Exploring the Impact of mRNA Modifications on Translation Efficiency and Immune Tolerance to Self-Antigens.

Therapeutic modified mRNAs are being developed for a broad range of human diseases. However, the impact of potential miscoding of modified mRNAs on self-tolerance remains unknown. Additionally, more studies are needed to explore the effects of nucleoside alkylation on translation. While all six tested modifications are tolerated as substrates by T7 RNA polymerase and inhibited mRNA immunogenicity, the translation efficiency varied significantly depending on the type of modification. In contrast to methylation, ethylation at the N1 position of pseudouridine (Ψ) hindered translation, suggesting that the C5-C1' glycosidic bond alone is not a critical element for high translation. Inhibition of mRNA translation was also observed with 5-methoxyuridine modification. However, this inhibition was partially alleviated through the optimization of mRNA coding sequences. BALB/c mice immunized with syngeneic ψ-modified mRNA encoding for Wilms' tumor antigen-1 (WT1) developed a low but significant level of anti-WT1 IgG antibodies compared to those immunized with either unmodified or N1-methyl ψ-modified mRNA. Overall, the data indicate that adding a simple ethyl group (-CH2CH3) at the N1 position of ψ has a major negative effect on translation despite its reduced immunogenicity. Additionally, mRNA containing Ψ may alter translation fidelity at certain codons, which could lead to a breakdown of immune tolerance to self-antigens. This concern should be taken into account during gene replacement therapies, although it could benefit mRNA-based vaccines by generating a diverse repertoire of antigens.

How the initial discovery of modified RNA enabled evasion of innate immune responses and facilitated the development of RNA therapeutics.

Besides being the physical link between DNA and proteins, RNAs play several other key roles, including RNA catalysis and gene regulation. Recent advances in the design of lipid nanoparticles have facilitated the development of RNA-based therapeutics. However, chemically and in vitro transcribed RNAs can activate innate immunity, leading to the production of proinflammatory cytokines and interferons, a response similar to the one induced by viral infections. Since these responses are undesirable for certain therapeutic applications, it is important to develop ways to block the sensing of exogenous RNAs by immune cells, such as monocytes, macrophages and dendritic cells. Fortunately, RNA sensing can be blocked by chemical modifications of certain nucleotides, particularly uridine, a finding that has facilitated the development of RNA-based therapeutics such as small interfering RNAs and mRNA vaccines. Here, I provide a backstory on how improved understanding of RNA sensing by innate immunity can be applied to develop more effective RNA therapeutics.

Tumor-Associated Macrophage Subsets: Shaping Polarization and Targeting.

The tumor microenvironment (TME) is a critical regulator of tumor growth, progression, and metastasis. Among the innate immune cells recruited to the tumor site, macrophages are the most abundant cell population and are present at all stages of tumor progression. They undergo M1/M2 polarization in response to signals derived from TME. M1 macrophages suppress tumor growth, while their M2 counterparts exert pro-tumoral effects by promoting tumor growth, angiogenesis, metastasis, and resistance to current therapies. Several subsets of the M2 phenotype have been observed, often denoted as M2a, M2b, M2c, and M2d. These are induced by different stimuli and differ in phenotypes as well as functions. In this review, we discuss the key features of each M2 subset, their implications in cancers, and highlight the strategies that are being developed to harness TAMs for cancer treatment.

Antibody Surface Profiling Identifies Glycoforms in Multiple Myeloma as Targets for Immunotherapy: From Antibody Derivatives to Mimetic Peptides for Killing Tumor Cells.

Despite therapeutic advances in recent years, there are still unmet medical needs for patients with multiple myeloma (MM). Hence, new therapeutic strategies are needed. Using phage display for screening a large repertoire of single chain variable fragments (scFvs), we isolated several candidates that recognize a heavily sulfated MM-specific glycoform of the surface antigen syndecan-1 (CD138). One of the engineered scFv-Fc antibodies, named MM1, activated NK cells and induced antibody-dependent cellular cytotoxicity against MM cells. Analysis of the binding specificity by competitive binding assays with various glycan ligands identified N-sulfation of glucosamine units as essential for binding. Additionally, site-directed mutagenesis revealed that the amino acids arginine and histidine in the complementarily determining regions (CDRs) 2 and 3 of the heavy chain are important for binding. Based on this observation, a heavy-chain antibody, known as a nanobody, and a peptide mimicking the CDR loop sequences were designed. Both variants exhibited high affinity and specificity to MM cells as compared to blood lymphocytes. Specific killing of MM cells was achieved by conjugating the CDR2/3 mimic peptide to a pro-apoptotic peptide (KLAKLAK)2. In a co-culture model, the fusion peptide killed MM cells, while leaving normal peripheral blood mononuclear cells unaffected. Collectively, the development of antibodies and peptides that detect tumor-specific glycoforms of therapeutic targets holds promise for improving targeted therapies and tumor imaging.

Precision Killing of M2 Macrophages with Phage-Displayed Peptide-Photosensitizer Conjugates.

Among the immunosuppressive cells recruited to the tumor microenvironment, macrophages are particularly abundant and involved in angiogenesis, metastasis, and resistance to current cancer therapies. A strategy that simultaneously targets tumor cells and macrophages, particularly pro-tumoral M2 macrophages, would have significant clinical impact for various types of solid malignancies. By the use of phage display technology, we have recently developed a synthetic peptide, named NW, which binds to M1 and M2 macrophages with high affinity. Additional affinity selection on M2 macrophages identified only dominant peptides whose binding motifs are similar to that of the NW peptide. To reduce the frequency of selecting such dominating peptides, the peptide library was affinity selected on M2 macrophages blocked with NW peptide. This approach resulted in the selection of peptides that bind to M2, but not M1 macrophages. To explore the therapeutic potential of the selected peptides, the M13 phage-displayed peptides were conjugated to the photosensitizer IR700, which has been used for cancer photoimmunotherapy. The phage displaying a dominant peptide (SPILWLNAPPWA) killed both M1 and M2 macrophages, while those displaying the M2-specific peptides killed M2 macrophages only upon near-infrared light exposure. A significant fraction of the M2 macrophages were also killed with the untargeted M13 phage-IR700 conjugates. Hence, M2 macrophages can also be selectively targeted by the wild type M13 phage, which displayed a significant tropism to these cells. The benefits of this photoimmunotherapy include an automatic self-targeting ability of the wild type M13 phage, and the option of genetic manipulation of the phage genome to include tumor targeting peptides, allowing the killing of both M2 macrophages and cancer cells.

Structural Requirements for the Binding of a Peptide to Prohibitins on the Cell Surface of Monocytes/Macrophages.

The screening of phage peptide libraries resulted in the identification of a sequence (named NW peptide, NWYLPWLGTNDW) that specifically binds to human monocytes and macrophages. Although the NW peptide can be used for the targeted delivery of therapeutics without knowledge of its receptor(s), the identification of-its binding partners will support future clinical applications-Here, we used the biotinylated NW peptide for cross-linking cell surface receptor(s) on live cells or as bait in pull-down assays with membrane proteins isolated from monocytes or human THP-1 cells differentiated into macrophages. Proteomic analysis of the captured proteins identified cell surface prohibitins (PHB1 and PHB2) and modified albumin as binding partners. Using flow cytometry and pull-down methods, we demonstrated that PHB1 and PHB2 interact directly with the NW peptide. Confocal imaging showed co-localization of the peptide with PHB1 on the surface of monocytes. Single replacement of either tryptophan or leucine with alanine completely inhibited binding, whereas the replacement of asparagine at position 1 or 10 and aspartic acid at position 11 with alanine did not affect the binding of the peptide variants. Neutral amino acid replacement of tryptophan at positions 2, 6, and 12 with tyrosine or phenylalanine also abolished the binding, implying that the indole ring of tryptophan is indispensable for the NW peptide to bind. Overall, the data suggest that membrane-associated prohibitins might be a useful target for the delivery of therapeutics to monocytes/macrophages and that tryptophan and leucine are key residues for peptide binding.

Correction: Sioud et al. Evaluation of In Vitro Phototoxicity of a Minibody-IR700 Conjugate Using Monolayer and Multicellular Tumor Spheroid Models. Cancers 2021, 13, 3356.

The authors wish to make the following corrections to this paper [...].

Evaluation of In Vitro Phototoxicity of a Minibody-IR700 Conjugate Using Cell Monolayer and Multicellular Tumor Spheroid Models.

Photodynamic therapy (PDT) is a treatment strategy that utilizes photosensitizers (PSs) and light of a specific wavelength to kill cancer cells. However, limited tumor specificity is still a drawback for the clinical application of PDT. To increase the therapeutic efficacy and specificity of PDT, a novel human minibody (MS5) that recognizes a cell surface receptor expressed on various cancer cells was labeled with the hydrophilic phthalocyanine PS IR700 to generate an MS5-IR700 conjugate that is activated by near-infrared (NIR) light. The phototoxicity of the conjugate was mainly tested against the PC3 prostate cancer cell line. The MS5-IR700 conjugate killed PC3 cells after NIR light irradiation as compared to untreated cells or cells treated with IR700 alone. Time-course analysis of cell viability revealed a high percentage of cell death during the first hour in PC3 cells exposed to the MS5-IR700 conjugate and NIR light irradiation. After irradiation, the MS5-IR700 conjugate-treated PC3 cells displayed cellular swelling, round shape, and rupture of the cell and nuclear membranes. In a co-culture model, the MS5-IR700 conjugate killed MS5-positive Ramos lymphoma cells specifically, while leaving MS5-negative cells unaffected. In line with the data obtained with the monolayer cultures, the MS5-IR700 conjugate also killed PC3 cancer cell spheroids. The treatment induced relocation of heat shock protein 70 and calreticulin to the cell surface, implying the induction of immunogenic cell death. Overall, the data suggest that the developed MS5-IR700 conjugate is a promising therapeutic agent that warrants further preclinical studies.

RNA Interference: Story and Mechanisms.

The discovery that gene expression can be silenced by exogenously introduced double-stranded RNAs into cells unveiled a hidden level of gene regulation by a variety of small RNA pathways, which are involved in regulating endogenous gene expression, defending against virus infections, and protecting the genome from invading transposons, both at the posttranscriptional and epigenetic levels. All endogenous RNA interference pathways share a conserved effector complex, which contains at least an argonaute protein and a short single-stranded RNA. Such argonaute-RNA complexes can repress the transcription of genes, target mRNA for site-specific cleavage, or block mRNA translation into proteins. This review outlines the history of RNAi discovery, function, and mechanisms of action. For comparison, it also touches on CRISPR interference.

Microbial sensing by haematopoietic stem and progenitor cells: Vigilance against infections and immune education of myeloid cells.

Bone marrow haematopoietic stem and progenitor cells (HSPCs) express pattern recognition receptors such as Toll-like receptors (TLRs) to sense microbial products and activation of these innate immune receptors induces cytokine expression and redirects bone marrow haematopoiesis towards the increased production of myeloid cells. Secreted cytokines by HSPCs in response to TLR ligands can act in an autocrine or paracrine manner to regulate haematopoiesis. Moreover, tonic activation of HSPCs by microbiota-derived compounds might educate HSPCs to produce superior myeloid cells equipped with innate memory responses to combat pathogens. While haematopoietic stem cell activation through TLRs meets the increased demand for blood leucocytes to protect the host against infection, persistent exposure to inflammatory cytokines or microbial products might impair their function and even induce malignant transformation. This review highlights the potential outcomes of HSPCs in response to TLR ligands.

Selective Killing of Activated T Cells by 5-Aminolevulinic Acid Mediated Photodynamic Effect: Potential Improvement of Extracorporeal Photopheresis.

Extracorporeal photopheresis (ECP), a modality that exposes isolated leukocytes to the photosensitizer 8-methoxypsoralen (8-MOP) and ultraviolet-A (UV-A) light, is used to treat conditions such as cutaneous T-cell lymphoma and graft-versus-host disease. However, the current procedure of ECP has limited selectivity and efficiency; and produces only partial response in the majority of treated patients. Additionally, the treatment is expensive and time-consuming, so the improvement for this modality is needed. In this study, we used the concept of photodynamic therapy (PDT) with 5-aminolevulinic acid (ALA), a precursor of an endogenously synthesized photosensitizer protoporphyrin IX (PpIX) in combination with blue light to explore the possibility of targeting activated human blood T cells ex vivo. With various T-cell activation protocols, a high ALA-induced PpIX production took place in activated CD3+, CD4+CD25+, and CD8+ T cell populations with their subsequent killing after blue light exposure. By contrast, resting T cells were much less damaged by the treatment. The selective and effective killing effect on the activated cells was also seen after co-cultivating activated and resting T cells. Under our clinically relevant experimental conditions, ALA-PDT killed activated T cells more selectively and efficiently than 8-MOP/UV-A. Monocyte-derived dendritic cells (DCs) were not affected by the treatment. Incubation of ALA-PDT damaged T cells with autologous DCs induced a downregulation of the co-stimulatory molecules CD80/CD86 and also upregulation of interleukin 10 (IL-10) and indoleamine 2,3-dioxygenase expression, two immunosuppressive factors that may account for the generation of tolerogenic DCs. Overall, the data support the potential use of ALA-PDT strategy for improving ECP by selective and effective killing of activated T cells and induction of immune tolerance.

RNA and CRISPR Interferences: Past, Present, and Future Perspectives.

RNA interference (RNAi), a natural gene silencing process, is a widely used technique in basic research, preclinical studies, and drug development strategies. Although the technique has great potential to generate new human therapies and treat undruggable diseases, the clinical application of RNAi is still challenging primarily because of the delivery problem and potential off-target effects. Over the past two decades, great efforts have been undertaken to develop delivery agents and chemical modifications to overcome these challenges. Such advances in RNA delivery and chemical modifications have benefited researchers who are developing gene-editing therapies based on CRISPR-Cas9, an RNA-guided endonuclease, which is already having a major impact on biology and medicine. Here, I review the discovery of these two interference tools, identify the technical challenges yet to be overcome and provide some perspectives on how these two RNA-based technologies can be harnessed to treat human diseases.

Optimized siRNA Delivery into Primary Immune Cells Using Electroporation.

Effective RNA delivery strategies for primary human monocytes and dendritic cells (DCs) are useful tools for both basic research and cancer immunotherapy applications. Compared to viral delivery, electroporation is a relatively safe and simple technique that has been established for most immune cells. This chapter describes the feasibility of introducing small interfering RNAs into human primary monocytes and DCs using either nucleofection or standard electroporation techniques. DC cancer vaccines that integrate siRNA targeting relevant DC-intrinsic immunosuppressive signals induced robust and durable anti-tumor immune responses.

Exploring 5'-Biotinylation of the Sense Strand to Improve siRNA Specificity and Potency.

Although RNA interference is widely used for gene silencing, unintended gene modulation generated by off-target effects represents a major barrier to its applications in biology and medicine. Off-targeting can be induced by both the sense and antisense siRNA strands. An approach to minimizing off-target gene silencing by the sense strand would be the blockade of the 5'-end phosphorylation, thereby impeding its entry into the RNA-induced silencing complex (RISC). In this chapter, a biotin group at the 5'-end of the sense strand was used to inhibit its incorporation into RISC, thereby facilitating the antisense strand selection and enhancing siRNA cleavage potency. Biotin is a naturally occurring compound, and its presence in siRNA sequences will not induce additional side effects.

Improving Dendritic Cell Cancer Vaccine Potency Using RNA Interference.

Dendritic cell cancer vaccines have already become a treatment modality for patients with various cancer types. However, the curative potential of this immunotherapy is limited by the existence of negative feedback mechanisms that control dendritic cells (DCs) and T-cell function. By inhibiting the expression of inhibitory factors using RNA interference technology, a new generation of DC vaccines was developed. Vaccine-stimulated T cells showed antitumor effects both in vitro and in cancer patients. Here, we describe the development and validation of a fully GMP-compliant production process of ex vivo DC cancer vaccines combined with the blockade of immunosuppressive pathways using small interfering RNAs. The protocol can be used for DC-based therapy for all cancer types.

Unleashing the Therapeutic Potential of Dendritic and T Cell Therapies Using RNA Interference.

Therapeutic dendritic cell (DC) cancer vaccines work to boost the body's immune system to fight a cancer. Although this type of immunotherapy often leads to the activation of tumor-specfic T cells, clinical responses are fairly low, arguing for the need to improve the design of DC-based vaccines. Recent studies revealed a promising strategy of combining DC vaccines with small interfering RNAs (siRNAs) targeting immunosuppressive signals such as checkpoint receptors. Similarly, incorporating checkpoint siRNA blockers in adoptive T-cell therapy to amplify cytotoxic T lymphocyte responses is now being tested in the clinic. The development of the next generation of cancer immunotherapies using siRNA technology will hopefuly benefit patients with various cancer types including those who did not respond to current therapies. This review highlights the latest advances in RNA interference technology to improve the therapeutic efficacy of DC cancer vaccines and T cell therapy.

Harnessing the Antiviral-Type Responses Induced by Immunostimulatory siRNAs for Cancer Immunotherapy.

When introduced into endosomes via cationic lipids, certain small interfering RNA (siRNA) sequences activate the interferon signaling pathways in immune cells such as dendritic cells (DCs), known as the most efficient antigen-presenting cells of the immune system. Human immature DCs produced high levels of the immune-response protein interferon-α and tumor necrosis factor- α upon incubation with siRNA/lipid formulations, resulting in their maturation and expression of co-stimulatory molecules like CD80, CD86, and CD40 on the cell surface. These molecules are used by mature DCs to co-stimulate T cells during antigen presentation in lymphoid organs. Ex vivo loading of immature DCs with DOTAP-formulated immunostimulatory siRNAs and tumor antigens has proven effective as a cancer vaccine in a rat model of acute myeloid leukemia. Here, we describe this new vaccination strategy that targets tumor cells by activating DCs and blocking the expression of immunosuppressive factors.

Next Generation of Adoptive T Cell Therapy Using CRISPR/Cas9 Technology: Universal or Boosted?

Adoptive T cell therapy (ACT) using either chimeric antigen receptor (CAR)- or T cell receptor (TCR)-engineered lymphocytes has emerged as a promising strategy to treat cancer. However, this therapy is still facing enormous challenges such as poor quality of autologous T cells, T cell exhaustion, and the immune suppressive tumor microenvironments. Additionally, graft-versus-host disease is an issue that must be addressed to allow the use of allogeneic T cells. Strategies to overcome these therapeutic challenges using gene editing technology are now being developed. One strategy is to disrupt TCR and/or MHC expression in healthy donor T cells to generate T cells for universal use. Another strategy is to improve the quality of patient's T cells by eliminating either the expression of selected immune checkpoint receptors or negative regulators of TCR signaling and/or T-cell homeostasis. Here, we review the use of CRISPR-Cas9 platform in T cell engineering with a focus on the development of universal T cells and boosted autologous cells for next-generation ACT.

Targeted Killing of Monocytes/Macrophages and Myeloid Leukemia Cells with Pro-Apoptotic Peptides.

Several cells of myeloid origin, such as monocytes and macrophages are involved in various human disorders, including cancer and inflammatory diseases. Hence, they represent attractive therapeutic targets. Here we developed three lytic hybrid peptides, by fusing a monocyte- and macrophage-binding peptide to pro-apoptotic peptides, and investigated their killing potency on blood monocytes, macrophages, and leukemia cells. We first showed that the targeting NW peptide is effective for depleting monocytes from whole peripheral blood mononuclear cells (PBMCs). Incubating the cells with biotin-conjugated NW peptide, and the subsequent capture on streptavidin-conjugated magnetic beads, depleted monocytes from the PBMCs. The NW peptide also depleted myeloid leukemia blasts from patient PBMCs. The treatment of the PBMCs with the lytic hybrid NW-KLA peptide killed monocytes, but not lymphocytes and primary mammary epithelial cells. Additionally, the fusion peptide exhibited a potent toxicity against macrophages and leukemia cells. The free lytic KLA peptide did not affect cells. Similarly, a second lytic hybrid peptide killed macrophages, leukemia cell lines, and blood leukemia blasts from patients with acute and chronic myeloid leukemia. The IC50 towards target cells were in the low macromolar range (4-12 µM). Overall, the data indicate that the NW peptide could be a potential drug delivery agent for monocytes, macrophages, and leukemia cells. Moreover, the engineered lytic hybrid peptides acting alone, or in combination with other therapeutic agents, might benefit many cancer patients and overcome drug resistance.