A region of the brain called the striatum is critical for many cognitive and motor functions, including decision-making, control of movement, habit formation, and processing of reward. It also plays a role in addiction and is significantly affected by Huntington’s disease, schizophrenia, and other disorders.

In work that could help scientists devise new treatments for those diseases, MIT researchers have generated a new atlas of the neurons found within the striatum. Using single-cell RNA sequencing and other techniques, they were able to identify 31 subgroups of neurons based on which genes they express.

These groups include neurons that are involved in addiction, depression, and schizophrenia. The researchers also discovered why some neurons of the striatum are more vulnerable to Huntington’s disease. All of these results, the researchers say, could help scientists develop new drugs to combat these conditions.

“We see this as the foundation that will allow more studies in our Huntington’s disease and opioid use disorder projects. We needed a roadmap of what is there,” says Myriam Heiman, the Picower Professor of Neuroscience and director of MIT’s Picower Institute for Learning and Memory.

Heiman; Manolis Kellis, a professor of computer science in MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and a member of the Broad Institute of MIT and Harvard; and Dana Gabuzda, a principal investigator at Dana-Farber Cancer Institute and a professor of neurology at Brigham and Women’s Hospital and Harvard Medical School, are the senior authors of the study, which appears today in Cell. MIT postdoc Raleigh Linville and MIT graduate student Benjamin James are the paper’s lead authors.

Mapping the striatum

The striatum, located deep within the brain, receives diverse inputs from the cortex, midbrain, hippocampus, and other regions, which it uses to coordinate planning, movement, and decision-making, as well as processing reward. In this study, the researchers focused on the most populous cell type in the striatum, a type of inhibitory neuron called the medium spiny neuron, which responds to dopamine.

Most of these medium spiny neurons belong to either the direct pathway, which helps to promote movement, or the indirect pathway, which suppresses unwanted movements. These pathways are distinguishable by what type of dopamine receptor they express — dopamine receptor 1 (D1) or dopamine receptor 2 (D2).

Beyond these two divisions, scientists knew that there were many subpopulations performing different roles, especially in the anatomically ventral (lower) regions of the striatum. However, it has been difficult to generate a consensus on how to classify these cells, in part because prior studies focused on specific subregions, meaning that overarching principles of striatal cellular organization were lacking.

To overcome that challenge, the researchers worked closely with brain banks in the United States and Canada to collect postmortem striatal samples representing diverse anatomical regions. 

Then, they used three different techniques to analyze the samples, including single-cell RNA sequencing — a method that can measure RNA molecules within individual cells to reveal which genes are being expressed. Two additional techniques — multiplexed fluorescent in situ hybridization and spatial transcriptomics — allowed the researchers to identify spatial principles of organization within the tissue.

Using these techniques, the researchers were able to identify 31 different subpopulations of neurons, including nine types of medium spiny neurons. Among their medium spiny neuron types are two “outlier” populations that appear to play important roles in schizophrenia, substance use disorder, and depression.

One of those populations, known as D1 outliers, showed high expression of genes involved in addiction and substance use disorder, especially genes related to opioid response. Another population, called D2 outliers, showed high expression of genes that respond to antidepressants. And, both populations appeared to respond strongly to clozapine, an antipsychotic drug used to treat schizophrenia.

Clozapine is among the most effective antipsychotics available, but it’s not widely used in the United States because it can cause a fatal blood disorder in a small percentage of patients. Now that researchers know which cells the drug acts on, they may be able to design more targeted therapeutics to overcome psychosis, but without the harmful side effects, Heiman says.

Huntington’s vulnerability

Another key finding of the paper helps to shed light on why the dorsal (upper) part of the striatum is more vulnerable to Huntington’s disease. The disease is caused by an inherited version of the huntingtin gene that carries too many repetitive DNA segments, called CAG repeats. 

The researchers found that dorsal populations of medium spiny neurons express higher levels of the genes MSH2 and MSH3, which play a role in increasing the number of CAG repeats found in the huntingtin gene. As more of those repeats accumulate, the mutated version of the huntingtin protein becomes more harmful to cells.

The researchers also found that a rare population of medium spiny neurons that forms island-like structures in the ventral striatum was more resistant to the accumulation of CAG repeats. Further study of this class of cells might help researchers learn how to induce other medium spiny neurons to become more resistant to the disease, Heiman says.

“Looking at the genes that these neurons express or don’t express might give us some clues as to how to make other medium spiny neurons resilient like them,” she says. 

Insights into substance use disorders

The researchers also compared their findings from human tissue samples to samples from mice and found several differences, especially in the expression of genes related to drug response and substance use disorders. One such gene, which encodes the mu opioid receptor (OPRM1), is highly expressed in the human D1 outlier population, but not in the corresponding population of neurons in mice. 

This means that standard mouse models may not fully capture the biology of opioid responses, and that engineering mice to express this receptor in a similar manner to humans could make those models significantly more accurate.

“Some of the diversity we’re seeing in the human ventral striatum is species-specific and has implications for modeling substance use disorder in rodents,” Heiman says. “Now that we understand better the species differences, we can use the rodent models for specific questions that apply for conserved genes, but we could also think about humanizing some models.”

The researchers hope that this map, built from tissue contributions by brain donors and their families, and assembled across disciplines and institutions, will provide an important starting point for researchers pursuing new treatments for some of the most difficult-to-treat brain disorders.

The research was funded, in part, by the National Institutes of Health, the G. Harold and Leila Y. Mathers Charitable Foundation, the Freedom Together Foundation, the Natalia Mental Health Foundation, the Biswas Family Foundation, and the Milken Institute.