Generation of Aorta Transcript Atlases of Wild-Type and Apolipoprotein E-null Mice by Laser Capture Microdissection-Based mRNA Expression Microarrays

Methods Mol Biol. 2015;1339:297-308. doi: 10.1007/978-1-4939-2929-0_20.


Atherosclerosis is a transmural chronic inflammatory disease of medium and large arteries. Though it is well recognized that immune responses contribute to atherosclerosis, it remains unclear whether these responses are carried out in secondary lymphoid organs such as the spleen and lymph nodes and/or within the arterial wall. Arteries are composed of three major layers, i.e., the laminae intima, media, and adventitia. However, each of these layers may play different roles in arterial wall biology and atherogenesis. We identified well-structured artery tertiary lymphoid organs (ATLOs) in the abdominal aorta adventitia but not in the intima of aged apolipoprotein E-null (ApoE(-/-)) mice. These observations suggested that disease-associated immune responses are highly territorialized within the arterial wall and that the adventitia may play distinct and hitherto unrecognized roles. Here, we set out to apply laser capture microdissection (LCM) to dissect plaque, media, adventitia, and adjacent aorta-draining lymph nodes (LN) in aged ApoE(-/-) mice in attempts to establish the territoriality of atherosclerosis immune responses. Using whole-genome mRNA expression microarrays of arterial wall tissues, we constructed robust transcript atlases of wild-type and ApoE(-/-) mouse aortas. Data were deposited in the National Center for Biotechnology Information's gene expression omnibus (GEO) and are accessible to the public through the Internet. These transcript atlases are anticipated to prove valuable to address a wide scope of issues ranging from atherosclerosis immunity and inflammation to the role of single genes in regulating arterial wall remodeling. This chapter presents protocols for LCM of mouse aorta and microarray expression analysis from LCM-isolated aorta laminae.

Keywords: Artery tertiary lymphoid organ (ATLO); Atherosclerosis; Gene expression omnibus (GEO); Laser capture microdissection (LCM); Microarrays; Transcriptome atlas.

MeSH terms

  • Access to Information
  • Animals
  • Aorta / metabolism*
  • Aortic Diseases / genetics*
  • Aortic Diseases / immunology
  • Aortic Diseases / metabolism
  • Apolipoproteins E / deficiency*
  • Apolipoproteins E / genetics
  • Atherosclerosis / genetics*
  • Atherosclerosis / immunology
  • Atherosclerosis / metabolism
  • Computational Biology
  • Databases, Genetic
  • Disease Models, Animal
  • Gene Expression Profiling / methods*
  • Genetic Predisposition to Disease
  • Internet
  • Laser Capture Microdissection*
  • Mice, Knockout
  • Oligonucleotide Array Sequence Analysis*
  • Phenotype
  • RNA, Messenger / genetics*
  • Transcriptome


  • Apolipoproteins E
  • RNA, Messenger