An integrative proteotranscriptomics approach reveals new ADAM9 substrates and downstream pathways.

Membrane protein shedding is a key regulatory mechanism for cell signaling and adhesion, and dysregulated shedding is associated with diseases. Many membrane proteases can catalyze shedding, but the substrate spectra and downstream targets of these "sheddases" remain largely elusive. While secretomics-based methods have been applied to the systematic identification of sheddase substrates, these methods are not always effective and do not provide much information on downstream targets. Here we developed an integrative proteotranscriptomics approach to uncover the transcriptional and post-transcriptional targets of the disintegrin metalloproteinase ADAM9, a sheddase that has been implicated in solid tumors, autoimmunity, inflammatory diseases and COVID-19. This systematic approach revealed signaling pathways downstream of ADAM9, including the oncogenic mTOR and tumor suppressor FOXO pathways. We further identified several direct and indirect substrates for ADAM9, which may mediate the pathophysiological roles of ADAM9 in various diseases. Of note, some of these substrates are difficult to detect by secretomics. This new approach can be applied to other sheddases to systematically identify their substrates and targets.