The rockefeller university

RNA is the driving force of biological complexity, determining which genes any given cell expresses at specific times and under specific circumstances. Darnell developed high-throughput sequencing and crosslinking methods to investigate how RNA binding proteins (RBPs) modulate gene expression. He discovered neuron-specific RNA-binding proteins in the mammalian brain, and studies their link to intellectual function and human disease.

Darnell’s interest in RNA and RNA-binding proteins arose from studies of paraneoplastic neurologic disorders (PNDs), a group of rare conditions that affect the nervous system in people with certain tumors. These disorders are thought to arise when tumors make proteins normally unique to the brain, triggering an immune response that thwarts the cancer but also causes collateral damage to the nervous system.

Darnell’s lab discovered that neuron-specific proteins are targeted by the immune system in PNDs. The team found that the immune systems of PND patients kill tumor cells with what is essentially an antiviral response: CD8+ killer T cells that recognize the neuron-specific proteins. The lab also found that dying apoptotic tumor cells instigate this anti-tumor response and has worked on developing cancer vaccines that mimic this effect.

Subsequent studies in the Darnell lab explored why tumors induce the expression of neuron-specific proteins, and these proteins’ normal roles in neurons. This work led the lab to discover and explore the function of neuron-specific RNA-binding proteins in the mammalian brain, including the Nova and Hu (nElavl) PND targets. Additional studies led to the discovery of the function of the Nova-related RNA-binding protein FMRP, whose function is lost in fragile X syndrome, the most common inherited form of intellectual disability. The lab further expanded these investigations to include other RNA-binding proteins, such as Argonaute (Ago, which works with microRNAs to regulate messenger RNA), as well as Ptbp2, Mbln2, and Rbfox. Finally, the lab has expanded their work to consider RNA regulation over time, and apply this to the study of autoimmune disease (rheumatoid arthritis) and infectious disease (including COVID-19).

To understand these proteins’ functions in the brain, the lab developed a general and powerful method called cross-linking immunoprecipitation (CLIP), which allowed the team to create precise, genome-wide maps of protein binding sites on RNAs in living tissue. They used CLIP, together with the analysis of knockout mice and bioinformatic approaches, to discover that where a protein binds influences how messenger RNAs are altered through processes called alternative splicing and polyadenylation. Recent computational improvements in the analysis of CLIP maps have allowed single-nucleotide and single cell-type resolution of RNA regulatory sites in different neurons, and robust genome-wide predictions of combinatorial RNA regulation in the non-coding genome.

The lab has revealed how disruptions in RNA-protein interactions contribute to common neurologic disorders, such as that mediated by FMRP in autism spectrum disorders, by Ago in stroke and hepatitis infection, by nElavl in Alzheimer’s disease, and by Nova in axonal guidance and brain development. Studies with Nova and FMRP have led to insight into the balance of neuronal inhibition, excitation, and control of gene expression, leading to new approaches to study protein-synthesis dependent synaptic plasticity during neuronal excitation, and to apply these findings to the study of neurodegenerative disorders such as Parkinson’s disease, epilepsy, and autism.

Darnell is a faculty member in the David Rockefeller Graduate Program, and the Tri-Institutional M.D.-Ph.D. Program.