Today we report in @NatureMedicine the development of a base editing strategy for prion disease, currently a fatal and rapidly progressing neurogenerative condition with no effective treatment. @PrionAlliance @DevermanLab (1/13)
drive.google.com/file/d/1DVpKrz… Prion disease is caused by the assembly of prion protein (PrP) into toxic fibrils, a process templated by spontaneously misfolded endogenous PrP or misfolding-prone PrP mutants, or initiated by infection with exogenous misfolded PrP. Depleting brain PrP to reduce substrate for aggregation is a promising therapeutic strategy. (2/13)
[PrP fibril structure from Wang, Liang et al. NSMB, 27, 598 (2020)]

Today we report in @natBME the eePASSIGE system, which uses evolved and engineered recombinases and prime editing to integrate large gene-sized DNA cargoes into the mammalian genome in an efficient, precise, and targeted manner. (1/13)
drive.google.com/file/d/1WDMVqL…
PASSIGE, which we first reported in 2021, couples prime editing with recombinase enzymes to mediate targeted gene integration. Although prime editing effectively installs the attachment site into the genome (>80%), the overall integration efficiency of PASSIGE is limited by recombinase activity. (2/13)

Today we report in @NatureBiotech an engineered virus-like particle system for in vivo delivery of prime editor protein-RNA complexes. This PE-eVLP platform can support therapeutic prime editing in animal models of genetic disease.
/1
drive.google.com/file/d/1xd7Yzz…
Virus-like particles (VLPs) offer several key features as an in vivo delivery method for gene editing agents, including very large cargo sizes, the absence of any DNA transgene, and short-lived protein or RNA cargo. VLPs thus have potential to enable single-particle, DNA-free, transient delivery of prime editor RNPs.
/2

Today we report in @NatureMedicine a study led by Christine & Jonathan Seidman’s lab in which we used adenine base editing in vivo to correct a common mutation that causes hypertrophic cardiomyopathy (HCM), a disease that occurs in ~1 in 500 people (1/8) We designed an adenine base editor to correct myosin R403Q. In vivo delivery of the adenine base editor into two mouse models of R403Q using AAV9 resulted in 30-80% correction of Myh6 transcripts, which are exclusively made in cardiomyocytes. 2/8

Today we report in @NatureComms the development of compact zinc-finger base editors that edit mitochondrial or nuclear DNA in human cells and in animals, building on our previous development of TALE BEs that enabled the first precise editing of mtDNA. 1/8
drive.google.com/file/d/1FBnvvn… In 2020 we reported in @Nature the use of a novel double-strand DNA cytidine deaminase discovered by Joseph Mougous's lab to create all-protein DdCBEs, enabling the first editing of DNA in mitochondria—a CRISPR-free zone—to specified other sequences. 2/8 drive.google.com/file/d/1b2asK4…

Today we report in @NatureBiotech the conversion of adenine base editors (ABE) into next-generation cytosine base editors (TadCBEs) with high on-target activity and reduced off-target activity using phage-assisted continuous evolution (PACE). 1/14
drive.google.com/file/d/1XY3QG-… Current ABEs, including those in clinical trials, use a laboratory-evolved deoxyadenosine deaminase that results in similar or higher on-target activity, smaller size, and lower Cas-independent DNA and RNA off-target editing activity compared to commonly used CBEs. 2/14

Today we report in @NatureComms the evolution of functionalized DNA polymers that bind a target molecule, and the use of machine learning to generate novel polymer sequences that bind the target—but are unrelated to any of the experimental sequences. 1/6
drive.google.com/file/d/1Hs5LWv… Using DNA-templated ligation to join side-chain-functionalized DNA trimers enables artificial 'translation' of DNA libraries into highly functionalized nucleic acid polymer (HFNAP) libraries that can be evolved through iterated selection, template PCR, translation & mutation. 2/6

Today we report in @ScienceMagazine the development of a continuous evolution system that can reprogram a family of clinically used proteases to selectively cleave protein targets of our choosing. 1/10
science.sciencemag.org/content/371/65…

drive.google.com/file/d/1PqaQSt… Proteases offer powerful features as therapeutics, including potency as catalysts & the ability to modulate protein function, localization, & lifetime. But the difficulty of generating proteases that cleave proteins of our choosing has been a key barrier to their broader use.2/10

Today we report the use of base editing in patient-derived cells and in mice to correct the most common cause of progeria, the devastating rapid aging disease. Progeria is typically caused by a dominant negative C•G-to-T•A point mutation in LMNA. 1/11 drive.google.com/file/d/1oH4W0z… The mutation (discovered by @NIHDirector’s lab in 2003) results in progerin, a toxic protein that damages nuclei. So providing more healthy LMNA is not a solution, and cutting the mutated gene with nucleases is also challenging due to indel mixtures & similarity with wt LMNA.2/11

Bizarrely, @CDCgov now says Americans don’t need to get tested even if they have been in close contact with a #COVID19 infection, and that asymptomatic people do not need a test. More Americans will needlessly die as a result. Here's a thread on why testing is essential. (1/12) From one of the most accurate #COVID19 models to date (@youyanggu's covid19-projections.com/#current-us-pr…), about 1 in 75 Americans today has an active #COVID19 infection. Many of these are asymptomatic and unaware they are infected, but can still infect others. (2/12) nejm.org/doi/full/10.10…

A new report by Hong Kong University documents an apparent case of #COVID19 reinfection by two different #SARSCoV2 strains. A 33-year-old male presented symptoms and tested positive by RT-PCR on Mar 26. Hospitalized Mar 29, discharged Apr 14 after two negative PCR tests. (1/6)

https://twitter.com/cwylilian/status/1297857565385093121

He returned to Hong Kong from Spain and upon RT-PCR entry screening at the HK airport tested positive again by RT-PCR on Aug 15 (4.5 months after his initial positive test), with Ct=26.7, a fairly high viral load. No symptoms the second time. Hospitalized again. (2/6)

Today we report in @nature, in collaboration with the labs of Joseph Mougous and @VamsiMootha, the development of a new class of CRISPR-free base editors that enable precision editing of mitochondrial DNA (mtDNA) for the first time. drive.google.com/file/d/1xHcs__… 1/7 The team discovered DddA, an interbacterial toxin that is a novel cytidine deaminase enzyme that operates on *double-stranded* DNA (dsDNA), unlike all previously known cytidine deaminases, which require single-stranded DNA (ssDNA). 2/7

A key piece of the #COVID19 #SARSCoV2 origin puzzle emerges: where did the virus's unusual spike protein RBD—the receptor-binding domain that engages human ACE2 protein and allows the virus to enter human cells—come from? A new study from Shen & coworkers provides an answer.(1/5) The authors isolated coronaviruses from pangolins dying from respiratory disease in a wildlife rescue center in Mar-Aug 2019. One CoV-positive pangolin had antibodies that cross-reacted with #SARSCoV2 antigens, suggesting the animal was infected with a SARS-CoV-2-like virus.(2/5)

As some communities begin to lift #COVID19 stay-at-home orders, let’s talk about #masks. There is extensive evidence that masks protect you, and thus protect those around you. For example, this meta-analysis of 51 studies and 49 publications: bmj.com/content/bmj/33… (1/9) But what type of mask should you wear? Any type of mask that serves as a barrier between your nose/mouth and the environment will likely help and is better than no mask, but data has been published on cloth masks vs surgical (medical) masks vs N95 masks (respirators). (2/9)

Let’s estimate the total # of people in the US who have been infected by #COVID19 #SARSCoV2 as of Apr 4, and the number of US fatalities that will result from these infections. To avoid testing coverage uncertainty, we will use fatality data, rather than positive test data. (1/9) Importantly, the # of fatalities that we end up estimating from the infections through Apr 4 turns out to be independent of the infection fatality rate we use, as shown below. The infection fatality rate only changes our estimate of how many people in the US are infected. (2/9)

Given the misreporting about the differences between chloroquine vs. chloroquine phosphate vs. hydroxychloroquine, here is a simple chemistry overview. All have side-effects and none should be taken without a prescription. Chloroquine is the molecule shown in the upper left.(1/5) Two of the three N (nitrogen) atoms in chloroquine each tend to grab an extra proton in neutral water. When that happens, chloroquine acquires two positive charges—it becomes a cation. Those positive charges must find negative charges (anions) in stable forms of chloroquine.(2/5)