Genome editing that avoids immune detection to integrate large DNA sequences @nature.com
www.nature.com/articles/d41... on paper released last week by @bkleinstiver.bsky.social
www.nature.com/articles/s41...
Immune-evasive cssDNA donors combined with recombinases facilitate kilobase-scale insertion of custom genetic cargos in human cells and mice. #NBThighlight www.nature.com/articles/s41...
Nature research paper: Immune evasive DNA donors and recombinases license kilobase-scale writing
go.nature.com/4b3e0E2
This was a collaborative effort between Kleinstiver Lab (@bkleinstiver.bsky.social, @ferreiradasilvaj.bsky.social, David Rufino-Ramos), Musolino Lab (Patricia Musolino, Palani Kalailingam), Artzi Lab (Natalie Artzi, Eliz Amar-Lewis, Will Sawyer), & Full Circle Therapeutics (Howard We, Keqiang Xie).
While this study establishes initial POC, we’re excited about next-gen INSTALL systems and solutions to the recombinase side of the problem. Stay tuned! 👀 🚀 (13/13)
Multiplexed immune marker assays and blood work further showed that INSTALL was largely immune-evasive at the physiological level. Minimization of CpG motifs, which are sensed by TLR9 in the endosome, further decreased markers to background levels in adult mice. (12/13)
A hallmark sign of infection is recruitment of monocytes / macrophages to the site of inflammation. We stained for CD68+ cells in the liver and saw dramatic differences between dsDNA-treated and INSTALL-treated liver, confirming that INSTALL evaded DNA innate immunity at the cellular level. (11/13)
Next, we stained liver tissue from our in vivo experiments for activated STING (= immune response): INSTALL looked very similar to PBS and mRNA-only controls, whereas dsDNA could make nearly every cell light up! This confirmed that INSTALL evaded DNA innate immunity at the molecular level. (10/13)
Next, we conducted experiments to characterize immune response. First, we performed RNA-seq from primary human T-cells or THP-1 derived macrophages that were treated with recombinase mRNA and various donor types. dsDNA induced stark transcriptomic disruption whereas INSTALL minimized this. (9/13)
INSTALL might enable non-viral DNA integration in vivo for the first time. We delivered INSTALL via LNPs into mice and saw striking differences in survival compared to dsDNA-treated mice, enabling us to detect in vivo integration. Further work to increase efficiencies is now underway. (8/13)
We found that using a chemically modified “ePIP” (INSTALL-2e) outperformed dsDNA donors in immune-proficient contexts and more modestly in immune-deficient contexts. INSTALL functioned independently of cell cycle arrest, hinting that its more compact structure might aid nuclear localization. (7/13)
By coupling recombinases and redesigned cssDNA in mammalian cells, we created INSTALL. We found that simple oligo annealing to reconstitute the recombinase binding site was sufficient for integration of a cssDNA donor. We call this oligo a “PIP” and the resulting molecule an “oDNA”. (6/13)
Circular single-stranded DNA (cssDNA) offers immune-evasive promise, showing far better tolerance than dsDNA in primary T cells and in mice. However, canonical recombinases are incompatible with ssDNA. We looked to how cssDNA viruses and mobile elements have evolved around this. (5/13)
Yet nearly all recombinase systems are bottlenecked by a key challenge: mammalian cells have evolved potent innate immune responses against double-stranded DNA (dsDNA) - the very form canonically required as a donor for integration. (4/13)
Recombinases are powerful enzymes capable of integrating kilobase-sized DNA into a human genome. Recent technological advances are starting to expand their therapeutic potential by retargeting them to desired genomic loci. (3/13)
A persistent challenge in genome editing is allelic heterogeneity: dozens, hundreds, or thousands of different mutations can cause the same genetic disease. To scale genome editing, mutation-agnostic strategies that can insert a healthy gene at a specific genomic site are needed. (2/13)
Today in @nature.com we introduce INSTALL, which bypasses mammalian DNA immune sensing to enable non-viral DNA integration with recombinases—a step toward safe, and mutation-agnostic genome editing. 🧬 🧵 (1/13)
www.nature.com/articles/s41...
@harvardmed.bsky.social @mgbresearch.bsky.social
Evolution navigated billions of challenges to get to us to where we are today. Directed evolution compresses this to a 1D axis.
Imagine if you could sample 200 dimensions at once, with data to boot 📈
First @chorylab.bsky.social PACE preprint on our new system to tackle this: bit.ly/turboprance
🔎 Special report: Gene editing’s toolbox problem. Endpoints Senior Science Correspondent @scienceboss.bsky.social spoke with dozens of biotech leaders and scientists about the promise of new tools — and the growing frustration over how few cures have followed.
STAT 2025 Wunderkinds Connor Tou he/him
Congrats to IGI alum Connor Tou on being named a 2025 #STATWunderkind! At the IGI, Connor worked on CRISPR EvolvR in John Dueber's lab and now, as a Ph.D. student at MIT, he's working on genome engineering with large insertions.
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Congrats to @connorjtou.bsky.social on being named a 2025 #STATWunderkind. His enthusiasm in the lab is contagious and he thrives on doing really hard things.
Really well deserved recognition for an innovator and emerging leader in our field! 👏 🙌
@mgbresearch.bsky.social @harvardmed.bsky.social
3 Wunderkinds sit on stage with a moderator
Taking the stage are three of this year's #STATWunderkinds!
Meet the class of 2025: www.statnews.com/wunderkinds/
#STATSummit
Thanks Dimitrios! 🙏
At a time when conflict and cynicism seem to be shadowing much of health and medicine, @statnews.com is recognizing some of the brightest young minds in their fields this morning.
www.statnews.com/wunderkinds/
Honored to be part of the 2025 #STATWunderkinds! Grateful for the many supportive mentors, colleagues, and friends with special shoutout to @bkleinstiver.bsky.social.
Full list: www.statnews.com/wunderkinds/
@statnews.com @mitdeptofbe.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social
How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense
www.biorxiv.org/content/10.1...
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...
If you like transposons...
If you you love genome editing...
Or if you just like random bird animations,
we have the paper for you!
We (@kedmonds.bsky.social et al) are happy to share our work turning a songbird retrotransposon into a genome editing tool. 🐣 (1/n)
