The advent of CRISPR technology has revolutionized genome editing, enabling precise modifications in various organisms. A significant study introduced a massively parallel variant annotation pipeline (MVAP) to dissect schizophrenia-associated noncoding genetic variants, revealing the complexities of genetic contributions to mental health disorders (ref: Rummel doi.org/10.1016/j.cell.2023.09.015/). Another innovative approach involved the development of a mouse model with high clonal barcode diversity, facilitating joint lineage, transcriptomic, and epigenomic profiling in single cells, which is crucial for understanding tissue development (ref: Li doi.org/10.1016/j.cell.2023.09.019/). Additionally, research on mitigating chromosome loss in CRISPR-Cas9-engineered T cells highlighted a modified manufacturing process that reduced chromosome loss while maintaining editing efficacy, addressing a major safety concern in clinical applications (ref: Tsuchida doi.org/10.1016/j.cell.2023.08.041/). The exploration of off-target effects, particularly how negative DNA supercoiling can induce genome-wide Cas9 off-target activity, underscores the need for improved specificity in CRISPR applications (ref: Newton doi.org/10.1016/j.molcel.2023.09.008/). Furthermore, advancements in genetic screening techniques, such as compressed Perturb-seq, have expanded the capabilities of functional genomics by allowing for scalable and cost-effective screening of regulatory circuits (ref: Yao doi.org/10.1038/s41587-023-01964-9/). The establishment of databases like CasPEDIA and SLKB provides essential resources for researchers navigating the diverse landscape of CRISPR-Cas enzymes and synthetic lethality, respectively (ref: Adler doi.org/10.1093/nar/; Gökbağ doi.org/10.1093/nar/). Overall, these studies illustrate the multifaceted applications and ongoing challenges of CRISPR technology in both basic and applied research.

Gene therapy has emerged as a promising avenue for treating various genetic disorders, with CRISPR-Cas9 technology at the forefront. A pivotal study demonstrated the potential of CRISPR-Cas9 to engineer the RAG2 locus, offering a therapeutic alternative for RAG2-SCID, a primary immunodeficiency disorder (ref: Allen doi.org/10.1038/s41467-023-42036-5/). This innovative approach involves complete coding sequence replacement to preserve the critical regulatory architecture of the gene. Additionally, integrative analyses of noncoding variants associated with neuropsychiatric diseases revealed 2,221 variants linked to disorders such as schizophrenia and bipolar disorder, emphasizing the role of regulatory elements in disease etiology (ref: Guo doi.org/10.1038/s41588-023-01533-5/). The study of CAR T cell therapies has also advanced, with findings indicating that CRISPR-mediated deletion of CTLA4 enhances T cell function, potentially improving outcomes for patients who have previously failed CAR T cell treatments (ref: Schelker doi.org/10.1016/j.immuni.2023.09.006/). Furthermore, the development of mRNA trans-splicing dual AAV vectors for gene therapy addresses the challenges of delivering large genes, showcasing the versatility of CRISPR technology in therapeutic applications (ref: Riedmayr doi.org/10.1038/s41467-023-42386-0/). Collectively, these studies highlight the transformative potential of gene therapy and the critical role of CRISPR technology in advancing treatment options for genetic and neuropsychiatric disorders.

Research into neuropsychiatric disorders has increasingly focused on the genetic underpinnings of these complex conditions. A comprehensive study utilized a massively parallel functional dissection approach to map schizophrenia-associated noncoding genetic variants, revealing insights into the genetic architecture of the disorder (ref: Rummel doi.org/10.1016/j.cell.2023.09.015/). This work complements findings from another study that identified 2,221 noncoding variants linked to various neuropsychiatric diseases, including autism and major depression, through integrative analyses of epigenomic and transcriptomic data (ref: Guo doi.org/10.1038/s41588-023-01533-5/). The application of compressed Perturb-seq has further enhanced the ability to conduct scalable genetic screenings, allowing researchers to explore regulatory circuits associated with these disorders in greater depth (ref: Yao doi.org/10.1038/s41587-023-01964-9/). These advancements underscore the importance of understanding the regulatory landscape of genetic variants in neuropsychiatric conditions, paving the way for targeted therapeutic strategies.

Synthetic biology has leveraged CRISPR technology to create innovative systems for gene regulation and protein degradation. A notable advancement is the development of compact engineered human mechanosensitive transactivation modules, which enable potent transcriptional control through programmable DNA binding platforms (ref: Mahata doi.org/10.1038/s41592-023-02036-1/). This technology facilitates the construction of enhanced activation modules that can be utilized in various applications, including gene therapy. Additionally, the use of lysosome-targeting chimeras (LYTACs) has emerged as a promising strategy for targeted protein degradation, with genome-wide CRISPR knockout screens identifying key cellular determinants of this process (ref: Ahn doi.org/10.1126/science.adf6249/). The development of a task-specific encoding algorithm for RNAs further enhances the understanding of RNA interactions and their biological implications, showcasing the versatility of synthetic biology approaches (ref: Wang doi.org/10.1093/nar/). Together, these studies illustrate the potential of engineered systems to revolutionize gene regulation and therapeutic strategies.

Cancer research has increasingly incorporated CRISPR technology to enhance immunotherapy strategies. A significant study demonstrated that the deletion of CTLA4 using CRISPR/Cas9 can restore the antitumor function of CAR T cells, addressing a major barrier to effective cancer treatment (ref: Schelker doi.org/10.1016/j.immuni.2023.09.006/). This finding is particularly relevant for patients who have previously experienced treatment failure. Additionally, the exploration of receptor-interacting protein kinase 2 as a target in pancreatic cancer highlights the need for novel therapeutic strategies in this aggressive malignancy (ref: Sang doi.org/10.1158/2159-8290.CD-23-0584/). The integration of pooled CRISPR knockout screening with dual host-microbe single-cell RNA sequencing has also provided insights into the transcriptional interactions between intracellular pathogens and host cells, further elucidating the complexities of cancer biology (ref: Butterworth doi.org/10.1016/j.chom.2023.09.003/). Collectively, these studies underscore the transformative potential of CRISPR technology in advancing cancer research and immunotherapy.

Functional genomics has been significantly advanced by the application of CRISPR technology, particularly in the context of genetic screening techniques. A key innovation is the development of compressed Perturb-seq, which allows for scalable genetic screening of regulatory circuits by measuring multiple random perturbations per cell (ref: Yao doi.org/10.1038/s41587-023-01964-9/). This method addresses the limitations of traditional pooled CRISPR screens, enabling more efficient exploration of gene function. Additionally, the construction of engineered transactivation modules has revolutionized synthetic transcriptional control, facilitating the development of all-in-one CRISPRa AAV systems (ref: Mahata doi.org/10.1038/s41592-023-02036-1/). The establishment of databases such as SLKB and CasPEDIA further supports researchers by providing comprehensive resources for synthetic lethality and CRISPR-Cas enzyme classification, respectively (ref: Gökbağ doi.org/10.1093/nar/; Adler doi.org/10.1093/nar/). These advancements highlight the ongoing evolution of functional genomics and the critical role of CRISPR technology in enhancing our understanding of gene function and regulation.

The field of RNA editing and regulation has gained momentum with the advent of CRISPR technology, enabling novel approaches to understanding RNA dynamics. The CasPEDIA database serves as a functional classification system for class 2 CRISPR-Cas enzymes, facilitating the exploration of RNA-guided bacterial immunity and its biotechnological applications (ref: Adler doi.org/10.1093/nar/). Additionally, the synthetic lethality knowledge base (SLKB) has emerged as a valuable resource for researchers investigating synthetic lethality interactions, highlighting the connectivity of gene pairs in various cellular contexts (ref: Gökbağ doi.org/10.1093/nar/). The comprehensive single-cell gene regulatory network platform (scGRN) further enhances our understanding of the regulatory interactions between transcription factors and their target genes, providing insights into disease mechanisms (ref: Huang doi.org/10.1093/nar/). Furthermore, the development of eRNAbase addresses the need for a comprehensive database of enhancer RNAs, which play critical roles in gene transcription regulation (ref: Song doi.org/10.1093/nar/). Together, these resources and studies underscore the importance of RNA regulation in cellular processes and disease etiology.

Plant genomics has increasingly utilized CRISPR technology to enhance crop traits and understand genetic functions. A critical study revealed that CRISPR-mediated deletions of tandemly arrayed genes (TAGs) in plants often result in deletion-inversion bi-alleles, which can be misidentified as simple homozygous deletions, highlighting the complexities of gene editing in plant systems (ref: Liu doi.org/10.1038/s41467-023-42490-1/). This finding emphasizes the need for careful genotyping strategies in plant biotechnology. Additionally, research on the loss-of-function properties of mutant TP53 demonstrated that the removal of various TP53 mutants did not affect the proliferation of cancer cells, suggesting that gain-of-function properties may not be as critical as previously thought (ref: Wang doi.org/10.1158/2159-8290.CD-23-0402/). The integration of CRISPR technology in plant genomics not only aids in understanding gene functions but also enhances the potential for developing crops with improved traits, thereby addressing agricultural challenges.