Core-shell mesoporous silica nanoparticles for gene delivery: Desing principles and strategies to overcome biological barriers

Abstract

Non-viral nanocarriers are increasingly adopted as safer alternatives to viral vectors for gene delivery, enabling scalability and improved manufacturability. Among them, mesoporous silica nanoparticles (MSiNPs) offer a promising platform due to their structural properties and versatility. This work extracts critical trends of recent literature to seek standardized design rules for MSiNPs-based systems, focusing on the optimisation of the proposed core-shell model architecture. The analysis examines the silica-based matrix core, which determines the morphology and nano-pore structure, and the engineered shell, which modulates the bio-interface through charge inversion, stimulus-responsive release mechanisms, protein corona regulation and active targeting. A formalized “golden-trio” concept is proposed highlighting the interdependence among the physico-chemical properties of MSiNPs, cellular uptake, and intracellular trafficking—key determinants of transfection efficiency. The study evaluates the adaptability of MSiNPs enabling stabilization and vectorization of diverse payloads, including small interfering RNAs and microRNAs for gene silencing, plasmid DNA for expression, and CRISPR/Cas9 systems for genome editing. Strategies for targeting specific cell types by matching surface functionalisation to the genetic payload are discussed, along with the potential for co-administration and theranostic applications to achieve synergistic results. This review concludes that designing the physico-chemical properties of MSiNPs through an integrated approach—combining the core matrix with the precise modulation of the shell surface chemistry to overcome biological barriers and guarantee reproducibility and patient safety—is essential for unlocking their clinical potential in gene therapy.

Introduction

1.1. Gene delivery: key concepts, targets, benefits and current strategies

Gene delivery refers to the introduction of exogenous genetic material into mammalian cells with the aim of modulating cellular function for research or therapeutic purposes [1]. Over the past decades, gene delivery has evolved from a conceptual experimental approach into a clinically relevant strategy capable of addressing a wide spectrum of diseases, ranging from rare monogenic disorders to complex and widespread conditions such as cardiovascular diseases, cancer, and hematological malignancies [2]. By acting directly at the genetic level, gene-based therapies enable highly targeted interventions that underpin modern precision medicine. Depending on the therapeutic objective, gene delivery strategies may involve plasmid DNA, messenger RNA (mRNA), or regulatory RNA species such as small interfering RNA (siRNA) and microRNA (miRNA), each presenting distinct structural and biological requirements for effective delivery and intracellular activity [2]. These approaches offer clear advantages, including high specificity and the possibility of sustained or long-lasting therapeutic effects. However, their clinical success is largely determined by the delivery vector rather than by the genetic cargo itself. Major challenges include safety concerns related to immune activation, constraints on cargo size and stability, and the difficulty of achieving efficient and controlled intracellular delivery [1], [2].

Current gene delivery platforms are broadly classified into viral and non-viral systems. Viral vectors, including adenoviral, lentiviral, and adeno-associated viral (AAV) vectors, have demonstrated high transduction efficiency and have been successfully translated into several approved clinical therapies [3]. Among these, AAV-based vectors are particularly attractive due to their relatively low immunogenicity, cell-specific targeting mediated by different serotypes, and low risk of genomic integration. Nevertheless, viral strategies present notable limitations, including restricted DNA packaging capacity, technical challenges associated with large-scale manufacturing, and the presence of pre-existing or treatment-induced neutralizing antibodies that may significantly reduce transduction efficiency, especially upon repeated administration [4], [5]. In parallel, non-viral gene delivery systems have been extensively explored as safer and more versatile alternatives. These approaches, which trace their origins to early studies on DNA-mediated cellular uptake [1], rely on synthetic carriers to transport genetic material without the use of viral components. Although traditionally associated with lower transfection efficiencies, non-viral systems offer important advantages, including improved safety profiles, greater flexibility in cargo design, and fewer constraints related to immunogenicity and manufacturing. As a result, considerable research efforts have focused on the development of advanced synthetic vectors capable of improving delivery efficiency while maintaining biocompatibility.

Among non-viral platforms, nanoparticle-based delivery systems have emerged as particularly promising strategies. Lipidic, polymeric, and inorganic nanoparticles have been investigated for the delivery of plasmid DNA and regulatory nucleic acids in a variety of biomedical applications [6], [7]. In this context, mesoporous silica-based nanomaterials have attracted increasing attention due to their favourable biocompatibility, tunable physicochemical properties, and versatile surface functionalization. These attributes enable controlled cargo loading, protection of nucleic acids, and tailored interactions with biological environments, positioning silica-based systems as attractive candidates for next-generation non-viral gene delivery platforms.
Ultimately, the effectiveness of both viral and non-viral gene delivery systems is governed by their ability to overcome multiple biological barriers, including efficient cellular uptake and intracellular processing. These challenges are particularly critical for nucleic acid cargos such as mRNA and miRNA and motivate the rational design of delivery systems capable of addressing cellular and endosomal barriers, as discussed in the following sections.

1.2. Emerging nanocarriers for gene delivery

Despite the significant therapeutic potential of gene delivery, the efficient transport of nucleic acids remains a major challenge due to their intrinsic physicochemical properties, including large size, negative charge, and susceptibility to enzymatic degradation [8]. Consequently, effective gene delivery critically depends on the availability of delivery systems capable of protecting the genetic cargo, promoting cellular uptake, and enabling controlled intracellular processing. In this context, nanomedicine has driven the development of nanoscale delivery platforms with high surface-to-volume ratios, offering enhanced cargo loading, surface functionalization, and the possibility to integrate multiple functionalities within a single carrier. Over the last two decades, mesoporous silica nanoparticles (MSiNPs) have emerged as promising non-viral nanocarriers for gene delivery owing to their high loading capacity, tunable mesostructure, and chemically tailorable surface. These properties enable the rational design of delivery systems capable of interacting with biological environments in a controlled manner. Beyond conventional therapeutic approaches, nanoparticle-based systems also provide multifunctional platforms for advanced applications such as theranostics, where diagnostic and therapeutic functions can be combined within a single nanostructure [9].

As gene delivery technologies continue to evolve, the development of efficient nanocarriers cannot be decoupled from this broader technological context. Historically, viral vectors represented the first effective gene delivery platforms and were widely explored for this purpose, mainly recombinant adeno-associated vectors (rAAV), which were approved for the treatment of several monogenic hereditary diseases, including spinal muscular atrophy (SMA), Duchenne muscular dystrophy (DMD), and haemophilia A and B [10], [11], [12], [13], as well as showing promise in clinical trials [11], [14]. These approaches exploit the tropism of various serotypes to transfer therapeutic genetic material into target tissues such as the liver or muscle, where the transgene remains predominantly in episomal form, ensuring prolonged expression. However, the use of high doses of vector, often necessary to achieve supraphysiological protein levels or sufficient systemic cross-correction, has raised safety and sustainability concerns [14]. Viral vectors face significant obstacles, primarily marked immunogenicity, characterized by the presence of pre-existing neutralising antibodies that limit the treatable patient population, as well as the development of innate and adaptive immune responses post-infusion [11], [12]. Such responses can manifest as hepatotoxicity (elevated transaminases) and thrombotic microangiopathy (TMA) mediated by complement system activation. In addition, challenges associated with structural complexity and product heterogeneity require rigorous quality controls to monitor impurities such as empty capsids or viral aggregates [10], while large-scale production remains difficult and costly. Collectively, these limitations have driven sustained efforts toward the development of safer, more scalable, and less immunogenic non-viral gene delivery systems, highlighting the urgent need for alternatives that are suitable for broader and chronic clinical applications.

Collectively, these limitations have driven sustained efforts toward the development of safer, more scalable, and less immunogenic non-viral gene delivery systems. In this context, nanocarrier-based platforms—including lipid-based [15], polymeric [16], and inorganic systems [17]—have emerged as promising alternatives, offering improved safety profiles, reduced immunogenicity, scalable production, and versatile chemical design for gene delivery [18]. To date, the lipid-based vectors—lipid nanoparticles (LNPs)— have largely driven the success of non-viral gene delivery and their historical milestones illustrate both progress and limitations. Lipofectin was the first commercially available transfection reagent capable of entrapping and expressing DNA, and small interfering RNA-loaded LNPs (Onpattro) became the first FDA-approved small interfering RNA (siRNA) therapy for amyloidosis, demonstrating clinical efficacy and safety [19]. This was further evidenced during the global mRNA vaccination campaign, where Moderna and Pfizer successfully deployed two LNP-based mRNA vaccines [20]. Although LNPs have achieved significant achievements, their inherent drawbacks—such as stability issues, limited cargo versatility, and potential immunogenicity—underscore the need for superior alternatives. In this context, inorganic non-viral vectors, particularly MSiNPs, have emerged as highly promising due to their unique properties and tunable architectures [21], [22], [23]. Nevertheless, their complex physicochemical structure and biological interactions require integrated strategies for safety, efficacy, and quality from early development stages [24].

1.3. Non-viral vectors – The promise of mesoporous silica nanoparticles

As noted above, LNPs present both strengths and limitations: they protect genetic cargo from degradation, facilitate cellular uptake, and promote efficient endosomal escape due to their tailored composition [25], [26]. Nonetheless, LNPs exhibit intrinsic physical instability, including fusion and aggregation, which can result in premature payload loss. Polymorphic transitions within their solid lipid structure further compromise long-term performance. Additionally, large-scale manufacturing of LNPs requires complex and costly technologies, and the widespread use of polyethylene glycol (PEG) for stabilization has raised concerns due to the “PEG dilemma” [27], encompassing accelerated blood clearance and hypersensitivity reactions, including anaphylaxis [28], [29].

Other polymers and peptides have also been investigated as non-viral vectors, polyethyleneimine (PEI), has the exceptional ability to condense DNA and has been exploited to promote endosomal escape via the “proton sponge” effect. However, the use of PEI presents insurmountable barriers to systemic application [30] as its high positive charge density causes severe toxicity [31]. The evolution towards biodegradable polymers, such as poly-beta-aminoesters (PBAEs) and polyoxazolines, has attempted to mitigate these risks by introducing hydrolysable bonds that allow the carrier to degrade into less toxic by-products after release of the payload [32]. However, these often suffer from limited stability in the bloodstream and complex chemical synthesis to balance hydrophobicity and cationic charge, making large-scale reproducibility difficult. In parallel, cell-penetrating peptides (CPPs) and fusogenic peptides have demonstrated an excellent ability to cross biological membranes and specifically target tissues [33]. However, their Achilles heel lies in their loading capacity and stability. Being small molecules, peptides struggle to condense large genetic plasmids without forming unstable aggregates; moreover, their biological nature makes them susceptible to rapid degradation by serum proteases [34]. As a result, peptides are rarely effective as stand-alone carriers, finding greater utility as auxiliary ligands rather than primary carriers.

While LNPs and liposomes have historically dominated the nanomedicine field, their intrinsic limitations present significant hurdles for consistent gene delivery. The reliance on lipids often leads to either therapeutic levels that are not enough for treating the disease or the need to administrate large amounts of lipids to reach those therapeutic levels [35]. Furthermore, the loading processes for lipid vectors can be highly problematic: if the loading process is inefficient, there would be a waste of the therapeutic agent and the need for an additional stage for removing the unentrapped drug. Therefore, in some cases, the use of certain liposomal formulations might become inefficient and uneconomical [35]. To address some of these limitations, MSiNPs offer a structurally robust alternative. Unlike lipid bilayers, the mesoporous framework of MSiNPs enables the loading, storage, and controlled release of therapeutic cargo under programmable conditions, which is advantageous for drug delivery applications [36]. In addition, MSiNPs solve the batch-to-batch variability prevalent in lipid vectors; independent studies show that the reproducibility of the loading process has been demonstrated through different loading procedures in different labs resulting in consistent encapsulation efficiency in all cases [35]. Their clinical viability is further supported by excellent biocompatibility profiles, as their intrinsic mesoporosity should accelerate the bioerosion and breakdown processes to small secretable fragments and final dissolution to silicic acid [35]. For gene delivery applications specifically, functionalized MSiNPs (e.g., chitosan-coated) effectively bind negatively charged nucleic acids, enhancing cellular uptake and notably improving transfection efficiency [36].

It is in this context of “imperfect compromises” that MSiNPs emerge as a superior synthetic solution representing not only an alternative, but also a technological evolution that integrates structural robustness, biological safety and functionalisation versatility, filling the gaps left open by lipidic, polymeric and peptide carriers. Their rigid inorganic framework prevents premature release and ensures mechanical and chemical stability, safeguarding genetic cargo under harsh biological condition [37], [38]. Key advantages include: i) high surface area, enabling encapsulation of large nucleic acid loads and co-delivery of therapeutic agents or imaging probes; ii) biocompatibility and biodegradability, as they degrade into non-toxic silicic acid excreted via renal clearance; iii) versatile functionalization, facilitated by surface silanol groups for covalent ligand anchoring and active targeting; iv) controlled release, achievable through pore capping with gatekeeper molecules responsive to specific stimuli. Furthermore, the inherent porosity of MSiNPs has been associated with reduced cytotoxicity [39] and hemolysis [22]. Table 1 comparatively summarizes the main properties and features of MSiNPs and the other non-viral vectors discussed.

Table 1. Critical comparison of mesoporous silica nanoparticles and other non-viral vectors for gene therapy.

When considering MSiNPs, a comprehensive and critical assessment of their design principles for gene therapy—spanning nearly two decades of research—remains lacking. Although a recent review by Huq et al. [19] has explored how MSiNPs may fit into the future landscape of gene therapy, we contend that the establishment of standardized guidelines addressing key physicochemical parameters is essential to accelerate clinical translation. These parameters include the mesoporous silica core matrix structure, the surface charge, and the ligand functionalization (considering both density and spatial distribution) in relation to specific therapeutic applications [40].Therefore, the primary objective of this critical analysis is to determine whether standard design principles can be established for MSiNPs across specific gene therapy contexts. This work adopts a material-centric “core-shell” perspective to decouple the structural requirements for cargo loading from the interfacial requirements for biological navigation. The review maps the evolution of MSiNPs technology and elucidates biological interactions governed by surface engineering, with a focus on controlled variations in pore size for gene loading, surface charge to enhance internalization and endosomal escape. Although at the preclinical stage, MSiNPs still address many limitations for efficient and safe gene delivery [41], [42]. By outlining predictive relationships for a clinically translatable platform, this work aims to demonstrate that MSiNPs are not merely passive carriers but programmable molecular vehicles [23], [43], capable of overcoming biological barriers, representing a robust and customizable solution to advance precision medicine.

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Giorgia Mano, Aránzazu Díaz-Cuenca, Core-shell mesoporous silica nanoparticles for gene delivery: Desing principles and strategies to overcome biological barriers, Journal of Drug Delivery Science and Technology, 2026, 108591, ISSN 1773-2247, https://doi.org/10.1016/j.jddst.2026.108591.

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