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R. Kishton et al.
10.4.2 Delivery Methods
There are three main categories of CRISPR delivery vehicles: viral, chemical, and mechanical. The nal application and therapeutic conditions will inuence the cargo format as well as the choice of vehicle for delivery. Compared to ex vivo therapies, in which cells are edited outside the body, invivo therapies present a much more challenging delivery scenario with minimal room for errors owing to patient safety requirements [33]. Moreover, invivo gene therapies typically require editing components to be targeted to specic organs or tissues, providing an addi­tional delivery challenge.
Viral vectors work on the basis of infecting target cells or tissue to introduce the editing components [34]. These vectors include lentiviruses (LVs; Retroviridae), adenoviruses (AdVs; Adenoviridae), and adeno-associated viruses (AAVs; Parvoviridae). These viral vectors act as chassis for the editing components to enter the cell and contain elements encoding for the nuclease and guide sequences, referred to as cargo. LVs and AdVs are large and can therefore carry considerable cargo; however, they have several undesirable effects, including integration into the host genome, adverse immune responses, and off-target effects. In contrast, AAVs are nonpathogenic and nonintegrating viruses in humans, causing very mild host immune responses. These safety advantages make them one of the most common delivery vehicles for invivo therapeutic use. However, they cannot package DNA above 4.7kb, limiting their application in knock-ins. Strategies to overcome this challenge include using smaller Cas9 variants such as SaCas9 to minimize the over­all cargo load and splitting the CRISPR components between two vectors. Engineered virus-like particles (eVLPs) have also recently been described as a highly efcient delivery vehicle for CRISPR RNP cargo [35].
Chemical delivery vehicles for CRISPR editing components include liposomes, lipid nanoparticles (LNPs), lipo- and poly-plexes, gold and other inorganic nanopar­ticles, and cell-penetrating peptides [36]. Nanoparticles such as LNPs are increasing in popularity and have been adapted for use in other non-CRISPR therapeutics, such as the delivery of mRNA vaccines. Mechanical vehicles for CRISPR delivery include microinjection into cells, electroporation, nucleofection, and microuidics. However, these are not compatible with invivo therapies and therefore are exclu­sively used for exvivo gene-edited cell therapies and invitro experiments.
10.5 CRISPR Therapeutics: Gene Therapies
andGene- Edited Cell Therapies
The development of CRISPR-based therapeutics has ushered in a new era of person­alized medicine, including both gene therapy and gene-edited cell therapy. In the decade since CRISPR was rst adapted as a gene editor, the eld has made
10 CRISPR Technology andIts Application inTherapeutics
astonishing progress, with the rst exvivo CRISPR gene-edited cell therapy begin­ning clinical trials in 2016, and the rst invivo gene therapy beginning trials in 2019.
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10.5.1 What Are Cell andGene Therapies?
Cell and gene therapies are a broad category of medical therapeutics based on the transfer of either whole cells (cell therapy) or genetic material (gene therapy) to patients to treat disease. Gene therapies are performed invivo and involve either introducing new genetic material to patients or disrupting genes that bear patho­genic mutations [37]. There are currently over 5000 known diseases caused by mutations in a single gene [38]. These monogenic disorders can theoretically be treated by either correcting the pathogenic mutation, known as gene correction ther­apy, or delivering a functional copy of part or all of the gene to alleviate the condi­tion, known as gene replacement therapy [39].
Cell therapies engineered using CRISPR or other technologies are known as gene-edited cell therapies. Gene-edited cell therapies include ex-vivo biologics that can be either autologous (patient-derived) or allogeneic (derived from a healthy donor) [40]. They aim to replace diseased cells, compensate for a lack of a particular cell type, or generate a desired functionality through engineered physiological activity. Many different types of gene-edited cell therapies have been developed, and they can be categorized by the types of cells used, for example, hematopoietic stem and progenitor cells (HSPCs), or primary immune cells like T cells. Gene­edited cell therapies are becoming increasingly common for the treatment of many different medical conditions, including cancer, infectious diseases, and genetic diseases.
10.5.2 Role ofCRISPR inCell andGene Therapy
The simplicity, accuracy, and wide range of potential targets of the CRISPR system make it ideal as a therapeutic agent for many different diseases. CRISPR’s adoption in the eld of cell and gene therapy has been rapid. The rst clinical trial of an exvivo CRISPR gene-edited cell therapy began in 2016, only 4 years after the origi­nal CRISPR paper was published, followed by another in 2018. The rst trial of a CRISPR-based invivo gene therapy began in 2019. The popularity and rapid clini­cal translation of CRISPR gene therapies and gene-edited cell therapies have only increased, with new trials beginning regularly. While currently no CRISPR thera­pies have been approved by the Federal Drug Administration (FDA), it is likely that many cell and gene therapies will be CRISPR-based in the near future.
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10.6 CRISPR inCancer Therapy
Cancer comprises a diverse, heterogeneous group of diseases, making it difcult to model and treat [41]. Cancers are driven by mutations in DNA, and various types of cancer are often characterized by commonly occurring signatures of mutations in oncogenes and tumor suppressor genes [41]. Heterogeneity in the drivers and fea­tures of tumors is observed between tumors arising from various tissue types and is also seen within tumors of similar tissue origin. Further, there can be considerable heterogeneity within a single tumor mass due in part to the variety of cell types that are contained within the complex tumor microenvironment [42]. The genetic com­plexity of cancer inuences not only how treatable the disease is but also how it spreads, the potential for drug resistance, and the likelihood of recurrence. Metastatic cancer, which has spread to multiple tissues and organs, presents challenges because each tumor may exhibit a heterogeneous mutational prole, potentially resulting in differential biological features and responses to treatment [42, 43]. Additionally, cancer cells have signicant capacity to either avoid detection by or otherwise sup­press the immune system [44].
CRISPR technology has quickly accelerated cancer research, both in terms of disease modeling and therapeutic strategies [45]. In therapeutic settings, CRISPR gene editing enables scientists to create better, safer, and more affordable gene­edited cell therapies. These therapies offer the ability to treat cancer in a highly specic manner and are highly desirable over traditional treatments like chemo­therapy and radiotherapy, which are toxic to healthy cells.
Cellular immunotherapies that have been broadly used in the clinic as cancer treatments include the infusion of expanded tumor-inltrating lymphocytes, T cell receptor (TCR) engineered T cells, and chimeric antigen receptor (CAR) engineered T cells [46]. These are often referred to as adoptive cell therapies, and each of these therapies generally involves harvesting T cells from patients and promoting or imbuing antitumor specicity. Following exvivo expansion to a large number of cells, the T cell products are infused into patients [47]. Cellular immunotherapies for the treatment of hematological cancers have generally shown more clinical ef­cacy to date than those used to treat solid tumors. CRISPR-mediated gene editing in T cell therapeutic products is now being explored as an avenue to generate cell therapies that are safer and more efcacious than previous iterations.
10.6.1 Tumor-Inltrating Lymphocyte Therapy
Tumor-inltrating lymphocytes (TIL) are T cells that are localized within a tumor, with a fraction of TIL exhibiting the capacity to recognize tumor antigens and kill tumor cells. The degree of TIL inltration in tumors can have positive prognostic
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value in several types of cancer, and TIL can be expanded exvivo and reinfused in patients as an autologous cancer therapy. The infusion of expanded TIL in lym­phodepleted patients in conjunction with interleukin-2 (IL-2) support can be clini­cally effective, with high rates of response reported in patients with metastatic melanoma. Despite the efcacy of TIL in certain settings, the expansion and ef­cacy of TIL can be limited in cancers that evade T cell surveillance and recognition [48]. Additionally, the antitumor activity of TIL may not be sufcient to mediate durable clinical responses in many patients. Consequently, CRISPR gene editing of TIL has been explored as a pathway to enhance T cell expansion and function, such as through the knockout of T cell intrinsic genes that inhibit antitumor function [49, 50].
10.6.2 TCR Engineered T Cell Therapy
T cell receptor (TCR) engineered T cell therapy uses T cells that are modied to express TCRs conferring the capacity for the specic recognition and destruction of tumor cells [51]. TCRs mediate T cell recognition of tumor cells through the major histocompatibility complex (MHC)/human leukocyte antigen (HLA) complex [52] presentation of antigenic peptides. The presented peptides can originate from either intracellular or membrane-bound proteins. TCR engineered T cells are produced by the engineered expression of exogenous TCRs with a known capacity to recognize tumor antigens in therapeutic cell products. The exogenous TCR has historically been introduced into T cells through viral transduction, but recent work has demon­strated that CRISPR-mediated knock in of a therapeutic TCR is a viable strategy to produce clinical products. As seen with TIL therapy, TCR engineered T cells can mediate clinical responses in select patients, but widespread efcacy is lacking. This is due to a number of factors, including tumor downregulation of HLA expres­sion and mispairing of engineered TCR protein components with endogenous TCR proteins. Mispairing of the transgenic TCR with the endogenous TCR is a particu­larly concerning issue, as it can result in inefcient antigen recognition or even autoimmunity and graft-versus-host disease [52].
CRISPR-Cas9 editing can be used to knock out the endogenous TCR as well as knock-in the transgenic TCR, eliminating mispairing and toxicity issues [47]. Recent research used CRISPR-Cas9 to knock out the endogenous TRAC (T cell Receptor Alpha Chain) locus in primary T cells and knock in a TCR with specicity to epitopes of Wilm’s tumor antigen 1, which is overexpressed in many types of cancer [53]. The resulting TCR cell therapy displayed potent activity against both hematological malignancies and solid tumors in mouse models, including acute myeloid leukemia, acute lymphoblastic leukemia, and glioblastoma, with no observ­able off-target editing [53].
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10.6.3 Chimeric Antigen Receptor T Cell Therapy
Chimeric antigen receptor T (CAR-T) cell therapy involves engineering T cells to express chimeric receptors on their surface to mediate recognition and killing of cancer cells [54]. Unlike TCRs, which are naturally occurring and recognize MHC/ HLA, chimeric antigen receptors are engineered proteins that recognize specic antigens expressed on the surface of cancer cells.
Similar to other cell immunotherapies, CAR-T is often inhibited by the cancer cells overexpressing immune checkpoint inhibitors, such as programmed cell death protein 1 ligand (PD-L1) on the cell surface. PD-L1 binds to the PD-1 receptor expressed on the surface of T cells, inhibiting immune cells [55]. Overcoming the PD-L1 inhibition pathway provides a promising avenue for next-generation cell therapies via a CRISPR knockout of PD-1 [55]. CRISPR can also be used for tar­geted knock-in of the CAR, which is then continuously expressed on the cell sur­face. Results of a Phase I trial of mesothelin-specic CAR-T cells with PD-1 and TCR gene knockouts have established the safety and feasibility of this method in human subjects [56].
Allogeneic CAR-T cells, although advantageous to manufacture relative to autologous cell products, are often unable to persist in hosts. This is due to recogni­tion and rejection by the host immune system or the presence of cytotoxic drugs. CRISPR has been employed in attempts to circumvent this issue by engineering universal allogeneic CAR-T therapy; by knocking out key genes involved in recog­nition by the host immune system, the cells can theoretically be used for any patient. Unlike previous technologies, CRISPR-Cas9 can be used to perform these complex edits; currently, several clinical trials are underway, in which multi-knockout allo­geneic CAR-T cells are being tested in human patients with various types of cancer [57, 58]. By generating CAR-T cells from iPSCs rather than from healthy donors, large stocks of “off-the-shelf” CAR-T cells are ready to treat patients with minimal wait times.
10.6.4 In Vivo CRISPR Editing ofSolid Tumors
In recent years, CRISPR has also been adapted for invivo editing of cancers by targeting cancer-specic mutations [59] or otherwise disrupting oncogenes. CRISPR can be used to disrupt the expression of key proteins that are overexpressed in can­cer cells, such as Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) [60]. NRF2 regulates hundreds of other genes, and its overexpression in cancer cells can result in resistance to chemotherapy. However, CRISPR-based knockout of the NRF2 pro­tein can restore chemosensitivity of the cancer cells. This strategy is being investi­gated in preclinical studies by researchers at the ChristianaCare Gene Editing Institute [60]. Other recent research in tumor editing includes improving delivery systems to efciently target tumors invivo. For example, one key study from Tel
10 CRISPR Technology andIts Application inTherapeutics
Aviv University developed targeted lipid nanoparticles (LNPs) for the delivery of CRISPR-Cas9 components [61] to target the KO of the PLK1 gene, resulting in high (~80%) editing efciencies, potent inhibition of tumor growth, and improved sur­vival rates [61].
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10.7 CRISPR Treatments forGenetic Disease
There are currently over 7000 known monogenic disorders that are ideal targets for CRISPR-mediated gene therapy [38]. CRISPR therapies for monogenic diseases can take several different forms based on the type of mutation(s) which cause the disease. For example, if a disease is caused by a gain-of-function mutation in a par­ticular gene, CRISPR knockout gene therapy can be used to delete the gene or the specic regions which bear the pathogenic mutations. Alternatively, if the disorder is caused by loss-of-function mutations in a gene that cause it to produce an abnor­mal protein or no protein at all, CRISPR knock-in can be used to correct the muta­tions, which is also referred to as gene correction therapy. Disorders in which a particular gene is overexpressed or underexpressed can also be therapeutically tar­geted using CRISPRi and CRISPRa, respectively. Many monogenic disorders are caused by single nucleotide polymorphisms (SNPs), making them possible to cor­rect using base- and prime-editing techniques which do not induce DSBs. Depending on the target organ or tissue, these methods can be performed invivo as gene thera­pies, or exvivo as gene-edited cell therapies. In this section, we cover these different therapeutic options with examples from proof-of-concept and preclinical studies.
10.7.1 CRISPR Gene Correction forMonogenic Diseases
SCD is perhaps one of the best-known monogenic disorders and was the rst genetic disease for which researchers attempted to generate a CRISPR cure. SCD is caused by a SNP mutation in the ß-globin gene (HBB), which normally produces adult hemoglobin (hemoglobin A) and oxygenates the blood [62]. The traditional treat­ments are blood transfusions or a bone marrow transplant from a healthy donor. CRISPR has offered several promising avenues for treating this debilitating condi­tion via autologous gene-edited HPSC therapy.
The rst and currently most popular method is sometimes referred to as gene switching or gene substitution. Fetal hemoglobin (hemoglobin F) is produced until ~6months of age in humans, at which time it is switched off by activation of the BCL11A transcription factor and replaced by hemoglobin A.Hemoglobin F is an adequate substitute for hemoglobin A [63]. Therefore, by performing CRISPR­Cas9 knockout of BCL11A, hemoglobin F production can be restored. This approach has been championed by several biotechnology companies, including CRISPR Therapeutics and Vertex Pharmaceuticals, who jointly ran the rst clinical trial
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based on this approach using their CTX-001 therapy [64]. Alternative approaches are being developed by Editas Medicine [65], using the Cas12a nuclease, and Beam Therapeutics, using base editing [66].
Therapies for SCD based on upregulating hemoglobin F can also be used to treat a related condition called beta-thalassemia. While they have similar symptoms and limited treatment options, beta-thalassemia is caused by multiple mutations in HBB rather than just one SNP. This makes it more difcult to cure with gene therapy because repairing many mutations is more challenging than correcting a single one. The ability to treat both diseases with a single therapy is why many companies have focused on the therapeutic upregulation of hemoglobin F.The CTX-001 therapy developed by CRISPR Therapeutics and Vertex Pharmaceuticals has also been tested on beta-thalassemia patients with similar levels of success [67].
Many genetic disorders require the correction of one or more pathogenic muta­tions in a particular gene. X-linked agammaglobulinemia (XLA) is an immunode­ciency disorder caused by a variety of mutations in the Bruton’s tyrosine kinase (BTK) gene [68]. Researchers at the University of California, Los Angeles created a CRISPR gene-edited cell therapy approach for XLA, correcting the majority of pathogenic mutations in the BTK gene in peripheral blood stem cells (PBSCs) [68]. The corrected PBSCs could therefore be used as an autologous cell therapy for XLA, with preclinical research being continued for this strategy.
10.7.2 CRISPR Knockout ofRepeat Hyperexpansions
Some genetic diseases are caused by multiple repeats of certain nucleotides that form hyperexpansions and interfere with the normal production of protein from the gene. Friedreich’s ataxia (FA) is an autosomal recessive disorder caused by muta­tions in the FXN gene which encodes frataxin, a mitochondrial protein responsible for aspects of energy production and iron metabolism [67]. The FXN gene bears a GAA trinucleotide repeat in its rst intron. Healthy individuals have ve to 30 repeats. FA patients have hyperexpansion of between 44 to 1700 repeats of this tri­nucleotide sequence [69]. The number of GAA repeats is correlated with the sever­ity of FA, as well as the age of onset.
CRISPR offers the potential to cure FA by excising the pathogenic trinucleotide hyperexpansion; researchers from the University of California, San Diego School of Medicine developed a CRISPR method to delete large sections of the expansion in patient-derived hematopoietic stem and progenitor cells (HSPCs). The treatment successfully increased the production of frataxin protein in the HSPCs, which then differentiated normally with no noticeable off-target editing or cellular toxicity [69]. Additional therapies are being developed by CRISPR Therapeutics and Capsida Biotherapeutics for FA [70]. As part of the collaboration, these companies are also creating a similar treatment for amyotrophic lateral sclerosis (ALS), a large number of cases of which are caused by a GGGGCC hexanucleotide repeat within the C9orf72 gene [71].
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10.7.3 CRISPR InVivo Gene Therapies
Leber’s congenital amaurosis (LCA) is a retinal disease caused by loss-of-function mutations in multiple genes affecting the rod and cone cells of the retina [72]. The most common causes are mutations in the RPE65 and CEP290 genes, making these genes prime targets for gene therapy. An early attempt to generate a cure for LCA was developed by Spark Therapeutics in a therapy known as Luxterna, which sim­ply provided a functional copy of RPE65 cDNA in an AAV vector via sub-retinal injection [73]. However, this therapy is not a one-time cure, and the patient group suitable for treatment with Luxterna is limited.
Editas Medicine more recently developed a CRISPR-based gene therapy known as EDIT-101, an RNP cargo packaged in an AAV5 delivery vehicle and adminis­tered via sub-retinal injection [74]. The BRILLIANCE clinical trial of EDIT-101 was the world’s rst-ever trial of an invivo CRISPR gene therapy, using CRISPR­Cas9 to edit the CEP290 gene, restoring healthy expression of the CEP290 protein and photoreceptor function. Interestingly, rather than correct the IVS26 mutation in CEP290, EDIT-101 uses two guide RNAs to create a DSB on either side of the mutation and delete it [75]. After repair, transcription and RNA splicing are restored, and the protein can be translated normally. Preliminary results of the ongoing Phase I/II trial of EDIT-101 indicate no serious toxicity or adverse events of the therapy and evidence for clinical benet [76]. Base editing is also being explored as an alternative therapy for LCA by researchers at the University of California, Irvine (UCI), with a proof-of-concept study demonstrating the correction of the RPE65 mutations invivo in a mouse model of the disease [77].
10.8 CRISPR inInfectious Disease Treatment
While cancer and genetic disease may appear the most obvious targets for CRISPR therapies, there is also signicant potential for this technology in the treatment of infectious diseases. Pathogenic microorganisms, including viruses, bacteria, fungi, and parasites, can all be targeted using CRISPR, and there has been signicant progress in this eld in recent years.
10.8.1 Circumventing Antibiotic Resistance inBacteria
CRISPR’s role in protecting bacteria from invading bacteriophages is now being used to turn the tables, targeting bacteria themselves. This can involve killing the target pathogenic bacteria or deleting or repressing the transcription of key genes in the bacterium, such as antibiotic resistance genes. A key strategy for the targeted kill­ing of pathogenic bacteria is to engineer bacteriophages using CRISPR systems [78]. The key benet of these therapies is that they eliminate the need for antibiotic
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treatments and can be used to target multi-drug resistant “superbugs” [78]. This approach has been pioneered by Locus Biosciences in their clinical trial of LBP-EC01, which uses CRISPR-Cas3 enhanced bacteriophages (termed crPhage™) for the ther­apeutic removal of Escherichia coli strains that cause urinary tract infections [79].
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10.8.2 CRISPR-Edited Cell Therapies fortheTreatment
ofViral Pathogens
CRISPR technology offers the possibility of targeting a variety of viral pathogens [80], including DNA viruses, such as human papillomavirus (HPV) and Epstein­Barr virus, as well as RNA viruses, such as SARS-CoV-2. The E6 and E7 genes of HPV have been the subject of many recent CRISPR studies due to their roles in causing cervical cancer, making them key targets for CRISPR-based knockout [81]. In preclinical research, CRISPR-Cas9 was used to knock out the E7 gene in a mouse model bearing HPV16 tumors; treatment was effective at clearing the tumors from the animals without causing liver or spleen toxicity [82].
Another promising option for the treatment of infectious diseases is CRISPR­edited B cell therapy. B cells produce antibodies and are an essential component of the adaptive immune system [83]. Vaccines are designed to prime the adaptive immune system by encouraging B cells to recognize new pathogens and produce antibodies for them [84]. CRISPR-edited B cells have been suggested as an alterna­tive to vaccines because they can be used to produce large quantities of neutralizing antibodies for pathogens via targeted gene knock-in [83, 84]. This strategy has been adopted to treat the respiratory syncytial virus, HIV, Epstein-Barr virus, and inu­enza viruses [85].
10.8.3 In Vivo CRISPR Therapy toExcise Integrated Viruses
fromtheHuman Genome
HIV is a retrovirus that infects human CD4 helper T cells, in which it reverse­transcribes its RNA genome and then inserts itself into the DNA genome of the host cells [86]. Due to its integration into the human genome and its ability to hide in dormant, noncirculating helper T cells for long periods of time, even antiretroviral drugs can never completely remove HIV from the body [87]. CRISPR now offers a potential cure for HIV, cutting it out of the human genome with minimal risk of off­target editing using a multi-guide approach successful for excising large DNA sequences [20]. Excision Bio is currently testing their invivo EBT-101 therapy for HIV in a Phase I/II trial [88] and is also developing similar therapies for other viruses. This includes EBT-103 therapy for JC virus, which can cause progressive
10 CRISPR Technology andIts Application inTherapeutics
multifocal leukoencephalopathy, EBT-104 for herpes simplex virus, and EBT-107 for hepatitis B virus [89].
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10.9 The Future ofCRISPR Therapeutics
Given the current trends around FDA approvals, the prediction is that in the near future, approximately one-third of medical treatments will be cell and gene thera­pies. Given the advantages of CRISPR over previous gene editing technologies, it is likely that many of these cell and gene therapies will be CRISPR-based. In the next section, the critical factors that will determine the future of CRISPR technology in medical therapeutics will be explained.
10.9.1 Industrialization ofCRISPR Editing: Increasing Safety
andLowering Costs
Many of the CRISPR cell and gene therapies currently in trials show promise. However, the size of patient groups in clinical studies is generally limited. If a trial is successful and the therapy in question gains FDA approval, there are often signi­cant obstacles in scaling up these therapeutics for widespread use in larger patient populations [90]. This includes accessing viral vectors for delivery, the necessary Good Manufacturing Practice (GMP)-grade reagents, and adequate production facilities. Signicant costs are associated with cell and gene therapies, making these medicines difcult for many patients to access. Due to the long wait times and high costs, cell and gene therapy developers often decide whether to build out GMP facilities for viral vector production. Commercial entities like Synthego, Editas and Agilent manufacture GMP sgRNA. Moreover, the inherent variability of gene­edited cell therapies and issues associated with invivo gene editing means that great care must be taken in order to ensure these medicines are safe and appropriately regulated [91].
10.9.2 Safety Considerations
An emerging concern is the safety of CRISPR therapies. Signicant efforts have been made by the scientic community to increase the safety of CRISPR therapies, including engineered Cas9 and other nuclease variants with increased accuracy. In late March, the FDA recently released updated guidelines on the topic of Human Gene Therapy Products Incorporating Human Genome Editing [92]. These guide- lines include the identication of off-target editing activity, including the type,