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☀️ Good morning.
To do nothing is sometimes a good remedy.
All of the featured studies this week are open access.
CRISPR Cuts Pain (in Mice): There are a handful of people that are completely insensitive to pain; about twenty cases have been reported in the scientific literature, according to Medline Plus. One of the ways to be “pain-free” is to have a hereditary mutation in a specific gene, called SCN9A, that encodes a voltage-gated sodium channel called Nav1.7. Scientists have tried for decades to develop drugs targeting SCN9A, which could dampen pain, minimize side-effects, and reduce people’s reliance on addictive opioids. But targeting Nav1.7 has proven difficult.
For a new study in Science Translational Medicine, researchers from the University of California, San Diego used a deactivated form of CRISPR-Cas9 — which can bind to DNA, but cannot cut it — to repress SCN9A in specific nerve cells. The team selected two guide RNAs that target SCN9A and cloned them into a single genetic construct. They then transfected the guides — together with the deactivated Cas9 — into mouse neuroblastoma cells expressing Nav1.7. The dual guide RNAs knocked down the protein’s expression by 71 per cent. The team also tested four different zinc finger nucleases, and found that one of them repressed Nav1.7 by 88 per cent in vitro.
After showing that the therapy worked on cells in a plastic dish, the researchers next delivered the CRISPR machinery into nerve cells, in living mice, using adeno-associated virus 9 (or AAV9, for short). Mice receiving AAV9 loaded with the CRISPR repression machinery had reduced expression of Nav1.7 in their lumbar dorsal root ganglia (a cluster of neurons in the spine), and felt less pain. The therapy did not affect the mice in any other way; the animals moved about normally, and the therapy was effective for about 44 weeks in one of the mouse models. This study was also covered in a brief Nature news story.
Why It Matters: Opioids are addictive. Alternative therapies for reducing pain are desirable. By showing that CRISPR can alleviate pain in mice (for several months), this study offers a starting point for future clinical trials, provided that patients are on board with having CRISPR-carrying viruses delivered into their spines.
CRISPR Treats Inflammatory Skin Disease (in Mice): There was a second impressive CRISPR therapy study this week. Instead of using the gene-editing tool to reduce pain, though, researchers used CRISPR to treat psoriasis and atopic dermatitis, two types of inflammatory skin disorders. Patients with these conditions are often treated with glucocorticoids (a type of steroid) or immunosuppressants.
For a new study in Science Advances, researchers from Zhejiang University, in China, built a patch, with itty-bitty needles, that can stick to skin and deliver CRISPR nanoparticles and glucocorticoids at the same time. They used the payload-packing patches to knock down the expression of a gene called NLRP3, which is often overexpressed when skin becomes inflamed, and is involved in glucocorticoid resistance.
To test the patch, the researchers rubbed a chemical on mice that caused them to develop skin inflammation. Then, they stuck a patch on the animals for five weeks. Mice with the patch had a significant reduction in itchiness and skin irritation. Cells in the epidermal and dermal tissues, where the patch was applied, had a disruption in the NLRP3 gene about 15 per cent of the time. Mice that received the treatment were generally healthy; they did not gain or lose weight.
Why It Matters: This study is about more than CRISPR-Cas9 for treating skin conditions. The researchers also meticulously designed and tested a patch to deliver these molecules into the skin, evaluating how deep the nanoparticles were able to penetrate and meticulously fine-tuning their approach until they came up with an effective patch. In the future, perhaps these transdermal patches could be used to deliver other medicines into the skin — not just gene-editing therapies.
Antimicrobials by Design: Antibiotic resistance is a growing problem. About 10 million people could die each year from antibiotic resistant infections by 2050 if current trends continue, according to a 2019 UN report. It is also difficult to create new types of antibiotics. The diversity of chemicals in nature that could have antimicrobial properties is impossibly vast; there are too many options to explore. Now, researchers have developed a quick way to build new types of antimicrobials.
For a study in Nature Biomedical Engineering, researchers from the IBM Thomas J. Watson Research Center and other institutions built a generative model — a type of statistical model that can predict how likely a random peptide sequence, for example, is likely to have come from a dataset — to design microbe-killing peptides. The math is, honestly, way above my pay grade. But the novelty of the approach seems to be this: the researchers merged their model with in silico physics equations, simulating hundreds of thousands of random peptide sequences, over about a week, to evaluate each of their physicochemical properties. After whittling down the peptide sequences to 20 candidates, the researchers tested each one against microbes, and also studied their toxicity in mice.
Two of the designed peptides, which were just 12 and 13 amino acids in length, were effective against “difficult-to-treat” microbes, and were not toxic to mice. Both peptides also happened to be positively charged, which is common for antimicrobials. Both peptide sequences were also compared to the library of known antimicrobials; neither of them were very similar to any sequence in the “training” database, which is an intriguing finding, and may suggest that an unexplored region of short peptide sequences could contain as-yet untapped antimicrobials.
Why It Matters: I have trouble understanding machine learning papers. But I chose to feature this study because the scale of the problem — antimicrobial resistance — is huge, and solutions are urgently needed. The entire experiment reported in this study, from training database to tested antimicrobials, was done in about 48 days. That is very impressive, and could help researchers unearth new antimicrobials on a short time-scale in the future.
🧫 Other Studies Published This Week
- A self-organized synthetic morphogenic liposome responds with shape changes to local light cues. Nature Communications. Open Access. Link
- A biosensor for detection of indole metabolites. bioRxiv (preprint). Link
- Sensitive and selective methanol biosensor using two-enzyme cascade reaction and fluorometry for non-invasive assessment of intestinal bacteria activity. Biosensors and Bioelectronics. Link
- Microfluidic based whole-cell biosensors for simultaneously on-site monitoring of multiple environmental contaminants (Perspective). Frontiers in Bioengineering and Biotechnology. Open Access. Link
- Application of cell-free protein synthesis system for the biosynthesis of l-theanine. ACS Synthetic Biology. Link
- Optimising protein synthesis in cell‐free systems, a review (Review). IET Engineering Biology. Open Access. Link
DNA Storage & Nanotechnology
- Functionalization of cellular membranes with DNA nanotechnology (Review). Trends in Biotechnology. Link
- Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming. npj Systems Biology and Applications. Open Access. Link
- A high-resolution protein architecture of the budding yeast genome. Nature. Link
- DNA origami patterning of synthetic T cell receptors reveals spatial control of the sensitivity and kinetics of signal activation. bioRxiv (preprint). Link
- Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning. eLife. Open Access. Link
- Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin. Science Advances. Open Access. Link
- Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation. Nature Communications. Open Access. Link
- Recombinant protein stability in cyanobacteria. ACS Synthetic Biology. Link
- A confinable home and rescue gene drive for population modification. eLife. Open Access. Link
Genetic Engineering & Control
- Lineage barcoding in mice with homing CRISPR. Nature Protocols. Link
- A CRISPR-Cas9–integrase complex generates precise DNA fragments for genome integration. Nucleic Acids Research. Open Access. Link
- Engineering transcriptional interference through RNA polymerase processivity control. ACS Synthetic Biology. Link
- CRISPR/Cas9 ribonucleoprotein-based genome editing methodology in the marine protozoan parasite Perkinsus marinus.Frontiers in Bioengineering and Biotechnology. Link
- Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering. Nature Communications. Open Access. Link
- Targeted genome reduction of Pseudomonas aeruginosa strain PAO1 led to the development of hypovirulent and hypersusceptible rDNA hosts. Frontiers in Bioengineering and Biotechnology. Open Access. Link
Medicine and Diagnostics
- Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids. Nature Protocols. Link
- Metabolic engineering of probiotic Escherichia coli for cytolytic therapy of tumors. Scientific Reports. Open Access. Link
- Switching metabolic flux by engineering tryptophan operon-assisted CRISPR interference system in Klebsiella pneumoniae. Metabolic Engineering. Link
- Biotechnological production of 2′-fucosyllactose: A prevalent fucosylated human milk oligosaccharide. ACS Synthetic Biology. Link
- Synthetic biology towards engineering microbial lignin biotransformation (Review). Trends in Biotechnology. Link
- Engineering the reductive TCA pathway to dynamically regulate the biosynthesis of adipic acid in Escherichia coli. ACS Synthetic Biology. Link
- Recent advances in producing sugar alcohols and functional sugars by engineering Yarrowia lipolytica (Review). Frontiers in Bioengineering and Biotechnology. Open Access. Link
- Hyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis. Nature Communications. Open Access. Link
- Biofoundry-assisted expression and characterisation of plant proteins. bioRxiv (preprint). Link
- Heterologous expression of mersacidin in Escherichia coli elucidates the mode of leader processing. ACS Synthetic Biology. Open Access. Link
- A computer-guided design tool to increase the efficiency of cellular conversions. Nature Communications. Open Access. Link
- Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes. Nature Communications. Open Access. Link
- Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Research. Open Access. Link (Press release from Wyss Institute.)
- Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nature Biotechnology. Link
- Target protein deglycosylation in living cells by a nanobody-fused split O-GlcNAcase. Nature Chemical Biology. Link
- Feedback ratiometric control of two microbial populations in a single chemostat. bioRxiv (preprint). Link
- Nanotechnology to advance CRISPR–Cas genetic engineering of plants. Nature Nanotechnology. Link (Read the blog post by first author, Gozde Demirer.)
- Enhanced vitamin E content in an Indica rice cultivar harbouring two transgenes from Arabidopsis thaliana involved in tocopherol biosynthesis pathway. Plant Biotechnology Journal. Open Access. Link
- Protein sequence design by conformational landscape optimization. PNAS. Open Access. Link
- Engineering alternate ligand recognition in the PurR topology: A system of novel caffeine biosensing transcriptional antirepressors. ACS Synthetic Biology. Link
Systems Biology & Modelling
- Significant non-existence of sequences in genomes and proteomes. Nucleic Acids Research. Open Access. Link
- Discovery of dynamical network models for genetic circuits from time-series data with incomplete measurements. bioRxiv (preprint). Link
- Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell (Comment). Nature Communications. Open Access. Link
- Genetically intact bioengineered spores of Bacillus subtilis. ACS Synthetic Biology. Link
- Rolling circle replication for biosensing, bioimaging, and biomedicine (Review). Trends in Biotechnology. Link
Until next time,