Insight into microvascular adaptive alterations in the Glisson system of biliary atresia after Kasai portoenterostomy using X-ray phase-contrast CT.

OBJECTIVES: To investigate microvascular alterations in the Glisson system of biliary atresia (BA) patients after Kasai portoenterostomy (KP) using three-dimensional (3D) virtual histopathology based on X-ray phase-contrast CT (PCCT). METHODS: Liver explants from BA patients were imaged using PCCT, and 32 subjects were included and divided into two groups: KP (n = 16) and non-KP (n = 16). Combined with histological analysis and 3D visualization technology, 3D virtual histopathological assessment of the biliary, arterial, and portal venous systems was performed. According to loop volume ratio, 3D spatial density, relative surface area, tortuosity, and other parameters, pathological changes of microvasculature in the Glisson system were investigated. RESULTS: In the non-KP group, bile ducts mostly manifested as radial multifurcated hyperplasia and twisted into loops. In the KP group, the bile duct hyperplasia was less, and the loop volume ratio of bile ducts decreased by 13.89%. Simultaneously, the arterial and portal venous systems presented adaptive alterations in response to degrees of bile duct hyperplasia. Compared with the non-KP group, the 3D spatial density of arteries in the KP group decreased by 3.53%, and the relative surface area decreased from 0.088 ± 0.035 to 0.039 ± 0.015 (p < .01). Deformed portal branches gradually recovered after KP, with a 2.93% increase in 3D spatial density and a decrease in tortuosity from 1.17 ± 0.06 to 1.14 ± 0.04 (p < .01) compared to the non-KP group. CONCLUSION: 3D virtual histopathology via PCCT clearly reveals the microvascular structures in the Glisson system of BA patients and provides key insights into the morphological mechanism of microvascular adaptation induced by biliary tract dredging after KP in BA disease. KEY POINTS: • 3D virtual histopathology via X-ray phase-contrast computed tomography clearly presented the morphological structures and pathological changes of microvasculature in the Glisson system of biliary atresia patients. • The morphological alterations of microvasculature in the Glisson system followed the competitive occupancy mechanism in the process of biliary atresia.

dbEssLnc: A manually curated database of human and mouse essential lncRNA genes.

Long non-coding RNAs (lncRNAs) play important roles in many biological processes. Knocking out or knocking down some lncRNAs will lead to lethality or infertility. These lncRNAs are called essential lncRNAs. Knowledges of essential lncRNAs are important in establishing minimal genomes of living cells, developing drug therapies and early diagnostic approaches for complex diseases. However, existing databases focus on collecting essential coding genes. Essential non-coding gene records are rare in existing databases. A comprehensive collection of essential non-coding genes, particularly essential lncRNA genes, is demanded. We manually curated 207 essential lncRNAs from literatures for establishing a database on essential lncRNAs, which is named as dbEssLnc (Database of essential lncRNAs). The dbEssLnc database has a web-based user-friendly interface for the users to browse, to search, to visualize and to blast search records in the database. The dbEssLnc database is freely accessible at https://esslnc.pufengdu.org. All data and source codes for mirroring the dbEssLnc database have been deposited in GitHub (https://github.com/yyZhang14/dbEssLnc).

XGEM: Predicting Essential miRNAs by the Ensembles of Various Sequence-Based Classifiers With XGBoost Algorithm.

MicroRNAs (miRNAs) play vital roles in gene expression regulations. Identification of essential miRNAs is of fundamental importance in understanding their cellular functions. Experimental methods for identifying essential miRNAs are always costly and time-consuming. Therefore, computational methods are considered as alternative approaches. Currently, only a handful of studies are focused on predicting essential miRNAs. In this work, we proposed to predict essential miRNAs using the XGBoost framework with CART (Classification and Regression Trees) on various types of sequence-based features. We named this method as XGEM (XGBoost for essential miRNAs). The prediction performance of XGEM is promising. In comparison with other state-of-the-art methods, XGEM performed the best, indicating its potential in identifying essential miRNAs.

SGII: Systematic Identification of Essential lncRNAs in Mouse and Human Genome With lncRNA-Protein-Protein Heterogeneous Interaction Network.

Long noncoding RNAs (lncRNAs) play important roles in a variety of biological processes. Knocking out or knocking down some lncRNA genes can lead to death or infertility. These lncRNAs are called essential lncRNAs. Identifying the essential lncRNA is of importance for complex disease diagnosis and treatments. However, experimental methods for identifying essential lncRNAs are always costly and time consuming. Therefore, computational methods can be considered as an alternative approach. We propose a method to identify essential lncRNAs by combining network centrality measures and lncRNA sequence information. By constructing a lncRNA-protein-protein interaction network, we measure the essentiality of lncRNAs from their role in the network and their sequence together. We name our method as the systematic gene importance index (SGII). As far as we can tell, this is the first attempt to identify essential lncRNAs by combining sequence and network information together. The results of our method indicated that essential lncRNAs have similar roles in the LPPI network as the essential coding genes in the PPI network. Another encouraging observation is that the network information can significantly boost the predictive performance of sequence-based method. All source code and dataset of SGII have been deposited in a GitHub repository (https://github.com/ninglolo/SGII).

Characterization and function analysis of Epinephelus coioides Hsp40 response to Vibrio alginolyticus and SGIV infection.

Heat shock protein 40 (Hsp40), a member of Heat shock proteins (Hsps) family, plays a crucial role in regulation of cell proliferation, survival and apoptosis in mammals. In this study, Hsp40, EcHsp40, was identified from Epinephelus coioides, an economically important marine-cultured fish in China and Southeast Asian counties. The full length of EcHsp40 was 2236 bp in length containing a 1026 bp open reading frame (ORF) encoding 341 amino acids, with a molecular mass of 37.88 kDa and a theoretical pI of 9.09. EcHsp40 has two conserved domains DnaJ and DnaJ_C. EcHsp40 mRNA was detected in all tissues examined, and the expression was significantly up-regulated response to challenged with Vibrio alginolyticus or Singapore grouper iridovirus (SGIV), one of the important pathogens of marine fish. EcHsp40 was distributed in both the cytoplasm and nucleus, over-expression of EcHsp40 can inhibit the activity of nuclear factor-κB (NF-κB) and activator protein-1 (AP-1), significantly promote SGIV-induced apoptosis, intracellular caspase-3 activity and viral replication, suggesting that the EcHsp40 may play an important role in pathogenic stimulation.

High-resolution three-dimensional visualization of hepatic sinusoids in cirrhotic rats via serial histological sections.

AIM: As a specialized intraparenchymal vascular conduit, hepatic sinusoids play a key role in liver microcirculation. This study aimed to explore the three-dimensional (3D) morphological changes of cirrhotic sinusoids by serial histological sections. METHODS: Cirrhosis was induced by tail vein injection of albumin in Wistar rats with a positive antibody. A total of 356 serial histological sections were prepared from liver tissue blocks of normal and cirrhotic rats. The optical microscope images were registered and reconstructed, and 3D reconstructions of the fine structures of fibrous tissues and sinusoids were subsequently visualized. RESULTS: The fibrosis area of the cirrhotic sample was 6-16 times that of the normal sample (P<0.001). Cirrhosis led to obvious changes in the distribution and morphology of sinusoids, which were mainly manifested as dilation, increased quantity and disordered distribution. Compared with normal liver, cirrhotic liver has a significantly increased volume ratio, number and volume of sinusoids (1.63-, 0.53-, and 1.75-fold, respectively, P<0.001). Furthermore, the samples were further divided into three zones according to the oxygen supply, and there were significant differences in the morphology of the sinusoids in the normal and cirrhotic samples (P<0.05). In particular, morphological parameters of the cirrhotic sinusoids near the portal area were obviously greater than those in the normal liver (P<0.05). CONCLUSION: 3D morphological structures of hepatic sinusoids were reconstructed, and the adaptive microstructure changes of cirrhotic sinusoids were accurately measured, which has an important implications for the study of hepatic microcirculation and pathological changes of cirrhosis.

Insight into Bile Duct Reaction to Obstruction from a Three-dimensional Perspective Using ex Vivo Phase-Contrast CT.

Background Biliary obstruction leads to an increase in biliary pressure within the biliary system, which induces the morphologic adaptation of the biliary tree. Purpose To observe and to quantify the morphologic characteristics of the adaptation in a bile duct ligation rat model and verify it in patients with biliary atresia in a three-dimensional (3D) manner using x-ray phase-contrast CT. Materials and Methods A bile duct ligation model was induced in 40 male Sprague-Dawley rats, which were divided into five groups: the control group (no ligation) and groups 2, 4, 6, and 8 weeks after bile duct ligation (eight animals in each group). Liver tissue samples (approximately 1.8 cm in length and 1.3 cm in height) were imaged by using phase-contrast CT and compared with histologic analysis. With a combination of phase-contrast CT and 3D visualization technology, the entire biliary system and the intrahepatic vascular system were quantitatively analyzed according to downstream, midstream, and upstream domains based on bile duct volume, surface area, and other parameters. Additionally, liver explant tissues from 28 patients with biliary atresia were studied to determine the impact of biliary tract reconstruction. Results To offset the increased biliary pressure within the biliary system, the ductular reaction in the downstream, midstream, and upstream domains manifested as dilatation, spiderweb-like looping, and interconnected honeycomb-like patterns, respectively. The most severe ductular reaction occurred in the upstream domain, and the relative surface area (mean, 0.02 µm-1 ± 0.01, 0.04 µm-1 ± 0.01, 0.07 µm-1 ± 0.02, and 0.10 µm-1 ± 0.02 for the 2-8-week groups, respectively; P < .01 among the groups) and volume fraction of ductules (mean, 16.54% ± 4.62, 19.69% ± 6.41, 26.92% ± 5.82, and 38.34% ± 10.36 for the 2-8-week groups, respectively; P < .01 among the groups except between the 2- and 4-week groups [P = .062]) significantly increased over time. In patients with biliary atresia, it was observed that both fibrosis and proliferative ductules regressed after successful biliary tract reconstruction following Kasai portoenterostomy. Furthermore, ductular reaction was accompanied by a progressive increase in the arterial supply but a loss of portal blood supply. Conclusion X-ray phase-contrast CT with three-dimensional rendering of the biliary system in a bile duct ligation rat model provides key insights into ductular reaction or biliary self-adaptation triggered by increased biliary pressure. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Vannier and Wang in this issue.

The Gut Microbiota and Its Relevance to Peripheral Lymphocyte Subpopulations and Cytokines in Patients with Rheumatoid Arthritis.

Growing experimental and clinical evidence suggests that a chronic inflammatory response induced by gut microbiome critically contribute to the development of rheumatoid arthritis (RA). Previous studies demonstrated the disturbance of lymphocyte subpopulations in RA patients. The purpose of this study was to explore the characteristics of gut microbiome and the associations between bacterium and lymphocyte subpopulations as well as cytokines in patients with RA. Fecal samples from 205 RA patients and 199 healthy controls (HCs) were collected for bacterial DNA extraction and 16S ribosomal RNA (rRNA) gene sequencing. The levels of peripheral lymphocyte subpopulation such as T, B, CD4+T, CD8+T, NK, T helper 1 (Th1), Th2, Th17, and regulatory T cells (Tregs) of these subjects were detected by flow cytometry combined with standard absolute counting beads. The serum levels of cytokines interleukin-2 (IL-2), IL-4, IL-6, IL-10, IL-17, tumour necrosis factor-α (TNF-α), and interferon-γ (INF-γ) were tested by flow cytometric bead array (CBA). Alpha and beta diversity of gut microbiome were explored by bioinformatics analysis. Spearman rank correlation test was used to explore the relationships between gut microbiome and lymphocyte subsets as well as serum cytokines. The diversity and relative abundance of intestinal microbiota in patients with RA were significantly different from those in HCs. Detailly, the abundant of phylum Proteobacteria in RA patients was more than that in HCs, while Firmicutes was less than in HCs. There was increased relative abundance of genus Clostridium_XlVa as well as genus Blautia, more abundance of Ruminococcus2 in patients with lower levels of T, B, CD4+T, and Tregs. In addition, the relative abundances of Pelagibacterium, Oxalobacter, ClostridiumXlVb, and ClostridiumXVIII were correlated with cytokines. Gut microbiome of RA patients was clearly different from that of HCs. Abnormal bacteria communities are associated with the altered levels of lymphocyte subpopulation and cytokines, which might be one of the pathogenesis of RA.

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy.

The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies.IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.

DDA-SKF: Predicting Drug-Disease Associations Using Similarity Kernel Fusion.

Drug repositioning provides a promising and efficient strategy to discover potential associations between drugs and diseases. Many systematic computational drug-repositioning methods have been introduced, which are based on various similarities of drugs and diseases. In this work, we proposed a new computational model, DDA-SKF (drug-disease associations prediction using similarity kernels fusion), which can predict novel drug indications by utilizing similarity kernel fusion (SKF) and Laplacian regularized least squares (LapRLS) algorithms. DDA-SKF integrated multiple similarities of drugs and diseases. The prediction performances of DDA-SKF are better, or at least comparable, to all state-of-the-art methods. The DDA-SKF can work without sufficient similarity information between drug indications. This allows us to predict new purpose for orphan drugs. The source code and benchmarking datasets are deposited in a GitHub repository (https://github.com/GCQ2119216031/DDA-SKF).

[Soluble expression, purification and bioactivity of recombinant human Era protein].

AIM: To prepare a soluble human Era(hEra) protein and to measure its bioactivity. METHODS: Human era cDNA gene from pUC19 plasmid was subcloned into the expression plasmid pMAL-p2x. pMAL-hEra was transducted to E.coli TB1 and the strain was induced by isopropyl beta-D-thiogalactopyranoside (IPTG). RESULTS: The expressed MBP-fused protein existed in a soluble form. The fused protein made up 23.9% of the total cell lysate. It was purified by amylose affinity chromotography and digested with Factor X. Although the fused segment was dissected, the remained hEra protein was unstable in the solution with the passage of time. The activity assay showed that hEra was a GTPase that could bind GTP and hydrolyze GTP to GDP. CONCLUSION: Human Era protein can be expressed in a soluble form and it has been proved to be a kind of G protein by the experiments in vitro. The study is important to further research into the function of human era gene.