B cell activation gene signature in blood and liver of HBeAg+ immune active chronic hepatitis B patients.

BACKGROUND: Immunological studies on chronic hepatitis B virus (HBV) infection have convincingly shown immune dysfunction involving multiple cell types. The focus of the majority of studies has been on the role of T cells and showed an impaired functional T cell response to HBV. B cells have been evaluated more recently, but in contrast to T cells, more pronounced activation of circulating B cells has been reported. To gain more insight into the activation status of B cells, we investigated the activation gene profile of B cells in the blood and liver of chronic HBV patients. METHODS: RNA-seq and flow cytometric analysis was performed on peripheral blood B cells of immune active chronic HBV patients, comparing them with samples from healthy controls. In addition, gene expression profiles of B cells in the liver were analyzed by bulk and single-cell RNA-seq. RESULTS AND CONCLUSIONS: Our data show a distinctive B cell activation gene signature in the blood of immune active chronic HBV patients, characterized by a significant upregulation of immune-related genes, including IRF1, STAT1, STAT3, TAP1, and TAPBP. This peripheral activation profile was also observed in B cells from the liver by single cell RNA-seq showing upregulation of IRF1, CD83 and significantly higher CD69 expression, with naive and memory B cell subsets being the primary carriers of the signature. Our findings suggest that B cell gene profiles reflect responsiveness to HBV infection, these findings are relevant for clinical studies evaluating immunomodulatory treatment strategies for HBV.

Intrahepatic plasma cells, but not atypical memory B cells, associate with clinical phases of chronic hepatitis B.

Studies have traditionally focused on the role of T cells in chronic hepatitis B (CHB), but recent evidence supports a role for B cells. The enrichment of so-called atypical memory (AtM) B cells, which show reduced signaling and impaired differentiation, is believed to be a characteristic feature of CHB, potentially contributing to the observed dysfunctional anti-HBsAg B-cell responses. Our study, involving 62 CHB patients across clinical phases, identified AtM B cells expressing IFNLR1 and interferon-stimulated genes. Contrary to previous reports, we found relatively low frequencies of AtM B cells in the liver, comparable to peripheral blood. However, liver plasma cell frequencies were significantly higher, particularly during phases with elevated viral loads and liver enzyme levels. Liver plasma cells exhibited signs of active proliferation, especially in the immune active phase. Our findings suggest a potential role for plasma cells, alongside potential implications and consequences of local proliferation, within the livers of CHB patients. While the significance of AtM B cells remains uncertain, further investigation is warranted to determine their responsiveness to interferons and their role in CHB.

Magmatism controls global oceanic transform fault topography.

Oceanic transform faults play an essential role in plate tectonics. Yet to date, there is no unifying explanation for the global trend in broad-scale transform fault topography, ranging from deep valleys to shallow topographic highs. Using three-dimensional numerical models, we find that spreading-rate dependent magmatism within the transform domain exerts a first-order control on the observed spectrum of transform fault depths. Low-rate magmatism results in deep transform valleys caused by transform-parallel tectonic stretching; intermediate-rate magmatism fully accommodates far-field stretching, but strike-slip motion induces across-transform tension, producing transform strength dependent shallow valleys; high-rate magmatism produces elevated transform zones due to local compression. Our models also address the observation that fracture zones are consistently shallower than their adjacent transform fault zones. These results suggest that plate motion change is not a necessary condition for reproducing oceanic transform topography and that oceanic transform faults are not simple conservative strike-slip plate boundaries.

Association of HBsAg levels with differential gene expression in NK, CD8 T, and memory B cells in treated patients with chronic HBV.

Background & Aims: HBsAg secretion may impact immune responses to chronic HBV infection. Thus, therapeutic approaches to suppress HBsAg production are being investigated. Our study aims to examine the immunomodulatory effects of high and low levels of circulating HBsAg and thereby improve our understanding of anti-HBV immunity. Methods: An optimized 10x Genomics single-cell RNA sequencing workflow was applied to blood samples and liver fine-needle aspirates from 18 patients undergoing tenofovir/entecavir (NUC) treatment for chronic HBV infection. They were categorized based on their HBsAg levels: high (920-12,447 IU/ml) or low (1-100 IU/ml). Cluster frequencies, differential gene expression, and phenotypes were analyzed. Results: In the blood of HBV-infected patients on NUC, the proportion of KLRC2+ "adaptive" natural killer (NK) cells was significantly lower in the HBsAg-high group and, remarkably, both KLRC2+ NK and KLRG1+ CD8 T cells display enrichment of lymphocyte activation-associated gene sets in the HBsAg-low group. High levels of HBsAg were associated with mild immune activation in the liver. However, no suppression of liver-resident CXCR6+ NCAM1+ NK or CXCR6+ CD69+ CD8 T cells was detected, while memory B cells showed signs of activation in both the blood and liver. Conclusions: Among NUC-treated patients, we observed a minimal impact of HBsAg on leukocyte populations in the blood and liver. However, for the first time, we found that HBsAg has distinct effects, restricted to NK-, CD8 T-, and memory B-cell subsets, in the blood and liver. Our findings are highly relevant for current clinical studies evaluating treatment strategies aimed at suppressing HBsAg production and reinvigorating immunity to HBV. Impact and implications: This study provides unique insight into the impact of HBsAg on gene expression levels of immune cell subsets in the blood and liver, particularly in the context of NUC-treated chronic HBV infection. It holds significant relevance for current and future clinical studies evaluating treatment strategies aimed at suppressing HBsAg production and reinvigorating immunity to HBV. Our findings raise questions about the effectiveness of such treatment strategies and challenge the previously hypothesized immunomodulatory effects of HBsAg on immune responses against HBV.

Cryptogenic non-cirrhotic HCC: Clinical, prognostic and immunologic aspects of an emerging HCC etiology.

The incidence of hepatocellular carcinoma (HCC) in non-cirrhotic livers is rising significantly, but clear risk factors for screening remain elusive. This study sought to characterize non-cirrhotic HCC etiologies. HCC cases from 2009 to 2020 in a Dutch referral center were examined, revealing 371 out of 1654 cases (22%) as non-cirrhotic. Notably, the incidence of non-cirrhotic HCC increased by 61% in the time frame between 2009 and 2020. Interestingly 39% of non-cirrhotic HCC cases had cryptogenic origins. Cryptogenic non-cirrhotic HCC exhibited similarities with non-cirrhotic NAFLD HCC, but displayed advanced tumor stages, lower surgical rates, and a more frequent presence of symptoms, which substantiated in poor survival rates. Advanced cryptogenic non-cirrhotic HCC stages exhibited elevated serum interleukin-6 levels compared to non-cirrhotic HCC with defined etiologies. Comparative analysis encompassing cryptogenic and NAFLD non-cirrhotic HCC cohorts and controls unveiled comparable circulating immune biomarker profiles and PNPLA3 polymorphisms. To conclude, the primary etiology of non-cirrhotic HCC in our cohort has not defined risk factors. This cryptogenic variant exhibits distinct traits, such as advanced tumors and increased symptoms, and most resemble burned-out NAFLD. Understanding this HCC variant is crucial for improving screening and management strategies.

Synthesis of N-acyl carbazoles, phenoxazines and acridines from cyclic diaryliodonium salts.

N-Acyl carbazoles can be efficiently produced through a single-step process using amides and cyclic diaryliodonium triflates. This convenient reaction is facilitated by copper iodide in p-xylene, using the commonly found activating ligand diglyme. We have tested this method with a wide range of amides and iodonium triflates, proving its versatility with numerous substrates. Beyond carbazoles, we also produced a variety of other N-heterocycles, such as acridines, phenoxazines, or phenazines, showcasing the robustness of our technique. In a broader sense, this new method creates two C-N bonds simultaneously based on a mono-halogenated starting material, thus allowing heterocycle formation with diminished halogen waste.

ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.

While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2-27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2-27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2-27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.

Validation and optimization of AFP-based biomarker panels for early HCC detection in Latin America and Europe.

BACKGROUND: HCC is a major cause of cancer death worldwide. Serum biomarkers such as alpha-fetoprotein (AFP), protein induced by vitamin K absence-II, and the Gender, Age, AFP-L3, AFP, Des-gamma-carboxy prothrombin (GALAD) score have been recommended for HCC surveillance. However, inconsistent recommendations in international guidelines limit their clinical utility. METHODS: In this multicenter study, over 2000 patient samples were collected in 6 Latin American and 2 European countries. The performance of the GALAD score was validated in cirrhotic cases, and optimized versions were tested for early-stage HCC and prediagnostic HCC detection. RESULTS: The GALAD score could distinguish between HCC and cirrhosis in Latin American patients with an AUC of 0.76, sensitivity of 70%, and specificity of 83% at the conventional cutoff value of -0.63. In a European cohort, GALAD had an AUC of 0.69, sensitivity of 66%, and specificity of 72%. Optimizing the score in the 2 large multicenter cohorts revealed that AFP-L3 contributed minimally to early-stage HCC detection. Thus, we developed a modified GALAD score without AFP-L3, the ASAP (age, sex, AFP, and protein induced by vitamin K absence-II), which showed promise for early-stage HCC detection upon validation. The ASAP score also identified patients with cirrhosis at high risk for advanced-stage HCC up to 15 months before diagnosis (p < 0.0001) and differentiated HCC from hemangiomas, with a specificity of 100% at 71% sensitivity. CONCLUSION: Our comprehensive analysis of large sample cohorts validates the GALAD score's utility in Latin American, Spanish, and Dutch patients for early-stage HCC detection. The optimized GALAD without AFP-L3, the ASAP score, is a good alternative and shows greater promise for HCC prediction.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer.

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.

How transform fault shear influences where detachment faults form near mid-ocean ridges.

Oceanic detachment faults represent an end-member form of seafloor creation, associated with relatively weak magmatism at slow-spreading mid-ocean ridges. We use 3-D numerical models to investigate the underlying mechanisms for why detachment faults predominantly form on the transform side (inside corner) of a ridge-transform intersection as opposed to the fracture zone side (outside corner). One hypothesis for this behavior is that the slipping, and hence weaker, transform fault allows for the detachment fault to form on the inside corner, and a stronger fracture zone prevents the detachment fault from forming on the outside corner. However, the results of our numerical models, which simulate different frictional strengths in the transform and fracture zone, do not support the first hypothesis. Instead, the model results, combined with evidence from rock physics experiments, suggest that shear-stress on transform fault generates excess lithospheric tension that promotes detachment faulting on the inside corner.

Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients.

BACKGROUND AND AIMS: HBV infection is restricted to the liver, where it drives exhaustion of virus-specific T and B cells and pathogenesis through dysregulation of intrahepatic immunity. Our understanding of liver-specific events related to viral control and liver damage has relied almost solely on animal models, and we lack useable peripheral biomarkers to quantify intrahepatic immune activation beyond cytokine measurement. Our objective was to overcome the practical obstacles of liver sampling using fine-needle aspiration and develop an optimized workflow to comprehensively compare the blood and liver compartments within patients with chronic hepatitis B using single-cell RNA sequencing. APPROACH AND RESULTS: We developed a workflow that enabled multi-site international studies and centralized single-cell RNA sequencing. Blood and liver fine-needle aspirations were collected, and cellular and molecular captures were compared between the Seq-Well S 3 picowell-based and the 10× Chromium reverse-emulsion droplet-based single-cell RNA sequencing technologies. Both technologies captured the cellular diversity of the liver, but Seq-Well S 3 effectively captured neutrophils, which were absent in the 10× dataset. CD8 T cells and neutrophils displayed distinct transcriptional profiles between blood and liver. In addition, liver fine-needle aspirations captured a heterogeneous liver macrophage population. Comparison between untreated patients with chronic hepatitis B and patients treated with nucleoside analogs showed that myeloid cells were highly sensitive to environmental changes while lymphocytes displayed minimal differences. CONCLUSIONS: The ability to electively sample and intensively profile the immune landscape of the liver, and generate high-resolution data, will enable multi-site clinical studies to identify biomarkers for intrahepatic immune activity in HBV and beyond.

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 Using Proximity Labeling and Affinity Purification.

The DNA repair scaffold SLX4 has pivotal roles in cellular processes that maintain genome stability, most notably homologous recombination. Germline mutations in SLX4 are associated with Fanconi anemia, a disease characterized by chromosome instability and cancer susceptibility. The role of mammalian SLX4 in homologous recombination depends critically on binding and activating structure-selective endonucleases, namely SLX1, MUS81-EME1, and XPF-ERCC1. Increasing evidence indicates that cells rely on distinct SLX4-dependent complexes to remove DNA lesions in specific regions of the genome. Despite our understanding of SLX4 as a scaffold for DNA repair proteins, a detailed repertoire of SLX4 interactors has never been reported. Here, we provide a comprehensive map of the human SLX4 interactome using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS). We identified 221 unique high-confidence interactors, of which the vast majority represent novel SLX4-binding proteins. Network analysis of these hits revealed pathways with known involvement of SLX4, such as DNA repair, and several emerging pathways of interest, including RNA metabolism and chromatin remodeling. In summary, the comprehensive SLX4 interactome we report here provides a deeper understanding of how SLX4 functions in DNA repair while revealing new cellular processes that may involve SLX4.

Synthesis and reactivity of azole-based iodazinium salts.

A systematic investigation of imidazo- and pyrazoloiodazinium salts is presented. Besides a robust synthetic protocol that allowed us to synthesize these novel cyclic iodonium salts in their mono- and dicationic forms, we gained in-depth structural information through single-crystal analysis and demonstrated the ring opening of the heterocycle-bridged iodonium species. For an exclusive set of dicationic imidazoiodaziniums, we show highly delicate post-oxidation functionalizations retaining the hypervalent iodine center.

Subduction initiation triggered the Caribbean large igneous province.

Subduction provides the primary driving force for plate tectonics. However, the mechanisms leading to the formation of new subduction zones remain debated. An example is the Lesser Antilles Arc in the Atlantic. Previous initiation mechanisms have implied the transmission of subduction from the Pacific Ocean or the impact of a plume head. Here, we use geodynamic models to simulate the evolution of the Caribbean region during the Cretaceous, where the eastern Pacific subduction triggered the formation of a new subduction zone in the Atlantic. The simulations show how the collision of the old Caribbean plateau with the Central America margin lead to the formation of a new Atlantic subduction zone by polarity reversal. The results further show how subduction renewal on the back of the old Caribbean plateau (present-day Central America) resulted in a major mantle flow reorganization that generated a subduction-induced plume consistent with the formation of the Caribbean Large Igneous Province.

Two-step continuous-flow synthesis of 6-membered cyclic iodonium salts via anodic oxidation.

We describe a multi-step continuous-flow procedure for the generation of six-membered diaryliodonium salts. The accompanying scalability and atom economy are significant improvements to existing batch methods. Benzyl acetates are submitted to this two-step procedure as highly available and cheap starting materials. An acid-catalyzed Friedel-Crafts alkylation followed by an anodic oxidative cyclization yielded a defined set of cyclic iodonium salts in a highly substrate-dependent yield.

Circulating Cytokines Reflect the Etiology-Specific Immune Environment in Cirrhosis and HCC.

Background and Aims: Chronic liver disease­from any etiology­can progress to fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The progression of liver cirrhosis to the end stages of disease is influenced by a variety of factors, including inflammatory cytokines. We pursued a study of cytokine-mediated inflammatory responses in hepatitis B (HBV), hepatitis C (HCV), alcoholic liver disease (ALD) and non-alcoholic fatty liver disease (NAFLD) patients with liver cirrhosis. Methods: Immune profiles were determined through the serum multiplex profiling of >100 cytokines in a 188 cirrhotic patients, 35 healthy controls and 196 early-stage HCC patients. Results: Patients with liver cirrhosis exhibited a vast upregulation of proinflammatory cytokines (p < 0.0001), including those with pro-oncogenic features, when compared to healthy individuals. In contrast to prevailing assumptions, each etiological cause of cirrhosis exhibited a unique cytokine profile in blood. Regardless of antiviral therapy, HBV cirrhosis patients had the largest number of upregulated proinflammatory mediators, compared to HCV, ALD and NAFLD (p < 0.0001). To further evaluate the etiology-dependent modulation of cytokine response in relation to liver cancer, we studied cytokine profiles in early-stage HCC patients strictly stratified by underlying liver disease. We observed unique sets of differentially expressed cytokines in each cohort of early-stage HCC patients of different cirrhosis etiologies. Conclusions: Our findings, therefore, underscore the importance of stratification by the etiological cause of liver cirrhosis in immune-based studies.

Eating Time as a Genetic Indicator of Methane Emissions and Feed Efficiency in Australian Maternal Composite Sheep.

Previous studies have shown reduced enteric methane emissions (ME) and residual feed intake (RFI) through the application of genomic selection in ruminants. The objective of this study was to evaluate feeding behaviour traits as genetic indicators for ME and RFI in Australian Maternal Composite ewes using data from an automated feed intake facility. The feeding behaviour traits evaluated were the amount of time spent eating per day (eating time; ETD; min/day) and per visit (eating time per event; ETE; min/event), daily number of events (DNE), event feed intake (EFI; g/event) and eating rate (ER; g/min). Genotypes and phenotypes of 445 ewes at three different ages (post-weaning, hogget, and adult) were used to estimate the heritability of ME, RFI, and the feeding behaviour traits using univariate genomic best linear unbiased prediction models. Multivariate models were used to estimate the correlations between these traits and within each trait at different ages. The response to selection was evaluated for ME and RFI with direct selection models and indirect models with ETE as an indicator trait, as this behaviour trait was a promising indicator based on heritability and genetic correlations. Heritabilities were between 0.12 and 0.18 for ME and RFI, and between 0.29 and 0.47 for the eating behaviour traits. In our data, selecting for more efficient animals (low RFI) would lead to higher methane emissions per day and per kg of dry matter intake. Selecting for more ETE also improves feed efficiency but results in more methane per day and per kg dry matter intake. Based on our results, ETE could be evaluated as an indicator trait for ME and RFI under an index approach that allows simultaneous selection for improvement in emissions and feed efficiency. Selecting for ETE may have a tremendous impact on the industry, as it may be easier and cheaper to obtain than feed intake and ME data. As the data were collected using individual feeding units, the findings on this research should be validated under grazing conditions.

Structure Elucidation of In Situ Generated Chiral Hypervalent Iodine Complexes via Vibrational Circular Dichroism (VCD).

The structure of in situ generated chiral aryl-λ3 -iodanes obtained under oxidative reaction conditions was not yet observable with experimental techniques and their proposed structures are purely based on DFT calculations. Herein, we establish vibrational circular dichroism (VCD) spectroscopy as an experimental technique to verify DFT-calculated chiral iodane structures. Based on a chiral triazole-substituted iodoarene catalyst, we were able to elucidate a yet undescribed cationic chiral iodane as the most populated intermediate under oxidative conditions with a significant intramolecular N-I-interaction and no significant interactions with tosylate or m-chlorobenzoic acid as potential anionic ligands. Instead, aggregation of these substrates was found, which resulted in the formation of a non-coordinating anionic hydrogen bonded complex. The importance of VCD as a crucial experimental observable is further highlighted by the fact that our initial structural proposal, that was purely based on DFT calculations, could be falsified.

One-Pot Synthesis of Heteroatom-Bridged Cyclic Diaryliodonium Salts.

Two one-pot procedures for the construction of O- and N-bridged diaryliodonium triflates are described. An effective aryne-mediated arylation of o-iodophenols and -sulfonamides provides diarylether and diarylamine intermediates, which are subsequently oxidized and cyclized to the corresponding diaryliodaoxinium and -iodazinium salts. Different derivatizations were applied to demonstrate their capacity as useful building blocks and gain a deeper understanding toward the general reactivity of these underdeveloped but potentially highly useful compounds.