Comparison of Ethanol Versus Formalin Fixation on Preservation of Histology and RNA in Laser Capture Microdissected Brain Tissues

Although RNA can be retrieved from formalin‐fixed, paraffin‐embedded (FFPE) tissues, the yield is low, and the RNA is fragmented. Recent advances in gene expression profiling underscore the importance of identifying a fixative that preserves histology and mRNA. We demonstrated that, for immersion fixation of brains, 70% ethanol is superior to formalin for mRNA preservation. RNA yield from ethanol‐fixed tissues was 70% of the yield from fresh frozen specimens, but only a negligible quantity was recovered from formalin‐fixed tissues. RNA from ethanol‐fixed brains showed integrity comparable to RNA from fresh frozen tissues, and RT‐PCR using RNA from ethanol‐fixed tissues was consistently successful. RNA from FFPE tissues composed of low‐molecular weight fragments, and their use in RT‐PCR failed repeatedly. The yield and quality of RNA from ethanol‐fixed brains were unaffected after immersion at 4°C for 2 weeks. In a blinded comparison to FFPE tissues, ethanol‐fixed specimens were judged to show comparable histology and superior immunostaining. After laser capture microdissection (LCM), we failed to recover mRNA from FFPE tissues but retrieved mRNA from ethanol‐fixed tissues for RT‐PCR and cDNA microarray analysis. We conclude that 70% ethanol preserves RNA integrity and is suitable for expression profiling of brain tissues by LCM and cDNA microarray.