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Center for Multiomic Human Brain Atlas to Tackle Methylation, Gene Expression for $500M NIH Project


CHICAGO – The second-largest slice of $500 million in funding for the US National Institutes of Health's new BRAIN Initiative Cell Atlas Network (BICAN) program has been allocated to a consortium led by the Salk Institute for Biological Studies. Some $126 million in grant funding over the next five years will support the creation of the Center for Multiomic Human Brain Atlas, which seeks to map the human brain on a cellular level to understand how neurotypical brains operate and age.

La Jolla, California-based Salk will receive about $77 million of the total, the largest single grant in the institute's history. Other key institutions behind the Center for Multiomic Human Brain Atlas include the University of California campuses in San Diego and Irvine, as well as Washington University in St. Louis.

The Salk-led consortium will conduct epigenomic studies of 50 regions of each of 30 human brains, for a total of 1,500 samples. It will include juvenile as well as adult subjects to study postnatal maturation of the brain.

UC Irvine will manage sample acquisition, with assistance from NIH NeuroBioBank collection centers at the universities of Maryland, Pittsburgh, and Florida, according to Margarita Behrens, a research professor in Salk's Computational Neurobiology Laboratory.

Salk will conduct single-cell sequencing of the samples and study chromatin architecture and DNA methylation, while UC San Diego researchers will study gene expression and chromatin modifications. WashU will primarily be responsible for data analytics.

NIH on Sept. 22 unveiled BICAN, backed by a series of 11 grants to support the creation of cell atlases of human and nonhuman brains and maps of cell interactions to inform research into neurological diseases. In addition, NIH made seven awards totaling $36 million over three years for the pilot phase of a related project called the Armamentarium for Precision Brain Cell Access.

BICAN awardees will build the atlases and maps through single-cell sequencing, noninvasive medical imaging, and advanced bioinformatic analysis. The program is part of the National Institute of Mental Health's ongoing Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative.

The largest share of the money, $173 million in five grants, is going to the Allen Institute to build the first-ever complete cell atlas for the human brain, as well as atlases for the brains of marmosets and macaques.

While the Allen Institute is looking at the human brain as well as the brains of two types of primates, the Center for Multiomic Human Brain Atlas is focusing on the human brain but from a different angle. Specifically, Salk will examine chromatin conformation at a single-cell level, while the laboratory of Bing Ren, professor of cellular and molecular medicine at UCSD, will look at histone modifications and RNA.

BICAN is the third phase of an ongoing effort to create a cellular map of the brain, following a pilot phase and the BRAIN Initiative Cell Census Network (BICCN). In 2017, the Salk Institute received $25 million in NIH BRAIN Initiative funding to establish the Center for Epigenomics of the Mouse Brain Atlas, which was tasked with performing single-cell epigenetic profiling on individual neurons throughout the mouse brain and linking cell types to anatomy for detailed characterization of their locations, morphology, and brain-wide connectivity and projections. 

BICCN participants including Salk described some of their efforts last year in a series of papers in Nature. A consortium led by Salk discussed the organization and connection of various cell types in mouse brains.

The Center for Multiomic Human Brain Atlas will be led by Joseph Ecker, director of the Salk Institute's Genomic Analysis Laboratory, with assistance from Behrens. The two, along with Ren, have previously collaborated on the Center for Epigenomics of the Mouse Brain Atlas.

Behrens described BICCN and now BICAN as "many different groups approaching the same problem from different sequencing modalities, such that we can create a very detailed map of the cells in the human brain."

The Salk consortium will build on techniques developed for the mapping of the mouse brain to make them "high-throughput and reliable" when examining human brains, according to Behrens. Data analysis is a key part of that strategy.

The Center for Multiomic Human Brain Atlas will create new analytics software along the way, incorporating new as well as existing data pipelines from the participating institutions including pipelines created for the earlier BICCN project.

BICAN is far more involved because the human brain is 100 times larger than the mouse brain, according to Behrens. "The cell types are not that different, but it's way more complicated," Behrens said.

"It's not just producing the data, but analyzing the data, finding the algorithms to analyze that data, trying to integrate data from different groups all together so we can create the common atlas of … the human brain," she added.

Quan Zhu, associate director of the UCSD Center for Epigenomics, is working closely with Ren on the Center for Multiomic Human Brain Atlas.

UCSD is handling the imaging and will perform two types of analysis using microscopes to examine cell types and gene expression profiles, as well as a high-throughput method that Ren's lab invented called Paired-Tag, short for parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing.

The researchers will also apply Harvard University spinout Vizgen's multiplex error-robust fluorescence in situ hybridization (MERFISH) imaging-based, single-cell spatial transcriptomics technology.

Zhu noted that sequencing does not provide any spatial information. "If we take the same genes, then look at the cells now with the microscope, we would be able to quantify how much each one of the genes are expressed, as well as their … location," she said.

MERFISH analysis will provide that key location information, though it will require some bioinformatics know-how as well as massive computing power, since each of the 1,500 analyses will generate as much as 3 terabytes of data, according to Zhu. WashU will help in this regard, providing data integration, harmonization, and visualization services.

Behrens said that the consortium will need freshly frozen brain tissue "in very, very good condition," not samples that have been sitting in biobanks for years. "There is too much variability in the RNA integrity of the different tissues, so we will need to collect that new," she said.

Collecting new brain samples will better allow the consortium to standardize its procedures, Behrens added.

Behrens said that the Salk consortium is meeting once or twice a week with the Allen Institute-led group right now to work out some basic procedures and standards for BICAN, including how they will slice up the brain samples into regions. "Then each group will do a different single-cell [sequencing] modality," she said.

Despite the millions in NIH funding, Behrens said that sequencing methods like RNA-seq and methylation still may be too expensive. "The number of nuclei that you're analyzing on each stage is enormous," she added. "There might be more than we think."

Behrens cautioned against having expectations for immediate results in the human brain atlas because of the sheer size of the human brain, likening the new effort to the Human Genome Project of two decades ago. "We declared victory and … we are still mapping" the human genome, she said.