Transcriptomic investigation reveals donor-specific gene signatures in human lung transplants

Systemic Inflammation Differences in Brain-vs. Circulatory-Dead Donors: Impact on Lung Transplant Recipients

Brain death triggers a systemic inflammatory response. Whether systemic inflammation is different in lung donors after brain- (DBD) or circulatory-death (DCD) is unknown, but this may potentially increase the incidence of primary graft dysfunction (PGD) after lung transplantation. We compared the plasma levels of interleukin (IL)-6, IL-8, IL-10 and TNF-α in BDB and DCD and their respective recipients, as well as their relationship with PGD and mortality after LT. A prospective, observational, multicenter, comparative, cohort-nested study that included 40 DBD and 40 DCD lung donors matched and their respective recipients. Relevant clinical information and blood samples were collected before/during lung retrieval in donors and before/during/after (24, 48 and 72 h) LT in recipients. Incidence of PGD and short-term mortality after LT was recorded. Plasma levels of all determined cytokines were numerically higher in DBD than in DCD donors and reached statistical significance for IL-6, IL-10 and IL-8. In recipients with PGD the donor's plasma levels of TNF-α were higher. The post-operative mortality rate was very low and similar in both groups. DBD is associated with higher systemic inflammation than DCD donors, and higher TNF-α plasma levels in donors are associated with a higher incidence of PGD.

Creating superior lungs for transplantation with next-generation gene therapy during ex vivo lung perfusion

Engineering donor organs to better tolerate the harmful non-immunological and immunological responses inherently related to solid organ transplantation would improve transplant outcomes. Our enhanced knowledge of ischemia-reperfusion injury, alloimmune responses and pathological fibroproliferation after organ transplantation, and the advanced toolkit available for gene therapies, have brought this goal closer to clinical reality. Ex vivo organ perfusion has evolved rapidly especially in the field of lung transplantation, where clinicians routinely use ex vivo lung perfusion (EVLP) to confirm the quality of marginal donor lungs before transplantation, enabling safe transplantation of organs originally considered unusable. EVLP would also be an attractive platform to deliver gene therapies, as treatments could be administered to an isolated organ before transplantation, thereby providing a window for sophisticated organ engineering while minimizing off-target effects to the recipient. Here, we review the status of lung transplant first-generation gene therapies that focus on inducing transgene expression in the target cells. We also highlight recent advances in next-generation gene therapies, that enable gene editing and epigenetic engineering, that could be used to permanently change the donor organ genome and to induce widespread transcriptional gene expression modulation in the donor lung. In a future vision, dedicated organ repair and engineering centers will use gene editing and epigenetic engineering, to not only increase the donor organ pool, but to create superior organs that will function better and longer in the recipient.

Applications of transcriptomics in ischemia reperfusion research in lung transplantation

Ischemia-reperfusion (IR) injury contributes to primary graft dysfunction, a major cause of early mortality after lung transplantation. Transcriptomics uses high-throughput techniques to profile the RNA transcripts within a sample and provides a unique view of the mechanisms underlying various biological processes. This review aims to highlight the applications of transcriptomics in lung IR injury studies, which have thus far revealed inflammatory responses to be the major event activated by IR, identified potential biomarkers and therapeutic targets, and investigated the mechanisms of therapeutic interventions. Ex vivo lung perfusion, together with advanced bioinformatic and transcriptomic techniques, including single-cell RNA-sequencing, microRNA profiling, and multi-omics, continue to expand the capabilities of transcriptomics. In the future, the construction of biospecimen banks and the promotion of international collaborations among clinicians and researchers have the potential to advance our understanding of IR injury and improve the management of lung transplant recipients.

Uncontrolled Donation after Circulatory Death Only Lung Program: An Urgent Opportunity

Uncontrolled donation after circulatory death (uDCD) represents a potential source of lungs, and since Steen's 2001 landmark case in Sweden, lungs have been recovered from uDCD donors and transplanted to patients in other European countries (France, the Netherlands, Spain and Italy) with promising results. Disparities still exist among European countries and among regions in Italy due to logistical and organizational factors. The present manuscript focuses on the clinical experiences pertaining to uDCD lungs in North America and European countries and on different lung maintenance methods. Existing experiences (and protocols) are not uniform, especially with respect to the type of lung maintenance, the definition of warm ischemic time (WIT) and, finally, the use of ex vivo perfusion (available in the last several years in most centers). In situ lung cooling may be superior to protective ventilation, but this process may be difficult to perform in the uDCD setting and is also time-consuming. On the other hand, the "protective ventilation technique" is simpler and feasible in every hospital. It may lead to a broader use of uDCD lung donors. To date, the results of lung transplants performed after protective ventilation as a preservation technique are scarce but promising. All the protocols comprise, among the inclusion criteria, a witnessed cardiac arrest. The detectable differences included preservation time (240 vs. 180 min) and donor age (<55 years in Spanish protocols and <65 years in Toronto protocols). Overall, independently of the differences in protocols, lungs from uDCD donors show promising results, and the possibility of optimizing ex vivo lung perfusion may broaden the use of these organs.

Modeling the Effects of IL-1β-mediated Inflammation During Ex Vivo Lung Perfusion Using a Split Human Donor Model

BACKGROUND

The association between interleukin-1β (IL-1β) concentrations during ex vivo lung perfusion (EVLP) with donor organ quality and post-lung transplant outcome has been demonstrated in several studies. The mechanism underlying IL-1β-mediated donor lung injury was investigated using a paired single-lung EVLP model.

METHODS

Human lung pairs were dissected into individual lungs and perfused on identical separate EVLP circuits, with one lung from each pair receiving a bolus of IL-1β. Fluorescently labeled human neutrophils isolated from a healthy volunteer were infused into both circuits and quantified in perfusate at regular timepoints. Perfusates and tissues were subsequently analyzed, with perfusates also used in functional assays.

RESULTS

Neutrophil numbers were significantly lower in perfusate samples collected from the IL-1β-stimulated lungs consistent with increased neutrophil adhesion ( P = 0.042). Stimulated lungs gained significantly more weight than controls ( P = 0.046), which correlated with soluble intercellular adhesion molecule-1 (R 2 = 0.71, P = 0.0043) and von-Willebrand factor (R 2 = 0.39, P = 0.040) in perfusate. RNA expression patterns for inflammatory genes were differentially regulated via IL-1β. Blockade of IL-1β significantly reduced neutrophil adhesion in vitro ( P = 0.025).

CONCLUSION

These data illustrate the proinflammatory functions of IL-1β in the context of EVLP, suggesting this pathway may be susceptible to therapeutic modulation before transplantation.

Circulating exosomes from brain death and cardiac death donors have distinct molecular and immunologic properties: A pilot study

BACKGROUND AND AIMS

Comparison of donation after brain death (DBD) and donation after cardiac death (DCD) lung tissue before transplantation have demonstrated activation of pro-inflammatory cytokine pathway in DBD donors. The molecular and immunological properties of circulating exosomes from DBD and DCD donors were not previously described.

METHODS

We collected plasma from 18 deceased donors (12 DBD and six DCD). Cytokines were analyzed by 30-Plex luminex Panels. Exosomes were analyzed for liver self-antigen (SAg), Transcription Factors and HLA class II (HLA-DR/DQ) using western blot. C57BL/6 animals were immunized with isolated exosomes to determine strength and magnitude of immune responses. Interferon (IFN)-γ and tumor necrosis factor-α producing cells were quantified by ELISPOT, specific antibodies to HLA class II antigens were measured by ELISA RESULTS: We demonstrate increased plasma levels of IFNγ, EGF, EOTAXIN, IP-10, MCP-1, RANTES, MIP-β, VEGF, and interleukins - 6/8 in DBD plasma versus DCD. MiRNA isolated from exosome of DBD donors demonstrated significant increase in miR-421, which has been reported to correlate with higher level of Interleukin-6. Higher levels of liver SAg Collagen III (p = .008), pro-inflammatory transcription factors (NF-κB, p < .05; HIF1α, p = .021), CIITA (p = .011), and HLA class II (HLA-DR, p = .0003 and HLA-DQ, p = .013) were detected in exosomes from DBD versus DCD plasma. The circulating exosomes isolated from DBD donors were immunogenic in mice and led to the development of Abs to HLA-DR/DQ.

CONCLUSIONS

This study provides potential new mechanisms by which DBD organs release exosomes that can activate immune pathways leading to cytokine release and allo-immune response.

Necroptosis in Organ Transplantation: Mechanisms and Potential Therapeutic Targets

Organ transplantation remains the only treatment option for patients with end-stage organ dysfunction. However, there are numerous limitations that challenge its clinical application, including the shortage of organ donations, the quality of donated organs, injury during organ preservation and reperfusion, primary and chronic graft dysfunction, acute and chronic rejection, infection, and carcinogenesis in post-transplantation patients. Acute and chronic inflammation and cell death are two major underlying mechanisms for graft injury. Necroptosis is a type of programmed cell death involved in many diseases and has been studied in the setting of all major solid organ transplants, including the kidney, heart, liver, and lung. It is determined by the underlying donor organ conditions (e.g., age, alcohol consumption, fatty liver, hemorrhage shock, donation after circulatory death, etc.), preservation conditions and reperfusion, and allograft rejection. The specific molecular mechanisms of necroptosis have been uncovered in the organ transplantation setting, and potential targeting drugs have been identified. We hope this review article will promote more clinical research to determine the role of necroptosis and other types of programmed cell death in solid organ transplantation to alleviate the clinical burden of ischemia-reperfusion injury and graft rejection.

Cell type- and time-dependent biological responses in ex vivo perfused lung grafts

In response to the increasing demand for lung transplantation, ex vivo lung perfusion (EVLP) has extended the number of suitable donor lungs by rehabilitating marginal organs. However despite an expanding use in clinical practice, the responses of the different lung cell types to EVLP are not known. In order to advance our mechanistic understanding and establish a refine tool for improvement of EVLP, we conducted a pioneer study involving single cell RNA-seq on human lungs declined for transplantation. Functional enrichment analyses were performed upon integration of data sets generated at 4 h (clinical duration) and 10 h (prolonged duration) from two human lungs processed to EVLP. Pathways related to inflammation were predicted activated in epithelial and blood endothelial cells, in monocyte-derived macrophages and temporally at 4 h in alveolar macrophages. Pathways related to cytoskeleton signaling/organization were predicted reduced in most cell types mainly at 10 h. We identified a division of labor between cell types for the selected expression of cytokine and chemokine genes that varied according to time. Immune cells including CD4⁺ and CD8⁺ T cells, NK cells, mast cells and conventional dendritic cells displayed gene expression patterns indicating blunted activation, already at 4 h in several instances and further more at 10 h. Therefore despite inducing inflammatory responses, EVLP appears to dampen the activation of major lung immune cell types, what may be beneficial to the outcome of transplantation. Our results also support that therapeutics approaches aiming at reducing inflammation upon EVLP should target both the alveolar and vascular compartments.

Transient hyperthermia during ex vivo lung perfusion has no protective effect in rat model

BACKGROUND

Although ex vivo lung perfusion (EVLP) is a useful technique for evaluating and repairing donor lungs for transplantation, EVLP itself can lead to inflammation in the lung. Heat shock proteins (HSPs) have anti-inflammatory effects and can reduce ischemic reperfusion injury in the donor's lungs after transplantation. In this study, the effects of transient hyperthermia during EVLP on the expression of HSPs and inflammatory pathways were examined.

METHODS

Fifteen male Sprague-Dawley rats were randomly divided into three groups: sham (n = 5), normothermic EVLP (37 °C, n = 5), and transient hyperthermia during EVLP (42 °C, n = 5). Lung function analyses regarding PaO2/FiO2 ratio, compliance, and pulmonary vascular resistance were conducted. The expression levels of HSPs and inflammatory cytokines were also evaluated. The degree of lung injury was histopathologically evaluated. Transcriptome analysis was performed on lung tissues from the sham (n = 2), normothermic EVLP (n = 2), and heat stress-EVLP (n = 2) groups.

RESULTS

There were no significant differences in functional or histological parameters between the three groups. The expression of HSPs had significantly increased, especially that of HSPs 40 and 60 in the heat stress EVLP group; this was consistent with the inflammatory response. Inflammatory cytokine levels were significantly higher during EVLP and intensified with transient hyperthermia.

CONCLUSION

Transient hyperthermia during EVLP has no protective effect on the donor lung graft or activation of the inflammatory pathway at the gene level.

Effects of donor source on transcriptomic profiles of human kidney tissue

Normal human tissue is a critical reference control in biomedical research. However, the type of tissue donor can significantly affect the underlying biology of the samples. We investigated the impact of tissue donor source type by performing transcriptomic analysis on healthy kidney tissue from three donor source types: cadavers, organ donors, and normal-adjacent tissue from surgical resections of clear cell renal cell carcinomas, and we compared the gene expression profiles to those of clear cell renal cell carcinoma samples. Comparisons among the normal samples revealed general similarity, with notable differences in gene expression pathways involving immune system and inflammatory processes, response to extracellular stimuli, ion transport, and metabolism. When compared to tumors, the transcriptomic profiles of the normal adjacent tissue were highly similar to the profiles from cadaveric and organ donor tissue samples, arguing against the presence of a field cancerization effect in clear cell renal cell carcinoma. We conclude that all three normal source types are suitable for reference kidney control samples, but important differences must be noted for particular research areas and tissue banking strategies.

Altered purine metabolism at reperfusion affects clinical outcome in lung transplantation

INTRODUCTION

Lung transplantation is an established treatment for patients with end-stage lung disease. However, ischaemia reperfusion injury remains a barrier to achieving better survival outcomes. Here, we aim to investigate the metabolomic and transcriptomic profiles in human lungs before and after reperfusion, to identify mechanisms relevant to clinical outcome.

METHODS

We analysed 67 paired human lung tissue samples collected from 2008 to 2011, at the end of cold preservation and 2 hours after reperfusion. Gene expression analysis was performed with R. Pathway analysis was conducted with Ingenuity Pathway Analysis. MetaboAnalyst and OmicsNet were used for metabolomics analysis and omics data integration, respectively. Association of identified metabolites with transplant outcome was investigated with Kaplan-Meier estimate and Cox proportional hazard models.

RESULTS

Activation of energy metabolism and reduced antioxidative biochemicals were found by metabolomics. Upregulation of genes related to cytokines and inflammatory mediators, together with major signalling pathways were revealed by transcriptomics. Purine metabolism was identified as the most significantly enriched pathway at reperfusion, based on integrative analysis of the two omics data sets. Elevated expression of purine nucleoside phosphorylase (PNP) could be attributed to activation of multiple transcriptional pathways. PNP catabolised reactions were evidenced by changes in related metabolites, especially decreased levels of inosine and increased levels of uric acid. Multivariable analyses showed significant association of inosine and uric acid levels with intensive care unit length of stay and ventilation time.

CONCLUSION

Oxidative stress, especially through purine metabolism pathway, is a major metabolic event during reperfusion and may contribute to the ischaemia reperfusion injury of lung grafts.

Diagnostic and Therapeutic Implications of Ex Vivo Lung Perfusion in Lung Transplantation: Potential Benefits and Inherent Limitations

Ex vivo lung perfusion (EVLP), a technique in which isolated lungs are continually ventilated and perfused at normothermic temperature, is emerging as a promising platform to optimize donor lung quality and increase the lung graft pool. Over the past few decades, the EVLP technique has become recognized as a significant achievement and gained much attention in the field of lung transplantation. EVLP has been demonstrated to be an effective platform for various targeted therapies to optimize donor lung function before transplantation. Additionally, some physical parameters during EVLP and biological markers in the EVLP perfusate can be used to evaluate graft function before transplantation and predict posttransplant outcomes. However, despite its advantages, the clinical practice of EVLP continuously encounters multiple challenges associated with both intrinsic and extrinsic limitations. It is of utmost importance to address the advantages and disadvantages of EVLP for its broader clinical usage. Here, the pros and cons of EVLP are comprehensively discussed, with a focus on its benefits and potential approaches for overcoming the remaining limitations. Directions for future research to fully explore the clinical potential of EVLP in lung transplantation are also discussed.

Donation after circulatory death and lung transplantation

Lung transplantation is the most effective modality for the treatment of patients with end-stage lung diseases. Unfortunately, many people cannot benefit from this therapy due to insufficient donor availability. In this review and update article, we discuss donation after circulatory death (DCD), which is undoubtedly essential among the strategies developed to increase the donor pool. However, there are ethical and legislative considerations in the DCD process that are different from those of donation after brain death (DBD). Among others, the critical aspects of DCD are the concept of the end of life, cessation of futile treatments, and withdrawal of life-sustaining therapy. In addition, this review describes a rationale for using lungs from DCD donors and provides some important definitions, highlighting the key differences between DCD and DBD, including physiological aspects pertinent to each category. The unique ability of lungs to maintain cell viability without circulation, assuming that oxygen is supplied to the alveoli-an essential aspect of DCD-is also discussed. Furthermore, an updated review of the clinical experience with DCD for lung transplantation across international centers, recent advances in DCD, and some ethical dilemmas that deserve attention are also reported.

Challenging the Ex Vivo Lung Perfusion Procedure With Continuous Dialysis in a Pig Model

BACKGROUND

Normothermic ex vivo lung perfusion (EVLP) increases the pool of donor lungs by requalifying marginal lungs refused for transplantation through the recovery of macroscopic and functional properties. However the cell response and metabolism occurring during EVLP generate a nonphysiological accumulation of electrolytes, metabolites, cytokines and other cellular byproducts which may have deleterious effects both at the organ and cell levels, with impact on transplantation outcomes.

METHODS

We analyzed the physiological, metabolic and genome-wide response of lungs undergoing a 6-hour EVLP procedure in a pig model in 4 experimental conditions: without perfusate modification, with partial replacement of fluid, and with adult or pediatric dialysis filters.

RESULTS

Adult and pediatric dialysis stabilized the electrolytic and metabolic profiles while maintaining acid-base and gas exchanges. Pediatric dialysis increased the level of IL-10 and IL-6 in the perfusate. Despite leading to modification of the perfusate composition, the 4 EVLP conditions did not affect the gene expression profiles which were associated in all cases with increased cell survival, cell proliferation, inflammatory response and cell movement, and with inhibition of bleeding.

CONCLUSIONS

Management of EVLP perfusate by periodic replacement and continuous dialysis has no significant effect on the lung function nor on the gene expression profiles ex vivo. These results suggest that the accumulation of dialysable cell products does not significantly alter the lung cell response during EVLP, a finding that may have impact on EVLP management in the clinic.

miR-214 Alleviates Ischemic Stroke-Induced Neuronal Death by Targeting DAPK1 in Mice

BACKGROUND

Ischemic stroke induces neuronal cell death and causes brain dysfunction. Preventing neuronal cell death after stroke is key to protecting the brain from stroke damage. Nevertheless, preventative measures and treatment strategies for stroke damage are scarce. Emerging evidence suggests that microRNAs (miRNAs) play critical roles in the pathogenesis of central nervous system (CNS) disorders and may serve as potential therapeutic targets.

METHODS

A photochemically induced thrombosis (PIT) mouse model was used as an ischemic stroke model. qRT-PCR was employed to assess changes in miRNAs in ischemic lesions of PIT-stroke mice and primary cultured neurons subjected to oxygen-glucose deprivation (OGD). 2,3,5-triphenyltetrazolium chloride (TTC) staining was performed to evaluate brain infarction tissues in vivo. TUNEL staining was employed to assess neuronal death in vitro. Neurological scores and motor coordination were investigated to evaluate stroke damage, including neurological deficits and motor function.

RESULTS

In vivo and in vitro results demonstrated that levels of miR-124 were significantly decreased following stroke, whereas changes in death-associated protein kinase 1 (DAPK1) levels exhibited the converse pattern. DAPK1 was identified as a direct target of miR-124. N-methyl-D-aspartate (NMDA) and OGD-induced neuronal death was rescued by miR-124 overexpression. Upregulation of miR-124 levels significantly improved PIT-stroke damage, including the overall neurological function in mice.

CONCLUSION

We demonstrate the involvement of the miR-124/DAPK1 pathway in ischemic neuronal death. Our results highlight the therapeutic potential of targeting this pathway for ischemic stroke.