[1] Ma Lijia's team at West Lake University developed a new CRISPR off-target and DNA translocation detection tool
2022-12-15 reported that on December 12, 2022, Ma Lijia's team from the School of Life Sciences of Westlake University published a research paper entitled: PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation in the journal Nature Communications. In this study, using the sequence insertion ability of Prime Editor (PE), Cas9 was used to replace Cas9n in PE, and it was fused with reverse transcriptase MMLV to develop a new off-target identification method - PEAC-seq (Prime Editor Assisted off- target Characterization).
PEAC-seq provides a comprehensive and streamlined strategy to identify CRISPR off-target edits in cells and in vivo, as well as Cas9-induced DNA translocations. This technology further enriches the toolkit for assessing CRISPR genotoxicity in basic research and clinical applications.
[2] The Institute of Oceanography used gene editing technology to obtain new germplasm of high-quality insect-resistant economic microalgae
It was reported on 2022-12-19 that recently, the algae physiological process and precision design breeding research team of the Institute of Oceanography, Chinese Academy of Sciences has made new progress in the research of gene editing technology to create new germplasm, and obtained a marine diatom that is resistant to insects and has a high oil content-Triangle The new germplasm of Phaeodactylum tricornutum was published in Biotechnology for Biofuels and Bioproducts, the TOP journal in the field of international biotechnology. At the same time, the team used gene editing technology to knock out the cryptochrome gene of Phaeodactylum tricornutum to obtain a new germplasm with high fucoxanthin content, which was recently published in the phycological journal Algal Research.
The first authors of the research paper published in Biotechnology for Biofuels and Bioproducts are Associate Researcher Gao Shan and Dr. Zhou Lu, and the corresponding author is Researcher Wang Guangce. The first author of the research paper published in Algal Research is Yang Wenting, a postgraduate student, and the corresponding authors are Associate Researcher Gao Shan and Researcher Wang Guangce. The research has been funded by the National Key R&D Program, the Key R&D Program of Shandong Province, the National Algae Industry Technology System and the National Natural Science Foundation of China.
【3】Theranostics: Specificity of Oligonucleotide Gene Therapy (OGT) Drugs
2022-12-12 Report, recently, researchers from ITMO University published a review article entitled "Specificity of oligonucleotide gene therapy (OGT) agents" in Theranostics, which summarized the oligonucleotide gene therapy (OGT) drug specificity.
In this study, we assessed the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTEs) in vitro, in animal models, and in clinical studies. With the exception of DNAzymes, all OGT reagents exhibited HD OTE in vitro, with the most comprehensive evidence showing poor specificity for siRNA and CRISPR/Cas9.
Original: doi: 10.7150/thno.77830.
[4] FDA asks Verve to provide evidence of whether its base editing therapy will be passed on to future generations
According to reports on 2022-12-07, Verve Therapeutics, a base-editing therapy company, issued a statement that the FDA has suspended the clinical trial investigational new drug application of its main candidate drug Verve-101.
On December 5, 2022, the FDA sent a formal letter to Verve Therapeutics explaining the reasons for suspending its base editing therapy. The FDA hopes that Verve will provide more data to alleviate people's concerns, including whether the patient's edited gene will be inherited to the patient. child. The FDA asked Verve to provide additional preclinical data on differences in efficacy between human and non-human cells, risk of germline editing and off-target analysis of non-hepatic cell types, as well as preliminary data from human clinical trials conducted in New Zealand. In addition, the FDA also required Verve to include additional birth control measures in clinical trial participants and to increase the interval between doses. In fact, these issues raised by the FDA have always been the concern of Verve. On October 31, 2022, Verve published a paper in the journal Circulation, and the experimental data in non-human primates confirmed that Verve-101 therapy edited PCSK9 The safety, effectiveness, durability, and tolerance of the gene have further confirmed that the therapy will not affect germ cells.
[5] FDA approves multiple base editing CAR-T clinical trial application
2022-12-05, Beam Therapeutics announced that the FDA has lifted the clinical hold for its base editing-based CAR-T cell therapy BEAM-201, and approved BEAM-201 for the treatment of relapsed/refractory T lymphocytic leukemia ( IND applications for T-ALL) and T-lymphoblastic lymphoma (T-LL).
John Evans, CEO of Beam, said the FDA's approval of the IND application for BEAM-201 is an exciting time for Beam and the gene editing field, as it represents the first investigational drug for multiple base editing. IND approval. We believe that multiple base editing technology can support the high-level cell engineering needs of future cell therapy. Combining four heavy-duty base editors, BEAM-201 has the potential to have a significant impact on these challenging T-cell tumor patients who currently lack innovative, new treatment options. We are pleased to have received this clearance, enabling us to advance this new drug into human clinical trials and look forward to providing further updates on this program in 2023.
BEAM-201 is a CD7-targeted quadruple base-edited CAR-T cell therapy based on Cytosine Base Editor (CBE) developed by Beam Therapeutics, which is designed for allogeneic CAR-T cells design
[6] Sub-journal of Nature: Construction of high-throughput gene editing platform for mammalian cells and progress in base editing AI prediction model
Reported on 2022-12-05, the high-throughput editing and screening platform laboratory led by Wang Meng, a researcher at the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, the synthetic biology technology laboratory led by researcher Bi Changhao, and the microbial metabolic engineering laboratory led by researcher Zhang Xueli cooperated, For the first time, an automated high-throughput gene manipulation platform for mammalian cells has been established, which can realize automatic editing of thousands of animal cell samples within a week, and the editing efficiency is equivalent to that of manual operation. Based on the massive in situ genome editing data of 293T cells obtained by a high-throughput platform, the researchers developed a machine learning model (CAELM) to predict the performance of cytosine base editors (BE4max). Compared with traditional machine learning modeling based on lentiviral integration targets, this study innovatively considered the real chromosomal environment of the target sequence in model construction, combined with editing target sequence information for machine learning, and proposed for the first time that chromatin accessibility The influence weight of sex on the editing result is 1/6 relative to the target sequence. In order to expand the compatibility of CAELM prediction and make the CAELM model applicable to more types of cells and different CBE base editors, researchers added relatively small different cell types (HepG2) and base editors (hyA3A- BE4max and Anc-BE4max) on the edited data set, the model is further trained and learned, expanding the prediction range of CAELM. This model can predict the base editing results of in situ targets in cells more accurately than existing models, and lays the foundation for the construction of machine learning models that accurately predict the base editing results of cells in humans or other species. This work is expected to accelerate the development and clinical application of BEs-based gene therapies.
Relevant research results were published in Nature Communications. The research work was supported by the National Natural Science Foundation of China, the National Key Research and Development Program, the Tianjin Municipal Synthetic Biotechnology Innovation Ability Improvement Action, and the Tianjin Natural Science Foundation of China.
【7】Science sub-journal: base editing, save fatal heart disease and prolong life
2022-12-01 reported that recently, researchers from the University of Texas Southwestern Medical Center published a research paper entitled: Precise genomic editing of pathogenic mutations in RBM20 rescues dilated cardiomyopathy in Science Translational Medicine, a sub-journal of Science.
This study verified the effect of base editing and lead editing in correcting RBM20 gene mutations in iPSCs, and further confirmed the adenine base editor (ABE) in a mouse model of dilated cardiomyopathy (DCM) with RBM20 gene mutations It can effectively correct gene mutations, restore its heart function and prolong life.
【8】Two Science reveals that RNA-guided CRISPR-Cas effector protein cleavage can trigger adaptive immune response
2022-11-30 In the first new study, researchers from the Massachusetts Institute of Technology demonstrated that the CRISPR-associated protease Csx29 exhibits programmable RNA-activated endopeptidase activity against sigma factor inhibitors to Regulates transcriptional responses. Cryo-EM structures of active substrate-bound Csx29 complexes reveal a heterogeneous activation mechanism that reorganizes the catalytic residues of Csx29 upon target RNA binding. The relevant research results were published in the journal Science on November 26, 2022. The title of the paper is "RNA-activated protein cleavage with a CRISPR-associated endopeptidase". This discovery reveals an RNA-guiding function in nature that can be exploited for RNA detection applications in vitro and in human cells.
In the second new study, researchers from the Massachusetts Institute of Technology and the University of Tokyo found that the type III-E CRISPR system includes the caspase-like protease Csx29, and when Cas7-11 recognizes the target When RNA is detected, Csx29 is activated to cleave another accessory protein called Csx30. This cleavage generates toxic Csx30 fragments that are hypothesized to inhibit the specialized sigma factor RpoE, regulate bacterial responses to phage infection, and lead to bacterial growth arrest, thereby clearing phage infection. The relevant research results were published in the journal Science on November 26, 2022. The title of the paper is "RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease".
Original: doi:10.1126/science.add7450.
doi:10.1126/science.add7347.
[9] Cell: CRISPR-Cas system discovered in thousands of viruses, is expected to improve cell genome editing
2022-11-28 In a new study, researchers from the University of California, Los Angeles found that the CRISPR-Cas system accounts for 0.4 of the publicly available genome sequences of viruses (called bacteriophages) that can infect these microorganisms. %. They suggest that these viruses use CRISPR-Cas to compete with each other -- and possibly also to manipulate the host's gene activity to their advantage. The relevant research results were published in the journal Cell on November 23, 2022, with the title of the paper "Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors".
Original: doi:10.1016/j.cell.2022.10.020.
【10】New base editor Td-CBE successfully developed
Reported on 2022-11-28, Yi Chengqi's research group from the School of Life Sciences of Peking University and collaborators jointly published online in Nature Biotechnology entitled "Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing” research results. In this study, by introducing the N46L mutation in TadA-8e adenine deaminase, it was successfully transformed into a specific and efficient cytosine deaminase, and based on this, a new type of base editor Td-CGBE was developed. with Td-CBEs.
Compared with the traditional CGBE/CBE base editors based on the AID/APOBEC family, Td-CGBE/CBEs editors exhibited a narrower editing window and lower insertion and deletion in the case of similar editing activity Editing features such as byproducts. At the same time, the study used the previously developed genome-wide, non-biased off-target detection technology Detect-seq to conduct an off-target assessment of Td-CBEs editors. The evaluation found that Td-CBEs caused far fewer off-target sites at the genome-wide level than traditional CBEs with the same editing activity; although Td-CBEs and the traditional base editor BE4max were constructed on different deaminases, Td-CBEs Compared with BE4max, no new off-target sites will be generated. It is worth noting that Td-CBEs will not produce the two new types of off-target edits (out-of-protospacer edits and target-strand edits) discovered by the previous research group.
【11】Nature: A CRISPR/Cas9-based non-viral precision genome editing clinical-grade therapy
It was reported on 2022-11-22 that recently, in a recent study published in "Nature", a research team from UCLA and other institutions developed a clinical-grade CRISPR/Cas9-based non-viral precision genome editing for the first time. A therapy that effectively redirects immune cells to recognize mutations in their own cancer cells. In first-in-human clinical trials, the therapy has shown promising results. This study demonstrates the feasibility and safety of non-viral precision genome engineering for the manufacture of clinical-grade genetically engineered adoptive cell transfer therapies.
In the new study, the team developed a clinical-grade method based on CRISPR/Cas9 non-viral precision genome editing. This approach simultaneously knocks out two endogenous TCR genes, TCRα (TRAC) and TCRβ (TRBC), and inserts two chains of a neoantigen-specific TCR (neoTCR) at the TRAC site. Then, a series of techniques were utilized to efficiently define T cell neoantigen responses to more than 60 human leukocyte antigen (HLA) class I allelic mutations.
This study demonstrates the feasibility of this novel approach, which involves isolating and cloning multiple immune cell receptors that recognize mutations in cancer cells, using one-step non-viral precision genome editing to simultaneously knock out endogenous immune cell receptors and knocking in Redirecting receptors and manufacturing clinical-grade TCR engineered T cells. In addition, the study also demonstrated the safety of infusing three gene-edited new TCR T cells, as well as the ability of genetically engineered T cells to be delivered to tumors.
[12] Editas, a CRISPR company founded by Zhang Feng, has suspended a clinical trial due to poor results and will seek partners for joint development
2022-11-21 reported that on November 17, 2022, Editas Medicine announced the data of the phase 1/2 clinical trial (BRILLIANCE) of the in vivo gene editing drug EDIT-101. At the same time, the company said it would stop the independent development plan of EDIT-101 and look for a partner. Until then, the company is suspending enrollment in the BRILLIANCE trial.
The drug EDIT-101 is designed to repair the mutation site IVS26 of the CEP290 gene through CRISPR/Cas9, thereby treating blindness caused by Leber congenital amaurosis type 10 (LCA10). There is currently no effective treatment for this serious rare disease. It is reported that the change in the clinical plan is mainly due to the lower than expected trial results. To date, the clinical trial BRILLIANCE has enrolled a total of 14 study participants, including 12 adults and 2 children. Only three patients had clinically meaningful improvements in corrected visual acuity. Other than that, other people's data is negligible. On the other hand, the patient population suitable for EDIT-101 is too small, which is one of the reasons why the company no longer independently develops the drug. Affected by the news, Editas shares fell more than 10%.
[13] One injection is effective for a long time, and the clinical data of the second in vivo CRISPR therapy released by the Nobel Prize-winning team
2022-11-18 report, on November 12, 2022, Intellia Therapeutics announced that its second in vivo CRISPR gene-editing therapy, NTLA-2002, is in the middle of a phase 1/2 clinical trial for the treatment of hereditary angioedema (HAE) The data is positive. These clinical data were obtained from 10 adult patients with hereditary angioedema (HAE) who received different doses of NTLA-2002 therapy, and the results showed that the pathogenic kallikrein in all patients treated with different doses (25mg, 50mg, 75mg) All decreased significantly, 64%, 81%, and 92% at the 32nd week, 22nd day, and 16th week, respectively.
In addition, the clinical trial also showed that the attack frequency of hereditary angioedema (HAE) decreased significantly after a single treatment, and the attack frequency of the 25mg and 75mg dose groups decreased by an average of 91% from the first week to the 16th week after treatment. % and 78% (50mg dose group has not yet reached the 16th week of observation time). The first three treated patients have been recurrence-free for 5.5-10.6 months to date. NTLA-2002 was generally well tolerated across all dose groups, with most adverse events being mild. Intellia said the clinical data showed a one-treatment, sustained response to NTLA-2002 and also confirmed the power of the company's CRISPR-based gene editing platform.