因表达进行高分辨率空间分析的潜力。新方法:在这里,我们描述了一种方案,即灌注固定和随后用多聚甲醛对小鼠大脑进行体外后固定,然后用蛋白酶消化从大脑切片中获得的免疫lcm获得的物质,从而可以分离出相对高完整性的RNA,这种RNA序列具有最小的技术变异性。结果:通过使用生物分析仪或磁带站测定RIN值,评估固定/免疫- lcm方案的各个步骤对RNA完整性的各自影响,发现不会产生显著的损害。利用固定/免疫- lcm方案评估靶脑微血管组织的基因表达,进一步显示了qRT-PCR和RNA-seq分析的高重复性,分别通过插值和Pearson相关性确定,后者检测到约22,000个基因,包括已建立的血脑屏障转录组中的基因。与现有方法的比较:迄今为止,还没有详细分析固定结合免疫- lcm如何影响RNA完整性和转录组学分析。结论:严格的分析表明,多聚甲醛固定-共价交联RNA和蛋白质-可以逆转,而不会对RNA完整性造成重大损害,并且可以与免疫- lcm相结合,实现全球基因表达的高分辨率空间分析。
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
Journal of Neuroscience Methods
Journal of Neuroscience Methods 医学-神经科学
CiteScore
7.10
自引率
3.30%
发文量
226
审稿时长
52 days
期刊介绍: The Journal of Neuroscience Methods publishes papers that describe new methods that are specifically for neuroscience research conducted in invertebrates, vertebrates or in man. Major methodological improvements or important refinements of established neuroscience methods are also considered for publication. The Journal''s Scope includes all aspects of contemporary neuroscience research, including anatomical, behavioural, biochemical, cellular, computational, molecular, invasive and non-invasive imaging, optogenetic, and physiological research investigations.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信