Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages

Molecular mechanisms of cadmium-induced cytotoxicity in human ovarian granulosa cells identified using integrated omics

Epidemiological and clinical data have demonstrated that exposure to cadmium (Cd), a toxic heavy metal, is associated with an increased risk of female infertility. Granulosa cells, the main somatic cells comprising ovarian follicles, are one of the main targets of Cd in the ovaries. However, the mechanism by which Cd induces cytotoxicity in granulosa cells has not been fully elucidated. In this study, we exposed human ovarian granulosa cells (KGN cells) to Cd and conducted in vitro cell experiments and multi-omics (metabolomics and transcriptomics) methods to elucidate these mechanisms. Cd exposure was found to not only induce the apoptosis of the KGN cells but also further reduced mitochondrial function by decreasing mitochondrial membrane potential, ATP production, and respiratory chain complex activity as well as increasing mitochondrial reactive oxygen species (ROS) production. A total of 443 differentially expressed metabolites (160 upregulated and 283 downregulated) and 5200 differentially expressed genes (4634 upregulated and 566 downregulated) were observed in the Cd exposed-cells. The multi-omics data showed that Cd interfered with citric acid cycle (TCA cycle), amino acid (including alanine, glycine, serine, threonine, arginine, and proline) metabolism, and calcium signaling. These findings help to better elucidate the potential toxicity mechanisms of Cd on granulosa cells and the ovary.

Potential Immunoregulatory Mechanism of Plant Saponins: A Review

Saponins are extracted from different parts of plants such as seeds, roots, stems, and leaves and have a variety of biological activities including immunomodulatory, anti-inflammatory effects, and hypoglycemic properties. They demonstrate inherent low immunogenicity and possess the capacity to effectively regulate both the innate and adaptive immune responses. Plant saponins can promote the growth and development of the body's immune organs through a variety of signaling pathways, regulate the activity of a variety of immune cells, and increase the secretion of immune-related cytokines and antigen-specific antibodies, thereby exerting the role of immune activity. However, the chemical structure of plant saponins determines its certain hemolytic and cytotoxicity. With the development of science and technology, these disadvantages can be avoided or reduced by certain technical means. In recent years, there has been a significant surge in interest surrounding the investigation of plant saponins as immunomodulators. Consequently, the objective of this review is to thoroughly examine the immunomodulatory properties of plant saponins and elucidate their potential mechanisms, with the intention of offering a valuable point of reference for subsequent research and advancement within this domain.

Bridging the Gap: Investigating the Link between Inflammasomes and Postoperative Cognitive Dysfunction

Postoperative cognitive dysfunction (POCD) is a cluster of cognitive problems that may arise after surgery. POCD symptoms include memory loss, focus inattention, and communication difficulties. Inflammasomes, intracellular multiprotein complexes that control inflammation, may have a significant role in the development of POCD. It has been postulated that the NLRP3 inflammasome promotes cognitive impairment by triggering the inflammatory response in the brain. Nevertheless, there are many gaps in the current literature to understand the underlying pathophysiological mechanisms and develop future therapy. This review article underlines the limits of our current knowledge about the NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome and POCD. We first discuss inflammasomes and their types, structures, and functions, then summarize recent evidence of the NLRP3 inflammasome's involvement in POCD. Next, we propose a hypothesis that suggests the involvement of inflammasomes in multiple organs, including local surgical sites, blood circulation, and other peripheral organs, leading to systemic inflammation and subsequent neuronal dysfunction in the brain, resulting in POCD. Research directions are then discussed, including analyses of inflammasomes in more clinical POCD animal models and clinical trials, studies of inflammasome types that are involved in POCD, and investigations into whether inflammasomes occur at the surgical site, in circulating blood, and in peripheral organs. Finally, we discuss the potential benefits of using new technologies and approaches to study inflammasomes in POCD. A thorough investigation of inflammasomes in POCD might substantially affect clinical practice.

Synergistic Antitumor Effect of Grifola frondose Polysaccharide—Protein Complex in Combination with Cyclophosphamide in H22 Tumor-Bearing Mice

Hepatocellular carcinoma (HCC) is the most common type of liver malignancy and remains a global health threat. The objective of the current study was to determine whether the combination of a cold-water extracted polysaccharide-protein complex from Grifolia frondosa (GFG) and cyclophosphamide (CTX) could inhibit tumor growth by suppressing the expression of angiogenesis-related proteins in H22 tumor-bearing mice. The results showed that the inhibition rate of GFG combined with CTX on H22 tumors was 65.29%, which was significantly higher than that of GFG treatment alone (24.82%). GFG combined with CTX significantly increased the expression levels of vascular endothelial growth factor, basic fibroblast growth factor, matrix metalloproteinase 2, and matrix metalloproteinase 9. Additionally, thymus index, spleen index, natural killer (NK) cell activity, interferon-γ (IFN-γ), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α) and interleukin-2 (IL-2) levels increased significantly after GFG treatment, especially after high-doses of GFG combined with CTX treatment (p < 0.05). The thymus index, spleen index, NK cell activity, IFN-γ, IL-1β, TNF-α, and IL-2 levels were 1.90, 1.46, 1.30, 2.13, 1.64, 2.03, and 1.24 times of those treated with CTX alone. Thus, we proposed that GFG can alleviate the side effects of CTX by relieving the immunosuppressive effect, liver/renal injury, and oxidative stress. In conclusion, the combination of GFG and CTX for cancer treatment may be a promising strategy, and GFG is expected to be a potential adjuvant alternative for the treatment of HCC.

Transcription factor nuclear factor erythroid 2 p45-related factor 2 (NRF2) ameliorates sepsis-associated acute kidney injury by maintaining mitochondrial homeostasis and improving the mitochondrial function

Mitochondrial dysfunction has a role in sepsis-associated acute kidney injury (S-AKI), so the restoration of normal mitochondrial homeostasis may be an effective treatment strategy. Transcription factor nuclear factor erythroid 2 p45-related factor 2 (NRF2) is a main regulator of cell-redox homeostasis, and recent studies reported that NRF2 activation helped to preserve mitochondrial morphology and function under conditions of stress. However, the role of NRF2 in the process of S-AKI is still not well understood. The present study investigated whether NRF2 regulates mitochondrial homeostasis and influences mitochondrial function in S-AKI. We demonstrated activation of NRF2 in an in vitro model: lipopolysaccharide (LPS) challenge of ductal epithelial cells of rat renal tubules (NRK-52e cells), and an in vivo model: cecal ligation and puncture (CLP) of rats. Over-expression of NRF2 attenuated oxidative stress, apoptosis, and the inflammatory response; enhanced mitophagy and mitochondrial biogenesis; and mitigated mitochondrial damage in the in vitro model. In vivo experiments showed that rats treated with an NRF2 agonist had higher adenosine triphosphate (ATP) levels, lower blood urea nitrogen and creatinine levels, fewer renal histopathological changes, and higher expression of mitophagy-related proteins [PTEN-induced putative kinase 1 (PINK1), parkin RBR E3 ubiquitin protein ligase (PRKN), microtubule-associated protein 1 light chain 3 II (LC3 II)] and mitochondrial biogenesis-related proteins [peroxisome proliferator-activated receptor γ coactivator-1 (PGC-1α) and mitochondrial transcription factor A (TFAM)]. Electron microscopy of kidney tissues showed that mitochondrial damage was alleviated by treatment with an NRF2 agonist, and the opposite response occurred upon treatment with an NRF2 antagonist. Overall, our findings suggest that mitochondria have an important role in the pathogenesis of S-AKI, and that NRF2 activation restored mitochondrial homeostasis and function in the presence of this disease. This mitochondrial pathway has the potential to be a novel therapeutic target for the treatment of S-AKI.

Structural characteristics and immunomodulatory effects of sulfated polysaccharides derived from marine algae

Marine algae are becoming an important source of valuable candidates of functional food that remain unexplored. Compositional analysis showed that marine algae contain essential nutrients, such as carbohydrates, proteins, fats, and minerals, of which polysaccharides are the main bioactive component. Depending on the source, marine algae polysaccharides are sulfated, which have diverse structures and compositions that influence their biological activities. A growing body of evidence has demonstrated that sulfated polysaccharides derived from marine algae (SPs) exhibit various bioactivities, especially immunomodulation. This review aims at summarizing the structural characteristics of SPs, their immunomodulatory effects, and the structural-immunomodulatory activity relationships between them from articles in recent decade, in order to provide a theoretical basis for the further applications of SPs as promising food or feed additives and possible health products to modulate the immune response.

Methodological Approaches To Assess Innate Immunity and Innate Memory in Marine Invertebrates and Humans

Assessing the impact of drugs and contaminants on immune responses requires methodological approaches able to represent real-life conditions and predict long-term effects. Innate immunity/inflammation is the evolutionarily most widespread and conserved defensive mechanism in living organisms, and therefore we will focus here on immunotoxicological methods that specifically target such processes. By exploiting the conserved mechanisms of innate immunity, we have examined the most representative immunotoxicity methodological approaches across living species, to identify common features and human proxy models/assays. Three marine invertebrate organisms are examined in comparison with humans, i.e., bivalve molluscs, tunicates and sea urchins. In vivo and in vitro approaches are compared, highlighting common mechanisms and species-specific endpoints, to be applied in predictive human and environmental immunotoxicity assessment. Emphasis is given to the 3R principle of Replacement, Refinement and Reduction of Animals in Research and to the application of the ARRIVE guidelines on reporting animal research, in order to strengthen the quality and usability of immunotoxicology research data.

Roles of Altered Macrophages and Cytokines: Implications for Pathological Mechanisms of Postmenopausal Osteoporosis, Rheumatoid Arthritis, and Alzheimer's Disease

Postmenopausal osteoporosis (PMOP) is characterized by the uncoupling of bone resorption and bone formation induced by estrogen deficiency, which is a complex outcome related to estrogen and the immune system. The interaction between bone and immune cells is regarded as the context of PMOP. Macrophages act differently on bone cells, depending on their polarization profile and secreted paracrine factors, which may have implications for the development of PMOP. PMOP, rheumatoid arthritis (RA), and Alzheimer's disease (AD) might have pathophysiological links, and the similarity of their pathological mechanisms is partially visible in altered macrophages and cytokines in the immune system. This review focuses on exploring the pathological mechanisms of PMOP, RA, and AD through the roles of altered macrophages and cytokines secretion. First, the multiple effects on cytokines secretion by bone-bone marrow (BM) macrophages in the pathological mechanism of PMOP are reviewed. Then, based on the thought of "different tissue-same cell type-common pathological molecules-disease pathological links-drug targets" and the methodologies of "molecular network" in bioinformatics, highlight that multiple cytokines overlap in the pathological molecules associated with PMOP vs. RA and PMOP vs. AD, and propose that these overlaps may lead to a pathological synergy in PMOP, RA, and AD. It provides a novel strategy for understanding the pathogenesis of PMOP and potential drug targets for the treatment of PMOP.

Essential Oils from Zingiber striolatum Diels Attenuate Inflammatory Response and Oxidative Stress through Regulation of MAPK and NF-κB Signaling Pathways

Zingiber striolatum Diels (Z. striolatum), a widely popular vegetable in China, is famous for its medicinal and nutritional values. However, the anti-inflammatory effects of essential oil from Z. striolatum (EOZS) remain unclear. In this study, EOZS from seven regions in China were extracted and analyzed by GC–MS. LPS-induced RAW264.7 cells and 12-O-Tetradecanoylphorbol 13-acetate (TPA)-stimulated mice were used to evaluate the anti-inflammatory effects of EOZS. Results show that 116 compounds were identified in EOZS from seven locations. Samples 2, 4 and 5 showed the best capability on DPPH radical scavenging and NO inhibition. They also significantly reduced the production of ROS, pro-inflammatory cytokines, macrophage morphological changes, migration and phagocytic capability. Transcriptomics revealed MAPK and NF-κB signaling pathways may be involved in the anti-inflammatory mechanism, and the predictions were proven by Western blotting. In TPA-induced mice, EOZS reduced the degree of ear swelling and local immune cell infiltration by blocking the activation of MAPK and NF-κB signaling pathways, which was consistent with the in vitro experimental results. Our research unveils the antioxidant capability and potential molecular mechanism of EOZS in regulating inflammatory response, and suggests the application of EOZS as a natural antioxidant and anti-inflammatory agent in the pharmaceutical and functional food industries.

Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification

Mass spectrometric profiling provides information on the protein and metabolic composition of biological samples. However, the weak efficiency of computational algorithms in correlating tandem spectra to molecular components (proteins and metabolites) dramatically limits the use of "omics" profiling for the classification of nosologies. The development of machine learning methods for the intelligent analysis of raw mass spectrometric (HPLC-MS/MS) measurements without involving the stages of preprocessing and data identification seems promising. In our study, we tested the application of neural networks of two types, a 1D residual convolutional neural network (CNN) and a 3D CNN, for the classification of three cancers by analyzing metabolomic-proteomic HPLC-MS/MS data. In this work, we showed that both neural networks could classify the phenotypes of gender-mixed oncology, kidney cancer, gender-specific oncology, ovarian cancer, and the phenotype of a healthy person by analyzing 'omics' data in 'mgf' data format. The created models effectively recognized oncopathologies with a model accuracy of 0.95. Information was obtained on the remoteness of the studied phenotypes. The closest in the experiment were ovarian cancer, kidney cancer, and prostate cancer/kidney cancer. In contrast, the healthy phenotype was the most distant from cancer phenotypes and ovarian and prostate cancers. The neural network makes it possible to not only classify the studied phenotypes, but also to determine their similarity (distance matrix), thus overcoming algorithmic barriers in identifying HPLC-MS/MS spectra. Neural networks are versatile and can be applied to standard experimental data formats obtained using different analytical platforms.

Applications of Multi-omics Approaches for Exploring the Molecular Mechanism of Ovarian Carcinogenesis

Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. The molecular mechanisms of ovarian carcinogenesis need to be explored in order to identify effective clinical therapies for ovarian cancer. Recently, multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (metabolites) levels. Multi-omics approaches can identify some diagnostic and prognostic biomarkers and therapeutic targets for ovarian cancer, and these molecular signatures are beneficial for clarifying the development and progression of ovarian cancer. Moreover, the discovery of molecular signatures and targeted therapy strategies could noticeably improve the prognosis of ovarian cancer patients.

Analysis of Nanotoxicity with Integrated Omics and Mechanobiology

Nanoparticles (NPs) in biomedical applications have benefits owing to their small size. However, their intricate and sensitive nature makes an evaluation of the adverse effects of NPs on health necessary and challenging. Since there are limitations to conventional toxicological methods and omics analyses provide a more comprehensive molecular profiling of multifactorial biological systems, omics approaches are necessary to evaluate nanotoxicity. Compared to a single omics layer, integrated omics across multiple omics layers provides more sensitive and comprehensive details on NP-induced toxicity based on network integration analysis. As multi-omics data are heterogeneous and massive, computational methods such as machine learning (ML) have been applied for investigating correlation among each omics. This integration of omics and ML approaches will be helpful for analyzing nanotoxicity. To that end, mechanobiology has been applied for evaluating the biophysical changes in NPs by measuring the traction force and rigidity sensing in NP-treated cells using a sub-elastomeric pillar. Therefore, integrated omics approaches are suitable for elucidating mechanobiological effects exerted by NPs. These technologies will be valuable for expanding the safety evaluations of NPs. Here, we review the integration of omics, ML, and mechanobiology for evaluating nanotoxicity.