Bulk and single-cell RNA sequencing analysis with 101 machine learning combinations reveal neutrophil extracellular trap involvement in hepatic ischemia-reperfusion injury and early allograft dysfunction

BACKGROUND

Hepatic ischaemia-reperfusion injury (HIRI) is a major clinical concern during the perioperative period and is closely associated with early allograft dysfunction (EAD), acute rejection (AR) and long-term graft survival. Neutrophil extracellular traps (NETs) are extracellular structures formed by the release of decondensed chromatin and granular proteins following neutrophil stimulation. There is growing evidence that NETs are involved in the progression of various liver transplantation complications, including ischaemia-reperfusion injury (IRI). This study aimed to comprehensively analyse the expression patterns of NET-related genes (NRGs) in HIRI, identify HIRI subtypes with distinct characteristics, and develop a reliable EAD prediction model.

METHODS

Microarray, bulk RNA-seq, and single-cell sequencing datasets were obtained from the GEO database. Initially, differentially expressed NRGs (DE-NRGs) were identified using differential gene expression analyses. We then utilised a non-negative matrix factorisation (NMF) algorithm to classify HIRI samples. Subsequently, we employed machine learning algorithms to screen the hub NRGs related to EAD and developed an EAD prediction model based on these hub NRGs. Concurrently, we assessed the expression patterns of hub NRGs at the single-cell level using the HIRI. Additionally, we validated C5AR1 expression and its effect on HIRI and NETs formation in a rat orthotopic liver transplantation (OLT) model.

RESULTS

In this study, we identified 11 DE-NRGs in the HIRI context. Based on these 11 DE-NRGs, HIRI samples were classified into two distinct clusters. Cluster1 exhibited a low expression of DE-NRGs, minimal neutrophil infiltration, mild inflammation, and a low incidence of EAD. Conversely, Cluster2 displayed the opposite phenotype, with an activated inflammatory subtype and a higher incidence of EAD. Furthermore, an EAD prediction model was developed using the four hub NRGs associated with EAD. Based on risk scores, HIRI samples were classified into high- and low-risk groups. The OLT model confirmed substantial upregulation of C5AR1 expression in the liver tissue, accompanied by increased formation of NETs. Treatment with a C5AR1 antagonist improved liver function, reduced tissue inflammation, and decreased NETs formation.

CONCLUSIONS

This study distinguished two apparent HIRI subtypes, established a predictive model for EAD, and validated the effect of C5AR1 on HIRI. These findings provide novel perspectives for the development of advanced clinical strategies to enhance the outcomes of liver transplant recipients.

A compact electron beam ion trap in support of high-temperature plasma diagnostics based on conduction-cooled superconducting coils

Spectroscopic diagnostics of future fusion reactor plasmas require information on impurity line emissions, especially for relevant high-Z metal elements (e.g., tungsten). These materials will be widely used as plasma facing components for their high heat tolerance and low sputtering yield. Based on an electron beam ion trap, a compact impurity spectra platform is developed to mimic the high-temperature environment of a fusion reactor. The proposed platform can deliver a focused e-beam at energies over 30 keV using a confining magnetic field of ∼1.0 T generated by two superconducting coils (NbTi). Cooled by a closed-loop cryocooler, the coils can avoid the usage of a complicated cryogenic system involving the handling of liquid helium. For spectroscopic studies of highly charged ions, a spherically curved crystal spectrometer is proposed to measure a wavelength range around 2-4 Å covering the typical wavelength range expected to be emitted by metal ions in a fusion plasma. This paper reports the design and development progress of the platform.

Development and preliminary test of a space-resolved vacuum-ultraviolet spectroscopy in EAST

The impurity radiation from the divertor region of the EAST tokamak is dominantly in the wavelength range of vacuum ultraviolet (VUV) due to the elevated edge electron temperature. A space-resolved VUV spectroscopy is developed to measure impurity radiation in the divertor region. An eagle-type VUV spectrometer with a focal length of 1 m is adopted in this system, equipped with a spherical grating and a charged-coupled device (CCD) detector. The performance of the VUV spectrometer is preliminarily tested on a synchrotron radiation facility. The wavelength calibration is conducted near 65 nm. It is found that the wavelength range observed by the CCD detector is about 11.07 nm around the central wavelength of about 65 nm. With a linear dispersion of 0.0053 nm/pixel, it is possible to measure the ion temperature lower than 20 eV at the edge region by analyzing the Doppler broadening of a carbon line. These test results show that the performance of the VUV spectrometer is capable of measuring divertor radiation and analyzing the ion temperature of edge impurity ions.

Prevention of lymphatic filariasis with insecticide-treated bednets in Cambodia

Potential risk factors for lymphatic filariasis (LF), including the failure to use insecticide-treated bednets (ITN), were studied in four north-eastern provinces of Cambodia, using 43 cases of LF and 248 apparently healthy controls who were matched with the cases in terms of age (+/-5 years), gender and village. The results of a univariate matched analysis indicated that lack of ITN [odds ratio (OR)=20.1; 95% confidence interval (CI)=2.2-182.4; P=0.008] and frequent overnight stays in forests or paddy fields outside the village (OR=3.6; CI=1.3-10.0; P=0.012) were the most important risk factors. In a multivariate matched analysis, frequent overnight stays outside the village combined with bednet use showed a clear dose-response relationship, with untreated nets offering significant protection during such stays but ITN offering significantly better protection. Even if villagers used ITN during such stays, they were significantly more likely to develop LF than villagers who did not travel (OR=5.0; CI=1.5-16.3; P=0.008), and if they used untreated or no nets while away they were even more likely than the non-travellers to develop the disease (OR=1413; CI=28.0-71,189; P<0.001). Taken together, these results provide further evidence for the importance of bednet use and their impregnation in the prevention of LF. At least in north-eastern Cambodia, the use of bednets and, preferably, ITN is particularly important during overnight stays outside the home village. In areas where LF is endemic, the sustained distribution of insecticide-treated bednets or hammock nets appears to be a very good idea.

[3H]Azidodantrolene: synthesis and use in identification of a putative skeletal muscle dantrolene binding site in sarcoplasmic reticulum

Dantrolene sodium is a medically important hydantoin derivative that interferes with release of Ca2+ from intracellular stores of skeletal muscle by an unknown mechanism. Identification of the molecular target of dantrolene would greatly aid in understanding both the mechanism of action of the drug and the dynamics of intracellular Ca2+ release in muscle. [3H]Azidodantrolene was designed and synthesized as a photoaffinity analogue in order to identify a putative dantrolene receptor in skeletal muscle. Introduction of 1 mole-atom of tritium into aldehyde 5b was required during radioligand synthesis in order to ensure high enough specific activity for detection of photo-cross-linked proteins by fluorographic methods. This was accomplished by reduction of ester 3 with custom synthesized, 100% tritium-labeled lithium triethylborotritide, followed by oxidation to 5b by manganese(IV) oxide. Compound 6b was demonstrated to be >/=95% tritium-labeled at the imine position by NMR spectroscopy, and the specific radioactivity of [3H]azidodantrolene sodium was empirically determined by HPLC and liquid scintillation counting to be 24.4 Ci/mmol, approximately 85% of theoretical maximum. [3H]Azidodantrolene was found to be pharmacologically active in ligand-receptor binding studies with skeletal muscle sarcoplasmic reticulum membranes. Photo-cross-linking experiments analyzed by SDS-PAGE and tritium fluorography have identified a approximately 160-kDa specifically labeled protein as the putative, intracellular, skeletal muscle dantrolene receptor. This photolabeled protein comigrates with a protein in Western blots immunologically cross-reactive to a polyclonal anti-rabbit skeletal muscle ryanodine receptor antibody. Thus, the putative dantrolene receptor may be related to the skeletal muscle ryanodine receptor.