Axon-Seq Decodes the Motor Axon Transcriptome and Its Modulation in Response to ALS

Stem Cell Reports. 2018 Dec 11;11(6):1565-1578. doi: 10.1016/j.stemcr.2018.11.005.


Spinal motor axons traverse large distances to innervate target muscles, thus requiring local control of cellular events for proper functioning. To interrogate axon-specific processes we developed Axon-seq, a refined method incorporating microfluidics, RNA sequencing (RNA-seq), and bioinformatic quality control. We show that the axonal transcriptome is distinct from that of somas and contains fewer genes. We identified 3,500-5,000 transcripts in mouse and human stem cell-derived spinal motor axons, most of which are required for oxidative energy production and ribogenesis. Axons contained transcription factor mRNAs, e.g., Ybx1, with implications for local functions. As motor axons degenerate in amyotrophic lateral sclerosis (ALS), we investigated their response to the SOD1G93A mutation, identifying 121 ALS-dysregulated transcripts. Several of these are implicated in axonal function, including Nrp1, Dbn1, and Nek1, a known ALS-causing gene. In conclusion, Axon-seq provides an improved method for RNA-seq of axons, increasing our understanding of peripheral axon biology and identifying therapeutic targets in motor neuron disease.

Keywords: RNA sequencing; amyotrophic lateral sclerosis; microfluidic devices; motor neurons; stem cells; transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amyotrophic Lateral Sclerosis / genetics*
  • Amyotrophic Lateral Sclerosis / pathology*
  • Animals
  • Axons / metabolism*
  • Gene Expression Regulation
  • Humans
  • Mice
  • Microfluidics
  • Mitochondria / metabolism
  • Motor Neurons / metabolism*
  • Mutation / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Ribosomes / metabolism
  • Sequence Analysis, RNA
  • Superoxide Dismutase-1 / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Transcriptome / genetics*


  • RNA, Messenger
  • Transcription Factors
  • Superoxide Dismutase-1