A machine learning approach to predict cellular uptake of pBAE polyplexes.

The delivery of genetic material (DNA and RNA) to cells can cure a wide range of diseases but is limited by the delivery efficiency of the carrier system. Poly ß-amino esters (pBAEs) are promising polymer-based vectors that form polyplexes with negatively charged oligonucleotides, enabling cell membrane uptake and gene delivery. pBAE backbone polymer chemistry, as well as terminal oligopeptide modifications, define cellular uptake and transfection efficiency in a given cell line, along with nanoparticle size and polydispersity. Moreover, uptake and transfection efficiency of a given polyplex formulation also vary from cell type to cell type. Therefore, finding the optimal formulation leading to high uptake in a new cell line is dictated by trial and error, and requires time and resources. Machine learning (ML) is an ideal in silico screening tool to learn the non-linearities of complex data sets, like the one presented herein, with the aim of predicting cellular internalisation of pBAE polyplexes. A library of pBAE nanoparticles was fabricated and the uptake studied in 4 different cell lines, on which various ML models were successfully trained. The best performing models were found to be gradient-boosted trees and neural networks. The gradient-boosted trees model was then analysed using SHapley Additive exPlanations, to interpret the model and gain an understanding into the important features and their impact on the predicted outcome.

Current progress in bionanomaterials to modulate the epigenome.

Recent advances in genomics during the 1990s have made it possible to study and identify genetic and epigenetic responses of cells and tissues to various drugs and environmental factors. This has accelerated the number of targets available to treat a range of diseases from cancer to wound healing disorders. Equally interesting is the understanding of how bio- and nanomaterials alter gene expression through epigenetic mechanisms, and whether they have the potential to elicit a positive therapeutic response without requiring additional biomolecule delivery. In fact, from a cell's perspective, a biomaterial is nothing more than an environmental factor, and so it has the power to epigenetically modulate gene expression of cells in contact with it. Understanding these epigenetic interactions between biomaterials and cells will open new avenues in the development of technologies that can not only provide biological signals (i.e. drugs, growth factors) necessary for therapy and regeneration, but also intimately interact with cells to promote the expression of genes of interest. This review article aims to summarise the current state-of-the-art and progress on the development of bio- and nanomaterials to modulate the epigenome.

Polyplex-Loaded Hydrogels for Local Gene Delivery to Human Dermal Fibroblasts.

Impaired cutaneous healing leading to chronic wounds affects between 2 and 6% of the total population in most developed countries and it places a substantial burden on healthcare budgets. Current treatments involving antibiotic dressings and mechanical debridement are often not effective, causing severe pain, emotional distress, and social isolation in patients for years or even decades, ultimately resulting in limb amputation. Alternatively, gene therapy (such as mRNA therapies) has emerged as a viable option to promote wound healing through modulation of gene expression. However, protecting the genetic cargo from degradation and efficient transfection into primary cells remain significant challenges in the push to clinical translation. Another limiting aspect of current therapies is the lack of sustained release of drugs to match the therapeutic window. Herein, we have developed an injectable, biodegradable and cytocompatible hydrogel-based wound dressing that delivers poly(ß-amino ester)s (pBAEs) nanoparticles in a sustained manner over a range of therapeutic windows. We also demonstrate that pBAE nanoparticles, successfully used in previous in vivo studies, protect the mRNA load and efficiently transfect human dermal fibroblasts upon sustained release from the hydrogel wound dressing. This prototype wound dressing technology can enable the development of novel gene therapies for the treatment of chronic wounds.

Spatiotemporal delivery of bioactive molecules for wound healing using stimuli-responsive biomaterials.

Wound repair is a fascinatingly complex process, with overlapping events in both space and time needed to pave a pathway to successful healing. This additional complexity presents challenges when developing methods for the controlled delivery of therapeutics for wound repair and tissue engineering. Unlike more traditional applications, where biomaterial-based depots increase drug solubility and stability in vivo, enhance circulation times, and improve retention in the target tissue, when aiming to modulate wound healing, there is a desire to enable localised, spatiotemporal control of multiple therapeutics. Furthermore, many therapeutics of interest in the context of wound repair are sensitive biologics (e.g. growth factors), which present unique challenges when designing biomaterial-based delivery systems. Here, we review the diverse approaches taken by the biomaterials community for creating stimuli-responsive materials that are beginning to enable spatiotemporal control over the delivery of therapeutics for applications in tissue engineering and regenerative medicine.

Prolonged Local In Vivo Delivery of Stimuli-Responsive Nanogels That Rapidly Release Doxorubicin in Triple-Negative Breast Cancer Cells.

Triple negative breast cancer patients remain with chemotherapy as their only viable therapeutic option. However, the toxicity of available anticancer drugs and their inefficient delivery have limited the development of effective chemotherapy administration protocols and combination therapies. Drug delivery devices that can properly target chemotherapy to the right cells with efficient cancer-cell killing may play a vital role in eliminating triple-negative breast cancer. While systemic delivery results in low drug accumulation at the tumor site and for a short period of time, local delivery enables sustained drug release. However, a system that is able to provide rapid, yet prolonged action, would enable efficient tumor elimination. Herein, the development of dual-sensitive nanogels is described that are designed to rapidly dislodge the chemotherapy drug, doxorubicin, inside cancer cells through dual-sensitive action-pH and redox sensitivities-enabling efficient cancer-cell killing while eliminating systemic side effects. Their embedding within a hydrogel injected next to a tumor in a triple-negative breast-cancer mouse model enables prolonged release of the drug with instantaneous action when inside the cells resulting in efficacious tumor elimination compared to sustained local delivery only. This technology can be used for the delivery of combination therapies and for the treatment of other solid tumors.

Biologically Inspired, Cell-Selective Release of Aptamer-Trapped Growth Factors by Traction Forces.

Biomaterial scaffolds that are designed to incorporate dynamic, spatiotemporal information have the potential to interface with cells and tissues to direct behavior. Here, a bioinspired, programmable nanotechnology-based platform is described that harnesses cellular traction forces to activate growth factors, eliminating the need for exogenous triggers (e.g., light), spatially diffuse triggers (e.g., enzymes, pH changes), or passive activation (e.g., hydrolysis). Flexible aptamer technology is used to create modular, synthetic mimics of the Large Latent Complex that restrains transforming growth factor-ß1 (TGF-ß1). This flexible nanotechnology-based approach is shown here to work with both platelet-derived growth factor-BB (PDGF-BB) and vascular endothelial growth factor (VEGF-165), integrate with glass coverslips, polyacrylamide gels, and collagen scaffolds, enable activation by various cells (e.g., primary human dermal fibroblasts, HMEC-1 endothelial cells), and unlock fundamentally new capabilities such as selective activation of growth factors by differing cell types (e.g., activation by smooth muscle cells but not fibroblasts) within clinically relevant collagen sponges.

Designing Hydrogels for On-Demand Therapy.

Systemic administration of therapeutic agents has been the preferred approach to treat most pathological conditions, in particular for cancer therapy. This treatment modality is associated with side effects, off-target accumulation, toxicity, and rapid renal and hepatic clearance. Multiple efforts have focused on incorporating targeting moieties into systemic therapeutic vehicles to enhance retention and minimize clearance and side effects. However, only a small percentage of the nanoparticles administered systemically accumulate at the tumor site, leading to poor therapeutic efficacy. This has prompted researchers to call the status quo treatment regimen into question and to leverage new delivery materials and alternative administration routes to improve therapeutic outcomes. Recent approaches rely on the use of local delivery platforms that circumvent the hurdles of systemic delivery. Local administration allows delivery of higher "effective" doses while enhancing therapeutic molecules' stability, minimizing side effects, clearance, and accumulation in the liver and kidneys following systemic administration. Hydrogels have proven to be highly biocompatible materials that allow for versatile design to afford sensing and therapy at the same time. Hydrogels' chemical and physical versatility can be exploited to attain disease-triggered in situ assembly and hydrogel programmed degradation and consequent drug release, and hydrogels can also serve as a biocompatible depot for local delivery of stimuli-responsive therapeutic cargo. We will focus this Account on the hydrogel platform that we have developed in our lab, based on dendrimer amine and dextran aldehyde. This hydrogel is disease-responsive and capable of sensing the microenvironment and reacting in a graded manner to diverse pathologies to render different properties, including tissue adhesion, biocompatibility, hydrogel degradation, and embedded drug release profile. We also studied the degradation kinetics of our stimuli-responsive materials in vivo and analyzed the in vitro conditions under which in vitro-in vivo correlation is attained. Identifying key parameters in the in vivo microenvironment under healthy and disease conditions was key to attaining that correlation. The adhesive capacity of our dendrimer-dextran hydrogel makes it optimal for localized and sustained release of embedded drugs. We demonstrated that it affords the delivery of a range of therapeutics to combat cancer, including nucleic acids, small molecules, and antibody drugs. As a depot for local delivery, it allows a high dose of active biomolecules to be delivered directly at the tumor site. Immunotherapy, a recently blooming area in cancer therapy, may exploit stimuli-responsive hydrogels to impart systemic effects following localized therapy. Local delivery would enable release of the proper drug dose and improve drug bioavailability where needed at the same time creating memory and exerting the therapeutic effect systemically. This Account highlights our perspective on how local and systemic therapies provided by stimuli-responsive hydrogels should be used to impart more precise, long-lasting, and potent therapeutic outcomes.

Local microRNA delivery targets Palladin and prevents metastatic breast cancer.

Metastasis is the primary cause for mortality in breast cancer. MicroRNAs, gene expression master regulators, constitute an attractive candidate to control metastasis. Here we show that breast cancer metastasis can be prevented by miR-96 or miR-182 treatment, and decipher the mechanism of action. We found that miR-96/miR-182 downregulate Palladin protein levels, thereby reducing breast cancer cell migration and invasion. A common SNP, rs1071738, at the miR-96/miR-182-binding site within the Palladin 3'-UTR abolishes miRNA:mRNA binding, thus diminishing Palladin regulation by these miRNAs. Regulation is successfully restored by applying complimentary miRNAs. A hydrogel-embedded, gold-nanoparticle-based delivery vehicle provides efficient local, selective, and sustained release of miR-96/miR-182, markedly suppressing metastasis in a breast cancer mouse model. Combined delivery of the miRNAs with a chemotherapy drug, cisplatin, enables significant primary tumour shrinkage and metastasis prevention. Our data corroborate the role of miRNAs in metastasis, and suggest miR-96/miR-182 delivery as a potential anti-metastatic drug.

Local triple-combination therapy results in tumour regression and prevents recurrence in a colon cancer model.

Conventional cancer therapies involve the systemic delivery of anticancer agents that neither discriminate between cancer and normal cells nor eliminate the risk of cancer recurrence. Here, we demonstrate that the combination of gene, drug and phototherapy delivered through a prophylactic hydrogel patch leads, in a colon cancer mouse model, to complete tumour remission when applied to non-resected tumours and to the absence of tumour recurrence when applied following tumour resection. The adhesive hydrogel patch enhanced the stability and provided local delivery of embedded nanoparticles. Spherical gold nanoparticles were used as a first wave of treatment to deliver siRNAs against Kras, a key oncogene driver, and rod-shaped gold nanoparticles mediated the conversion of near-infrared radiation into heat, causing the release of a chemotherapeutic as well as thermally induced cell damage. This local, triple-combination therapy can be adapted to other cancer cell types and to molecular targets associated with disease progression.

Revisiting the 'One Material Fits All' Rule for Cancer Nanotherapy.

The promise of (nano)biomaterials for the treatment of cancer can only be realized following a comprehensive scrutiny of the tumor microenvironment. The generic use of 'inert' vehicles that deliver a specific cargo to treat a range of cancer types and disease states obeys the 'one material fits all' rule. However, this approach leads to suboptimal and unpredictable clinical outcomes. The key factors constructing the tumor milieu should guide the design of disease-responsive materials. Given the growing availability of nanomaterials for cancer therapy, a material that responds to each patient's needs and, hence, reacts in a graded manner based on disease cues, would pave the way to precision materials for cancer therapy.

Self-assembled RNA-triple-helix hydrogel scaffold for microRNA modulation in the tumour microenvironment.

The therapeutic potential of miRNA (miR) in cancer is limited by the lack of efficient delivery vehicles. Here, we show that a self-assembled dual-colour RNA-triple-helix structure comprising two miRNAs-a miR mimic (tumour suppressor miRNA) and an antagomiR (oncomiR inhibitor)-provides outstanding capability to synergistically abrogate tumours. Conjugation of RNA triple helices to dendrimers allows the formation of stable triplex nanoparticles, which form an RNA-triple-helix adhesive scaffold upon interaction with dextran aldehyde, the latter able to chemically interact and adhere to natural tissue amines in the tumour. We also show that the self-assembled RNA-triple-helix conjugates remain functional in vitro and in vivo, and that they lead to nearly 90% levels of tumour shrinkage two weeks post-gel implantation in a triple-negative breast cancer mouse model. Our findings suggest that the RNA-triple-helix hydrogels can be used as an efficient anticancer platform to locally modulate the expression of endogenous miRs in cancer.

Personalizing Biomaterials for Precision Nanomedicine Considering the Local Tissue Microenvironment.

New advances in (nano)biomaterial design coupled with the detailed study of tissue-biomaterial interactions can open a new chapter in personalized medicine, where biomaterials are chosen and designed to match specific tissue types and disease states. The notion of a "one size fits all" biomaterial no longer exists, as growing evidence points to the value of customizing material design to enhance (pre)clinical performance. The complex microenvironment in vivo at different tissue sites exhibits diverse cell types, tissue chemistry, tissue morphology, and mechanical stresses that are further altered by local pathology. This complex and dynamic environment may alter the implanted material's properties and in turn affect its in vivo performance. It is crucial, therefore, to carefully study tissue context and optimize biomaterials considering the implantation conditions. This practice would enable attaining predictable material performance and enhance clinical outcomes.

Implantable hydrogel embedded dark-gold nanoswitch as a theranostic probe to sense and overcome cancer multidrug resistance.

Multidrug resistance (MDR) in cancer cells is a substantial limitation to the success of chemotherapy. Here, we describe facile means to overcome resistance by silencing the multidrug resistance protein 1 (MRP1), before chemotherapeutic drug delivery in vivo with a single local application. Our platform contains hydrogel embedded with dark-gold nanoparticles modified with 5-fluorouracil (5-FU)-intercalated nanobeacons that serve as an ON/OFF molecular nanoswitch triggered by the increased MRP1 expression within the tumor tissue microenvironment. This nanoswitch can sense and overcome MDR prior to local drug release. The nanobeacons comprise a 5-FU intercalated DNA hairpin, which is labeled with a near-infrared (NIR) dye and a dark-quencher. The nanobeacons are designed to open and release the intercalated drug only upon hybridization of the DNA hairpin to a complementary target, an event that restores fluorescence emission due to nanobeacons conformational reorganization. Despite the cross-resistance to 5-FU, more than 90% tumor reduction is achieved in vivo in a triple-negative breast cancer model following 80% MRP1 silencing compared with the continuous tumor growth following only drug or nanobeacon administration. Our approach can be applied to reverse cross-resistance to other chemotherapeutic drugs and restore treatment efficacy. As a universal nanotheranostic probe, this platform can pave the way to early cancer detection and treatment.

Regulation of dendrimer/dextran material performance by altered tissue microenvironment in inflammation and neoplasia.

A "one material fits all" mindset ignores profound differences in target tissues that affect their responses and reactivity. Yet little attention has been paid to the role of diseased tissue on material performance, biocompatibility, and healing capacity. We assessed material-tissue interactions with a prototypical adhesive material based on dendrimer/dextran and colon as a model tissue platform. Adhesive materials have high sensitivity to changes in their environment and can be exploited to probe and quantify the influence of even subtle modifications in tissue architecture and biology. We studied inflammatory colitis and colon cancer and found not only a difference in adhesion related to surface chemical interactions but also the existence of a complex interplay that determined the overall dendrimer/dextran biomaterial compatibility. Compatibility was contextual, not simply a constitutive property of the material, and was related to the extent and nature of immune cells in the diseased environment present before material implantation. We then showed how to use information about local alterations of the tissue microenvironment to assess disease severity. This in turn guided us to an optimal dendrimer/dextran formulation choice using a predictive model based on clinically relevant conditions.

Hydrogel doped with nanoparticles for local sustained release of siRNA in breast cancer.

Of all the much hyped and pricy cancer drugs, the benefits from the promising siRNA small molecule drugs are limited. Lack of efficient delivery vehicles that would release the drug locally, protect it from degradation, and ensure high transfection efficiency, precludes it from fulfilling its full potential. This work presents a novel platform for local and sustained delivery of siRNA with high transfection efficiencies both in vitro and in vivo in a breast cancer mice model. siRNA protection and high transfection efficiency are enabled by their encapsulation in oligopeptide-terminated poly(ß-aminoester) (pBAE) nanoparticles. Sustained delivery of the siRNA is achieved by the enhanced stability of the nanoparticles when embedded in a hydrogel scaffold based on polyamidoamine (PAMAM) dendrimer cross-linked with dextran aldehyde. The combination of oligopeptide-terminated pBAE polymers and biodegradable hydrogels shows improved transfection efficiency in vivo even when compared with the most potent commercially available transfection reagents. These results highlight the advantage of using composite materials for successful delivery of these highly promising small molecules to combat cancer.

Natural tissue microenvironmental conditions modulate adhesive material performance.

We designed and optimized tissue-responsive adhesive materials by matching material and tissue properties. A two-component material based on dextran aldehyde and dendrimer amine provides a cohesive gel through aldehyde-amine cross-linking and an adhesive interface created by a dextran aldehyde-selective reaction with tissue amines. By altering aldehyde-amine chemistry, we examined how variations in tissue surfaces (serosal amine density in the duodenum, jejunum, and ileum) affect interactions with adhesive materials of varied compositions (aldehyde content). Interestingly, the same adhesive formulation reacts differentially with the three regions of the small intestine as a result of variation in the tissue amine density along the intestinal tract, affecting the tissue-material interfacial morphology, adhesion strength, and adhesive mechanical properties. Whereas tissues provide chemical anchors for interaction with materials, we were able to tune the adhesion strength for each section of the small intestine tissue by altering the adhesive formulation using a two-component material with flexible variables aimed at controlling the aldehyde/amine ratio. This tissue-specific approach should be applied to the broad spectrum of biomaterials, taking into account specific microenvironmental conditions in material design.

In vivo and in vitro tracking of erosion in biodegradable materials using non-invasive fluorescence imaging.

The design of erodible biomaterials relies on the ability to program the in vivo retention time, which necessitates real-time monitoring of erosion. However, in vivo performance cannot always be predicted by traditional determination of in vitro erosion, and standard methods sacrifice samples or animals, preventing sequential measures of the same specimen. We harnessed non-invasive fluorescence imaging to sequentially follow in vivo material-mass loss to model the degradation of materials hydrolytically (PEG:dextran hydrogel) and enzymatically (collagen). Hydrogel erosion rates in vivo and in vitro correlated, enabling the prediction of in vivo erosion of new material formulations from in vitro data. Collagen in vivo erosion was used to infer physiologic in vitro conditions that mimic erosive in vivo environments. This approach enables rapid in vitro screening of materials, and can be extended to simultaneously determine drug release and material erosion from a drug-eluting scaffold, or cell viability and material fate in tissue-engineering formulations.