INTRODUCTION
Spinal pain is a prevalent issue arising from degenerative musculoskeletal changes, disc disorders, neuropathic conditions, inflammation, or trauma [1]. It often progresses into a neuropathic pain despite the availability of various treatments [2-4]. Pharmacological therapies such as painkillers, anti-inflammatory medicines, and muscle relaxants can provide temporary relief but may cause adverse side effects [5,6]. While opioid analgesics are effective, issues such as significant addictions could be entailed. Spinal injections or advanced techniques, including radiofrequency ablation and spinal cord stimulation (SCS), provide alternative pain management options but involve high costs, complex procedures, and potentially diminishing effectiveness over time. Currently, significant challenges remain in developing effective solutions to provide long-term effectiveness for neuropathic pain [7].
Recently, development of novel therapies emerged as promising approaches to manage neuropathic pain, presenting attractive alternatives to conventional treatments. Antisense oligonucleotides (ASOs), RNA interference (RNAi), and the CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) systems enabled specific control of pain-related genes and, therefore, provided highly valuable tools applicable for overcoming chronic pain. Gene therapy can restore dysregulated biological pathways caused by genetic mutations to their normal functional state, some of which are unachievable by conventional pharmaceutical therapies. Indeed, various studies demonstrated the application of the advanced tools for pain-related genetic interventions focusing on the pain-related targets including voltage-gated sodium channels (Nav), transient receptor potential (TRP) channels, and purinergic receptors.
Among these strategies, CRISPR can facilitate precise and specific suppression of select genes by accurate targeting of defined DNA sequences, offering greater efficiency and persistence compared to ASOs and RNAi. Some CRISPR systems enable single-base substitutions in DNA sequences and specific RNA targeting. Moreover, CRISPR activation (CRISPRa) and interference (CRISPRi) allow precise regulation of gene expression without changes in the DNA sequences.
The versatility of CRISPR have been harnessed in clinical CRISPR-based approaches for developing pain relief therapies. Genes encoding receptors in neuropathic pain represent potential therapeutic targets for applications of CRISPR tools. We discuss the feasibility of CRISPR-based treatments while addressing the current hurdles that must be overcome for successful clinical applications, such as target specificity, off-target effects, and longterm safety issues. Furthermore, this review provides a perspective on how CRISPR may be applied in novel therapy options for gene-based pain management.
In this review, we aim to bridge the gap between advances in CRISPR-based genome editing and their specific applications in spinal and neuropathic pain. We provide an integrated perspective on CRISPR technologies and pain pathways that highlights therapeutic targets, delivery strategies, and translational challenges unique to pain-related gene therapies.
GENETIC MODULATION OF PAIN: MOLECULAR TARGETS AND CONVENTIONAL THERAPEUTICS TOOLS
Spinal pain transmission involves a variety of cellular components, among which primary sensory neurons located in the dorsal root ganglia (DRG) and trigeminal ganglia (TG) are especially critical. These neurons comprise nociceptors—specialized sensory cells responsible for detecting harmful thermal, mechanical, and chemical stimuli. Nociceptors are broadly classified into unmyelinated C-fibers and thinly myelinated Aδ-fibers, each defined by distinct expression profiles of ion channel, receptor, and signaling molecules [8].
Genetic studies have identified several key molecular targets within these neurons, some of which have attracted interest in developing novel analgesics. The sodium voltage-gated channel alpha subunit 9 (SCN9A) gene, which encodes the Nav1.7 sodium channel, plays a crucial role in pain signaling [9,10]. Mutations in this gene are associated with inherited pain syndromes and compounds like vixotrigine and VX-548 targeting Nav1.7 are in clinical trials [11,12]. TRP vanilloid receptor 1 (TRPV1), which responds to noxious heat and contributes to inflammatory pain, has been pharmacologically modulated through capsaicin formulations and selective inhibitors [13,14]. The opioid receptor mu 1 (OPRM1) gene, encoding the μ-opioid receptor, regulates the efficacy of opioids like morphine and fentanyl, and clinical responses of therapies targeting the receptor vary depending on individual genetic backgrounds [15]. Other promising molecular targets being explored for their therapeutic potential include purinergic receptors (P2X3) —the focus of drugs such as gefapixant— as well as acid-sensing ion channel, Nav1.8, and several types of G protein-coupled receptors [16].
However, even with recent progress in the drug development, traditional pharmacological methods have been insufficient in providing the effective potency, selectivity, and tolerability for chronic pain control. In this regard, genetic approaches represent novel tools for selective modulation of pain-associated genes in a cell-type-specific manner. Advances in transcriptome analysis using single-cell RNA sequencing have expanded the knowledge of gene expression patterns across individual neuronal subtypes, allowing for the identification of highly selective molecular targets. The data-assisted development of targeted genetic strategies may help overcome the limitations of conventional pharmacological approaches and provide sustained pain relief with minimal side effects.
The advances in knowledge of pain-related genes target led to the application of gene-silencing tools such as ASOs and RNAi, which have been extensively explored in both preclinical and clinical pain research. Both ASO and RNAi approaches provide suppression of gene expression at the posttranscriptional level by targeting messenger RNA and continue to serve as important references for the development of more recent gene-regulating technologies for pain therapies.
THERAPIES TARGETING PAIN-RELATED PATHWAYS AT THE MOLECULAR LEVEL
1. ASOs and RNAi as Gene-Silencing Tools
ASOs are chemically synthesized single-stranded oligonucleotides designed to bind specific mRNA sequences and regulate gene expression. This binding can either recruit RNase H, resulting in degradation of the transcript, or interfere with normal mRNA splicing processes (Fig. 1A). Whereas, RNAi represents a distinct gene-silencing mechanism that employs small interfering RNAs (siRNAs) or short hairpin RNAs. These molecules are incorporated into the RNA-induced silencing complex, where they direct sequence-specific degradation of target mRNA transcripts (Fig. 1B).
These gene-silencing approaches offer a high degree of specificity and can be tailored to selectively downregulate pain-associated genes, making them especially valuable in the context of chronic or treatment-resistant pain. Recent studies have demonstrated their efficacy in modulating key molecular targets involved in nociceptive signaling, both in preclinical models and early-phase clinical trials. The following section highlights representative examples of ASO- and RNAi-based strategies applied to pain research, with a focus on their therapeutic relevance and translational potential.
2. Research on Therapeutic Targeting of Nociceptive Pathway
Notably, ASO and RNAi technologies have been widely applied to investigate and therapeutically modulate primary painrelated targets such as Nav1.8, Nav1.9, TRPV1, and P2X3 (Fig. 1C). Their selective suppression in primary sensory neurons has yielded significant insights into the molecular basis of chronic pain.
In the targeted regulation of voltage-gated sodium channels in nociceptors, ASO-mediated knockdown of Nav1.8 has been reported to effectively reduce neuropathic pain behaviors and suppress the redistribution of Nav1.8 channels in injured sciatic nerves [17]. These results were particularly evident in models where chemically stabilized ASOs targeting exon regions were delivered by intrathecal administration. However, other studies using different administration routes or targeting noncoding regions have reported limited analgesic effects, indicating that therapeutic efficacy may depend on factors such as oligonucleotide design, target site selection, and the specific pain model [18]. Similarly, ASO-mediated suppression of Nav1.9 has shown promising results in reducing mechanical pain sensitivity in rodent models, without eliciting significant adverse effects [19]. In contrast, earlier studies utilizing antisense oligodeoxynucleotides (ODNs) failed to achieve comparable outcomes [18]. This discrepancy may stem from fundamental differences in oligo chemistry—ODNs are typically unmodified and more susceptible to nuclease degradation, resulting in reduced stability and efficacy compared to chemically modified ASOs. Furthermore, ODNs often exhibit lower affinities and specificities for their target RNAs, which can limit their functional potency in vivo [20]. Adding to the complexity, the role of Nav1.9 in pain processing appears to be context-dependent. While Nav1.9-deficient mice display attenuated inflammatory pain responses without developing neuropathic phenotypes [21], increased Nav1.9 expression has been implicated in trigeminal neuralgia following infraorbital nerve injury [22]. These contrasting findings suggest that Nav1.9 may exert distinct functional roles across different neuronal circuits and pain subtypes.
Among TRP channels, both ASO and RNAi approaches have been explored to suppress TRPV1, a key mediator of thermal hypersensitivity and inflammatory pain. Studies have shown that intrathecal administration of TRPV1-specific siRNA significantly reduced capsaicin-induced visceral and neuropathic pain [23], while TRPV1 ASOs reversed mechanical hypersensitivity in spinal nerve-ligated rats [24]. Additionally, TRPV4 knockdown via ASOs showed a reduction of pain responses to hypotonic stimuli, further supporting its role as a therapeutic target for pain relief [25,26].
The P2X3 purinergic receptor, a ligand-gated ion channel activated by extracellular ATP, plays a crucial role in chronic pain, particularly neuropathic and inflammatory pain conditions [27]. P2X3 receptors are primarily expressed in DRG and TG neurons, contributing to nociceptive signaling and hypersensitivity. Excessive activation of P2X3 receptors following nerve injury or inflammation leads to increased pain transmission and abnormal neuronal excitability [28], making it an attractive target for gene therapy in chronic pain treatment. Studies have demonstrated that intrathecal administration of ASOs targeting P2X3 led to significant attenuation of mechanical hyperalgesia in both neuropathic and inflammatory pain models [29]. The important findings of the above studies are summarized in Table 1, which outlines the representative pain-related genes targeted by ASO and RNAi technologies, the observed therapeutic effects, and the corresponding preclinical models.
Beyond classical protein-coding targets, recent studies have revealed that noncoding RNAs and epigenetic mechanisms also exert significant influences on nociceptive gene regulation. Several studies showed that specific long noncoding RNAs (lncRNAs) and microRNAs influence pain-related gene expression in sensory neurons [30-32]. However, despite the high potential of siRNA and lncRNA-based therapies as targeted neuropathic pain treatments, challenges in delivery specificity and off-target effects remain significant obstacles to clinical translation. In response to the limitations of transient gene-silencing tools, CRISPR-based technologies have emerged as a next-generation strategy for precise and sustainable gene editing in pain research by directly modifying the DNA sequences or epigenetically controlling gene expression. Since researchers including Emmanuelle Charpentier and Jennifer Doudna, who were awarded the 2020 Nobel Prize, discovered the influential CRISPR-based geneediting technology, it has enabled targeted modifications of the endogenous DNA sequences, making it one of the most potent therapeutic tools available. Pioneering works on elucidating the molecular mechanism of CRISPR led to the development of clinical application strategies of the CRISPR system for advancing pain treatment. This technological evolution—from ASOs and RNAi to CRISPR—is illustrated in Fig. 1D, which outlines major scientific and clinical milestones in the development of gene regulation strategies [33-44].
THE MOLECULAR MECHANISMS AND THERAPEUTIC APPLICATIONS OF CRISPR GENE-EDITING TECHNOLOGY
1. Mechanisms of CRISPR-Cas Systems
The CRISPR-Cas system shares some similarities with ASO and RNAi as gene-targeting technologies, while there are distinct aspects such as the mechanisms, delivery formats, and clinical applications (Table 2). The CRISPR-Cas9 system from Streptococcus pyogenes has been one of the most widely used CRISPR gene-editing tools. In this system, the genome editing is conducted by the enzymatic function of CRISPR-Cas9 (SpCas9) protein that introduces a double-strand break (DSB) at the target DNA sequence. In the process, SpCas9 forms an active ribonucleoprotein nuclease complex with crRNA and tracrRNA, or alternatively, a single-guide RNA (sgRNA) (Fig. 2A, left panel). The crRNA or sgRNA sequences are complementary to the 20-nt DNA sequences of the target genomic locus. The NGG sequence, in which ‘N’ represents any nucleotide and each ‘G’ represents guanine, is known as the short protospacer adjacent motif (PAM) sequence and is recognized uniquely by SpCas9. Upon recognition of the target DNA, SpCas9 induces a DSB in the defined location at the target DNA by cleaving the target and the nontarget strands by distinct HNH and RuvC nuclease domains of Cas9, respectively [45].
A few years after the breakthroughs of type II Cas9, Cas12 nucleases were discovered and classified as a distinct group of type V CRISPR-Cas systems [39,46]. Unlike SpCas9, the AsCas12a system shows the characteristic TTTV PAM sequences, and the DSB occurs in a PAM-distal region via a single catalytic site of the RuvC domain (Fig. 2A, right panel). While Cas9 systems utilize both crRNA and tracrRNA to activate target sequence cleavage with blunt ends, Cas12 uses only a single crRNA to induce DNA cleavage with staggered ends. In addition to SpCas9 and Cas12a, various engineered or orthologous Cas9 and Cas12 variants have been recently developed to expand PAM compatibility, improve editing precision, and enable application in diverse biological contexts (Table 3).
2. Conventional Genome-Editing Approaches by Double-strand DNA Breaks
Conventional genome-editing approaches are mediated by deliberately inducing DSBs at specific sites in the genome. Subsequently, the target DNA sequences are modified during the intracellular DSB recovery process by endogenous DNA repair machineries, such as nonhomologous end joining (NHEJ) or homology-directed repair (HDR) [47,48]. Generally, the NHEJ pathway is primarily activated to repair for DSBs introduced by Cas9 or Cas12a. DNA repair by NHEJ is inherently an error-prone mechanism that ligates the broken DNA ends without homolo-gous template as a reference. During this process, insertions or deletions (indels) are frequently introduced at the DSB sites [49]. These indels often lead to frameshift mutations within the targeted gene that result in disruption of gene expression or complete knockout of the gene (Fig. 2B). The efficiency of NHEJmediated knockout depends on factors such as cell types and the characteristics of their DNA repair pathways [50].
HDR is an alternative cellular DSB repair process that is primarily activated in cells undergoing active cell division because the HDR repair factors are typically expressed exclusively during the S and G2 phases of the cell cycle [51]. As HDR requires a homologous DNA molecule to facilitate accurate DNA repair, knock-in of exogenous DNA at the DSB site can be achieved by providing a synthetic repair template with desired genetic modifications (Fig. 2B). HDR-mediated knock-in can be utilized for translational research such as introducing functional tags, fixing pathogenic mutations, or generating disease models.
3. CRISPR-based Base Editing and Prime Editing Technologies Without DSBs
While DSB-mediated CRISPR genome engineering enabled groundbreaking research, subsequent studies revealed the risks of unintended genomic alterations such as large deletions [52] and chromosomal abnormalities [47-49,53-55]. To overcome the issues, engineered CRISPR systems known as base editors were developed to enable precise single-nucleotide conversions without inducing DSB [56]. In this approach, nickase Cas9 (nCas9) is fused to a deaminase enzyme, allowing targeted conversion of specific bases within a defined editing window. The editing window typically spans positions 4 to 8 or 4 to 10 relative to the PAM on the nontarget DNA strand [57,58]. Cytosine base editors convert cytosine to thymine (C• G to T• A), while adenosine base editors convert adenine to guanine (A• T to G• C) (Fig. 2C), enabling efficient and predictable point mutations with reduced insertion or deletion byproducts.
Prime editing is an advanced CRISPR-based genome-editing approach that enables versatile and precise introduction of targeted insertions, deletions, and all possible base substitutions without inducing DSBs [59]. This system employs a fusion of an nCas9 and a reverse transcriptase enzyme, guided by a specially designed prime editing guide RNA (pegRNA). The pegRNA not only directs the Cas9 to the target site but also contains an extended sequence encoding the desired edit, along with a primer binding site and reverse transcription template. Upon nicking the DNA strand, the reverse transcriptase uses the pegRNA template to synthesize the edited DNA sequence at the nick site, enabling modifications such as point mutations, small insertions (~40 bp), or deletions (~80 bp) with high precision and fewer unintended byproducts compared to conventional CRISPR methods [60] (Fig. 2D).
4. CRISPR Technologies for Targeted Regulation of Gene Expression
CRISPRa is a powerful genetic engineering tool that enables the targeted upregulation of gene expression without altering the underlying DNA sequence. Unlike traditional CRISPR-Cas9 systems that induce DSBs, CRISPRa employs a catalytically inactive Cas9 (dCas9) protein fused to transcriptional activators, such as VP64, p65, and Rta, to increase the transcription at specific genomic loci [61-63] (Fig. 2E). When guided to the promoter or enhancer regions of a target gene by a sgRNA, the CRISPRa complex recruits RNA polymerase and other transcriptional cofactors to initiate and amplify gene transcription. SgRNA sequence determines the specificity of the target site, enabling researchers to selectively enhance the expression of almost any gene of interest. Its nonmutagenic nature minimizes the risk of off-target effects associated with DNA breaks, making it a safer alternative for therapeutic applications. Additionally, the modularity of the dCas9 fusion system allows combining various activators to achieve synergistic effects [64,65], further expanding its potential in both research and clinical settings.
CRISPRi is a gene-silencing technology that repress the expression of target gene by inhibiting transcription in a targeted and reversible manner, without causing permanent changes to the DNA sequence. CRISPRi uses a dCas9 protein fused to transcriptional repressors such as the Krüppel-associated box (KRAB) domain, and histone demethylases such as LSD1 or KDM1A [65,66]. The CRISPRi complex is guided by a sgRNA to specific promoter or regulatory regions of the target gene (Fig. 2F). Once bound, the dCas9-KRAB complex sterically blocks the binding of RNA polymerase, transcription factors, or other transcriptional cofactors required for gene activation. Additionally, the KRAB domain recruits chromatin-modifying enzymes, such as histone deacetylases and histone methyltransferases, which induce repressive chromatin environments that further suppress transcription. CRISPRi is a versatile tool for functional genomics, enabling researchers to study loss-of-function phenotypes by silencing specific genes. Unlike traditional gene knockout approaches, CRISPRi allows partial or tunable suppression of gene expression, providing insights into dose-dependent gene functions [67]. This feature of CRISPRi is particularly useful for studying essential genes, where complete knockout would be lethal.
The important features of the different CRISPR modalities, including nuclease-based genome editors (Cas9), base editors, prime editors, and transcriptional regulators (CRISPRa/i), are summarized in Table 4 focusing on their mechanisms, components, and potential applications.
5. CRISPR-based Gene Therapy for Pain-related Receptors
Nav1.7, a voltage-gated sodium channel encoded by the SCN9A gene, plays a crucial role in the signaling of inflammatory and neuropathic pain within the primary sensory neurons [68]. Gain-of-function mutations in SCN9A lead to severe pain dis-orders such as inherited erythromelalgia and paroxysmal extreme pain disorder, while loss-of-function mutations result in complete insensitivity to pain, even in cases of fractures and burns [68-70].
Based on preclinical studies, targeted regulation of Nav1.7 by CRISPR-based technologies has demonstrated promising pain relief outcomes. Recent research has explored CRISPR-dCas9-based epigenetic repression of Nav1.7 to modulate its expression without altering the genomic sequence. By using CRISPR-dCas9 and zinc-finger proteins, researchers have successfully silenced Nav1.7 in nociceptors, reducing pain responses in preclinical models71 (Fig. 3A). Intrathecal delivery of CRISPR-dCas9 led to significant pain relief in carrageenan-induced inflammatory pain, paclitaxel-induced neuropathic pain, and BzATP-induced pain models [71]. Importantly, Nav1.7 suppression attenuated the pain hypersensitivity without impairing normal sensory functions. These findings suggest that Nav1.7 can be a viable target of CRISPR gene therapy for chronic pain, and further research is anticipated to refine the delivery strategies and ensure clinical safety.
The TRPV1 receptor is a key mediator of thermal pain and inflammation-induced hyperalgesia [72,73]. It is activated by heat, capsaicin, and inflammatory mediators, and has been extensively studied for its role in pain perception and chronic pain conditions. Mutations in TRPV1 have been linked to severe, long-lasting pain following corneal surgery, highlighting its relevance in postoperative and neuropathic pain [74]. In an inflammatory in vivo pain model, CRISPR-Cas9-mediated editing of TRPV1 phosphorylation sites (Ser801Ala) reduced the pain caused by masseter muscle inflammation, without impairing the normal physiological function of TRPV1 [75] (Fig. 3B). These findings suggest that precise genetic interventions targeting TRPV1 could offer long-term relief for mechanical allodynia, inflammatory pain, and nerve injury-induced hypersensitivity.
In summary, CRISPR-based gene therapy offers effective approaches for targeted modulation of pain receptors such as Nav1.7 and TRPV1, which play critical roles in nociceptive signaling and chronic pain conditions. The current scope and therapeutic potential of gene-specific CRISPR strategies in pain research are summarized in Table 1, which includes the key painrelated genes, their known roles in pain signaling, the types of CRISPR interventions used, and the preclinical models in which they have been tested. By utilizing CRISPR-Cas9 for gene knockout and CRISPR-dCas9 for epigenetic repression, researchers have successfully reduced pain hypersensitivity in preclinical models. As CRISPR-based gene therapies have demonstrated significant promise, researchers are expanding the application of CRISPR genome engineering therapeutic tools to a broader range of diseases. The first CRISPR therapies for other diseases have now reached the clinic, and further development of CRISPR-based methods for pain relief in under investigation. As of now, no CRISPR therapy has been approved for pain, but identification of novel targets and overcoming the technical challenges will lead to improved therapies for pain control. The next section will review these landmark clinical successes and remaining challenges on the path to CRISPR-based pain treatments.
RECENT DEVELOPMENT OF CRISPRBASED GENE THERAPIES: INSIGHTS FROM APPROVED AND ONGOING CLINICAL TRIALS
As described in the previous sections, CRISPR-Cas9 emerged as a transformative tool in developing therapies for genetic and intractable diseases at their root, offering unprecedented precision. In recent years, CRISPR therapy has succeeded in diverse classes of diseases and its rapid advancement has catalyzed a surge of active research across a wide range of biomedical fields. CRISPR technology facilitates personalized medicine, as treatments can be tailored to a patient’s unique genetic profile. Moreover, it allows for flexible and rapid development, as altering only the guide RNA enables targeting of different genetic sequences (Fig. 2A). This adaptability is especially promising for diseases characterized by high genetic heterogeneity, such as various cancers and rare inherited disorders. Importantly, gene editing via CRISPR leads to permanent genomic alterations, potentially eliminating the need for repeated treatment and thereby significantly improving the life quality of patients.
Furthermore, the therapeutic applications of CRISPR are not limited to monogenic genetic disorders. Preclinical and clinical research using CRISPR have demonstrated promising results in cancer immunotherapy, particularly through the combination of CRISPR with CAR-T-cell engineering [76-79], as well as in the treatment of infectious diseases like HIV [80]. This versatility suggests that CRISPR is a platform that could also be adapted for complex conditions like chronic pain, which often have multifactorial genetic underpinnings.
Additionally, several CRISPR-based therapies rely on autologous cell sources, where a patient’s own cells are harvested, edited ex vivo, and reintroduced. This approach minimizes the risk of immune rejection and eliminates the need for immunosuppression. Since autologous cells are naturally compatible with the host environment, they tend to exhibit high engraftment efficiency and stable function after reinfusion [81]. We introduce the recent developments of autologous cell-based CRISPR gene therapy, such as Casgevy, which is clinically approved for the treatment of sickle cell disease (SCD) in patients [82]. An overview of approved and ongoing CRISPR-based clinical trials is provided in Table 5.
In parallel, we will address the key challenges associated with CRISPR therapies, including indirect issues such as viral deliv-ery methods and preconditioning regimens, as well as other safety concerns related to the off-target effects and potential immune responses induced by in vivo CRISPR delivery.
1. Approved CRISPR-Based Therapy
CRISPR-based therapies are being actively developed for genetic diseases, with SCD and transfusion-dependent β-thalassemia (TDT) at the forefront. Both are severe monogenic disorders caused by mutations in the hemoglobin subunit beta (HBB) gene. SCD results from a point mutation that produces abnormal hemoglobin S, leading to impaired oxygen transport and sickled, fragile red blood cells. TDT arises from mutations that reduce or eliminate β-globin production, causing ineffective erythropoiesis and transfusion-dependent anemia. In both cases, symptoms emerge when fetal hemoglobin (HbF) levels drop after birth, a switch regulated by the transcription factor BCL11A, which suppresses γ-globin expression.
Casgevy (exagamglogene autotemcel), developed by Vertex Pharmaceuticals and CRISPR Therapeutics [82], became the first approved CRISPR therapy by the United Kingdom’s Medicines and Healthcare products Regulatory Agency in November 2023, followed by U.S. Food and Drug Administration approval in the U.S. in December 2023 for the treatment of SCD, and in January 2024 for TDT. It uses CRISPR-Cas9 to disrupt an enhancer in the BCL11A gene in autologous CD34+ stem cells [83], reactivating γ-globin and restoring HbF production (Fig. 4). In parallel, Bluebird Bio’s lentiviral therapy Lyfgenia received approval for SCD as well. It introduces HbAT87Q, a functional HbA mimic, into autologous stem cells. While both therapies offer significant clinical benefits, Lyfgenia received a boxed warning due to leukemia in two participants. Casgevy has not received such a warning but long-term safety data remains limited.
The clinical application of CRISPR gene therapies may entail the potential safety risks related to the off-target effects. Continued monitoring and extended follow-up will be essential for ensuring safety and durability, and we therefore discuss the main safety issues in the next section.
2. Clinical Adverse Events Associated With CRISPR-Based Therapies
Despite these successes, serious adverse events have occurred in some CRISPR trials, underscoring the need for caution. A case report described the death of a male patient in his twenties, who had Duchenne muscular dystrophy (DMD) [84,85], after receiving a high dose of recombinant adeno-associated virus to deliver the CRISPR-Cas9 system. The patient died from an innate immune reaction, likely triggered by the extremely high viral dose. The vectors accumulated to unusually high levels in the lungs, leading to a fatal immune response. Another reported case involved BEAM-101 [85], a base editing therapeutic candidate which utilizes a modified CRISPR-Cas9 system, developed by Beam Therapeutics. According to an official statement by the company, the patient died approximately four months after receiving the infusion due to respiratory failure. The clinical investigator concluded that the adverse event was likely related to the busulfan-based preconditioning regimen rather than the gene-editing product itself. Accordingly, investigators assessed the death to be unrelated to BEAM-101.
Notably, neither adverse event was attributed to the gene-editing mechanism per se. However, they highlight the importance of maintaining vigilance regarding all components of CRISPRbased therapies including but not limited to the delivery systems, conditioning regimens, and dosing strategies. Comprehensive risk assessment and long-term monitoring are necessary for ongoing and future trials, and regulators now require robust safety data for these novel therapies.
STRATEGIES FOR THE POTENTIAL SAFETY ISSUES IN THERAPEUTIC APPLICATION OF CRISPR
In the preceding section, we reviewed the recent clinical applications of CRISPR-based therapies. To date, no adverse events of treated patients have been directly attributed to the CRISPR genome-editing mechanism itself. However, the long-term effects of CRISPR therapies are not completely understood as most are in clinical trials or have been recently approved. In this section, we explain the potential safety concerns associated with CRISPR genome editing—off-target effects [86] and immunogenicity [87]— and discuss the strategies to mitigate the problems, drawing on the findings from foundational research.
1. CRISPR Genome Editing at Unintended Loci by off-target Effects
Although translational application of CRISPR provided versatile tools for correcting the disease-causing DNA sequence, as DNA editing is irreversible, any permanent off-target modifications may result in unpredictable side effects [88]. Previous studies have shown that off-target mutations can occur at many sites across the genome [89-91], potentially hitting critical genomic loci unintentionally. Previous studies showed that CRISPR-Cas9 can unintendedly edit DNA sequences that are partially complementary to the gRNA [89-91]. In some cases, DNA with no seeming complementarity to the gRNA could also be subject to off-target editing [89-91]. The unpredictable nature of off-target poses significant difficulties in analyzing the off-target effects of CRISPRbased therapy in the whole genome for each cell in vivo and ex vivo treatments, because every cell’s genome would need to be checked for rare mutations, which is not currently feasible.
1) Use of nCas9 to minimize off-target effects
Previous studies have shown that the unwanted by-product genome editing by Cas9 off-target effects could be reduced by using nCas9 [92], a Cas9 mutant that makes single-strand cuts. However, the nickase solution did not completely eliminate the off-target effects throughout the genome.
2. Immune Issues Associated with in vivo CRISPR Delivery
Adaptive and humoral immune responses caused by CRISPR delivery to humans are also major obstacles in the clinical applications. Most widely utilized CRISPR genome engineering system originates from bacteria such as Streptococcus pyogenes and Staphylococcus aureus. Since S. pyogenes and S. aureus frequently colonize humans, pre-existing immunity against bacterial CRISPR-Cas9 proteins is found in more than 80% of healthy individuals [97]. For example, 78% and 58% of healthy human donors possess immunoglobulin G (IgG) antibodies against SaCas9 and SpCas9, respectively [87]. Moreover, researchers found high incidences of cytokine-positive antigen-reactive T cells against SaCas9 (78% donors) and SpCas9 (67% donors). The activated T cells with the expression of CD137 or CD154 on the cell surface were also identified by interferon-γ enzyme-linked immunospot (ELISpot) assays [87,98] and intracellular cytokine staining [87]. Preclinical models have shown similar concerns. In mice, SaCas9 delivery triggered cytotoxic CD8+ T-cell responses that eliminated Cas9-expressing hepatocytes [99]. In a canine model of DMD, SpCas9 induced therapeutic effects but was later associated with muscle inflammation and Cas9-specific immune responses, which could not be prevented by transient immunosuppression [100].
1) Peptide engineering and computational optimization of Cas proteins to reduce immunogenicity
To overcome these issues, researchers are engineering the CRISPR-Cas proteins to reduce immunogenicity. One group mutated immunodominant peptide regions in SpCas9, achieving a 25–30-fold reduction in immune recognition without compromising editing efficiency [101].
2) Computational optimization of Cas proteins for decreasing immunogenic responses
Raghavan et al. [102] showed that computational modeling to redesign SaCas9 and AsCas12a resulted in lowering their MHCbinding potential and improving immune tolerance.
With these versatile approaches to reducing the immune response to the CRISPR systems, the translation of the CRISPR technology from the laboratory to the clinic is becoming increasingly feasible. By mitigating the immune rejection and improving the overall safety profile of CRISPR-based treatments, researchers are paving the way for more practical and patient-specific applications (Fig. 5). In addition to immune-related barriers, several nonimmunological factors also complicate the translation of CRISPR-based therapeutics for pain. Among these, the absence of validated biomarkers and variability in gene expression profiles are critical limitations. The integration of high-resolution approaches—such as single-cell RNA sequencing, spatial transcriptomics, and epigenomic profiling—may facilitate the identification and prioritization of pain-relevant biomarkers for CRISPR-based interventions. These multi-omics tools can help uncover cell-type-specific mechanisms and refine therapeutic strategies for spinal pain treatment. As these innovations continue to mature, CRISPR genome engineering tools are anticipated to be effectively integrated into clinical treatments for a wide range of diseases, potentially including pain conditions.
CONCLUSION
Neuropathic pain affects hundreds of millions of people worldwide, highlighting the urgent need for more effective and targeted therapeutic strategies. Conventional pain management approaches often exhibit limited efficacy, variability in patient response, and potential adverse effects, necessitating the development of alternative treatment modalities. Despite progress in the conventional pain management strategies, many patients suffering from neuropathic pain continue to experience inadequate relief. Pharmacological treatments, including opioids, anticonvulsants, and antidepressants, often provide only partial symptom control and are frequently associated with significant side effects such as sedation, dependency, and tolerance. Interventional approaches like SCS offer alternative therapeutic options; however, their efficacy varies, and the long-term success rates remain suboptimal, with some patients experiencing diminishing benefits over time. These limitations highlight substantial unmet clinical needs for novel and more effective pain management strategies.
Advances in neurobehavioral studies showed that the identification of receptors that detect noxious stimuli has become increasingly crucial in elucidating pain mechanisms and identifying novel therapeutic targets. Additionally, progress in functional genomics and transcriptomic regulation has expanded the potential for genetic interventions in various chronic pain conditions. Despite these advancements, the translation of basic research into clinical applications remains challenging. Key obstacles include the absence of reliable pain biomarkers, the high placebo effect in pain treatment trials, biocompatibility concerns, and the limited precision of genetic interventions.
To address these limitations, biochemical and biophysical studies integrating clinical trial data have become increasingly crucial for the development of precision medicine approaches. CRISPR technology has emerged as a powerful tool that enables researchers to test hypotheses with high specificity and efficiency, and has been successfully applied in biochemical studies leveraging clinical trial data to identify and validate therapeutic targets for pain management.
In this review, we examined the mechanistic basis of CRISPR technology, highlighting its ability to precisely edit genetic material and regulate the expression of target genes. We next introduced the application of CRISPR in preclinical models to investigate the therapeutic potential of the pain-related ion channels, such as Nav and TRP channels, which play key roles in nociceptive signaling and chronic pain conditions. Furthermore, we have summarized the ongoing research efforts aimed at overcoming the major challenges in gene therapy, including the mitigation of off-target effects, enhancement of target specificity, and reduction of immunogenic responses, all of which are crucial for the successful clinical translation of CRISPR-based therapeutics.
In addition to the technical difficulties, the development of CRISPR-based therapies will need to address important ethical and regulatory challenges. Ethically, these interventions necessitate thorough societal discussion and consensus before approval, particularly regarding long-term safety, intergenerational effects, and potential misuse. Clear guidelines must be established to define which diseases are appropriate for gene-editing therapies; otherwise, indiscriminate application may raise serious concerns, including those related to enhancement or eugenics. From a regulatory perspective, the lack of unified international standards and the complexity of monitoring genomeediting outcomes highlight the need for robust oversight frameworks.
Future progress in CRISPR-based pain therapeutics will require not only the refinement of the CRISPR system itself but also the development of complementary technologies. One critical area is the delivery method. Recent advances include virusbased systems such as virus-like particles [103,104], DIRECTED (Delivery to Intended Recipient Cells Through Envelope Design) [105], and Cas9-packaging enveloped delivery vehicles [106], as well as nonviral strategies using biocompatible lipid [107] or lipid-like nanoparticles [108,109]. Another essential component is the optimization of guide RNA (gRNA) design. Machine learning–based tools have been developed to predict gRNA efficiency and editing outcomes, enabling more precise and efficient gene modulation. Lastly, the identification of spinal pain-specific biomarkers is crucial for enabling patient stratification and targeted therapeutic approaches. Recent studies have begun to explore potential biomarkers such as CCL5, OPRL1, SST, and CXCL13 in the context of chronic pain [110]. These advancements, when integrated with CRISPR-based technologies, may accelerate the development of personalized, effective treatments for spinal and neuropathic pain.
Looking ahead, the therapeutic landscape for chronic pain may benefit from combinatorial strategies that integrate CRISPR-based gene editing with advanced neuromodulation techniques. For example, the convergence of CRISPR and optogenetics could allow for temporally precise control of gene expression in pain-relevant circuits. Additionally, targeting non-neuronal cell types such as astrocytes and microglia may provide new entry points for modulating neuroinflammation and central sensitization. Finally, integrating gene-editing approaches with real-time spinal cord neuromodulation platforms—such as electrical stimulation of ascending pathways—could enable dynamic, feedback-driven therapeutic systems tailored to individual pain profiles. These interdisciplinary approaches hold promise for expanding the precision and efficacy of future pain interventions.
With the continuous expansion of viable molecular targets and advancements in gene-editing methodologies, the field of chronic pain management is poised for significant progress. Based on the research and technological innovations discussed in this review, CRISPR-based gene therapy is anticipated to play a pivotal role in shaping a new paradigm for more precise and effective pain treatment strategies.
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