SnapShot: CRISPR-RNA-guided adaptive immune systems

A comprehensive review on the current status of CRISPR based clinical trials for rare diseases

A considerable fraction of population in the world suffers from rare diseases. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its related Cas proteins offer a modern form of curative gene therapy for treating the rare diseases. Hereditary transthyretin amyloidosis, hereditary angioedema, duchenne muscular dystrophy and Rett syndrome are a few examples of such rare diseases. CRISPR/Cas9, for example, has been used in the treatment of β-thalassemia and sickle cell disease (Frangoul et al., 2021; Pavani et al., 2021) [1,2]. Neurological diseases such as Huntington's have also been focused in some studies involving CRISPR/Cas (Yang et al., 2017; Yan et al., 2023) [3,4]. Delivery of these biologicals via vector and non vector mediated methods depends on the type of target cells, characteristics of expression, time duration of expression, size of foreign genetic material etc. For instance, retroviruses find their applicability in case of ex vivo delivery in somatic cells due to their ability to integrate in the host genome. These have been successfully used in gene therapy involving X-SCID patients although, incidence of inappropriate activation has been reported. On the other hand, ex vivo gene therapy for β-thalassemia involved use of BB305 lentiviral vector for high level expression of CRISPR biological in HSCs. The efficacy and safety of these biologicals will decide their future application as efficient genome editing tools as they go forward in further stages of human clinical trials. This review focuses on CRISPR/Cas based therapies which are at various stages of clinical trials for treatment of rare diseases and the constraints and ethical issues associated with them.

Utilization of CRISPR-Cas genome editing technology in filamentous fungi: function and advancement potentiality

Filamentous fungi play a crucial role in environmental pollution control, protein secretion, and the production of active secondary metabolites. The evolution of gene editing technology has significantly improved the study of filamentous fungi, which in the past was laborious and time-consuming. But recently, CRISPR-Cas systems, which utilize small guide RNA (sgRNA) to mediate clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), have demonstrated considerable promise in research and application for filamentous fungi. The principle, function, and classification of CRISPR-Cas, along with its application strategies and research progress in filamentous fungi, will all be covered in the review. Additionally, we will go over general matters to take into account when editing a genome with the CRISPR-Cas system, including the creation of vectors, different transformation methodologies, multiple editing approaches, CRISPR-mediated transcriptional activation (CRISPRa) or interference (CRISPRi), base editors (BEs), and Prime editors (PEs).

Genome editing in rice using CRISPR/Cas12i3

The CRISPR/Cas type V-I is a family of programmable nuclease systems that prefers a T-rich protospacer adjacent motif (PAM) and is guided by a short crRNA. In this study, the genome-editing application of Cas12i3, a type V-I family endonuclease, was characterized in rice. We developed a CRIPSR/Cas12i3-based Multiplex direct repeats (DR)-spacer Array Genome Editing (iMAGE) system that was efficient in editing various genes in rice. Interestingly, iMAGE produced chromosomal structural variations with a higher frequency than CRISPR/Cas9. In addition, we developed base editors using deactivated Cas12i3 and generated herbicide-resistant rice plants using the base editors. These CRIPSR/Cas12i3-based genome editing systems will facilitate precision molecular breeding in plants.

A CG@MXene nanocomposite-driven E-CRISPR biosensor for the rapid and sensitive detection of Salmonella Typhimurium in food

In this study, we developed a novel electrochemical biosensor based on CRISPR/Cas12a (E-CRISPR) for the rapid and sensitive detection of Salmonella Typhimurium (S. Typhimurium). The CRISPR/Cas12a system was applied to identify S. Typhimurium gene and induce signal changes in electrochemical measurement. The colloidal gold and MXene (CG@MXene) nanocomposites were synthesized and immobilized to improve the performance of the biosensor by decreasing the background noise. The formation process of CG@MXene was well characterized, and experiment conditions were fully optimized. Under the optimal conditions, the proposed E-CRISPR biosensor exhibited excellent sensitivity for S. Typhimurium, with a limit of detection (LOD) of 160 CFU/mL, and great specificity against other common foodborne pathogens. Furthermore, the feasibility of the E-CRISPR biosensor was evaluated by analyzing S. Typhimurium-spiked chicken samples, with a recovery rate ranging from 100.46% to 106.37%. In summary, this research proposed a novel E-CRISPR biosensor from a new perspective to detect S. Typhimurium which can be an alternative approach for bacterial detection in the food supply chain.

Applications of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) as a Genetic Scalpel for the Treatment of Cancer: A Translational Narrative Review

Cancer remains a global health challenge with high prevalence and mortality rates, imposing significant financial and emotional burdens on affected families. However, hope lies in genetic manipulation, with a focus on innovative approaches to combat genetically linked cancers. Clustered regularly interspaced short palindromic repeats (CRISPR), an adaptive immune system found in various bacteria and archaea, hold immense potential. We searched articles on PubMed Central, Medline, and PubMed databases indexed journals. The keywords from the research topic, i.e., "CRISPR AND genetic therapy," were searched, and we found 3397 articles. Following this, we explored the medical subject headings (MeSH) glossary and created a search strategy "Clustered Regularly Interspaced Short Palindromic Repeats"[Mesh] AND "Genetic Therapy"[Majr] and after applying a variety of filters we included 30 studies in our review. CRISPR consists of unique spacers and CRISPR-associated (Cas) genes, operating through acquisition, CRISPR ribonucleic acid (crRNA) biogenesis, and target interference phases. The type II CRISPR-Cas9 system is a well-researched avenue for gene editing, with Cas9 cleaving specific genomic regions and initiating deoxyribonucleic acid (DNA) repair mechanisms. Cancer results from genetic alterations, leading to tumor development with properties like metastasis. CRISPR/Cas9 offers precise genome editing to inhibit tumor formation by removing specific genomic sequences and promoting DNA repair. Challenges in CRISPR's use for cancer therapy, including delivery methods, cell adaptation, and ethical concerns, are recognized. Beyond cancer, CRISPR finds diverse applications in infectious diseases and non-cancerous conditions, signifying its transformative potential in modern medicine. CRISPR technology represents a groundbreaking frontier in cancer therapy and beyond, offering insights into genetic editing, disease mechanisms, and potential cures. Despite challenges and ethical considerations, precise genome editing promises improved cancer treatments and innovative medical interventions in the future.

Current trends of clinical trials involving CRISPR/Cas systems

The CRISPR/Cas9 system is a powerful genome editing tool that has made enormous impacts on next-generation molecular diagnostics and therapeutics, especially for genetic disorders that traditional therapies cannot cure. Currently, CRISPR-based gene editing is widely applied in basic, preclinical, and clinical studies. In this review, we attempt to identify trends in clinical studies involving CRISPR techniques to gain insights into the improvement and contribution of CRISPR/Cas technologies compared to traditional modified modalities. The review of clinical trials is focused on the applications of the CRISPR/Cas systems in the treatment of cancer, hematological, endocrine, and immune system diseases, as well as in diagnostics. The scientific basis underlined is analyzed. In addition, the challenges of CRISPR application in disease therapies and recent advances that expand and improve CRISPR applications in precision medicine are discussed.

A CRISPR/Cas12a-mediated, DNA extraction and amplification-free, highly direct and rapid biosensor for Salmonella Typhimurium

CRISPR/Cas-based biosensors were typically used for nucleic-acid targets detection and complex DNA extraction and amplification procedures were usually inevitable. Here, we report a CRISPR/Cas12a-mediated, DNA extraction and amplification-free, highly direct and rapid biosensor (abbreviated as "CATCHER") for Salmonella Typhimurium (S. Typhimurium) with a simple (3 steps) and fast (∼2 h) sensing workflow. Magnetic nanoparticle immobilized anti-S. Typhimurium antibody was worked as capture probe to capture the target and provide movable reaction interface. Colloidal gold labeled with anti-S. Typhimurium antibody and DNase I was used as detection probe to bridge the input target and output signal. First, in the presence of S. Typhimurium, an immuno-sandwich structure was formed. Second, DNase I in sandwich structure degraded the valid, complete activator DNA to invalid DNA fragments which can't trigger the trans-cleavage activity of Cas12a. Finally, the integrity of reporter DNA was preserved presenting a low fluorescence signal. Conversely, in the absence of S. Typhimurium, strong fluorescence recovery appeared owing to the cutting of reporter by activated Cas12a. Significantly, the proposed "CATCHER" showed satisfactory detection performance for S. Typhimurium with the limit of detection (LOD) of 7.9 × 101 CFU/mL in 0.01 M PBS and 6.31 × 103 CFU/mL in spiked chicken samples, providing a general platform for non-nucleic acid targets.

CRISPR/Cas9 is a powerful tool for precise genome editing of legume crops: a review

Legumes are an imperative source of food and proteins across the globe. They also improve soil fertility through symbiotic nitrogen fixation (SNF). Genome editing (GE) is now a novel way of developing desirable traits in legume crops. Genome editing tools like clustered regularly interspaced short palindromic repeats (CRISPR) system permits a defined genome alteration to improve crop performance. This genome editing tool is reliable, cost-effective, and versatile, and it has to deepen in terms of use compared to other tools. Recently, many novel variations have drawn the attention of plant geneticists, and efforts are being made to develop trans-gene-free cultivars for ensuring biosafety measures. This review critically elaborates on the recent development in genome editing of major legumes crops. We hope this updated review will provide essential informations for the researchers working on legumes genome editing. In general, the CRISPR/Cas9 novel GE technique can be integrated with other techniques like omics approaches and next-generation tools to broaden the range of gene editing and develop any desired legumes traits. Regulatory ethics of CRISPR/Cas9 are also discussed.

Genes encoding bile salt hydrolase differentially affect adhesion of Lactiplantibacillus plantarum AR113

BACKGROUND

Adhesion is considered important for Lactiplantibacillus to persist in the human gut and for it to exert probiotic effects. Lactiplantibacillus plantarum contains a considerable number and variety of genes encoding bile salt hydrolases (bsh), but their effects on microbial adhesion remain poorly understood. To clarify the effects of four bsh on adhesion, we tried to knock out bsh (Δbsh) of L. plantarum AR113 using the CRISPR-Cas9 method, and compared the growth, auto-aggregation (R_AA ), co-aggregation (R_CA ), surface hydrophobicity (A_HC ) of AR113 wild-type and Δbsh strains and their adhesion abilities to HT29 cells.

RESULTS

We first obtained the AR113 Δbsh1,3,2,4 strain with four bsh knocked out. Their growth was significantly slower than the wild-type strain cultured in De Man, Rogosa, and Sharpe medium (MRS) with 3.0 g L^-1 glyco- or tauro-conjugated bile acid. Bsh had no significant effect on the growth of ten strains cultured in MRS, but Δbsh1 inhibited their growth when cultured in MRS containing 3.0 g L^-1 sodium glycocholate, whereas Δbsh4 instead promoted their growth in MRS with 3.0 g L^-1 sodium glycocholate and sodium taurocholate. R_CA and R_AA were linearly positive for all strains except AR113 Δbsh2,4, and A_HC and R_AA were negatively correlated for most strains excluding AR113 Δbsh2, with R_AA  = 6.38-25.05%, R_CA  = 5.17-9.22%, and A_CH  = 3.22-47.71%. The adhesion ability of ten strains cultured in MRS was higher than that of strains cultured in MRS with 3.0 g L^-1 bovine bile, and it was related to bsh2.

CONCLUSION

Bsh differentially affected the adhesion of AR113 series strains. This adds to the available information about substrate-gene-performance, and provides new information to enable engineering to regulate the colonization of Lactiplantibacillus. © 2021 Society of Chemical Industry.

Integration of the Ligase Chain Reaction with the CRISPR-Cas12a System for Homogeneous, Ultrasensitive, and Visual Detection of microRNA

The ligase chain reaction (LCR), as a classic nucleic acid amplification technique, is popular in the detection of DNA and RNA due to its simplicity, powerfulness, and high specificity. However, homogeneous and ultrasensitive LCR detection is still quite challenging. Herein, we integrate the LCR with a CRISPR-Cas12a system to greatly promote the application of the LCR in a homogeneous fashion. By employing microRNA as the model target, we design LCR probes with specific protospacer adjacent motif sequences and the guide RNA. Then, the LCR is initiated by target microRNA, and the LCR products specifically bind to the guide RNA to activate the Cas12a system, triggering secondary signal amplification to achieve ultrasensitive detection of microRNA without separation steps. Moreover, by virtue of a cationic conjugated polymer, microRNA can not only be visually detected by naked eyes but also be accurately quantified based on RGB ratio analysis of images with no need of sophisticated instruments. The method can quantify microRNA up to 4 orders of magnitude, and the determination limit is 0.4 aM, which is better than those of other reported studies using CRISPR-Cas12a and can be compared with that of the reverse-transcription polymerase chain reaction. This study demonstrates that the CRISPR-Cas12a system can greatly expand the application of the LCR for the homogeneous, ultrasensitive, and visual detection of microRNA, showing great potential in efficient nucleic acid detection and in vitro diagnosis.

Visualization Analysis of CRISPR Gene-editing Knowledge Map based on Citespace

CRISPR is an adaptive immune defense system found in bacteria and archaea that is resistant to heterologous invasive genetic material. Later studies showed that the CRISPR system can be used for gene-editing. This study used the Web of Science database as a search object, then visually analyzed the literature related to CRISPR gene-editing technology with CiteSpace IV. The results show that publications had increased year by year. USA ranked first in terms of publications. China is second, but the centrality is very low. Doudna JA and Zhang F have made outstanding contributions. There are close connections between the internal institutions of the various states, but there are few links between the states. The hot spot and frontier are the application of CRISPR in animals, plants, detection, diagnosis, and clinical treatment.

Improving FnCas12a Genome Editing by Exonuclease Fusion

Among current reported Cas12a orthologs, Francisella novicida Cas12a (FnCas12a) is less restricted by protospacer adjacent motif (PAM). However, the activity of FnCas12a nuclease is relatively low or undetectable in human cells, limiting its application as desirable genome engineering tools. Here, we describe TEXT (Tethering EXonuclease T5 with FnCas12a)-a fusion strategy that significantly increased the knockout efficiency of FnCas12a in human cells at multiple genomic loci in three different cell lines. TEXT results in higher insertion and deletion efficiency than FnCas12a under different spacer lengths from 18 nt to 23 nt. Deep sequencing shows that TEXT substantially increased the deletion frequency and deletion size at the targeted locus. Compared to other Cas12a orthologs, including AsCas12a and LbCas12a, TEXT achieves the highest on-targeting efficiency and shows minimal off-targeting effects at all tested sites. TEXT enhances the activity of FnCas12a nuclease and expands its targeting scope and efficiency in human cell genome engineering.

Application of CRISPR/Cas9 System to Reverse ABC-Mediated Multidrug Resistance

Multidrug resistance (MDR) is the main obstacle in cancer chemotherapy. ATP-binding cassette (ABC) transporters can transport a wide range of antitumor drugs out of cells, which is the most common reason in the development of resistance to drugs. Currently, various therapeutic strategies are used to reverse MDR, among which CRISPR/Cas9 gene editing technique is expected to be an effective way. Here, we reviewed the research progress of reversing ABC-mediated drug resistance by CRISPR/Cas9 system.

Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity

The type I-F CRISPR adaptive immune system in Pseudomonas aeruginosa (PA14) consists of two CRISPR loci and six CRISPR-associated (cas) genes. Type I-F systems rely on a CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease (i.e., Cas2/3) for target degradation. In most type I systems, Cas2 and Cas3 are separate proteins involved in adaptation and interference, respectively. However, in I-F systems, these proteins are fused into a single polypeptide. Here we use biochemical and structural methods to show that two molecules of Cas2/3 assemble with four molecules of Cas1 (Cas2/3₂:Cas1₄) into a four-lobed propeller-shaped structure, where the two Cas2 domains form a central hub (twofold axis of symmetry) flanked by two Cas1 lobes and two Cas3 lobes. We show that the Cas1 subunits repress Cas2/3 nuclease activity and that foreign DNA recognition by the Csy complex activates Cas2/3, resulting in bidirectional degradation of DNA targets. Collectively, this work provides a structure of the Cas1-2/3 complex and explains how Cas1 and the target-bound Csy complex play opposing roles in the regulation of Cas2/3 nuclease activity.

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter revisiting, mutated viruses, and plasmids. Here we have determined how new spacers are produced and selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step, PAM-associated manner. The helicase-nuclease Cas3 pre-processes target DNA into fragments of about 30-100 nt enriched for thymine-stretches in their 3' ends. The Cas1-2 complex further processes these fragments and integrates them sequence-specifically into CRISPR repeats by coupling of a 3' cytosine of the fragment. Our results highlight that the selection of PAM-compliant spacers during priming is enhanced by the combined sequence specificities of Cas3 and the Cas1-2 complex, leading to an increased propensity of integrating functional CTT-containing spacers.

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

CRISPR-Cas systems are bacterial adaptive immune systems, each typically composed of a locus of cas genes and a CRISPR array of spacers flanked by repeats. Processed transcripts of CRISPR arrays (crRNAs) play important roles in the interference process mediated by these systems, guiding targeted immunity. Here we developed computational approaches that allow us to characterize the expression of many CRISPRs in their natural environments, using community RNA-seq (metatranscriptomic) data. By exploiting public human gut metatranscriptomic data sets, we studied the expression of 56 repeat-sequence types of CRISPRs, revealing that most CRISPRs are transcribed in one direction (producing crRNAs). In rarer cases, including a type II system associated with Bacteroides fragilis, CRISPRs are transcribed in both directions. Type III CRISPR-Cas systems were found in the microbiomes, but metatranscriptomic reads were barely found for their CRISPRs. We observed individual-level variation of the crRNA transcription, and an even greater transcription of a CRISPR from the antisense strand than the crRNA strand in one sample. The orientations of CRISPR expression implicated by metatranscriptomic data are largely in agreement with prior predictions for CRISPRs, with exceptions. Our study shows the promise of exploiting community RNA-seq data for investigating the transcription of CRISPR-Cas systems.