With a bold new plan of recording complex biological information in living cells and genomes, over time, the Allen Institute, the Chan Zuckerberg Initiative (CZI), and the University of Washington (UW) announced the launch of the Seattle Hub for Synthetic Biology in December of last year.
Their goal is to, “Capture the entire biography, instead of just the last page,” Jay Shendure, MD, PhD, and the Hub’s executive director, told Inside Precision Medicine. The Hub launched with $75 million in funding from the Allen Institute and the CZI.
This initiative builds on technology that the Allen Institute and Shendure’s lab at UW have been developing: DNA Typewriter and ENGRAM (ENhancer-driven Genomic Recording of transcriptional Activity in Multiplex), a method of “recording cellular experiences, as opposed to human memories,” said Shendure. They are very different approaches, “It is very analogous to language—we are taking advantage of the native machinery of the cell,” he added.
Shendure has a remarkably storied career. His doctoral thesis, completed in George Church’s lab at Harvard, included one of the first successful examples of next generation DNA sequencing. After he joined faculty of the Department of Genome Sciences at UW in 2007, his lab pioneered exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism, cell-free DNA diagnostics for cancer and reproductive medicine, massively parallel molecular profiling of single cells, and more.
He is now a professor of genome sciences at the UW School of Medicine and an investigator at the Howard Hughes Medical Institute. The primary mission of his lab today is to develop and apply new technologies at the interface of genomics, molecular biology, and developmental biology.
“I’m a technology developer in genomics,” he said, pointing out that this is an aspect of biomedicine we tend to underinvest in. “Our lab has a culture of brainstorming, and with the right culture of creative people, eventually a half-baked idea turns into something,” he added.
It’s a compelling vision. When the Allen Institute announced the Hub, he said, “Imagine being able to put a smart watch into each of your cells to record the genome itself and everything that cell is experiencing.”
He explained the challenge to Inside Precision Medicine. “We generally use our eyes or microscopes to see things. The other aspect is sampling. When you break things open, even if you are using fluorescence, you can only see what has happened at that time.” Shendure and his colleagues hope to overcome limitations in visualization and sampling, among other things. “We want to learn how various cell types evolve, understand the experience of each cell, and the pathophysiological mechanism across disease,” he said.
The DNA Typewriter, for example, “sounds like it’s science fiction, but it’s not,” said Shendure. Just as 1s and 0s encode the letters on a computer or phone screen, DNA’s building blocks, labeled A, C, T, and G, can be used as the basis for a multitude of coded messages. This new method “writes” information into cells’ DNA.
The teams at UW and the Allen Discovery Center for Cell Lineage Tracing described their proof-of-concept DNA Typewriter method in a study published in Nature (July, 2022), led by UW researchers Junhong Choi, PhD, and Shendure.
They write: “… contemporary DNA-based memory devices are constrained in terms of the number of distinct ‘symbols’ that can be concurrently recorded and/or by a failure to capture the order in which events occur.”
DNA Typewriter is designed to overcome these drawbacks. The blank recording medium (“DNA Tape”) is a tandem array of partial CRISPR–Cas9 target sites, with all but the first site truncated at their 5′ ends and therefore inactive. The “symbols” are short insertional edits that record the identity of the prime editing guide RNA while also shifting the position of the “type guide” by one unit along the DNA Tape.
In their study, the team demonstrated “recording and decoding of thousands of symbols, complex event histories and short text messages.” They were also able to evaluate the performance of dozens of orthogonal tapes and construct “long tape” potentially capable of recording as many as 20 serial events. In addition, they used DNA Typewriter with single-cell RNA-seq to reconstruct a monophyletic lineage of 3,257 cells and found that “… sequential edits to multicopy DNA tape can be maintained across at least 20 generations and 25 days of in vitro clonal expansion.”
Meanwhile, through ENGRAM, the activity and dynamics of multiple transcriptional reporters are stably recorded to DNA. The system is based on the prime editing-mediated insertion of signal- or enhancer-specific barcodes to a genomically encoded recording unit.
In a 2021 preprint (bioRxiv), Shendure’s team described how ENGRAM could be used to record the relative genomic effects of at least hundreds of enhancers with high fidelity, sensitivity, and reproducibility. Leveraging specific synthetic enhancers, the team also showed time- and concentration-dependent genomic recording of Wnt, NF-κB, and Tet-On activity. Finally, by coupling ENGRAM to sequential genome editing, they documented serially occurring molecular events.
Shendure predicts molecular editing will emerge as a new field.
“We are at a transformational moment,” he said. “Increasingly exome and NGS is a mainstay of pediatric rare diseases, early detection of cancer, prenatal diagnosis, and now advancing CAR T with a new era of genome editing. Increasingly we will see that the future is genome engineering. We’ll be able to detect pathology early and respond to it.”
He added that “There are still plenty of challenges. We would not have entered this area if we weren’t a bit naive. A lot of the challenges are in the technical needs and the way ENGRAM and DNA Typewriter work is fundamentally different from what we already have.”
Besides Shendure, the other leaders of the new Hub are Marion Pepper, PhD, Cole Trapnell, PhD, and Jesse Gray, PhD, all from UW Medicine’s Brotman Baty Institute for Precision Medicine, where Shendure serves as scientific director. The Hub will build on technology pioneered at the Allen Discovery Center for Cell Lineage Tracing and the Baty Institute.
Malorye Branca is a contributing editor at Inside Precision Medicine and a freelance medical science journalist. She has written hundreds of articles, as well as managed and launched health and science magazines, newsletters, and market research report businesses. She has also co-authored two books: “Moneyball Medicine” and “Walmart’s Second Opinion.”
