Use of RNA interference to minimize ischemia reperfusion injury

Extracellular matrix gene set and microRNA network in intestinal ischemia-reperfusion injury: Insights from RNA sequencing for diagnosis and therapy

Intestinal ischemia-reperfusion injury (IIRI) is a complex and severe pathophysiological process characterized by oxidative stress, inflammation, and apoptosis. In recent years, the critical roles of extracellular matrix (ECM) genes and microRNAs (miRNAs) in IIRI have garnered widespread attention. This review aims to systematically summarize the diagnostic and therapeutic potential of ECM gene sets and miRNA regulatory networks in IIRI. First, we review the molecular mechanisms of IIRI, focusing on the dual role of the ECM in tissue injury and repair processes. The expression changes and functions of ECM components such as collagen, elastin, and matrix metalloproteinases during IIRI progression are deeply analyzed. Second, we systematically summarize the regulatory roles of miRNAs in IIRI, particularly the mechanisms and functions of miRNAs such as miR-125b and miR-200a in regulating inflammation, apoptosis, and ECM remodeling. Additionally, this review discusses potential diagnostic biomarkers and treatment strategies based on ECM genes and miRNAs. We extensively evaluate the prospects of miRNA-targeted therapy and ECM component modulation in preventing and treating IIRI, emphasizing the clinical translational potential of these emerging therapies. In conclusion, the diagnostic and therapeutic potential of ECM gene sets and miRNA regulatory networks in IIRI provides new directions for further research, necessitating additional clinical and basic studies to validate and expand these findings for improving clinical outcomes in IIRI patients.

Recent insights into mitochondrial targeting strategies in liver transplantation

Ischemia/reperfusion (I/R) injury in liver transplantation can disrupt the normal activity of mitochondria in the hepatic parenchyma. This potential dysfunction of mitochondria after I/R injury could be responsible for the initial poor graft function or primary nonfunction observed after liver transplantation. Thus, determining the mechanisms that lead to human hepatic mitochondrial dysfunction might contribute to improving the outcome of liver transplantation. Furthermore, early identification of novel prognostic factors involved in I/R injury could serve as a key endpoint to predict the outcome of liver grafts and also to promote the early adoption of novel strategies that protect against I/R injury. Here, we briefly review recent advances in the study of mitochondrial dysfunction and I/R injury, particularly in relation to liver transplantation. Next, we highlight various pharmacological therapeutic strategies that could be applied, and discuss their relationship to relevant mitochondrion-related processes and targets. Lastly, we note that although considerable progress has been made in our understanding of I/R injury and mitochondrial dysfunction, further investigation is required to elucidate the cellular and molecular mechanisms underlying these processes, thereby identifying biomarkers that can help in evaluating donor organs.

Blockade of Inflammation and Apoptosis Pathways by siRNA Prolongs Cold Preservation Time and Protects Donor Hearts in a Porcine Model

In donor hearts from mini pigs, overtime cold preservation and ischemia-reperfusion injury cause poor graft quality and impaired heart function. Blockage of complement, apoptosis, and inflammation is considered a strategy for attenuating ischemia-reperfusion injury and protecting cardiac function. Minipig donor hearts were perfused and preserved in Celsior solution or transfection reagent containing Celsior solution with scramble siRNA or siRNAs targeting complement 3, caspase-8, caspase-3, and nuclear factor κB-p65 genes at 4°C and subsequently hemo-reperfused ex vivo (38°C) or transplanted into recipients. The protective effect of the siRNA solution was evaluated by measuring cell apoptosis, structural alteration, protein markers for tissue damage and oxidative stress, and cardiac function. We found a reduction in cell apoptosis, myocardial damage, and tissue inflammation by reduced biochemistry and markers and protein expression of proinflammatory cytokines and improvement in cardiac function, as shown by the improved hemodynamic indices in 12-hr-preserved siRNA-treated hearts of both ex vivo and orthotopic transplantation models. These findings demonstrate that blockade of inflammation and apoptosis pathways using siRNA can prolong cold preservation time and better protect donor heart function in cardiac transplantation of large animals, which may be beneficial for human heart preservation.

Down-regulation of nuclear HMGB1 reduces ischemia-induced HMGB1 translocation and release and protects against liver ischemia-reperfusion injury

Hepatocyte-specific HMGB1 deletion has been found to worsen the injury and inflammation in liver ischemia-reperfusion injury (IRI), highlighting a role for intracellular HMGB1 in cellular protection. Down-regulation of nuclear HMGB1 by small interfering RNA (siRNA) might not only decrease its injurious extracellular role by reducing its release but also serve to maintain its beneficial intracellular role, thus protecting against IRI. We established a non-lethal liver IRI model in mice via segmental hepatic warm ischemia for 1 h and reperfusion for 6 h. HMGB1-siRNA achieved a reduction of ~60–70% in the nuclear HMGB1 expression in the liver at 48 h post-treatment. Knockdown of nuclear HMGB1 expression dramatically reduced both the degree of nuclear-cytoplasmic translocation of HMGB1 during hepatic ischemia and of HMGB1 release after hepatic reperfusion, resulting in significant preservation of liver function and a marked reduction in pathological damage. Also, HMGB1-siRNA pretreatment markedly inhibited the increases in hepatic expression of TLR4, TLR2, RAGE, TNF-α, IL-1β, IL-6, MCP-1, iNOS, and COX-2 seen in control mice after hepatic reperfusion. We demonstrated for the first time that down-regulation of nuclear HMGB1 reduces ischemia-induced HMGB1 release and protects against liver IRI, which is helpful for better understanding the role of HMGB1 in organ IRI.

siRNA technology in kidney transplantation: current status and future potential

Kidney transplantation is one of the most common transplantation operations in the world, accounting for up to 50 % of all transplantation surgeries. To curtail the damage to transplanted organs that is caused by ischemia-reperfusion injury and the recipient's immune system, small interfering RNA (siRNA) technology is being explored. Importantly, the kidney as a whole is a preferential site for non-specific systemic delivery of siRNA. To date, most attempts at siRNA-based therapy for transplantation-related conditions have remained at the in vitro stage, with only a few of them being advanced into animal models. Hydrodynamic intravenous injection of naked or carrier-bound siRNAs is currently the most common route for delivery of therapeutic constructs. To our knowledge, no systematic screens for siRNA targets most relevant for kidney transplantation have been attempted so far. A majority of researchers have arrived at one or another target of interest by analyzing current literature that dissects pathological processes taking place in transplanted organs. A majority of the genes that make up the list of 53 siRNA targets that have been tested in transplantation-related models so far belong to either apoptosis- or immune rejection-centered networks. There is an opportunity for therapeutic siRNA combinations that may be delivered within the same delivery vector or injected at the same time and, by targeting more than one pathway, or by hitting the same pathways within two different key points, will augment the effects of each other.

Additives to preservation solutions

As the impact of ischemia reperfusion injury on graft outcome is now well defined, efforts are made towards decreasing these lesions, typically through the improvement of preservation techniques. The use of pharmacological supplements which could be compatible with any preservation solution used by the transplant center and target specific pathways of IR is an interesting strategy to improve graft quality. However, the extensive number of studies showing the benefits a molecule in an animal model of IR without thorough mechanistic determination of the effects of this agent make it difficult to opt for specific pharmaceutical intervention. Herein we expose studies which demonstrate the benefits of several molecules relying on a thorough mechanical analysis of the events occurring during preservation, both at the cellular and the systemic levels. We believe this approach is the most appropriate to truly understand the potential benefits of a molecule and particularly to design a comprehensive pharmaceutical regiment, with several agents acting synergistically against IR, to improve organ preservation and graft outcome.

Emerging therapies targeting intra-organ inflammation in transplantation

Over the past several years, the field of transplantation has witnessed significant progress on several fronts; in particular, achievements have been made in devising novel immunosuppressive strategies. An under-explored area that may hold great potential to improve transplantation outcomes is the design of novel strategies to apply specifically to organs to reduce intra-graft inflammation. A growing body of evidence indicates a key role of intra-graft inflammatory cascade in potently instigating the alloimmune response. Indeed, controlling the activation of innate immunity/inflammatory responses has been shown to be a promising strategy to increase the graft acceptance and survival. In this minireview, we provide an overview of emerging targeted strategies, which can be directly applied to grafts to down-regulate intra-graft inflammation prior to transplantation.

Innate immunity activation involved in unprotected porcine auto-transplant kidneys preserved by naked caspase-3 siRNA

Background

The naked caspase-3 small interfering RNA (siRNA) infused into the renal artery during cold preservation was effective, but did not protect auto-transplant porcine kidneys with increased inflammation and apoptosis in our previous study. The mechanisms involved, in particular, whether siRNA or complementary systemic feedback eliciting innate immune responses are worthy to be further investigated.

Methods

The protein and mRNA expression of innate immunity-related molecules were detected by western blotting and quantitative PCR in the tissues previously collected from 48 h auto-transplant kidneys. The donor kidneys were retrieved from mini pigs and cold preserved by University of Wisconsin solution with/without 0.3 mg caspase-3 siRNA for 24 h.

Results

The protein level of Toll like receptor (TLR) 3, TLR7, and their main adapters, TRIF and MyD88, was up-regulated in the siRNA preserved auto-transplant kidneys. The mRNA level of NF-κB and c-Jun was increased, as well as pro-inflammatory cytokines, including IL-1β, IL-6, TNF-α and interferon (IFN)-α, β and γ. In addition, the non-TLR RNA sensor PKR protein, but not RIG1, was also increased in the siRNA preserved auto-transplant kidneys.

Conclusions

The activation of innate immunity with amplified inflammatory responses in the caspase-3 siRNA preserved auto-transplant kidneys are associated with increased TLR3, TLR7 and PKR, which might be due to complementary systemic feedback, although persistent actions initiated by short-acting caspase-3 siRNA cannot be completely ruled out. These results provided valuable evidence to guide future siRNA design and pre-clinic studies.

An in silico approach to design potential siRNA molecules for ICP22 (US1) gene silencing of different strains of human herpes simplex 1

BACKGROUND

The herpes simplex virus (HSV-1) is a virus that manifests itself in viral infection with painful, watery blisters in the skin or on the genitals as well as mucous membrane such as the mouth or lips. During an outbreak, the disease is contagious particularly and is irredeemable with present technology. Genetic studies of HSV-1 have shown that ICP22 (US1) gene is an immediate early gene and is responsible for genome replication and also has contribution in viral infection.

METHOD

For disease diagnosis, ICP22 (US1) gene may be suitable target. Viral activity can be controlled through RNA interference technology, a significant method for the post-transcriptional gene silencing. However, in different viral isolates there is a genetic variability; it is very challenging to design possible siRNA molecules which can silence the respective target genes. The work was done by using various computational tools as similarity search, target alignment, secondary structure prediction and RNA interaction evaluation.

RESULT

In our study two effective siRNA molecules for ICP22 (US1) gene silencing of seven different strains of HSV-1 were rationally designed and authenticated using computational methods, which might lead to knockdown the viral activity.

CONCLUSION

siRNA molecules were foreseen against ICP22 (US1) gene of different strains of HSV-1 as effective aspirant using computational methods. Thus, the approach may deliver a vision for the chemical synthesis of antiviral RNA molecule for treatment of HSV-1, at genomic level.

Role of complement and perspectives for intervention in transplantation

The complement cascade is a major contributor to the innate immune response. It has now been well accepted that complement plays a critical role in hyperacute rejection and acute antibody-mediated rejection of transplanted organ. There is also increasing evidence that complement proteins contribute to the pathogenesis of organ ischemia-reperfusion injury, and even to cell-mediated rejection. Furthermore, the chemoattractants C3a and C5a and the terminal membrane attack complex that are generated by complement activation can directly or indirectly mediate tissue injury and trigger adaptive immune responses. Here, we review recent findings concerning the role of complement in graft ischemia-reperfusion injury, antibody-mediated rejection and accommodation, and cell-mediated rejection. We also discuss the current status of complement intervention therapies in clinical transplantation and describe potential new therapeutic strategies for clinical application.

Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.