CRISPR Cas-Based Diagnostics and Gene Therapy
CRISPR Cas-Based Diagnostics and Gene Therapy
Keywords
Clinical trails, CRISPR/Cas, diagnostics, gene therapy, point-of-care-testing. *Correspondence to: Pei Li.
E-mail: lipei@kaist.ac.kr
Figure 1 Discovery of CRISPR/Cas and the milestones of CRISPR/Cas development in diagnostics and gene therapy.
in Spain discovered repeated-spacer clusters in archaea in Besides diagnostics, CRISPR/Cas systems revolution-
1993 [18]. From 2000 to 2011, more evidence showed that ized the area of gene therapy-based healthcare. In 2013,
the CRISPR/Cas system is involved in bacterial immunity Cong et al. engineered a CRISPR/Cas system and proved
[19, 20]. that Cas9 could precisely induce cleavage in mamma-
Despite the numerous discoveries in the CRISPR/Cas lian cells [29]. This study raised the possibility of the
system, its applications in diagnostics and gene therapies implementation of CRISPR-Cas9 as a therapeutic tool
have only been developed in recent decades. As recently for gene-editing. Since then, CRISPR/Cas technology
as 2012, it was reported that a CRISPR nuclease can be has been tested in many clinical trials for a large variety
programmed by merely varying its guide RNA (gRNA) of diseases, such as metastatic gastrointestinal epithelial
sequence, which makes it extremely useful for genome cancer, T-cell malignancies, and refractory B-cell malig-
editing [21]. In 2013, scientists successfully edited differ- nancies [30]. In 2017, the first CRISPR/Cas-based clini-
ent types of cells by using a specific Type II Cas protein cal trial to treat the human immunodeficiency virus (HIV)
termed Cas9 [22]. The gRNA is the key for CRISPR-Cas9 was carried out by several Chinese scientists [31]. In 2018,
systems. It can recognize the target sequence with high a T-cell receptor (TCR) gene-modified T cell was tested in
specificity [2, 5]. clinical trials to treat patients with different cancers [32].
Subsequently, Cas9 protein cuts the targeted sequence This study proved the possibility of using CRISPR-Cas9
near a protospacer adjacent motif (PAM) [2]. In 2015, in cancer treatment [33]. In 2019, the treatment of Leber’s
two Type V CRISPR/Cas proteins, Cas-12a and Cas- congenital amaurosis (LCA) based on in vivo CRISPR-
13a, were discovered for genome editing, and they were Cas9 gene therapy was tested in clinical trials [34].
initially named Cpf1 and C2c2, respectively [23–25]. This article reviews the recent progress of the CRISPR/
Notably, Science named the powerful genome-editing Cas system in clinical diagnostics and gene therapy-based
technique–CRISPR as the breakthrough of the year [26]. treatments in clinical trials. We also discuss the CRISPR/Cas
In 2016, Abudayyeh et al. discovered that Cas-13a is an systems’ strengths as well as its limitations, such as off-target
RNA-guided RNase, which provides protection against effects (OTEs), tissue accessibility, and ethical concerns for
RNA phages [27, 28]. their future applications.
Figure 2 Illustration of CRISPR-Cas-12a and 13a sensing mechanisms and their diagnostic applications.
DETECTR enabled selective detection of human pap- Also, the CRISPT/Cas system has been utilized in the
illomavirus (HPV) in patient samples in a short time diagnosis of noninfectious diseases, such as identifying
[46]. Similarly, Li et al. developed one-Hour Low-cost oncogenes and other mediators in almost all areas of cancers
Multipurpose highly Efficient System (HOLMES) based [57]. Additionally, CRISPR-based genome editing strategies
on Cas-12a for fast human SNP genotype detection [37]. show high-accuracy in the identification of single-base var-
Recently, Yin et al. reported a dynamic aqueous multiphase iation in target sequences. Therefore it provides a sufficient
reaction (DAMR) system for quantitative HPV detection distinction of specific alleles, which is crucial for early dis-
with sensitivity based on CRISPR-Cas-12a and recombi- ease diagnosis [58, 59].
nase polymerase amplification (RPA) [38].
Notably, CRISPR/Cas has emerged as a sensing tool
for rapidly developed severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) RNA for quick, on-site
CRISPR-Cas9-based gene
diagnosis in the current pandemic of coronavirus disease therapy
2019 (COVID-19) [16, 47–49] (Figure 1) The current
“gold-standard” COVID-19 detection method is reverse Gene therapies, which deliver nucleic acids to patients’
transcription polymerase chain reaction (RT-PCR) [50]. cells, have been utilized to treat diseases that are not cur-
This method is highly sensitive and specific, and it can able with conventional medicines [60]. Current gene ther-
quantify viral RNA. However, it requires proper sampling apies use nucleases to modify genomes by generating DNA
procedures, and it suffers from PCR inhibition, and a long lesions and initiating endogenous DNA repair systems [61].
detection time [51, 52]. Conventional nucleases for gene therapy include zinc finger
CRISPR-Cas12a and 13a combined with isothermal nucleases (ZFNs), and transcription activator-like effector
nucleic acid amplification strategies, such as RPA and nucleases (TALENs) [62]. ZFNs and TALENs are engi-
loop-mediated isothermal amplification (LAMP), can pro- neered enzymes that are made by fusing binding and cleav-
vide sensitive detection results within an hour [48, 49, 53]. age domains. Substitution of the natural cleavage domain
To improve the sample-to-result time, Ramachandran et with engineered enzymes enables ZFNs and TALENs to
al. developed an electric field gradient for automatically target specific DNA sequences [63]. However, it is challeng-
purifying target RNA in raw nasopharyngeal swab samples ing to predict the target’s final arrangement by using ZENs
based on a selective ionic focusing technique, termed iso- [63]. DNA target cloning is a complicated design process
tachophoresis (ITP) implemented on a microfluidic chip and the low genome screening efficiency has limited the
[53]. They combined the ITP technology with a LAMP application of TALENs in gene therapy [64]. Recently, gene
CRISPR assay to detect SARS-CoV-2 RNA. It can be therapy based on CRISPR-Cas9 has been applied to treat
achieved in about 35 min from raw sample-to-result-time various diseases in clinical trials due to its simplicity, var-
[53]. Additionally, CRISPR/Cas has been utilized for the ious genomic target sites, multiplex genomic modification,
multiplex detection of SARS-CoV-2 and HIV. Ding et al. and the possibility of easy off-target site prediction [65, 66].
developed an all-in-one dual CRISPR-Cas-12a (AIOD- Different from ZFNs and TALENs, the process of CRISPR-
CRISPR) assay for detecting SARS-CoV-2 and HIV in Cas9 is easier and faster because it only requires one Cas9
one-spot. They achieved sensitive detection of virus RNAs endonuclease and a short single gRNA [67]. In addition to
down to a few copies. It has achieved comparable results this, unlike traditional methods that introduce functional
with real-time RT-PCR in human plasma samples [54]. genetic materials via direct viral vector-mediated over-ex-
Recently, Fozouni et al. reported a CRISPR-Cas13a-based pression, CRISPR-Cas9 can introduce functional genes in
direct SARS-CoV-2 RNA detection strategy, eliminating patients that can be expressed in their natural context [68].
the viral RNA’s pre-amplification step. The authors meas- Therefore, CRISPR/Cas therapy is promising for treating
ured the fluorescence by utilizing a smart phone camera in diseases related to gene disorders [22].
a compact device, which yields quantitative results in real- Since its discovery, CRISPR/Cas-based therapy has been
time. They achieved sensitivity of ∼100 copies/μL within investigated in a wide spectrum of cells types and in various
30 min for SARS-CoV-2 RNA detection [55]. This sensing animals. In brief, CRISPR-Cas9-based gene-editing can be
platform has the potential to allow fast, cost-effective and accomplished by inserting, deleting, or replacing sections of
accurate COVID diagnostics at POC [55]. the DNA sequence in the DNA double-strand breaks DSBs’
Moreover, the CRISPR/Cas system has been exploited in locus. (Figure 3). In ex vivo CRISPR-Cas9 gene therapies,
the field of bacterial detection, such as for identifying anti- cells are isolated from the patient, applied to the gene-ed-
microbial drug-resistant bacteria [16]. One strategy termed iting process, and then injected back into the patient. It is
finding low abundance sequences by hybridization (FLASH) possible to choose the cells with high viability to increase
employs Cas9 and different gRNAs to identify pathogens the survival rate of cells after transplantation to achieve its
using gene sequencing [56], which achieved sub-attomolar therapeutic effect [69]. In terms of in vivo CRISPR-Cas9
sensitivity. Although the authors only applied this strategy gene therapies, CRISPR components are directly deliv-
to examine the antimicrobial resistance genes in respiratory ered to specific tissues (such as the eye, brain, or muscle)
fluid and dried blood spots, in theory, FLASH next-genera- through systematic administration or local injection [69].
tion genes sequencing can be applied to other samples that Subsequently, CRISPR-Cas9-based gene-editing systems
rely on multiplex PCR [56]. recognize particular target DNA sequences by gRNA,
CRISPR/Cas9-based therapies
Ex vivo In vivo
Pr
om
Correction of blood
oter
disorders or blood-related Immunotherapies for cancer CRISPR
diseases by targeting immune cells plasmids
by targeting HSPCs (T cells/B cells)
Construction of CRISPR-
CRISPR-Cas9 is delivered CRISPR-Cas9 is delivered Cas9 plasmid
to HPSCs ex vivo for desired to immune cells ex vivo for
gene editing desired gene editing
Ex vivo culture of
Ex vivo culture of CRISPR- therapeutically modified
Cas9-edited HSPCs immune cells
Target Cell
T
A
generating DSBs using the cas9 protein, which then initi- Ex vivo CRISPR-Cas9-based gene
ates endogenous DNA repair pathways. Nonhomologous
end-joining (NHEJ) is the major DNA repair mechanism
therapy for blood disorders
that induces indels to deactivate gene functions. Homology-
Initially CRISPR-Cas9 was applied for the treatment inher-
directed repair (HDR) is essential for precise editing, such as
replacing a gene sequence with a desired sequence with the ited blood disorders [71]. Sickle-cell disease (SCD) and
low possibility of introducing random mutations [68, 70]. Ex β-thalassemia genetic disorders are caused by mutations in a
vivo CRISPR-Cas9 gene therapies have been widely utilized single gene, which affect the production of β-globin, a com-
to treat several blood diseases, acquired immunodeficiency ponent of fetal hemoglobin (HbF) [72, 73]. These two dis-
syndrome (AIDS), and cancer. In vivo CRISPR-Cas9 gene eases can be alleviated by re-expressing the γ-globin gene,
therapy technology is only at its initial stage. To the best of the paralogous gene of HbF. Wu et al. applied CRISPR-Cas9
our knowledge, it has only been tested to treat LCA10 [34]. to human hematopoietic stem cells to increase the expres-
Below, we present the up-to-date progress of CRISPR-Cas9- sion of γ-globin by modifying the enhancer of a gene called
based gene therapy and its clinical applications according to B-cell lymphoma 11 A (BCL11A), which is a repressor gene
specific diseases. of γ-globin [71].
Ex vivo CRISPR-Cas9-based gene gene therapy [82]. CRISPR-Cas9-based in vivo gene ther-
apy that employs AAV vectors has been applied in treating
therapy for AIDS Duchenne muscular dystrophy (DMD) in mouse models
through intramuscular, intraperitoneal, or intravenous injec-
Another ex vivo CRISPR-Cas9 therapy approach has been
tion to rescue the disease phenotype [83–86]. These stud-
applied to patients infected with HIV [74]. Continuous
ies showed the potential of using AAV vectors for in vivo
deduction of CD4+ T lymphocytes is the main symptom
CRISPR-Cas9 delivery in human clinical trials. Recently,
in HIV patients. This reduction leads to the inability of
for the very first time, THE CRISPR-Cas9 technique was
the immune system to defend against pathogens [75]. HIV
employed in a clinical trial through direct delivery of the
can bind and enter macrophages or CD4+ T lymphocytes.
CRISPR/Cas9 component to the target tissue of human body
Transmembrane C–C chemokine receptor type 5 (CCR5)
by using AAV vectors. This trial is aiming to treat LCA10 by
plays an important role in mediating the entry of HIV into
correcting a defective gene named centrosomal protein 290
lymphocytes [76]. Previous studies showed that a specific
(CEP290) [34].The outcome of this clinical trial is of great
mutation (the deletion of particular 32-base pair of the gene)
importance for the further applications of in vivo CRISPR/
of the CCR5 gene could destroy its function, thus suppress-
Cas gene therapies.
ing the expression of CCR5 on the cell surface [77, 78].
Xu et al. applied CRISPR/Cas9 to ablate CCR5 with same
strategy which has been utilized in hematopoietic stem and
progenitor cells (HSPCs). The results of this study showed
that these edited HSPCs in mice could resist HIV for up to
Future perspective and
47 weeks [31]. challenges of CRISPR/
Cas-based diagnostics and
Ex vivo CRISPR-Cas9-based gene therapeutic applications
therapy for cancer
CRISPR/Cas technology has been regarded as a versatile
Furthermore, CRISPR-Cas9-based ex vivo gene therapies genome-editing tool with significant potential for diagnos-
combined with immunotherapy advanced the clinical trials tic and therapeutic applications. CRISPR/Cas-based mole-
for cancer treatment. Chimeric antigen receptor (CAR)- cular assays provide fast, sensitive, and specific diagnostics
engineered T-cell therapy is the most commonly used immu- in patient samples suitable for POCT. Moreover, CRISPR/
notherapy that modifies T cells’ genes from patients to kill Cas-based diagnostics can be easily transformed into a uni-
cancer cells [79]. Firstly, T lymphocytes were isolated from versal diagnostic platform by simply changing the design of
patients’ blood. Next, target genes (TCR and PD-1) were the specific sgRNA for different pathogens and cancer cell
deleted to attenuate the immune response. Subsequently, lines. CRISPR/Cas-based SARS-CoV-2 detection strategies
a specific TCR encoding gene for the NY-ESO-1 antigen, for POCT have rapidly emerged since the outbreak of the
which is highly up-regulated in the relapsed tumor, was COVID-19 pandemic due to the simplicity of its design.
transduced into the T lymphocytes using a lentivirus [33]. Despite the high sensitivity and specificity, CRISPR/Cas-
Therefore, immune cells can be transformed into trained based fluorescent nucleic acid detection has several limita-
“soldier cells” to locate and kill cancer cells through gene tions, including the necessity of pre-amplification methods,
modification. This clinical trial paved the way for a broader such as LAMP and RPA, expensive fluorescent signal read-
implication of CRISPR/Cas-based gene therapies. A recent out devices, and expertise in biotechnology. On the other
study published in Nature Medicine showed favorable results hand, although CRISPR/Cas-based lateral flow colorimet-
in the treatment of late-stage lung cancer patients with these ric detection provides merely qualitative detection results,
modified T cells. Donor cells exist in patients for more than it has been regarded as a rapid, robust, and cost-effective
19 months. This trial confirmed the feasibility and safety of approach for on-site diagnosis by the naked-eye. Moreover,
CAR T-cell therapy in treating late-stage lung cancer [80]. the CRISPR/Cas-based electrochemical biosensors also pro-
The authors also used PD-1 deleted-T cells for the treatment vide a highly desirable free pre-amplification method for
of different kinds of cancers in clinical trials [80]. rapid nucleic acid diagnostics.
In terms of therapeutic applications, despite the remarka-
ble advances of CRISPR/Cas-based gene therapies and their
Recent advances in in vivo CRISPR/ clinical applications, several challenges should be addressed.
Cas-based gene therapy A significant concern of utilizing CRISPR-Cas9 gene ther-
apy in the clinic is the OTEs. The binding of gRNA to a sim-
Ex vivo CRISPR-Cas9 gene therapy has been extensively ilar region with target sequence of genome can lead to the
reviewed, however in vivo gene therapy based on CRISPR- deletions or insertions in an unwanted locus. Notably, these
Cas9 has been less extensively employed [80]. Risk-free random deletions and insertions of the genome can cause
and efficient delivery of the CRISPR-Cas9 element to the detrimental mutations [87]. Since undetectable OTEs are
target tissue is the foundation of successful treatment [81]. not understood completely, the method for the detection and
Currently, adeno-associated viral (AAV) vectors are the fre- evaluation of the consequences of OTEs for various organs
quently used delivery vehicles for in vivo CRISPR/Cas-based needs to be explored further [88].
In addition to OTEs, different delivery methods of specific tissues. Compared with local injections, systematic
CRISPR/Cas gene therapy have their own merits and chal- administration is more capable of reaching different organs
lenges. Compared with in vivo delivery, ex vivo delivery through the circulatory system. Besides, it is also possible
exhibits several advantages, including technical feasibility, to control the expression of Cas9 precisely in desired tis-
clinical safety, and the possibility of a tight quality check sue [91]. However, CRISPR components delivered in vivo
on transplanted cells. But this approach was challenged by might be degraded by various enzymes and thus lose their
the viability and time limitation of retaining functional cells function [80].
in vitro after genetic editing and a lengthy culture process Besides the technical challenges, several ethical (moral)
[80]. Moreover, ex vivo therapy is limited to specific cell and safety concerns limited the CRISPR applications, such
types, such as HSPCs and T lymphocytes, because of their as germline editing [92, 93]. Firstly, OTEs over the lifetime
ability to survive and expand in culture. In contrast, many caused by germline gene editing remains critical for utilizing
other tissues are not suited for this method [89, 90]. In vivo this technology broadly in the human body. Also, the pos-
gene therapy is a promising technology that can expand sibility of artificial selection of humans has raised concern
CRISPR/Cas technology application to treat genetic disor- for ethicists and the public. Therefore, a good documentation
ders with a widespread range. Methods of in vivo CRISPR guideline will be of great help to support the further clinical
components delivery include intravenously injecting to applications of CRISPR-Cas9 technology.
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