John L. Bixby, Ph.D.

Phenotypic Screening, Axon Regeneration, and Drug Discovery

Transcription factors in Axon Growth
Our focus is on understanding and overcoming barriers to axon regeneration after injury to the central nervous system (CNS). We use various strategies to identify and manipulate molecular targets to promote this regeneration. When Dr. Vance Lemmon and I established our joint lab in 2003, we adopted two core technologies: phenotypic screening and transcriptomics. This combination was powerful and resulted in the identification of KLF family members as important regulators of CNS axon regeneration (Moore et al, 2010, Science, 326: 298; Blackmore et al, 2012, PNAS (USA) 109: 7517). We also did extensive work on other transcription factors such as  STAT3 and Jun family members (Smith et al, 2011, Mol Cell Neurosci 46: 32; Lerch et al, 2014, Mol Cell Neurosci, 59: 97; Luo et al, 2016, Cell Rep, 15: 398; Mehta et al, 2016, Exp Neurol, 280: 115; Danzi et al, 2018, Mol Cell Neurosci 92: 114).

Kinases in Axon Growth
In the past 12 years or so, we have focused increasingly on the roles of kinases in CNS regeneration. Kinases regulate most aspects of cell function, including axon growth and regeneration. Because of their critical roles in cancer, there are many drugs and compounds as well as cDNA and RNAi libraries that can be used to interrogate the kinome. We have done a large kinase overexpression screen in primary hippocampal neurons (Buchser et al, 2010, Molec Syst Biol 6: 391). Besides identifying interesting individual targets for further study, our pathway and gene ontology analysis of these results led to a surprise. Kinase pathways involved in cancer are also important in regulating axon growth!

Kinase Inhibitors for Drug Discovery
More recently, together with Dr. Hassan Al-Ali, we have been using kinase inhibitors (KIs) to identify target (those to inhibit) and liability (those to avoid) kinases to promote regeneration (Al-Ali et al, 2015, ACS Chem Biol 10: 1939; Beckerman et al, 2015, Assay Drug Dev Technol 13: 377; Al-Ali et al., 2017, J Neurosci 37: 7079; Patel et al, 2020, PNAS (USA) 117: 33597). This work exploits KI polypharmacology, combining biochemical profiling of KIs with their phenotypic effects, using bioinformatic and machine learning approaches. This approach has led us to identify a KI that enhances axon growth/regeneration in vivo, which we are developing into a potential therapeutic with the help of a Blueprint Neurotherapeutics (UG3/UH3) grant from NIH/NINDS.

Rigor and Reproducibility
For some time, we have been concerned about rigor and reproducibility in SCI research.  In 2012, we organized “Growth Cones and Axon Regeneration: Entering the Age of Informatics”, a meeting supported by the NICHD/NINDS U.S.-JAPAN Brain Research Cooperative Program.  At that meeting the participants began work on “Minimum Information About a Spinal Cord Injury Experiment”, a reporting standard for the SCI field (Lemmon et al, 2014, J. Neurotrauma, 31:1354). Together with Dr. Ubbo Visser, we subsequently developed an ontology and knowledgebase for the SCI domain (Callahan et al, 2016, Database (Oxford), Apr 7, pii: baw040; Lemmon et al, 2014, Neural Regeneration Research 9: 6).  We have helped organize other workshops and meetings on this issue (Fouad et al, 2020, J Neurotrauma, 37: 831; Callahan et al, 2017, Exp Neurol, 295:135), served on the Executive Board (now on the Community Board) of the Open Data Commons for Spinal Cord Injury (odc-sci.org), and are part of the “Pan-Neurotrauma Data Commons” which will unify the ODC-SCI with the ODC-TBI, funded by a U24 grant from NINDS.