Multiplexing Biology
Shendure Shares Trek Along ‘New Frontiers in Genomics’
Photo: Credit Ernesto Del Aguila
Remember when the cineplex concept debuted and a family could pile into the car for a trip to one big theater where everyone could see a different movie at the same time in the same place? Saved a lot of time, effort and angst, didn’t it?
In recent years, longtime NIH grantee Dr. Jay Shendure has been focused on applying a similar idea to genome science. He discussed his work recently in Lipsett Amphitheater at the 15th installment of the Jeffrey M. Trent Lecture in Cancer Genomics.
“A common thread that runs through our work is, can we multiplex biology—at every level and in as many flavors as we can?” Shendure began. “Think about technologies like next-gen sequencing, exome sequencing, massively parallel reporter assays…the performance of multiple experiments within a single volume…It’s a very technical theme as opposed to a disease or a particular physiologic mechanism, but still one that I think is very powerful.”
HHMI researcher and professor of genome sciences at the University of Washington, Shendure also serves as director of the Allen Discovery Center for Cell Lineage and director of the Brotman-Baty Institute for Precision Medicine.
“I regard Jay as one of the most highly accomplished genome researchers of this decade—full stop,” said NHGRI director Dr. Eric Green, who introduced the guest speaker.
Shendure joined a long, storied list of speakers delivering the annual talk named for NHGRI’s founding scientific director.
“This is really a lecture series of rock stars in honor of a rock star,” enthused current NHGRI scientific director Dr. Dan Kastner, opening the event. “Through his vision, through his energy, through the dint of his hard work, Jeff quickly created an entity that was an engine that transformed the intramural program of NIH.”
Also former chief of NHGRI’s Cancer Genetics Branch, Trent “infused genetics and genomics into the culture of the campus science community” and his influence eventually spread to research enterprises globally, Kastner recalled. “It became a powerhouse of genetics and genomics not only in the United States but around the world.”
Photo: Ernesto Del Aguila
In his 50-minute lecture, “New Frontiers in Genomics,” Shendure briefed the audience on three starkly different projects—all funded by NIH—in which his technology development lab is “trying to answer old questions with new methods. But a common theme is this idea of multiplexing biology.”
It’s been established for several decades now that having genetic variation in the BRCA1 gene can put a person at greater risk of developing cancer; people can be readily tested to see whether they carry such variants. What still puzzles scientists, however, is that not all genetic variants in BRCA1 and related genes increase risk of cancer. How can we better distinguish the benign variants versus those that will require treatment?
“The challenge is that even though we have implicated the gene, we do not always know which variants are pathogenic,” Shendure explained.
He described how his colleagues developed a CRISPR-driven saturation genome editing method to systematically test more than 96 percent of all possible variants within key regions of the BRCA1 gene. When compared to the widely used ClinVar database of classified variants in actual cancer patients, the Shendure group results matched well for accuracy.
“We see very strong agreement between our data and those calls,” Shendure said. “We’re hoping that this is a paradigm potentially moving forward, if we can scale this further.”
For the second project, he asked a completely different question: How do we identify what genes an enhancer regulates?
Scientists commonly use expression quantitative trait locus (eQTL) studies to determine which genes an enhancer regulates. But this method is time-consuming, expensive and has other important limitations.
Inspired by this technique but seeking a more general solution, Shendure’s group designed “crisprQTL mapping, which enables testing of many candidate enhancers against many transcripts.”
Describing a third project in fewer than 10 minutes, rock star researcher Shendure—who is also a member of the advisory committee to the NIH director and had just spent the previous day and a half attending the ACD’s biannual meeting—talked about how to merge what scientists have learned about organism genomes with data from genome-wide association studies (GWAS) in humans.
In the past 5 years or so, Shendure and collaborators developed a technique—single cell combinatorial indexing (sci, pronounced “sky”)—to profile the molecular contents of large numbers of single cells without ever isolating single cells.
Since then, various colleagues have adapted sci and used the method to make, for example, an atlas transcriptome of the C. elegans worm and, in the space of about a week and a half, profile 2 million cells from mouse embryos in one experiment.
“The stuff you can see around development of all the various cell lineages of the organism—we’ve only scratched the surface of what we could potentially look at with these data,” Shendure said.
His group then placed a sci-derived mouse atlas on top of GWAS data to try to discern what cell types underlie common human diseases and conditions such as gout, emphysema, systolic blood pressure and pain on walking.
“We are related,” he said wryly, showing strong matches of his group’s results with those on file in the UK BioBank. “And you can just lift the coordinates over [from the mouse genome to the human] and it works, amazingly.
“This is giving you a glimpse of these multiplex methods,” he concluded, “that still have a lot of runway in terms of how we can apply them to contemporary and important questions in genomics and biology in general.”