Gene expression profiling of individual hypothalamic nuclei from single animals using laser capture microdissection and microarrays

J Neurosci Methods. 2009 Feb 15;177(1):87-93. doi: 10.1016/j.jneumeth.2008.09.024. Epub 2008 Oct 8.


In order to identify novel genes involved in appetite and body weight regulation we have developed a microarray based method suitable for detecting small changes in gene expression in discrete groups of hypothalamic neurons. The method is based on a combination of stereological sampling, laser capture microdissection (LCM), PCR based amplification (SuperAmp), and one-color cDNA microarray analysis. To validate the method we assessed and compared fasting induced changes in mRNA levels of Neuropeptide Y (NPY) and proopiomelanocortin (POMC) in the hypothalamic arcuate nucleus (ARC) of diet-induced obese rats using cDNA microarrays, quantitative PCR and in situ hybridization. All methods revealed statistically significant fasting-induced changes in NPY and POMC expression. An additional 3480 differentially expressed probes (fold change >1.22, t-test p=0.05) were identified in the microarray analysis. Our findings demonstrate a consistent gene expression pattern across three different gene expression detection methods and strongly suggest that LCM coupled microarray analysis combined with SuperAmp can be used as a semi-quantitative mRNA profiling tool. Importantly, the sensitivity of the method greatly improves the usefulness of the microarray technology for gene expression profiling in non-homogeneous tissues such as the brain.

MeSH terms

  • Analysis of Variance
  • Animals
  • Arcuate Nucleus of Hypothalamus / metabolism*
  • Dietary Fats / adverse effects
  • Fasting / physiology
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation / physiology*
  • Male
  • Microarray Analysis / methods*
  • Microdissection / methods*
  • Neuropeptide Y / genetics
  • Neuropeptide Y / metabolism
  • Obesity / etiology
  • Obesity / metabolism
  • Obesity / pathology
  • Pro-Opiomelanocortin / genetics
  • Pro-Opiomelanocortin / metabolism
  • RNA, Messenger / metabolism
  • Rats
  • Transcription, Genetic / physiology*


  • Dietary Fats
  • Neuropeptide Y
  • RNA, Messenger
  • Pro-Opiomelanocortin