Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease

Cell. 2020 Aug 20;182(4):976-991.e19. doi: 10.1016/j.cell.2020.06.038. Epub 2020 Jul 22.


Although complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer's disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here, in an AD mouse model, the transcriptional changes occurring in tissue domains in a 100-μm diameter around amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIGs), whereas a multicellular gene co-expression network of plaque-induced genes (PIGs) involving the complement system, oxidative stress, lysosomes, and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomics analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.

Keywords: Alzheimer’s disease; amyloid plaque; astrocyte; cellular phase; complement cascade; in situ sequencing; microglia; myelination; oligodendrocyte; spatial transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alzheimer Disease / genetics
  • Alzheimer Disease / pathology*
  • Amyloid / metabolism
  • Amyloid beta-Peptides / genetics
  • Amyloid beta-Peptides / metabolism
  • Animals
  • Brain / metabolism
  • Brain / pathology
  • Complement System Proteins / genetics
  • Complement System Proteins / metabolism
  • Disease Models, Animal
  • Gene Expression Profiling
  • Humans
  • Lysosomes / genetics
  • Lysosomes / metabolism
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Myelin Sheath / genetics
  • Myelin Sheath / metabolism
  • Oxidative Stress / genetics
  • Sequence Analysis, DNA / methods*
  • Transcriptome*


  • Amyloid
  • Amyloid beta-Peptides
  • Complement System Proteins