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A heterologous marker-free selection approach for CRISPR/Cas9-based gene editing in the malaria parasite Plasmodium falciparum.
CRISPR/Cas9-based gene editing of the malaria parasite Plasmodium falciparum has emerged as a transformative tool for advancing functional studies on parasite biology and identifying new therapeutic targets. Currently applied CRISPR/Cas9 methodologies depend on a limited set of heterologous drug resistance markers for the selection of transgenic parasites, which restricts the potential for iterative genetic modifications. Here, we developed a heterologous marker-free CRISPR/Cas9 gene editing strategy (CRISPR/Cas9pyrR) for P. falciparum based on the simultaneous editing of a gene of interest and introduction of pyrimethamine (PYR) resistance-conferring mutations into the dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) gene. By providing a pfdhfrpyrR donor sequence and the Cas9 expression cassette on separate plasmids, CRISPR/Cas9pyrR ensures that only parasites acquiring both plasmids survive under PYR pressure. As a proof of principle, we applied CRISPR/Cas9pyrR to generate two transgenic parasite lines expressing GFP-tagged versions of the putative nuclear envelope protein PfGEX1 and nuclear pore protein PfNUP116, respectively. We show that PfGEX1-GFP marks the nuclear envelope specifically in gametocytes, but not in asexual blood stage parasites. Similarly, and against previous reports, we find PfNUP116-GFP expression is undetectable in asexual parasites but instead localizes to a distinct perinuclear region in early gametocytes. These results suggest dynamic compositional changes of the nuclear periphery during sexual differentiation. We further demonstrate sequential genetic engineering of the PfNUP116-GFP-expressing line using the human dhfr drug resistance marker combined with WR99210-based selection by additionally tagging PfAP2-G, the master transcriptional regulator of sexual commitment, and the nuclear pore protein PfNUP313. Hence, CRISPR/Cas9pyrR provides a versatile and effective new method that enhances and complements the current genetic toolkit for malaria research.IMPORTANCEMalaria tropica, which is caused by the unicellular parasite Plasmodium falciparum, is one of the most devastating infectious diseases worldwide. The development of urgently needed effective vaccines and new antimalarial drugs with novel modes of action requires a profound understanding of parasite biology. CRISPR/Cas9-based genome engineering is beyond doubt the most important experimental approach to study the function and essentiality of parasite proteins and to identify and validate new vaccine and drug targets. In this study, we developed and successfully applied a modified CRISPR/Cas9 strategy, termed CRISPR/Cas9pyrR, that avoids the use of a heterologous drug resistance marker for the selection of genetically modified parasites. CRISPR/Cas9pyrR thus complements the CRISPR/Cas9 toolbox available for gene editing in P. falciparum and overcomes some of the limitations of currently employed protocols.
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Gene editing in birds takes flight.
The application of gene editing (GE) technology to create precise changes to the genome of bird species will provide new and exciting opportunities for the biomedical, agricultural and biotechnology industries, as well as providing new approaches for producing research models. Recent advances in modifying both the somatic and germ cell lineages in chicken indicate that this species, and conceivably soon other avian species, has joined a growing number of model organisms in the gene editing revolution.
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The Applications of CRISPR/Cas9 System for Urinary System Tumor.
Tumors of the urinary system include those in the urinary and reproductive systems, of which tumors of the prostate, bladder, and kidney have the highest incidence. In recent years, due to changes in dietary structure, prostate cancer has become the most common type of male genitourinary system cancer. Furthermore, due to tobacco consumption, increases in industrialization, and the age of the population, the incidence of bladder cancer in both males and females in both urban and rural areas, has shown an increasing trend. The incidence and mortality of kidney cancer have also increased and negatively affected the lives and health of all residents. While surgery, radiotherapy, and chemotherapy have greatly improved the cure and survival rates of patients with urinary tumors, we lack methods for early detection and effective long-term treatment. New tools and methods for diagnosis and treatment are thus urgently needed. Recently, CRISPR/Cas9 has become an efficient method to alter the genome in many organisms. It can be used to activate or inhibit gene expression, which greatly facilitates the editing of targeted genes, both in vivo and in vitro. It provides a powerful scientific research tool to analyze the mechanisms of disease occurrence and development and to develop advanced targeted drug delivery. The diagnosis and treatment of human tumors will consequently be improved as this technology will surely accelerate cancer research. In this article, we discuss how CRISPR/Cas9 technology can be used to research and treat genitourinary system tumors will consequently be improved as this technology will surely accelerate cancer research. Here, we review the current applications of CRISPR/Cas9 technology for genitourinary system tumor research and therapy.
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing.
Conventional cancer treatment modalities such as radiation and chemotherapy, cause cancer cell death by inducing DNA damage, particularly DNA strand breaks. Over the years, newer avenues have emerged for overcoming radio/chemoresistance by harnessing repair proteins as targets for small molecule inhibitors. Analysis of genome-wide expression data in cancer subtypes and understanding synthetic lethal interactions among repair pathways are important stepping-stones. Several inhibitors targeting DNA strand break repair proteins have yielded good effects in preclinical studies, and have the potential to be developed as therapeutics in cancer as monotherapy or in combination with radiation and chemotherapy. Furthermore, these small molecule inhibitors can aid in precise genome editing (using CRISPR) by harnessing the differential levels of repair inside cells. Shifting the repair balance towards homology-directed repair using inhibitors of NHEJ or stimulators of HR has yielded promising effects alongside CRISPR in cells and several disease models. In short, DNA strand break repair inhibitors are the forerunners in cancer therapy and genome editing, working in concert with the established artillery in the field.
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Biolistic Delivery of CRISPR/Cas9 with Ribonucleoprotein Complex in Wheat.
The great advances in exploiting the CRISPR/Cas9 system are paving the way for targeted genome engineering in plants. Genome editing by direct delivery of CRISPR/Cas9 ribonucleoprotein complexes (RNPs) into plant cells reduces off-target mutations and avoids the integration of foreign DNA fragments, thus providing an efficient and accurate method for precision crop breeding. Here we describe an RNP-based genome editing protocol for wheat. The protocol covers the in vitro transcription of sgRNA, purification of Cas9 protein, biolistic delivery of CRISPR/Cas9 RNPs, and tissue culture procedures for regenerating testable seedlings.
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Gene therapy beats premature-aging syndrome in mice.
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Phenotyping first-generation genome editing mutants: a new standard?
The unprecedented efficiency of the CRISPR/Cas9 system in genome engineering has opened the prospect of employing mutant founders for phenotyping cohorts, thus accelerating research projects by circumventing the requirement to generate cohorts using conventional two- or three-generation crosses. However, these first-generation mutants are often genetic mosaics, with a complex and difficult to define genetic make-up. Here, we discuss the potential benefits, challenges and scientific validity of such models.
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Enhanced production of D-pantothenic acid in Corynebacterium glutamicum using an efficient CRISPR-Cpf1 genome editing method.
BACKGROUND: Corynebacterium glutamicum has industrial track records for producing a variety of valuable products such as amino acids. Although CRISPR-based genome editing technologies have undergone immense developments in recent years, the suicide-plasmid-based approaches are still predominant for C. glutamicum genome manipulation. It is crucial to develop a simple and efficient CRISPR genome editing method for C. glutamicum. RESULTS: In this study, we developed a RecombinAtion Prior to Induced Double-strand-break (RAPID) genome editing technology for C. glutamicum, as Cpf1 cleavage was found to disrupt RecET-mediated homologous recombination (HR) of the donor template into the genome. The RAPID toolbox enabled highly efficient gene deletion and insertion, and notably, a linear DNA template was sufficient for gene deletion. Due to the simplified procedure and iterative operation ability, this methodology could be widely applied in C. glutamicum genetic manipulations. As a proof of concept, a high-yield D-pantothenic acid (vitamin B5)-producing strain was constructed, which, to the best of our knowledge, achieved the highest reported titer of 18.62 g/L from glucose only. CONCLUSIONS: We developed a RecET-assisted CRISPR-Cpf1 genome editing technology for C. glutamicum that harnessed CRISPR-induced DSBs as a counterselection. This method is of great importance to C. glutamicum genome editing in terms of its practical applications, which also guides the development of CRISPR genome editing tools for other microorganisms.
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Investigating the Potential of Gene Editing Technologies in Enhancing Stem Cell Therapy for Alzheimer's Disease.
Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by progressive cognitive decline and memory loss, significantly affecting the quality of life for millions of people worldwide. Current therapeutic options primarily focus on symptomatic relief, with limited effectiveness in addressing the underlying pathophysiology. Recent advancements in gene editing technologies, particularly CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats), offer promising opportunities to enhance stem cell therapy for AD. This review explores the potential of gene editing to target genetic risk factors associated with AD, such as APOE4 (Apolipoprotein E) and TREM2 (Triggering Receptor Expressed on Myeloid Cells 2), and to improve the differentiation and functionality of induced pluripotent stem cells (iPSCs) derived from AD patients. By creating more accurate disease models and humanized animal systems, researchers can gain a deeper understanding of the mechanisms of AD and evaluate novel therapeutic strategies. Moreover, combining gene editing with stem cell therapy may facilitate cell replacement therapies and the development of exosome-based treatments that modulate neuroinflammation and promote neuroprotection. Despite the promise of these approaches, challenges, such as off-target effects, delivery efficiency, and ethical considerations, remain significant hurdles. This review aims to provide a comprehensive overview of the current state of research, emphasizing the potential of gene editing technologies to revolutionize stem cell therapy for AD and improve patient outcomes.
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[Type II CRISPR-Cas System Nucleases: A Pipeline for Prediction and In Vitro Characterization].
The use of CRISPR-Cas bacterial adaptive immunity system components for targeted DNA changes has opened broad prospects for programmable genome editing of higher organisms. The most widely used gene editors are based on the Cas9 effectors of the type II CRISPR-Cas systems. In complex with guide RNAs, Cas9 proteins are able to directionally introduce double-stranded breaks into DNA regions that are complementary to guide RNA sequences. Despite the wide range of characterized Cas9s, the search for new Cas9 variants remains an important task, since the available Cas9 editors have several limitations. This paper presents a workflow for the search for and subsequent characterization of new Cas9 nucleases developed in our laboratory. Detailed protocols describing the bioinformatical search, cloning, and isolation of recombinant Cas9 proteins, testing for the presence of nuclease activity in vitro, and determining the PAM sequence, which is required for recognition of DNA targets, are presented. Potential difficulties that may arise, as well as ways to overcome them, are considered.
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