2026 Gruber Neuroscience Prize

For John L.R. Rubenstein, Nina Ireland Distinguished Professor in Child Psychiatry at the University of California, San Francisco (UCSF), growing up with a scientist-physician father meant having a first-hand view of how research is done, as well as what impact it can have. “My father told me to pick an important problem and focus on that,” Rubenstein said. 

Rubenstein decided to focus on gene regulation in the developing brain after attending a lecture during his sophomore year as at Stanford. However, after talking with a neuroscientist John Nicholls, who was also a family friend, Rubenstein decided to wait to study brain development, due to the fact that the field was not yet advanced enough to study his intended problem. “He told me to wait, that it was premature to study gene regulation in the brain,” Rubenstein said. 

Instead, Rubenstein spent his undergraduate years working on a variety of research problems. This included studying how the immune system responded to heart transplantation with the physician-scientists Norman Shumway and Randall Morris; researching DNA replication with Arthur Kornberg and William Wickner; as well as projects supervised by the scientists A. T. Ganesan, David Clayton and Douglas Brutlag, that looked at bacteriophage replication and mitochondrial DNA. 

As an MD/Ph.D. student at Stanford, Rubenstein’s research focused on the biophysics of cell membranes, which included studying the dynamics of lipids and proteins, as well as biogenesis. This work was conducted under the guidance of Harden McConnell and James Rothman; he also benefited from the advice and expertise of Hiroto Okayama and Paul Berg. “It was great foundational scientific training,” Rubenstein said. 

Rubenstein then did his postdoctoral training at the Pasteur Institute in Paris with Francois Jacob, Jean Francois Nicholas and Josh Sanes, where he worked on developing tools to study developmental biology including the use of antisense RNA. At first, his work had nothing to do with studying the development of the brain, but the tools they developed would later become useful. “It was there that we applied retroviral lineage analyses to developmental biology,” Rubenstein said. 

After finishing his postdoctoral training, Rubenstein returned to Stanford, to do his residency. During his residency was when he turned his attention to studying the development of the mammalian forebrain. Over a period of two years, Rubenstein and his collaborators developed a technique to identify genes that were differentially regulated in the developing forebrain. This technique, called subtractive hybridization, used antisense RNA to identify RNA strands that were expressed in the developing forebrain but not the adult forebrain.

“It took a long time to get that procedure working properly, but it worked great,” Rubenstein said. “The first gene that we identified was Dlx2, which became the center of most of my work.” In follow-up experiments, Rubenstein with Luis Puelles and his trainees found that Dlx2 was expressed in a very specific subset of regions in the developing forebrain and provided evidence for a fundamental topological framework for forebrain organization (Prosomeric Model). 

Rubenstein later identified a second gene, called Tbr1, that was also central to forebrain development. In follow-up experiments, they discovered that the excitatory neurons and the inhibitory neurons were being produced in two separate parts of the forebrain, that corresponded with Tbr1 and Dlx2  expression, respectively. “That  was a fundamental discovery,” Rubenstein said. 

Following the discovery that inhibitory and excitatory neurons are produced in two separate parts of the developing brain, this raised the question of how these neurons ended up in other parts of the fully developed brain. In later experiments, Rubenstein and his collaborators were able to show that inhibitory neurons migrate from the basal ganglia to the hippocampus and cerebral cortex, during early development. “That’s how we discovered that the basal ganglia was the source of most inhibitory neurons in the cortex and the hippocampus,” Rubenstein said. 

As an outgrowth of this research, Rubenstein and his collaborators hypothesized that disruption to the cortical interneuron development may underlie conditions such as epilepsy and certain psychiatric disorders. Rubenstein, along with his collaborators Scott Baraban, Arturo Alvarez-Buylla, Arnold Kriegstein, and Cory Nicholas did preclinical experiments at UCSF that led to founding the company Neurona Therapeutics. This company has treated 31 patients with epilepsy to date. It is now embarking on a Phase 3 clinical trial to looking at the effectiveness of transplanting cortical interneurons, as a treatment for focal epilepsy. 

In another clinical translation, focused on the function of Tbr1 in the postnatal cortex. Tbr1 mutations can underlie intellectual disability and autism. The Rubenstein lab discovered that Tbr1 deficiency reduces synapse development and reduces Wnt signaling in postnatal cortex. They found that the synapse defects could be rescued using a molecule that is FDA-approved. Currently, a group in France is investigating whether this molecule can help patients with a mutation in Tbr1.