Single-cell resolution unravels spatial alterations in metabolism, transcriptome and epigenome of ageing liver

Epigenetic ageing clocks have revealed that tissues within an organism can age with different velocity. However, it has not been explored whether cells of one type experience different ageing trajectories within a tissue depending on their location. Here, we employed lipidomics, spatial transcriptomics and single-cell ATAC-seq in conjunction with available single-cell RNA-seq data to address how cells in the murine liver are affected by age-related changes of the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. Particularly periportal hepatocytes were characterized by decreased mitochondrial function and strong alterations in the epigenetic landscape, while pericentral hepatocytes,despite accumulation of large lipid droplets, did not show apparent functional differences. In general, chromatin alterations did not correlate well with transcriptional changes, hinting at post-transcriptional processes that shape gene expression during ageing. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.

Palm Oil-Rich Diet Affects Murine Liver Proteome and S-Palmitoylome

Palmitic acid (C16:0) is the most abundant saturated fatty acid in animals serving as a substrate in synthesis and β-oxidation of other lipids, and in the modification of proteins called palmitoylation. The influence of dietary palmitic acid on protein S-palmitoylation remains largely unknown. In this study we performed high-throughput proteomic analyses of a membrane-enriched fraction of murine liver to examine the influence of a palm oil-rich diet (HPD) on S-palmitoylation of proteins. HPD feeding for 4 weeks led to an accumulation of C16:0 and C18:1 fatty acids in livers which disappeared after 12-week feeding, in contrast to an accumulation of C16:0 in peritoneal macrophages. Parallel proteomic studies revealed that HPD feeding induced a sequence of changes of the level and/or S-palmitoylation of diverse liver proteins involved in fatty acid, cholesterol and amino acid metabolism, hemostasis, and neutrophil degranulation. The HPD diet did not lead to liver damage, however, it caused progressing obesity, hypercholesterolemia and hyperglycemia. We conclude that the relatively mild negative impact of such diet on liver functioning can be attributed to a lower bioavailability of palm oil-derived C16:0 vs. that of C18:1 and the efficiency of mechanisms preventing liver injury, possibly including dynamic protein S-palmitoylation.

Inhibition of COX-2 Ameliorates Murine Liver Schistosomiasis Japonica Through Splenic Cellular Immunoregulation

We have reported the positive association of cyclooxygenase 2 (COX-2)/prostaglandin E2 (PGE2) axis with liver fibrosis induced by Schistosoma japonicum (Sj) infection, and TLR4 signaling controlled this axis. However, how COX-2 regulated immune response during Sj infection is still unclear. Here we further studied the effect of COX-2 specific inhibitor-NS398 on liver granulomatous inflammation, fibrosis and explored the mechanisms via evaluating different immune cell during Sj infection.The results showed that NS398 significantly reduced the size of liver granuloma, spleen and mesenteric lymph node (MLN) and alleviated chronic granulomatous inflammation. Mechanically, it might be via decreasing the numbers of Sj-induced T helper type 1 (Th1), Th2, T follicular helper (Tfh), T follicular regulatory cells (Tfr) and germinal center B (GCB) cells to alleviate the liver inflammation and fibrosis. In addition, there were no difference of the numbers of macrophages, neutrophils, MDSCs,Th17 and total B cells in the spleen of the mice with or without NS-398 treatment. Our above data suggests that COX-2/PGE2 inhibition may represent a potential therapeutic approach to schistosomiasis japonica.

Nuclear morphology is a deep learning biomarker of senescence across tissues and species

Cellular senescence is a critical component of aging and many age-related diseases, but understanding its role in human health is challenging in part due to the lack of exclusive or universal markers. Using neural networks, we achieve high accuracy in predicting senescence state and type from the nuclear morphology of DAPI-stained human fibroblasts, murine astrocytes, murine neurons, and fibroblasts derived from premature aging diseases in culture. After generalizing this approach, the predictor recognizes an increasing rate of senescent cells with age in H&E-stained murine liver tissue and human dermal biopsies, suggesting that alterations in nuclear morphology is a universal feature of senescence. Evaluating corresponding medical records reveals that individuals with a higher rate of senescent cells have a significantly decreased rate of malignant neoplasms, lending support for the protective role of senescence in limiting cancer development. Additionally, we find a positive association with lower significance for other conditions, including osteoporosis, osteoarthritis, hypertension, cerebral infarction, hyperlipidemia, and hypercholesteremia. In sum, we introduce a predictor of cellular senescence based on nuclear morphology that is applicable across tissues and species and is associated with health outcomes in humans.

There Is Strength in Numbers: Quantitation of Fc Gamma Receptors on Murine Tissue-Resident Macrophages

Many of the effector functions of antibodies rely on the binding of antibodies/immune complexes to cellular Fcγ receptors (FcγRs). Since the majority of innate immune effector cells express both activating and inhibitory Fc receptors, the outcome of the binding of immune complexes to cells of a given population is influenced by the relative affinities of the respective IgG subclasses to these receptors, as well as by the numbers of activating and inhibitory FcγRs on the cell surface. A group of immune cells that has come into focus more recently is the various subsets of tissue-resident macrophages. The central functions of FcγRs on tissue macrophages include the clearance of opsonized pathogens, the removal of small immune complexes from the circulation and the depletion of antibody-opsonized cells in the therapy of autoimmunity and cancer. Despite these essential functions of FcγRs on tissue-resident macrophages, an in-depth quantification of FcγRs is lacking. Thus, the aim of our current study was to quantify the various Fcγ receptors on macrophages in murine liver, lung, kidney, brain, skin and spleen. Our study identified a pronounced heterogeneity between FcγR expression patterns of the different tissue macrophages, which may reflect their specialized functions within their unique niches in different organ environments.

Potential Role for Combined Subtype-Selective Targeting of M1 and M3 Muscarinic Receptors in Gastrointestinal and Liver Diseases

Despite structural similarity, the five subtypes comprising the cholinergic muscarinic family of G protein-coupled receptors regulate remarkably diverse biological functions. This mini review focuses on the closely related and commonly co-expressed M1R and M3R muscarinic acetylcholine receptor subtypes encoded respectively by CHRM1 and CHRM3. Activated M1R and M3R signal via Gq and downstream initiate phospholipid turnover, changes in cell calcium levels, and activation of protein kinases that alter gene transcription and ultimately cell function. The unexpectedly divergent effects of M1R and M3R activation, despite similar receptor structure, distribution, and signaling, are puzzling. To explore this conundrum, we focus on the gastrointestinal (GI) tract and liver because abundant data identify opposing effects of M1R and M3R activation on the progression of gastric, pancreatic, and colon cancer, and liver injury and fibrosis. Whereas M3R activation promotes GI neoplasia, M1R activation appears protective. In contrast, in murine liver injury models, M3R activation promotes and M1R activation mitigates liver fibrosis. We analyze these findings critically, consider their therapeutic implications, and review the pharmacology and availability for research and therapeutics of M1R and M3R-selective agonists and antagonists. We conclude by considering gaps in knowledge and other factors that hinder the application of these drugs and the development of new agents to treat GI and liver diseases.

FTIR Spectroscopy for Evaluation and Monitoring of Lipid Extraction Efficiency for Murine Liver Tissues Analysis

Over the past several decades, growing research on lipids and lipidomic technologies have shown the important role played by lipids in many different situations. A powerful technique used for lipids detection and characterization in biological tissues is Fourier Transform Infrared (FTIR) spectroscopy. The main goal of the present work is to exploit FTIR spectroscopy as a tool for monitoring lipid extraction efficiency by evaluating three different lipid extraction methods in murine liver tissues. In particular, infrared spectra have been obtained in the 4000–600 cm−1 wavenumber region and the contributions of different functional groups have been evidenced. The ratio values estimated using the absorbance of selected bands related to different liver constituents have been used for a quantitative comparison of the efficiency of the different extraction methods.

Multiplexed ultrasound imaging using clustered gas vesicles and spectral imaging

Current advances in ultrasound imaging techniques including super-resolution ultrasound imaging allows us to visualize microvasculature in biological specimens using microbubbles. However, microbubbles diffuse in blood stream limiting imaging acquisition and frame subtraction scheme of super-resolution ultrasound imaging cannot improve spatial resolution without moving microbubbles. Fluorescent proteins revolutionized to understand molecular and cellular functions in biological systems. Here, we devised a panel of gas vesicles to realize multiplexed ultrasound imaging to uniquely visualize locations of different species of gas vesicles. Mid-band fit spectral imaging technique demonstrated that stationary gas vesicles were efficiently localized in gel phantom and murine liver specimens by visualizing three-dimensional vessel structures. Clustered and unclustered gas vesicles were phagocytosed by murine macrophages to serve as carriers and beacons for the proposed multiplexed and single cell level imaging technique. The spatial distribution of macrophages containing clustered and unclustered gas vesicles were reconstructed by mid-band fit spectral imaging with pseudo-coloring scheme.

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here, we present a spatial proteogenomic atlas of the healthy human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and bile-duct macrophages. We also uncover the respective spatially-resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that bile-duct macrophages are induced by local lipid exposure, while Kupffer cells crucially depend on their crosstalk with hepatic stellate cells via the evolutionarily-conserved ALK1-BMP9/10 axis.