Professor Giulia Palermo and colleagues from the University of California, Riverside and the University of Rochester have developed high-fidelity Cas13a variants with increased sensitivity for base pair mismatches.The activation of these Cas13a variants can be inhibited with a single mismatch between guide-RNA and target-RNA, a property that can be used for the detection of SNPs associated with diseases or specific genotypic sequences.  

Researchers from UC San Diego have engineered human zinc finger-containing fusion proteins that target and can destroy or modify human RNA transcripts that contain expanded G4C2 hexanucleotide repeats. This approach, which they have termed zinc fingerdirected RNA targeting, provides a means to, depending on the fusion protein, 1) target and degrade disease-causing RNA transcripts containing G4C2 expansions and to 2) target, label, and track the same transcripts in living cells.

Brief description not available

Brief description not available

Reseachers from UC San Diego demonstrated a proof of principle for a CAGEX RNA-targeting CRISPR–Cas13d system as a potential allele-sensitive therapeutic approach for HD, a strategy with broad implications for the treatment of other neurodegenerative disorders.

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Understanding the function of RNAs requires visualizing their location and dynamics in live cells. However, direct labeling and imaging individual endogenous RNAs in living cells is still needed. UC Berkeley researchers have developed a method to directly resolve individual endogenous RNA transcripts in living cells using programmable RNA-guided and RNA-targeting CRISPR-Csm complexes coupled with a variety of crRNAs that collectively span along the transcripts of interest.  The researchers demonstrated robust labeling of MAP1B and NOTCH2 mRNAs in several cell lines. We tracked NOTCH2 and MAP1B transcript transient dynamics in living cells, captured distinct mobilities of individual transcripts in different subcellular compartments, and detected translation dependent and independent RNA motions.  

Rapid virus evolution generates proteins essential to infectivity and replication but with unknown function due to extreme sequence divergence. Using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, it was found that 62% of viral proteins are structurally distinct and lack homologs in the Alphafold database. Structural comparisons suggested putative functions for >25% of unannotated viral proteins.  UC Berkeley researcher have created new single stranded DNA (ssDNA) bindingproteins and double stranded (dsDNA) binding proteins, and methods and compositions for using them, such as binding to target DNA.   

UC Berkeley researchers have indentified and characterized a novel CRISPR Cas13 subtype that exhibits unique and advantageous features for transcriptome editing applications. At approximately half the size of the smallest known Cas13 subtype, this novel subtype is the smallest CRISPR Cas effector identified to date. The compactness of this novel Cas13 subtype facilitates its delivery into a wide array of cell types using various delivery mechanisms, significantly enhancing its utility in genomic research and therapeutic applications. The novel Cas13 subtype retains the hallmark programmable RNA-targeting capability of the Cas13 family, enabling precise and efficient editing of RNA sequences. This feature is particularly valuable in the context of transcriptome engineering, where specific alterations to RNA molecules can modulate gene expression, correct genetic errors, or modulate the function of non-coding RNAs. The discovery of this compact Cas13 subtype opens new avenues for transcriptome editing, offering potential applications in functional genomics, gene therapy, and the development of novel therapeutic strategies targeting RNA. Its ease of delivery and potent RNA-editing capabilities position this novel Cas13 subtype as a valuable tool for both basic research and clinical applications in the field of genetic engineering and precision medicine.

Class 2 CRISPR-Cas are streamlined versions in which a single Cas protein bound to RNA is responsible for binding to and cleavage of a targeted sequence. Theprogrammable nature of these minimal systems has facilitated their use as a versatile technology for genome editing.  CRISPR-Cas enzymes with reduced requirements for a protospacer-adjacent motif (PAM) sequence adjacent to the target site could improve the breadth of target sites available for genome editing.  UC Berkeley researchers have developed a novel PAM-loose 12a variants, nucleic acids encoding the variant Cas12a proteins and systems using these variants that make the Cas12a-based CRISPR technology much easier to design a DNA target for carrying out genome editing in human cells. 

The strategy employed by the invention is inspired by splicing factors, a category of RNA-binding protein that influence alternative splicing outcomes. These splicing factors are trans-acting, and act to enhance or silence exon inclusion by binding near or on the target exon and promoting or repressing the activity of splicing machinery. Scientifically, a highly programmable, minimally disruptive system to increase exon inclusion could allow for higher-throughput identification of functional roles of specific exons than have been previously shown.

UC Berkeley researchers have created variant CRISPR-Cas effector polypeptides (e.g., variant Cas9 proteins) with improved properties, such as improved editing efficiency and/or improved PAM sequence flexibility, as well as methods of modifying a target nucleic acid using a variant CRISPR-Cas effector polypeptide and methods of generating variant CRISPR-Cas effector polypeptides.

Researchers at the University of California, Davis have developed a virally derived homolog to increase the inflammatory response desirable in cancer immunotherapy.

Researchers at the University of California, Davis have developed a viral peptide therapeutic that targets MYC-based cancerous tumors.

A primary reason behind the lack of progress in heart therapeutics is the inability to use phenotypic human tissue-level approaches to discover novel therapies. In recent years, there have been significant advances in the development microphysiological systems (MPS), which recapitulate organ-level and even organism-level functions.   MPS are quickly becoming representative of the future of disease modeling and drug screening, therefore paving the way for complex in vitro models to dominate the preclinical drug discovery landscape. However, there has yet to be an effective LNP formulation for therapeutic mRNA delivery to the heart. Therefore, despite progress in this area, one of the remaining challenges is to develop a LNP formulation capable of diffusing within human cardiac muscle, transfecting cardiomyocytes, and escaping the endo-lysosome before degradation more efficiently than current strategies. UC Berkeley researchers and others have developed compositions and methods using lipid nanoparticles for delivery of a payload (e.g., messenger RNA (mRNA)) to the heart, for delivery of mRNA for transfection of cells and methods of treatment.

Researchers at UC Irvine have identified and tested a molecular target that regulates T cell function during chronic viral infection and cancer. The molecular target is one of the high mobility group proteins (HMGB2). HMGB2 is a DNA binding protein that regulates transcriptional processes, meaning that its modulation will have profound effects on T cell differentiation and ultimate function by altering the expression of many genes.

Brief description not available

Brief description not available

Brief description not available

RNA-mediated adaptive immune systems in bacteria and archaea rely on Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) genomic loci and CRISPR associated (Cas) proteins that function together to provide protection from invading viruses and plasmids. Genome editing can be carried out using a CRISPR-Cas system comprising a CRISPR-Cas effector polypeptide and a guide nucleic acid, such as a guide RNA. However, unintended chromosomal abnormalities following on-target genome editing, such as chromosome loss, are potential concerns for genome editing. UC Berkeley researchers and others have developed a method to modulate the expression levels of the DNA damage response factor p53 in order to mitigate chromosomal abnormalities that occur after genome editing by nucleases like Cas9. The invention provides treatment methods by generating a modified cell and then administering the modified cell to an individual in need thereof and compositions having a CRISPR-Cas effector polypeptide, a guide nucleic acid, and an agent that increases the level of a p53 polypeptide in a mammalian cell.

Scientists have developed a CRISPR-Cas9 based genome editing method for universal correction of disease-causing mutations in the CTLA4 gene, which most commonly manifest as a Primary Immunodeficiency. Current treatment involves monthly IV injections or weekly subcutaneous injections of a recombinant CTLA4-Ig fusion protein abatacept. This invention includes one-time infusion of a CTLA4-corrected autologous T cell therapy. The corrected patient cells are generated by ex vivo electroporation of a specific gRNA:Cas9 ribonucleoprotien (RNP) complex and cognate homology-directed-repair template (HDRT) targeting a functional copy of the CTLA4 gene within an intronic region of the endogenous CTLA4 gene. This combination allows for (1) highly efficient knockin (up to 70% in patient cells), (2) cell-type and context specific regulation of CTLA4 expression under natural promoter and regulatory elements, and (3) preservation of endogenous CTLA4 expression in uncorrected cells.

Researchers at the University of California, Davis have developed a method to stop bacterial growth while maintaining desirable metabolic functions for therapeutic and biotechnological applications.

Manipulation of eukaryotic genomes, particularly the integration of multi-kilobase DNAsequences, remains challenging and limits the rapidly growing fields of synthetic biology andcell engineering. Large serine recombinases (LSRs) are enzymes that recognize specific targetsequences on a DNA donor sequence and DNA target sequence to catalyze a recombinationreaction that results in the insertion of a DNA donor in a sequence-specific manner. Genomeediting can be carried out using an LSR system and a DNA donor nucleic acid, such as a plasmidor double-stranded DNA. However, in a human genome, these systems can exhibit variableefficiency and specificity.In this invention, UC Berkeley researchers and others have developed optimized compositionsto significantly increase the efficiency and specificity of LSRs to target a specific genomic locusin human cells. Via fusion to additional protein systems, this engineered composition retainsthe simplicity of a single protein for gene delivery. The invention also encompasses use in invivo or ex vivo gene therapy and the creation of modified cell lines or transgenic animals.

The CRISPR-Cas system is now understood to confer bacteria and archaea with acquired immunity against phage and viruses. CRISPR-Cas systems consist of Cas proteins, which are involved in acquisition, targeting and cleavage of foreign DNA or RNA, and a CRISPR array, which includes direct repeats flanking short spacer sequences that guide Cas proteins to their targets. The programmable nature of these systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation. There is a need in the art for additional CRISPR-Cas systems with improved cleavage and manipulation under a variety of conditions and ones that are particularly thermostable under those conditions. UCB researchers created a set of efficient CRISPR-Cas9 proteins from a thermostable Cas9 from the thermophilic bacterium Geobacillus stearothermophilus (GeoCas9) through directed evolution. The gene editing activity of the evolved mutant proteins was improved by up to four orders of magnitude compared to the wild-type GeoCas9. The researchers showed that the gene editors based on the evolved GeoCas9 can be effectively assembled into lipid nanoparticles (LNP) for the rapid delivery to different cell lines in vitro as well as different organs or tissues in vivo. The LNP-based delivery strategy could also be extended to other gene editors.  

Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool.