Bio

Professional Education


  • Bachelor of Arts, Earlham College (2008)
  • Doctor of Philosophy, University of California Berkeley (2015)

Stanford Advisors


Publications

All Publications


  • Differential and convergent utilization of autophagy components by positive-strand RNA viruses. PLoS biology Abernathy, E., Mateo, R., Majzoub, K., van Buuren, N., Bird, S. W., Carette, J. E., Kirkegaard, K. 2019; 17 (1): e2006926

    Abstract

    Many viruses interface with the autophagy pathway, a highly conserved process for recycling cellular components. For three viral infections in which autophagy constituents are proviral (poliovirus, dengue, and Zika), we developed a panel of knockouts (KOs) of autophagy-related genes to test which components of the canonical pathway are utilized. We discovered that each virus uses a distinct set of initiation components; however, all three viruses utilize autophagy-related gene 9 (ATG9), a lipid scavenging protein, and LC3 (light-chain 3), which is involved in membrane curvature. These results show that viruses use noncanonical routes for membrane sculpting and LC3 recruitment. By measuring viral RNA abundance, we also found that poliovirus utilizes these autophagy components for intracellular growth, while dengue and Zika virus only use autophagy components for post-RNA replication processes. Comparing how RNA viruses manipulate the autophagy pathway reveals new noncanonical autophagy routes, explains the exacerbation of disease by starvation, and uncovers common targets for antiviral drugs.

    View details for DOI 10.1371/journal.pbio.2006926

    View details for PubMedID 30608919

  • The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy AUTOPHAGY Delorme-Axford, E., Abernathy, E., Lennemann, N. J., Bernard, A., Ariosa, A., Coyne, C. B., Kirkegaard, K., Klionsky, D. J. 2018; 14 (5): 898–912

    Abstract

    Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast Saccharomyces cerevisiae and in mammalian cells. In yeast, chromosomal deletion of XRN1 enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (ATG) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.

    View details for DOI 10.1080/15548627.2018.1441648

    View details for Web of Science ID 000438287700011

    View details for PubMedID 29465287