Codon Digest: Injected Gene Editors

Also, there's no such thing as a "blood microbiome."

This is Codon Digest, a weekly roundup of research papers, news articles, and industry highlights about engineered biology. Thanks for skimming. ❤️

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“A hen is only an egg's way of making another egg.”

— Samuel Butler, 1878

(* = My picks)

AI + Bio

• Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Peng X. Nature Machine Intelligence. Read

  T-cell receptors (TCRs) are the cornerstone proteins used to build CAR-T immunotherapies. This deep learning tool, called TEIM-Res, predicts how TCRs interact with other proteins, which may be useful to design more nuanced, or specific, cellular medicines.

Basic Science

• *No evidence for a common blood microbiome based on a population study of 9,770 healthy humans. Tan C.C.S. Nature Microbiology. Read

  Prior studies had suggested the existence of a blood microbiome. But now, by studying DNA extracted from microbes in the blood of almost 10,000 healthy people, this paper shows that there is no such thing. The scientists found 117 types of microbes, mostly from the gut, mouth, and genitourinary tract, in the blood; but most people had no microbes or only one species in their bloodstreams. The likeliest explanation is that microbes occasionally, and temporarily, enter the bloodstream from other parts of the body.

• Transcription factor clusters enable target search but do not contribute to target gene activation. Meeussen J.V.W. Nucleic Acids Research. Read

  Transcription factors bind to DNA and control gene expression. They tend to “group up” in cells. This study suggests that these clusters help the proteins find an appropriate DNA sequence, but if the cluster is too large, it can cause negative effects on gene activation.

• T cell immunotherapies engage neutrophils to eliminate tumor antigen escape variants. Hirschhorn D. Cell. Read

• A neutrophil response linked to tumor control in immunotherapy. Gungabeesoon J. Cell. Read

• Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. Sen P. Nature Aging. Read

Biological Engineering

• mScarlet3: a brilliant and fast-maturing red fluorescent protein. Gadella Jr, T.W.J. Nature Methods. Read

  A brighter red fluorescent protein that causes no “apparent” toxicity to living cells.

• Identification of tagged glycans with a protein nanopore. Li M. Nature Communications. Read

  Proteins are often tagged with sugar molecules, but we don’t usually “see” these sugars when we study proteins. A new technique does the job.

• A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Klenk C. Nature Communications. Read

• A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks. English M.A. Molecular Systems Biology. Read

• De novo design of stable proteins that efficaciously inhibit oncogenic G proteins. Cummins M.C. bioRxiv. Read

• Switchable hydrophobic pockets in DNA protocells enhance chemical conversion. Liu W. JACS. Read

The Brain

• *High-speed low-light in vivo two-photon voltage imaging of large neuronal populations. Platisa J. Nature Methods. Read

  A new way to track the activity of large groups of neurons with a special microscope and algorithm. Deep-tissue imaging of over 100 neurons for one hour in awake mice!

• Rapid detection of neurons in widefield calcium imaging datasets after training with synthetic data. Zhang Y. Nature Methods. Read

  A deep-learning tool, called DeepWonder, can accurately “pick out'“ neurons from dense brain images. The algorithm is superior to prior tools. It detected 14,000 neurons in 17 hours.

• A consensus protocol for functional connectivity analysis in the rat brain. Grandjean J. Nature Neuroscience. Read

  You love to see it! A giant dataset about the rat brain, and how neurons connect to each other, was collected and pooled together from 20 different research laboratories.

• Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics. Kim S. Neuron. Read

DNA Sequencing & Synthesis

• An atlas of genetic scores to predict multi-omic traits. Xu Y. Nature. Read

  An incredibly deep analysis of DNA sequences, transcriptomics, and proteomics data from thousands of people. Machine learning was used to correlate the data with 17,227 molecular traits, and everything is kept in a public database (https://www.omicspred.org/).

• A dual-purpose polymerase engineered for direct sequencing of pseudouridine and queuosine. Huber L.B. Nucleic Acids Research. Read

  A new DNA polymerase variant, called RT-KTq I614Y, can directly detect RNA modifications, including pseudouridine (Ψ) and queuosine (Q). By combining this new variant with standard sequencing methods, it’s possible to identify RNA modifications in a really simple way.

Gene Editing & All Things CRISPR

• *Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing. Li B. Nature Biotechnology. Read

  Inhalable nanoparticles, packaged with mRNA or CRISPR systems, efficiently edit lung cells. The authors tested 720 different ionizable lipids to make the perfect nanoparticles. They achieved high gene-editing efficiencies in airway epithelial cells (which are normally hard to target.)

• *Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Lampe G.D. Nature Biotechnology. Read

  A new method to accurately insert large DNA sequences into mammalian cells with minimal off-target effects. This paper is a legitimate game changer for genome editing.

• Programmable protein delivery with a bacterial contractile injection system. Kreitz J. Nature. Read

  Proteins were engineered to “inject” various other proteins (including Cas9 or base editors) into mice or human cells.

• Prime editing with genuine Cas9 nickases minimizes unwanted indels. Lee J. Nature Communications. Read

  Prime editing is a tool to make small DNA insertions or deletions without cleaving the genome. Sometimes, these proteins "break" the genome at off-target sites. Protein engineering was used to make a prime editing protein with high activity & that causes fewer off-target breaks.

• Specific targeting of plasmids with Argonaute enables genome editing. Esyunina D. Nucleic Acids Research. Read

  Argonaute proteins are programmable tools to cut DNA. They use single-stranded DNA as a guide. In cells, Argonautes preferentially cut plasmids, but this study adapted them into a tool that can integrate plasmid sequences into the genome.

• Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice. Yan N. Nature Communications. Read

  An incredible paper. Base editors were tested in "400 transgenic mice over 15 months" to assess their long-term effects on the animals. The results? Mice offspring had random mutations scattered across their genomes. Some base editor proteins caused much fewer off-target effects, including one version called ABE7.10 F148A.

• Massively parallel profiling of RNA-targeting CRISPR-Cas13d. Kuo H-C. bioRxiv. Read

  Scientists measured the specificity of CRISPR-Cas13d (an RNA-editing protein) against 10,000 RNA targets. The resulting data reveals that Cas13d is "exquisitely sensitive to secondary structure within the target RNA.”

• Collateral activity of the CRISPR/RfxCas13d system in human cells. Shi P. Communications Biology. Read

  A specific version of Cas13, called RfxCas13d, also cuts up nearby RNA strands after it binds to, and cuts, its normal target.

• CRISPRi-mediated tunable control of gene expression level with engineered single-guide RNA in Escherichia coli. Byun G. Nucleic Acids Research. Read

• Continuous multiplexed phage genome editing using recombitrons. Fishman C.B. bioRxiv. Read

• An efficient, scarless, selection-free technology for phage engineering. Goren M.G. bioRxiv. Read

• [Review] Prime editing: advances and therapeutic applications. Zhao Z. Trends in Biotechnology. Read

Health

• *Base editing rescue of spinal muscular atrophy in cells and in mice. Arbab M. Science. Read

  A one-time gene therapy injection for spinal muscular atrophy. Mice and human cells that were given the therapy had normal levels of the survival motor neuron protein, and no symptoms. When delivered using AAV9 in mice, the treatment significantly improved motor function and extended average lifespan.

• Turning universal O into rare Bombay type blood. Anso I. Nature Communications. Read

  A special enzyme, found in bacteria, can change a common blood type (O) into a very rare blood type (called Bombay).

• Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Thakku S.G. Nature Communications. Read

  A diagnostic tool to detect a pathogenic bacterium in blood plasma, again using a Cas13 protein.

• mRNA vaccines and hybrid immunity use different B cell germlines against Omicron BA.4 and BA.5. Andreano E. Nature Communications. Read

  How well do different antibodies, created by people who got two or three doses of the COVID-19 mRNA vaccine, fight off new viral variants, such as BA.4 and BA.5? Only about 15% of antibodies actually neutralize the new variants.

• Therapeutic neutralizing monoclonal antibody administration protects against lethal yellow fever virus infection. Ricciardi M.J. Science Translational Medicine. Read

• Safety and pharmacokinetics of escalating doses of neutralising monoclonal antibody CAP256V2LS administered with and without VRC07-523LS in HIV-negative women in South Africa (CAPRISA 012B): a phase 1, dose-escalation, randomised controlled trial. Mahomed S. The Lancet HIV. Read

Plants

• Design of an Arabidopsis thaliana reporter line to detect heat-sensing and signaling mutants. Guihur A. bioRxiv. Read

  This is a cool paper! Plants were engineered to emit light when they became overheated. Might be useful for tracking crop responses to heatwaves.

• Multi-Knock—a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants. Hu Y. Nature Plants. Read

  The first step in plant gene-editing is to figure out which genes to edit. This paper presents a massive CRISPR screen, in Arabidopsis, that identifies many genes with previously "hidden functions." The authors tested 59,000+ gRNAs, each targeting 2-10 genes, and ultimately identified a new type of transporter protein in the plant cells.

• Designer grass pea for transgene-free minimal neurotoxin-containing seeds with CRISPR-Cas9. Saha T. bioRxiv. Read

Software & Computational Models

• Functional comparison of metabolic networks across species. Ramon C & Stelling J. Nature Communications. Read

Tools and Methods

• Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Neikes H.K. Nature Biotechnology. Read

  A method to measure how the binding energy between proteins (called transcription factors) and DNA in the genome.

• Large-scale purification of functional AAV particles packaging the full genome using short-term ultracentrifugation with a zonal rotor. Wada M. Gene Therapy. Read

  A really simple way to isolate AAVs, which are a type of virus often used to deliver gene therapies into cells.

• Deep learning-enabled segmentation of ambiguous bioimages with deepflash2. Griebel M. Nature Communications. Read

  A general, deep learning tool to segment “ambiguous” biological images and datasets. Might be useful!

• An open-source FACS automation system for high-throughput cell biology. Wiener D.M. bioRxiv. Read

  The authors of this paper took a commercial instrument, and then added a robotic arm and custom software to automate part of the experiment and send updates to Slack. It apparently “reduces hands-on effort by 93%.” Blueprints are available in the paper.

• Adaptable, turn-on monobody (ATOM) fluorescent biosensors for multiplexed detection in cells. Sekhon H. bioRxiv. Read

• Accessible light-controlled knockdown of cell-free protein synthesis using phosphorothioate-caged antisense oligonucleotides. Hartmann D & Booth M.J. Communications Chemistry. Read

• Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop. Cummins B. Synthetic Biology. Read

• Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities. Xu A.M. Cell Systems. Read

• Small-molecule aptamer for regulating RNA functions in mammalian cells and animals. Fukunaga K. JACS. Read

Random Stuff

• Prime factorization via localized tile assembly in a DNA origami framework. Zhang Y. Science Advances. Read

  DNA strands were used to build a “computer” that can factor prime numbers.

• Comparing the economic terms of biotechnology licenses from academic institutions with those between commercial firms. Shah P. PLoS One. Read

  Economic terms were compared for 239 biotechnology licenses issued to academic institutions and 916 similar licenses at commercial firms. Academic licenses had lower royalty rates, deal sizes, and pre-commercial payments compared to corporate licenses.

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📰 News

• A blood test to detect about 50 different cancers. Will Bedingfield. WIRED. Read

  • A company, called Grail, has developed a test that looks for trace amounts of DNA in the blood. If the test has a ‘hit,’ “there’s a 45 percent likelihood that it’s cancer.” DNA sequences are also linked with specific parts of the body, and so the company says its device can also “predict where a cancer is in the body with 90 percent accuracy.” Clinical trials are underway.

• “Stressed plants ‘cry’ — and some animals can probably hear them.” Emma Marris. Nature. Read

  • This one made the rounds on Twitter.

• “3D-printable glass is made from proteins and biodegrades.” Jude Coleman. Nature. Read

  • Chemically modified peptides were melted into a supercooled liquid and quenched to form "biomolecular glass." The glass disintegrates in soil after ~7.5 months. Normal glass takes 1 million years (seriously). Read the paper online.

• “David Liu’s lab shows new base editing SMA therapy could lead to a one-time therapy.” Max Bayer. Fierce Biotech. Read

• “A remotely operated lab is taking shape 2.5 km under the sea.” Dhananjay Khadilkar. Ars Technica. Read

  • Off the coast of Marseille, this autonomous laboratory is unmanned and runs experiments 2,450 meters beneath the ocean’s waves.

• “Human cells hacked to act like squid skin cells could unlock key to camouflage.” Jennifer Ouellette. Ars Technica. Read

• “The professor trying to protect our private thoughts from technology.” Edward Helmore. The Guardian. Read

• “The quest for injectable brain implants has begun.” Grace Huckins. WIRED. Read

• “Rick Berke on building a biotech journalism outlet to last.” Luke Timmerman. Timmerman Report. Read

  • The co-founder of STAT talks about his work. (h/t Raphael Ferreira)

• “Cultured meat firm resurrects woolly mammoth in lab-grown meatball.” Paul Sawers. Tech Crunch. Read

  • The startup, from Australia, is called Vow. They make meatballs using “molecular engineering;” the meat products include myoglobin proteins based on the DNA sequence of extinct mammoths.

• “10 women founders taking the synthetic biology world by storm.” John Cumbers. Forbes. Read

• “Musk's brain implant company in search of human trials partner.” Marisa Taylor & Rachael Levy. Reuters. Read

• “Meet the three Berkeley dropouts empowering biotechs with low-code cloud-based biocomputing.” John Cumbers. Forbes. Read

📰 Musings

• “Scientists gain insights into Old Master artists’ use of egg in oil paintings.” Nicola Davis. The Guardian. Read

  • da Vinci and Botticelli both used eggs in their oil paints, according to a study in Nature Communications.

• “NASA lays out vision for robotic Mars exploration.” Paul Voosen. Science. Read

• “Fast-growing open-access journals stripped of coveted impact factors.” Jeffrey Brainard. Science. Read

  • MDPI journals are no longer given a Web of Science impact factor. According to the article:

    “MDPI’s practice of publishing large numbers of special issues is likely at the heart of the concern, outsiders say. “[Clarivate’s] announcement suggests we are approaching the high-water mark for the use of special issues as a growth model,” Johnson says.”

• “Virgin Orbit to lay off 85 percent of staff, freeze operations.” Aaron Gregg. The Washington Post. Read

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🏘️ Events

Send me your events.

• Future of Synthetic Biology Conference.

  • Free for college and high school students on April 22. And it’s online! Register online.

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🏭 Industry

• “SR One closes biotech fund at $600M.” Labiotech. Read

• Private investments for biotechnology companies have been “more discriminate, disciplined and demanding” over the last few months. Nature Biotechnology. Read

• The FDA is reviewing a “controversial cell therapy for ALS,” developed by BrainStorm Cell Therapeutics. STAT. Read

• A company that uses AI to design small molecule therapeutics for cancer and immune-related conditions, called Athos Therapeutics, has gotten the green light to commence a Phase I clinical trial. Press release. Read

• Eisai and Biogen — companies behind the controversial, FDA-approved drug for Alzheimer’s, called Aduhelm — have published three additional papers with “detailed analyses” from their phase 2 trials. Press release. Read

• GenScript, a company that does everything from DNA synthesis to cell line manufacturing, increased revenue by 27.7% from 2021 to 2022, up to $625 million. Press release. Read

• “Codiak files for bankruptcy after exosome-focused biotech unable to satisfy 'financial needs.’” Fierce Biotech. Read

• “Boehringer puts $481M on the line to pursue emerging cancer target in Covant team-up.” Fierce Biotech. Read

• “Vertex and CRISPR Therapeutics announce licensing agreement to accelerate development of Vertex’s hypoimmune cell therapies for the treatment of Type 1 Diabetes.” Press release. Read

• “Nanoscope's phase 2 win for gene therapy shows potential of light-sensitive approach to eye disease.” Fierce Biotech. Read

  • A trial of 27 patients, injected with “light-sensitive molecules to treat retinal disease,” had improvements in vision.

• “Viking Therapeutics announces results from Phase 1 clinical trial of dual GLP-1/GIP receptor agonist VK2735.” Press release. Read

  • Some good data for the obesity drug. Those who received the drug lost weight compared to those on placebo; up to 6% more. The drug has a half-life exceeding 7 days, which is pretty incredible.

• “Sonoma Biotherapeutics and Regeneron announce collaboration to discover, develop and commercialize T_reg cell therapies for autoimmune diseases.” Press release. Read

  • Sonoma receives $75 million in upfront payments.

• “Bicycle Therapeutics announces a strategic collaboration with Novartis to discover, develop and commercialize Bicycle® radio-conjugates.” Press release. Read

• “Moderna's gene therapy expansion picks up pace with $76M upfront Generation Bio collab.” Fierce Biotech. Read

Thanks for skimming,

— Niko McCarty

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Disclosure: The views expressed in this blog are entirely my own and do not represent the views of any company or university with which I am affiliated.