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Mouldy Sioud

Publications and source records attributed to Mouldy Sioud.

At least 19 recordsLinked to original sources

Main approaches to target discovery and validation.

The identification and validation of disease-causing target genes is an essential first step in drug discovery and development. Genomics and proteomics technologies have already begun to uncover novel functional pathways and therapeutic targets in several human diseases such as cancers and autoimmunity. Also, bioinformatics approaches have highlighted several key targets and functional networks. In contrast to gene-profiling approaches, phenotype-oriented target identification allows direct link between the genetic alterations and a disease phenotype. Therefore, identified genes are more likely to be a cause rather than a consequence of the disease. Once a gene target or a mechanistic pathway is identified, the next step is to demonstrate that it does play a critical role in disease initiation, perpetuation, or both. A range of strategies exists for modulating gene expression in vitro and in vivo. These strategies include the use of antibodies, negative dominant controls, antisense oligonucleotides, ribozymes, and small-interfering RNAs. In contrast to in vitro assays, mouse reverse genetics such as knockout phenotypes has become a powerful approach for deciphering gene function and target validation in the context of mammalian physiology. In addition to disease-causing genes, the identification of antigens that stimulate both arms of the immune system is the major goal for effective vaccine development. The hope is that target discovery and validation processes will concurrently identify and validate therapeutic targets for drug intervention in human diseases.

Animals↗

Discovery of differentially expressed genes: technical considerations.

Identification and characterization of differentially expressed genes may be an important first step toward the understanding of both normal physiology and disease. A multitude of techniques belonging to two main categories have been developed to identify the differences in gene expression between samples from different biological origin: selection techniques and global techniques. Whereas the selection techniques strive to identify specific differentially expressed genes, the global techniques analyze the total transcriptome or a major part of the RNA population in a defined biological material. By exploiting the known sequences of the adaptors used in suppressive subtraction hybridization technique, a strategy named novel rescue-suppression-subtractive hybridization was developed. It should facilitate the discovery of differentially expressed genes.

Cloning, Molecular↗

An overview of the immune system and technical advances in tumor antigen discovery and validation.

The ability of the immune system to distinguish between self- and nonself antigens is controlled by mechanisms of central and peripheral tolerance. Although the induction and maintenance of tolerance is important for preventing autoimmunity, breaking self-tolerance is a crucial constituent for combating cancers. Cancer patients are able to develop spontaneous immune responses to tumors that they bear, however these responses are not suboptimal for eradicating tumors. Moreover, none of the current immune strategies is able to activate the immune system to respond against tumor cells as it responds against infectious agents. These observations have raised the question of how to activate immunity in cancer patients to a threshold required for tumor rejection. Because tolerance is emerging as a central obstacle for immune recognition of human tumor antigens, this chapter describes how T- and B-cells are generated and activated in the periphery. It also outlines the technical advances in tumor antigen discovery and validation.

Animals↗

Protein arrays: a versatile toolbox for target identification and monitoring of patient immune responses.

Functional proteomics is a promising technique for the rational identification of novel therapeutic targets and biological markers. The studies of protein-protein interactions have been gained from the development of high-throughput technologies such as the yeast two-hybrid system, protein arrays, phage display, and systematic analysis of interaction maps for the prediction of protein functions. Because antibodies are used extensively as diagnostic and clinical tools, the characterization of their antigen specificity is of prime importance. Indeed, screening protein arrays with sera from patients with either cancer or autoimmune diseases would facilitate the identification of autoantibody signatures that can be used for diagnosis and/or prognosis of patients. The usefulness of multiplexed measurements lies not only in the ability to screen many individual marker candidates but also in evaluating the use of multiple markers in combination. Here, we review the advantage of protein and serum screening of peptides and cDNA repertoires displayed on phages as well as the fabrication of protein microarrays for probing immune responses in patients.

Autoantibodies↗

Druggable signaling proteins.

In normal cells, signaling pathways are tightly regulated. However, when they are aberrantly activated, certain pathways are capable of causing diseases. In many tumors, the aberrantly activated signaling proteins include members of the epidermal growth factor receptor family, the Ras proteins, protein kinase C isoenzymes, BCR-ABL fusion protein as well as transcription factors such as signal transducers and activators of transcriptions and Myc. Accordingly, deregulation of these signaling proteins holds promise for the development of new anticancer drugs. Studies in vitro and in disease-relevant models demonstrated that blocking the activation of a key target in a constitutively activated signaling pathway could reverse disease phenotype. Moreover, constitutive activation of the target alone is sufficient to induce relevant disease phenotype. Notably, the most dramatic therapeutic advances in cancer therapy during the last decade have come from agents targeted against active thyrosine kinases. These include imatinib (anti-BCR-ABL), gefitinib (anti-EGF receptor), and herpetin (anti-ErbB-2). Here, some selected validated and drugable targets are summarized.

Animals↗

Target validation using RNA interference in solid tumors.

Reverse genetics is one strategy that is currently used to establish a link between a target gene and a disease phenotype. In this process, the function of a gene is inhibited and the consequence of its loss on a desired biological function, such as tumor growth and metastasis, is monitored. RNA interference (RNAi) has been found to be the most effective method to specifically inhibit gene expression. Notably, interactions between cancer cells, stromal cells, and the extracellular matrix (ECM) are crucial to angiogenesis and tumorigenesis. Tumor cells and the surrounding stroma are the principle source of growth factors and cytokines, which induce remodeling of the ECM mediated by metalloproteases (MMPs) secreted by macrophages. The production of macrophages is regulated by colony-stimulating factor (CSF)-1, which is overexpressed in several tumors. When short-interfering RNAs (siRNAs) targeting either the CSF-1 or its receptors were delivered into colon and breast cancer xenografts in mice, tumor growth was inhibited. Associated with this suppression, we observed decreased tumor vascularity, reduced expression of angiogenic factors and MMPs, and decreased macrophage recruitment to the tumors. The suppression of CSF-1 by RNA interference is therefore a powerful tool to block gene function and influence tumor-stroma interactions in solid tumor development.

Animals↗

Treatment options and individualized medicine.

Although several drug targets are identified, current strategies in therapy do not take into account that patients vary in their response to drugs, both with respect to efficacy and toxic side effects. Whereas both clinical and histopathologic predictors of prognosis are established in some diseases, a better understanding of the molecular mechanisms that determine treatment response should play an important role in the development of individualized medicine. Treatment optimization will rely on the ability to adjust treatment algorithms for use in the individual patient based on the identification and validation of the factors that critically determine treatment outcomes, including diagnosis, disease phase and characteristics, organ functions, age, and gender. Although the analysis of a single genetic marker (e.g., CYP polymorphisms) may yield significant information that predicts drug response, the prediction obtained from the analysis of several genetic and epigenetic markers is potentially more powerful in selecting patients for effective therapy, whereas sparing those who would not respond or would suffer undesirable side effects. In this chapter, several relevant examples are presented.

Age Factors↗

Design of bifunctional siRNAs: combining immunostimulation and gene-silencing in one single siRNA molecule.

Active suppression of T lymphocyte activation can limit the efficacy of immune surveillance and immunotherapy. Here we have explored the possibility of designing bifunctional small interfering RNAs (siRNAs) capable of inducing innate immunity through Toll-like receptors and simultaneously inhibiting the expression of immunosuppressive factors. Using interleukin (IL) 10 as a model, we found that liposomal delivery of IL10 siRNAs could efficiently activate the expression of cytokines (e.g. TNF-alpha, IL6, and IL12) and interferons (e.g. IFN-alpha) in peripheral blood mononuclear cells (PBMCs) and immature monocyte-derived dendritic cells (iMoDCs). Moreover, the designed siRNAs inhibited IL10 gene expression. Transfection of iMoDCs with either chemically or in vitro transcribed IL10 siRNAs induced their differentiation into mature MoDCs (mMoDCs) characterized by the expression of costimulatory molecules CD80/CD86 and the chemokine receptor CCR7. Lipid delivery of either chemically synthesized or T7-transcribed immunostimulatory siRNAs induced cytokine production. However, in contrast to chemically synthesized siRNAs, electroporation of in vitro transcribed siRNAs also induced cytokine production in iMoDCs. Interestingly, IL10 siRNA-transfected iMoDCs were capable for enhancing the response of allogeneic T cells, providing support for the rational design of bifunctional siRNAs as immune modulating therapy.

Cells, Cultured↗

Transcriptional targeting of small interfering RNAs into cancer cells.

Small interfering RNAs (siRNAs) are widely used for analyzing gene function and have the potential to be developed into human therapeutics. However, persistent siRNA expression in normal cells may cause toxic side effects. Therefore, the therapeutic applications of RNAi in cancer require either the specific delivery of synthetic siRNAs into cancer cells or the control of siRNA expression. Accordingly, we have developed a cancer-specific vector that expresses siRNAs from the human survivin promoter. A plasmid vector expressing siRNAs under this promoter enabled efficient gene silencing of gene expression in different cancer cell lines. The levels of inhibition were comparable to that obtained with the constitutively active U6 promoter. By contrast to U6 promoter, no significant gene silencing was obtained with the Survivin promoter in normal mammary epithelial cells. Collectively, these data indicate that the survivin promoter is suitable for directing siRNA expression in cancer cells, but not normal cells.

Cell Line, Tumor↗

Signaling through toll-like receptor 7/8 induces the differentiation of human bone marrow CD34+ progenitor cells along the myeloid lineage.

Toll-like receptors (TLRs) play a key role in pathogen recognition and regulation of the innate and adaptive immune responses. Although TLR expression and signaling have been investigated in blood cells, it is currently unknown whether their bone marrow ancestors express TLRs and respond to their ligands. Here we found that TLRs (e.g. TLR4, TLR7 and TLR8) were expressed by freshly isolated human bone marrow (BM) hematopoietic CD34+ progenitor cells. Incubation of these primitive cells with TLR ligands such as immunostimulatory small interfering RNAs and R848, a specific ligand for TLR7/8, induced cytokine production (e.g. IL1-beta, IL6, IL8, TNF-alpha, GM-CSF). Moreover, TLR7/8 signaling induced the differentiation of BM CD34+ progenitors into cells with the morphology of macrophages and monocytic dendritic precursors characterized by the expression of CD13, CD14 and/or CD11c markers. By contrast, R848 ligand did not induce the expression of glycophorin A, an early marker for erythropoiesis. Collectively, the data indicate for the first time that human BM CD34+ progenitor cells constitutively express functional TLR7/TLR8, whose ligation can induce leukopoiesis without the addition of any exogenous cytokines. Thus, TLR signaling may regulate BM cell development in humans.

Adult↗

Gene expression analysis in blood cells in response to unmodified and 2'-modified siRNAs reveals TLR-dependent and independent effects.

Ribonucleic nucleic acid recognition by Toll-like receptors (TLRs) induces innate immune responses. However, no comprehensive analysis of gene expression in human blood cells in response to unmodified and 2'-modified immunostimulatory RNAs has been reported. Using oligonucleotide microarrays, we show that around 400 genes were significantly (P<0.001) altered in peripheral blood mononuclear cells (PBMC) in response to either single-stranded (ss) or double-stranded (ds) small interfering RNAs (siRNAs). Most of the upregulated genes encode proteins involved in innate and adaptive immune responses, including proinflammatory cytokines, interferons, chemokines and chemokine receptors. Genes encoding proteins involved in lymphocyte activation (e.g. CD80, CD40, and CD69) and in regulation of the immune responses (e.g. SOCS proteins) were upregulated. Also, genes encoding for antiviral proteins (Mx1, Mx2, TRIM proteins), and interferon regulatory factors (e.g. IRF7) were upregulated. Around 90% of the genes (140 out of 160) affected by R-848, a specific ligand for TLR7 and TLR8, were also affected by ss siRNAs or ds siRNAs, indicating that the signaling pathways activated by R-848 are also activated by immunostimulatory siRNAs. In addition to immunoactivation via TLRs, ss siRNAs and ds siRNAs induced TLR-independent gene alterations. Surprisingly, replacement of only uridine bases with either 2'-fluoro or 2'-O-methyl modified counterparts abrogated all the observed bystander effects. Collectively, these microarray data offer for the first time an insight into human PMBC response to immunostimulatory RNAs such as ss siRNAs and ds siRNAs. The data should help to define strategies to either enhance or avoid the non-specific effects of siRNAs in order to develop safe therapeutics.

Gene Expression Profiling↗

Innate sensing of self and non-self RNAs by Toll-like receptors.

Toll-like receptors (TLRs) have an important role in innate immunity in mammals by recognizing conserved microbial components that are known as pathogen-associated molecular patterns (PAMPs). Although the majority of these receptors sense pathogen components on the cell surface, a subset of them (TLR3, TLR7, TLR8 and TLR9) senses viral and bacterial nucleic acids in endosomal compartments. Of considerable interest is the recent finding that TLR7 and TLR8 can also recognize small interfering RNA (siRNA), which is the main effector in RNA interference. This immune activation by siRNAs can be abrogated by the 2'-ribose modification of uridines. Here, we discuss the recent developments that have expanded the understanding of self-non-self discrimination of RNAs by the innate immune system, and consider future directions for therapeutic applications of these findings.

Animals↗

Single-stranded small interfering RNA are more immunostimulatory than their double-stranded counterparts: a central role for 2'-hydroxyl uridines in immune responses.

It has recently become apparent that certain small interfering RNA (siRNA) sequences stimulate the innate immunity through endosomal Toll-like receptors (TLR), particularly TLR7 and TLR8. However, it remains unclear whether siRNA duplexes act as specific ligands for these receptors. To address this question and to overcome the problem of immune activation by siRNA, several RNA sequences were chemically synthesized and their effects were investigated. Results indicate that human peripheral blood mononuclear cells (PBMC) recognize and respond to a large number of sense or antisense single-stranded (ss) siRNA. In most cases immunostimulatory RNA motifs are more effectively recognized by innate immunity in the context of ss siRNA as compared to siRNA duplexes. Novel immunostimulatory RNA motifs were identified and their replacement with adenosines abrogated immune activation. Most notably, replacement of the 2'-hydroxyl uridines with either 2'-fluoro, 2'-deoxy or 2'-O-methyl uridines abrogated immune activation. Thus, immune recognition of RNA by TLR can be evaded by 2'-ribose modifications of only uridines. Collectively, the data should facilitate the development of siRNA therapeutics and expand the understanding of how RNA is sensed by innate immunity.

Adjuvants, Immunologic↗

Molecular basis for the immunostimulatory potency of small interfering RNAs.

Small interfering RNAs (siRNAs) represent a new class of antigene agents, which has emerged as a powerful tool for functional genomics and might serve as a potent therapeutic approach. However, several studies have showed that they could trigger several bystander effects, including immune activation and inhibition of unintended target genes. Although activation of innate immunity by siRNAs might be beneficial for therapy in some instances, uncontrolled activation can be toxic, and is therefore a major challenging problem. Interestingly, replacement of uridines in siRNA sequences with their 2'-modified counterparts abrogated siRNA bystander effects. Here we highlight these important findings that are expected to facilitate the rational design of siRNAs that avoid the induction of bystander effects.

Journal Article↗

RNA interference.

Explore the source record for details and available documents.

Editorial↗

Influence of light fluence rate on the effects of photodynamic therapy in an orthotopic rat glioma model.

OBJECT: Failure of treatment for high-grade gliomas is usually due to local recurrence at the site of resection, indicating that a more aggressive local therapy could be beneficial. Photodynamic therapy (PDT) is a local treatment involving the administration of a tumor-localizing photosensitizing drug, in this case aminolevulinic acid (ALA). The effect depends on the total light energy delivered to the target tissue, but may also be influenced by the rate of light delivery. METHODS: In vitro experiments showed that the sensitivity to ALA PDT of BT4C multicellular tumor spheroids depended on the rate of light delivery (fluence rate). The BT4C tumors were established intracranially in BD-IX rats. Microfluorometry of frozen tissue sections showed that photosensitization is produced with better than 200:1 tumor/normal tissue selectivity after ALA injection. Four hours after intraperitoneal ALA injection (125 mg/kg), 26 J of 632 nm light was delivered interstitially over 15 (high fluence rate) or 90 (low fluence rate) minutes. Histological examination of animals treated 14 days after tumor induction demonstrated extensive tumor necrosis after low-fluence-rate PDT, but hardly any necrosis after high-fluence-rate treatment. Neutrophil infiltration in tumor tissue was increased by PDT, but was similar for both treatment regimens. Low-fluence-rate PDT administered 9 days after tumor induction resulted in statistically significant prolongation of survival for treated rats compared with nontreated control animals. CONCLUSIONS: Treatment with ALA PDT induced pronounced necrosis in tumors only if the light was delivered at a low rate. The treatment prolonged the survival for tumor-bearing animals.

Aminolevulinic Acid↗

Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization.

The potential induction of inflammatory cytokines and interferon responses by small-interfering RNAs (siRNAs) represents a major obstacle for their use as inhibitors of gene expression. Therapeutic applications of siRNAs will require a better understanding of the mechanisms that trigger such unwanted effects, especially in freshly isolated human cells. Surprisingly, the induction of tumor necrosis factor (TNF-alpha) and interleukin-6 (IL-6) in adherent peripheral blood mononuclear cells (PBMC) was not restricted to double-stranded siRNAs, because induction was also obtained with single-stranded siRNAs (sense or antisense strands). The immunostimulatory effects were sequence-dependent, since only certain sequences are prone to induce inflammatory responses while others are not. The induction of TNF-alpha, IL-6 and interferon alpha (IFN-alpha) was chloroquine-sensitive and dependent more likely on endosomal Toll-like receptor signaling in particular TLR8. Indeed, no significant immunostimulatory effects were detected when either double or single-stranded siRNAs were delivered directly to cytoplasm via electroporation. Both RNA types activated a NF-kappaB promoter-driven luciferase gene in transiently transfected human adherent PBMC. Moreover, culture of immature dendritic cells with either double or single-stranded siRNAs stimulated interleukin-12 production and induced the expression of CD83, an activation marker. Interestingly, several double-stranded siRNAs did not induce TNF-alpha, IL-6 and IFN-alpha production, however, their single-stranded sense or antisense did. Taken together, the present data indicate for the first time that the induction of inflammatory cytokines and IFN-alpha responses by either double-stranded or single-stranded siRNAs in adherent PBMC is sequence-dependent and requires endosomal intracellular signaling. The finding that endosomal localization of self-RNAs (sense strands) can trigger Toll-like receptor signaling in adherent human PBMC is intriguing because it indicates that endosomal self-RNAs can display a molecular pattern capable for activating innate immunity.

Cells, Cultured↗