Probing the unseen structure and function of liver cells through atomic force microscopy

Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress

BACKGROUND

Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT.

RESULTS

Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT.

CONCLUSIONS

Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.

Single-cell transcriptome reveals a novel mechanism of C-Kit+-liver sinusoidal endothelial cells in NASH

AIM

To understand how liver sinusoidal endothelial cells (LSECs) respond to nonalcoholic steatohepatitis (NASH).

METHODS

We profiled single-LSEC from livers of control and MCD-fed mice. The functions of C-Kit+-LSECs were determined using coculture and bone marrow transplantation (BMT) methods.

RESULTS

Three special clusters of single-LSEC were differentiated. C-Kit+-LSECs of cluster 0, Msr1+-LSECs of cluster 1 and Bmp4+Selp+-VECs of cluster 2 were revealed, and these cells with diverse ectopic expressions of genes participated in regulation of endothelial, fibrosis and lipid metabolism in NASH. The number of C-Kit+-primary LSECs isolated from MCD mice was lower than control mice. Immunofluorescence co-staining of CD31 and C-KIT showed C-Kit+-LSECs located in hepatic sinusoid were also reduced in NASH patients and MCD mice, compared to AIH patients and control mice respectively. Interestingly, lipotoxic hepatocytes/HSCs cocultured with C-Kit+-LSECs or the livers of MCD mice receipting of C-Kit+-BMCs (bone marrow cells) showed less steatosis, inflammation and fibrosis, higher expression of prolipolytic FXR and PPAR-α, lower expression of TNF-α and α-SMA. Furthermore, coculturing or BMT of C-Kit+-endothelial derived cells could increase the levels of hepatic mitochondrial LC3B, decrease the degree of mitochondrial damage and ROS production through activating Pink1-mediated mitophagy pathway in NASH.

CONCLUSIONS

Hence, a novel transcriptomic view of LSECs was revealed to have heterogeneity and complexity in NASH. Importantly, a cluster of C-Kit+-LSECs was confirmed to recovery Pink1-related mitophagy and NASH progression.

Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis

LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.

Three-Dimensional Cell Co-Culture Liver Models and Their Applications in Pharmaceutical Research

As the primary site for the biotransformation of drugs, the liver is the most focused on organ type in pharmaceutical research. However, despite being widely used in pharmaceutical research, animal models have inherent species differences, while two-dimensional (2D) liver cell monocultures or co-cultures and three-dimensional (3D) liver cell monoculture in vitro liver models do not sufficiently represent the complexity of the human liver’s structure and function, making the evaluation results from these tools less reliable. Therefore, there is a pressing need to develop more representative in vitro liver models for pharmaceutical research. Fortunately, an exciting new development in recent years has been the emergence of 3D liver cell co-culture models. These models hold great promise as in vitro pharmaceutical research tools, because they can reproduce liver structure and function more practically. This review begins by explaining the structure and main cell composition of the liver, before introducing the potential advantages of 3D cell co-culture liver models for pharmaceutical research. We also discuss the main sources of hepatocytes and the 3D cell co-culture methods used in constructing these models. In addition, we explore the applications of 3D cell co-culture liver models with different functional states and suggest prospects for their further development.

Proton irradiation induced reactive oxygen species promote morphological and functional changes in HepG2 cells

The increased use of proton therapy has led to the need of better understanding the cellular mechanisms involved. The aim of this study was to investigate the effects induced by the accelerated proton beam in hepatocarcinoma cells. An existing facility in IFIN-HH, a 3 MV Tandetron™ accelerator, was used to irradiate HepG2 human hepatocarcinoma cells with doses between 0 and 3 Gy. Colony formation was used to assess the influence of radiation on cell long-term replication. Also, the changes induced at the mitochondrial level were shown by increased ROS and ATP levels as well as a decrease in the mitochondrial membrane potential. An increased dose has induced DNA damages and G₂/M cell cycle arrest which leads to caspase 3/7 mediated apoptosis and senescence induction. Finally, the morphological and ultrastructural changes were observed at the membrane level and the nucleus of the irradiated cells. Thus, proton irradiation induces both morphological and functional changes in HepG2 cells.

Optimized Isolation and Characterization of C57BL/6 Mouse Hepatic Stellate Cells

To obtain meaningful results of hepatic stellate cell (HSC) function, it is crucial to use highly pure HSC populations. Our aim was to optimize HSC isolation from mice livers without exploiting the characteristically transient vitamin A autofluorescence of HSC. HSCs were isolated from C57BL/6 mice using a two-step collagenase digestion and Nycodenz gradient separation followed by CD11b-negative sorting step in order to remove contaminating macrophages and dendritic cells. Isolated cells were analyzed for yield, viability, purity, and potential new markers using immunofluorescence and flow cytometry. We obtained a yield of 350,595 ± 100,773 HSC per mouse liver and a viability of isolated cells of 92.4 ± 3.1%. We observed a low macrophage/dendritic cell contamination of 1.22 ± 0.54%. Using flow cytometry, we demonstrated that CD38 was expressed at the surface of HSC subpopulations and that all expressed intracellular markers specific for HSC in the liver. This isolation method, avoiding fluorescent activated cell sorting (FACS), allowed isolation of HSCs with high purity. Further, flow cytometry analysis suggests that CD38 may be a reliable marker of HSCs and may include subpopulations of HSCs without retinoid droplets.

Chain-Like Structures of Biogenic and Nonbiogenic Magnetic Nanoparticles in Vascular Tissues

In this paper, slices of organs from various organisms (animals, plants, fungi) were investigated by using atomic force microscopy and magnetic force microscopy to identify common features of localization of both biogenic and nonbiogenic magnetic nanoparticles. It was revealed that both biogenic and nonbiogenic magnetic nanoparticles are localized in the form of chains of separate nanoparticles or chains of conglomerates of nanoparticles in the walls of the capillaries of animals and the walls of the conducting tissue of plants and fungi. Both biogenic and nonbiogenic magnetic nanoparticles are embedded as a part of the transport system in multicellular organisms. In connection with this, a new idea of the function of biogenic magnetic nanoparticles is discussed, that the chains of biogenic magnetic nanoparticles and chains of conglomerates of biogenic magnetic nanoparticles represent ferrimagnetic organelles of a specific purpose. Besides, magnetic dipole-dipole interaction of biogenic magnetic nanoparticles with magnetically labeled drugs or contrast agents for magnetic resonance imaging should be considered when designing the drug delivery and other medical systems because biogenic magnetic nanoparticles in capillary walls will serve as the trapping centers for the artificial magnetic nanoparticles. The aggregates of both artificial and biogenic magnetic nanoparticles can be formed, contributing to the risk of vascular occlusion. Bioelectromagnetics. 43:119-143, 2022. © 2021 Bioelectromagnetics Society.

Single-cell RNA transcriptome landscape of hepatocytes and non-parenchymal cells in healthy and NAFLD mouse liver

Nonalcoholic fatty liver disease (NAFLD) is a global health-care problem with limited therapeutic options. To obtain a cellular resolution of pathogenesis, 82,168 single-cell transcriptomes (scRNA-seq) across different NAFLD stages were profiled, identifying hepatocytes and 12 other non-parenchymal cell (NPC) types. scRNA-seq revealed insights into the cellular and molecular mechanisms of the disease. We discovered a dual role for hepatic stellate cells in gene expression regulation and in the potential to trans-differentiate into myofibroblasts. We uncovered distinct expression profiles of Kupffer cells versus monocyte-derived macrophages during NAFLD progression. Kupffer cells showed stronger immune responses, while monocyte-derived macrophages demonstrated a capability for differentiation. Three chimeric NPCs were identified including endothelial-chimeric stellate cells, hepatocyte-chimeric endothelial cells, and endothelial-chimeric Kupffer cells. Our work identified unanticipated aspects of mouse with NAFLD at the single-cell level and advanced the understanding of cellular heterogeneity in NAFLD livers.

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Of all, 82,168 single-cell transcriptomes across different NAFLD stages were profiled

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Hepatocytes and 12 non-parenchymal cell types were identified in mouse liver

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Three chimeric NPCs were identified in mouse liver

Effects of Lipid Deposition on Viscoelastic Response in Human Hepatic Cell Line HepG2

Hepatic steatosis is associated with various liver diseases. The main pathological feature of steatosis is the excessive lipid accumulation. Ultrasound has been extensively used for the diagnosis of hepatic steatosis. However, most ultrasound-based non-invasive methods are still not accurate enough for cases with light lipid infiltration. One important reason is that the extent to which lipid infiltration may affect mechanical properties of hepatocytes remains unknown. In this work, we used atomic force microscope and in vitro dose-dependent lipid deposition model to detect the quantitative changes of mechanical properties under different degrees of steatosis in a single-cell level. The results show that hepatic cells with lipid deposition can be treated as linear viscoelastic materials with the power law creep compliance and relaxation modulus. Further analysis showed that even slight accumulation of lipid can lead to measurable decrease of stiffness and increased fluidity in liver cells. The accurate detection of viscoelastic properties of hepatocytes and the analysis methods may provide novel insights into hepatic steatosis grading, especially in the very early stage with reversible liver lesion. The application of viscoelasticity index for grading fat deposition might be a new detection indicator in future clinical diagnosis.

Fibrotic Events in the Progression of Cholestatic Liver Disease

Cholestatic liver diseases including primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are associated with active hepatic fibrogenesis, which can ultimately lead to the development of cirrhosis. However, the exact relationship between the development of liver fibrosis and the progression of cholestatic liver disease remains elusive. Periductular fibroblasts located around the bile ducts seem biologically different from hepatic stellate cells (HSCs). The fibrotic events in these clinical conditions appear to be related to complex crosstalk between immune/inflammatory mechanisms, cytokine signalling, and perturbed homeostasis between cholangiocytes and mesenchymal cells. Several animal models including bile duct ligation (BDL) and the Mdr2-knockout mice have improved our understanding of mechanisms underlying chronic cholestasis. In the present review, we aim to elucidate the mechanisms of fibrosis in order to help to identify potential diagnostic and therapeutic targets.

Investigation into morphological and electromechanical surface properties of reduced-graphene-oxide-loaded composite fibers for bone tissue engineering applications: A comprehensive nanoscale study using atomic force microscopy approach

We decided to implement an extensive atomic force microscopy study in order to get deeper understanding of surface-related nanoscale properties of 3D printed pristine polycaprolactone and its reduced-graphene-oxide-loaded composites. The study included surface visualization and roughness quantification, elastic modulus and adhesion force assessment with force spectroscopy, along with kelvin probe force microscopy evaluation of local changes of surface potential. Atomic force microscopy examination was followed by scanning electron microscopy visualization and wettability assessment. Moreover, systematic examination of reduced graphene oxide flakes fabricated exclusively for this study was performed, including: scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy and combustion elemental analysis. The addition of reduced graphene oxide resulted in thickening of the composite fibers and surface roughness enhancement. In addition, elastic modulus of composite fibers was higher and at the same time adhesion forces between scanning probe and tested surface was lower than for pristine polymeric ones. Lastly, we recorded local (nanoscale) alterations of surface potential of fibers with addition of graphene-derivative. The results clearly suggest graphene derivative's dose-dependent alteration of elastic modulus and adhesion force recorded with atomic force microscope. Moreover, changes of the material's surface properties were followed by changes of its electrical properties.

Characterizing liver sinusoidal endothelial cell fenestrae on soft substrates upon AFM imaging and deep learning

BACKGROUND

Liver sinusoidal endothelial cells (LSECs) display unique fenestrated morphology. Alterations in the size and number of fenestrae play a crucial role in the progression of various liver diseases. While their features have been visualized using atomic force microscopy (AFM), the in situ imaging methods and off-line analyses are further required for fenestra quantification.

METHODS

Primary mouse LSECs were cultured on a collagen-I-coated culture dish, or a polydimethylsiloxane (PDMS) or polyacrylamide (PA) hydrogel substrate. An AFM contact mode was applied to visualize fenestrae on individual fixed LSECs. Collected images were analyzed using an in-house developed image recognition program based on fully convolutional networks (FCN).

RESULTS

Key scanning parameters were first optimized for visualizing the fenestrae on LSECs on culture dish, which was also applicable for the LSECs cultured on various hydrogels. The intermediate-magnification morphology images of LSECs were used for developing the FCN-based, fenestra recognition program. This program enabled us to recognize the vast majority of fenestrae from AFM images after twice trainings at a typical accuracy of 81.6% on soft substrate and also quantify the statistics of porosity, number of fenestrae and distribution of fenestra diameter.

CONCLUSIONS

Combining AFM imaging with FCN training is able to quantify the morphological distributions of LSEC fenestrae on various substrates.

SIGNIFICANCE

AFM images acquired and analyzed here provided the global information of surface ultramicroscopic structures over an entire cell, which is fundamental in understanding their regulatory mechanisms and pathophysiological relevance in fenestra-like evolution of individual cells on stiffness-varied substrates.

Applications of atomic force microscopy in immunology

Cellular mechanics, a major regulating factor of cellular architecture and biological functions, responds to intrinsic stresses and extrinsic forces exerted by other cells and the extracellular matrix in the microenvironment. Cellular mechanics also acts as a fundamental mediator in complicated immune responses, such as cell migration, immune cell activation, and pathogen clearance. The principle of atomic force microscopy (AFM) and its three running modes are introduced for the mechanical characterization of living cells. The peak force tapping mode provides the most delicate and desirable virtues to collect high-resolution images of morphology and force curves. For a concrete description of AFM capabilities, three AFM applications are discussed. These applications include the dynamic progress of a neutrophil-extracellular-trap release by neutrophils, the immunological functions of macrophages, and the membrane pore formation mediated by perforin, streptolysin O, gasdermin D, or membrane attack complex.

Biophysical nanocharacterization of liver sinusoidal endothelial cells through atomic force microscopy

The structural-functional hallmark of the liver sinusoidal endothelium is the presence of fenestrae grouped in sieve plates. Fenestrae are open membrane bound pores supported by a (sub)membranous cytoskeletal lattice. Changes in number and diameter of fenestrae alter bidirectional transport between the sinusoidal blood and the hepatocytes. Their physiological relevance has been shown in different liver disease models. Although the structural organization of fenestrae has been well documented using different electron microscopy approaches, the dynamic nature of those pores remained an enigma until the recent developments in the research field of four dimensional (4-D) AFM. In this contribution we highlight how AFM as a biophysical nanocharacterization tool enhanced our understanding in the dynamic behaviour of liver sinusoidal endothelial fenestrae. Different AFM probing approaches, including spectroscopy, enabled mapping of topography and nanomechanical properties at unprecedented resolution under live cell imaging conditions. This dynamic biophysical characterization approach provided us with novel information on the 'short' life-span, formation, disappearance and closure of hepatic fenestrae. These observations are briefly reviewed against the existing literature.

Actin-spectrin scaffold supports open fenestrae in liver sinusoidal endothelial cells

Fenestrae are open transmembrane pores that are a structural hallmark of healthy liver sinusoidal endothelial cells (LSECs). Their key role is the transport of solutes and macromolecular complexes between the sinusoidal lumen and the space of Disse. To date, the biochemical nature of the cytoskeleton elements that surround the fenestrae and sieve plates in LSECs remain largely elusive. Herein, we took advantage of the latest developments in atomic force imaging and super‐resolution fluorescence nanoscopy to define the organization of the supramolecular complex(es) that surround the fenestrae. Our data revealed that spectrin, together with actin, lines the inner cell membrane and provided direct structural support to the membrane‐bound pores. We conclusively demonstrated that diamide and iodoacetic acid (IAA) affect fenestrae number by destabilizing the LSEC actin‐spectrin scaffold. Furthermore, IAA induces rapid and repeatable switching between the open vs closed state of the fenestrae, indicating that the spectrin‐actin complex could play an important role in controlling the pore number. Our results suggest that spectrin functions as a key regulator in the structural preservation of the fenestrae, and as such, it might serve as a molecular target for altering transendothelial permeability.

Atomic Force Microscopy on Biological Materials Related to Pathological Conditions

Atomic force microscopy (AFM) is an easy-to-use, powerful, high-resolution microscope that allows the user to image any surface and under any aqueous condition. AFM has been used in the investigation of the structural and mechanical properties of a wide range of biological matters including biomolecules, biomaterials, cells, and tissues. It provides the capacity to acquire high-resolution images of biosamples at the nanoscale and allows at readily carrying out mechanical characterization. The capacity of AFM to image and interact with surfaces, under physiologically relevant conditions, is of great importance for realistic and accurate medical and pharmaceutical applications. The aim of this paper is to review recent trends of the use of AFM on biological materials related to health and sickness. First, we present AFM components and its different imaging modes and we continue with combined imaging and coupled AFM systems. Then, we discuss the use of AFM to nanocharacterize collagen, the major fibrous protein of the human body, which has been correlated with many pathological conditions. In the next section, AFM nanolevel surface characterization as a tool to detect possible pathological conditions such as osteoarthritis and cancer is presented. Finally, we demonstrate the use of AFM for studying other pathological conditions, such as Alzheimer's disease and human immunodeficiency virus (HIV), through the investigation of amyloid fibrils and viruses, respectively. Consequently, AFM stands out as the ideal research instrument for exploring the detection of pathological conditions even at very early stages, making it very attractive in the area of bio- and nanomedicine.

Actin Depolymerization in Dedifferentiated Liver Sinusoidal Endothelial Cells Promotes Fenestrae Re-Formation

Liver sinusoidal endothelial cells (LSECs) possess fenestrae, which are key for the exchange between blood and hepatocytes. Alterations in their number or diameter have important implications for hepatic function in liver diseases. They are lost early in the development of hepatic fibrosis through a process called capillarization. In this study, we aimed to demonstrate whether in vitro dedifferentiated LSECs that have lost fenestrae are able to re-form these structures. Using stimulated emission depletion super-resolution microscopy in combination with transmission electron microscopy, we analyzed fenestrae formation in a model mimicking the capillarization process in vitro. Actin is known to be involved in fenestrae regulation in differentiated LSECs. Using cytochalasin D, an actin-depolymerizing agent, we demonstrated that dedifferentiated LSECs remain capable of forming fenestrae. Conclusion: We provide a new insight into the complex role of actin in fenestrae formation and in the control of their size and show that LSEC fenestrae re-formation is possible, suggesting that this process could be used during fibrosis regression to try to restore exchanges and hepatocyte functions.

Nanoindentation of Soft Biological Materials

Nanoindentation techniques, with high spatial resolution and force sensitivity, have recently been moved into the center of the spotlight for measuring the mechanical properties of biomaterials, especially bridging the scales from the molecular via the cellular and tissue all the way to the organ level, whereas characterizing soft biomaterials, especially down to biomolecules, is fraught with more pitfalls compared with the hard biomaterials. In this review we detail the constitutive behavior of soft biomaterials under nanoindentation (including AFM) and present the characteristics of experimental aspects in detail, such as the adaption of instrumentation and indentation response of soft biomaterials. We further show some applications, and discuss the challenges and perspectives related to nanoindentation of soft biomaterials, a technique that can pinpoint the mechanical properties of soft biomaterials for the scale-span is far-reaching for understanding biomechanics and mechanobiology.

Multi-scale characterization and biological evaluation of composite surface layers produced under glow discharge conditions on NiTi shape memory alloy for potential cardiological application

NiTi shape memory alloys are characterized by relatively good biocompatibility primarily thanks to their ability to self-passivate. However, before they can be used as medical implants for long term use, they need to undergo treatment aimed at producing layers on their surface that are superior to spontaneously formed oxide layers and that would increase their resistance to corrosion, limit nickel ion release from the surface (metallosis) and have the capability to shape their biological properties depending on the application. Furthermore, cardiac implants require addressing the issue of blood clotting on the surface. Treatment in glow-discharge low temperature plasma makes it possible to produce titanium layers with a structure and properties that are controlled via process parameters. In addition, antithrombogenic properties can be improved by depositing a carbon coating via the RFCVD process. The aim of the study was to investigate the structure, surface topography, adhesive properties, wettability, surface free energy and evaluate metallosis after producing TiO₂ and a-C:N:H + TiO₂ composite layers on NiTi alloy. The capabilities of AFM microscopes in studying the adhesive properties of a surface were also highlighted in the study. The study shows that the produced surface layers are capable of significantly reducing metallosis. Furthermore, in contrast to NiTi in its initial state, layers of nanocrystalline TiO₂ titanium oxide (rutile) with a homogeneous structure demonstrate greater adhesion strength and more developed surface in the microscale, which facilitates the formation of an a-C:N:H coating. Therefore the formation of a coating of a-C:N:H amorphous carbon on NiTi alloy that has previously been oxidised in low-temperature plasma may prove to be a favourable solution in terms of using NiTi alloy to produce cardiac implants.