Screening of quorum sensing peptides for biological effects in neuronal cells

The Gut Microbiota and Chronic Pain

PURPOSE OF REVIEW

To examine the effects and interactions between gut microbia and chronic pain.

RECENT FINDINGS

The gut microbiome has been an area of interest in both the scientific and general audience due to a growing body of evidence suggesting its influence in a variety of health and disease states. Communication between the central nervous system (CNS) and gut microbiome is said to be bidirectional, in what is referred to as the gut-brain axis. Chronic pain is a prevalent costly personal and public health burden and so, there is a vested interest in devising safe and efficacious treatments. Numerous studies, many of which are animal studies, have been conducted to examine the gut microbiome's role in the pathophysiology of chronic pain states, such as neuropathy, inflammation, visceral pain, etc. As the understanding of this relationship grows, so does the potential for therapeutic targeting of the gut microbiome in chronic pain.

PSRQSP: An effective approach for the interpretable prediction of quorum sensing peptide using propensity score representation learning

Quorum sensing peptides (QSPs) are microbial signaling molecules involved in several cellular processes, such as cellular communication, virulence expression, bioluminescence, and swarming, in various bacterial species. Understanding QSPs is essential for identifying novel drug targets for controlling bacterial populations and pathogenicity. In this study, we present a novel computational approach (PSRQSP) for improving the prediction and analysis of QSPs. In PSRQSP, we develop a novel propensity score representation learning (PSR) scheme. Specifically, we utilized the PSR approach to extract and learn a comprehensive set of estimated propensities of 20 amino acids, 400 dipeptides, and 400 g-gap dipeptides from a pool of scoring card method-based models. Finally, to maximize the utility of the propensity scores, we explored a set of optimal propensity scores and combined them to construct a final meta-predictor. Our experimental results showed that combining multiview propensity scores was more beneficial for identifying QSPs than the conventional feature descriptors. Moreover, extensive benchmarking experiments based on the independent test were sufficient to demonstrate the predictive capability and effectiveness of PSRQSP by outperforming the conventional ML-based and existing methods, with an accuracy of 94.44% and AUC of 0.967. PSR-derived propensity scores were employed to determine the crucial physicochemical properties for a better understanding of the functional mechanisms of QSPs. Finally, we constructed an easy-to-use web server for the PSRQSP (http://pmlabstack.pythonanywhere.com/PSRQSP). PSRQSP is anticipated to be an efficient computational tool for accelerating the data-driven discovery of potential QSPs for drug discovery and development.

Bacterial Quorum-Sensing Peptides as Immune Modulators Present in Systemic Circulation

Quorum-sensing peptides (QSPs) are bacterial peptides traditionally considered only as inter-bacterial communication molecules. Recently, their involvement in microbiome-host interactions influencing host diseases such as cancer and sarcopenia were explored. However, it is still unknown to what extent these peptides have the potential to modulate the immune system. In this proof-of-concept study, we screened 89 QSPs for their potential to induce IL-6 and TNFα in murine splenocytes and J774 macrophages. Confirmatory experiments on the positive screening-hits were conducted using murine splenocytes and human PBMCs of different ages. Finally, to investigate the biological relevance of immunomodulatory QSPs, we analysed plasma in a human cohort for the presence of the immunomodulatory QSP Q010. To do this, we used a newly developed UHPLC-MS/MS method. Our findings indicated that specific QSPs activate immune cells in vitro, with Q007, Q010, Q017 and Q212 being the top four screening hits. Q007 and Q010 were affirmed in subsequent confirmatory experiments using murine splenocytes and human PBMCs. Finally, Q010 was detected in human plasma, demonstrating for the first time the presence of an immunomodulatory QSP in human circulation. In conclusion, our data are the first evidence indicating the potential of biologically relevant quorum-sensing peptides to modulate the immune system.

The Crosstalk between Microbiome and Mitochondrial Homeostasis in Neurodegeneration

Mitochondria are highly dynamic organelles that serve as the primary cellular energy-generating system. Apart from ATP production, they are essential for many biological processes, including calcium homeostasis, lipid biogenesis, ROS regulation and programmed cell death, which collectively render them invaluable for neuronal integrity and function. Emerging evidence indicates that mitochondrial dysfunction and altered mitochondrial dynamics are crucial hallmarks of a wide variety of neurodevelopmental and neurodegenerative conditions. At the same time, the gut microbiome has been implicated in the pathogenesis of several neurodegenerative disorders due to the bidirectional communication between the gut and the central nervous system, known as the gut-brain axis. Here we summarize new insights into the complex interplay between mitochondria, gut microbiota and neurodegeneration, and we refer to animal models that could elucidate the underlying mechanisms, as well as novel interventions to tackle age-related neurodegenerative conditions, based on this intricate network.

Application of quorum sensing system in microbial synthesis of valuable chemicals: a mini-review

With advantages of low substrates cost, high optical purity of end products and environmentally friendly fermentation process, microbial production of valuable chemicals grow rapidly. Compared with static microbial strain engineering strategies, such as gene deletion, overexpression and mutation, dynamic pathway regulation is a new approach that balances cellular growth and chemical production. Quorum sensing is a natural microbial communication system responsible for cell-density-related cell behaviors. Accordingly, quorum sensing systems can be employed to achieve dynamic regulation in microorganisms without the need for manual intervention or the use of chemical inducers. In this review, natural quorum sensing systems are firstly summarized. Then, recent progress in using quorum sensing circuits in the field of metabolic engineering is highlighted. The current application challenges of quorum sensing systems and future perspectives in microbial synthesis of chemicals are also discussed.

An insight into reactivity and bioactivity properties of quorum sensing peptides against PDE10A: a computational peptidology approach

Peptides are currently the most promising lead molecules. Quorum sensing peptides have a variety of structural features and are regularly exposed to post-translational modifications. Antiparkinsonian drugs lose their efficacy after a long period of use, and patients develop motor problems such as drug-induced dyskinesia (DIDs). The interaction between PDE10A and cAMP is necessary for dopamine neurotransmission and may play a role in Parkinson's disease pathogenesis. cAMP and cGMP are cyclic nucleotides that act as secondary messengers in the signal transduction pathway, influencing a range of CNS activities. PDE enzymes hydrolyze phosphodiester bonds to break down cAMP and cGMP, allowing them to control intracellular levels of these second messengers effectively. PDE expression, and hence cyclic nucleotide levels and their downstream targets, may change with age and in numerous age-related illnesses, including Parkinson's disease, according to mounting evidence. At the peak of dyskinesias, cyclic nucleotide levels were lower, and using phosphodiesterase inhibitors before antiparkinsonian medicines reduced the severity of dyskinesias. In a recent study, PapRIV was found to have the ability to activate BV-2 microglia cells, indicating that this quorum sensing peptide may play a role in gut-brain contact. As a result of the current in silico work, mainly focused on QSPs as a lead molecule for inhibiting PDE10A, the SRNAT QSP sequence has been a potent molecule in molecular docking and molecular dynamics simulations. Furthermore, we can test the efficiency of therapeutic components in vitro and in vivo utilizing this computational approach against PDE10A.

The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction

Background

Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far.

Results

Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis.

Conclusion

Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01317-z.

Microbiome in cancer: Role in carcinogenesis and impact in therapeutic strategies

Cancer is the world's second-leading cause of death, and the involvement of microbes in a range of diseases, including cancer, is well established. The gut microbiota is known to play an important role in the host's health and physiology. The gut microbiota and its metabolites may activate immunological and cellular pathways that kill invading pathogens and initiate a cancer-fighting immune response. Cancer is a multiplex illness, characterized by the persistence of several genetic and physiological anomalies in malignant tissue, complicating disease therapy and control. Humans have coevolved with a complex bacterial, fungal, and viral microbiome over millions of years. Specific long-known epidemiological links between certain bacteria and cancer have recently been grasped at the molecular level. Similarly, advances in next-generation sequencing technology have enabled detailed research of microbiomes, such as the human gut microbiome, allowing for the finding of taxonomic and metabolomic linkages between the microbiome and cancer. These investigations have found causative pathways for both microorganisms within tumors and bacteria in various host habitats far from tumors using direct and immunological procedures. Anticancer diagnostic and therapeutic solutions could be developed using this review to tackle the threat of anti-cancer medication resistance as well through the wide-ranging involvement of the microbiota in regulating host metabolic and immunological homeostasis. We reviewed the significance of gut microbiota in cancer initiation as well as cancer prevention. We look at certain microorganisms that may play a role in the development of cancer. Several bacteria with probiotic qualities may be employed as bio-therapeutic agents to re-establish the microbial population and trigger a strong immune response to remove malignancies, and further study into this should be conducted.

Quorum sensing: a new perspective to reveal the interaction between gut microbiota and host

Quorum sensing (QS), a chemical communication process between bacteria, depends on the synthesis, secretion and detection of signal molecules. It can synchronize the gene expression of bacteria to promote cooperation within the population and improve competitiveness among populations. The preliminary exploration of bacterial QS has been completed under ideal and highly controllable conditions. There is an urgent need to investigate the QS of bacteria under natural conditions, especially the QS of intestinal flora, which is closely related to health. Excitingly, growing evidence has shown that QS also exists in the intestinal flora. The crosstalk of QS between gut microbiota and the host is systematically clarified in this review.

Microbiota and body weight control: Weight watchers within?

Background

Despite several decades of research, managing body weight remains an unsolved clinical problem. Health problems associated with dysregulated body weight, such as obesity and cachexia, exhibit several gut microbiota alterations. There is an increased interest in utilising the gut microbiota for body weight control, as it responds to intervention and plays an important role in energy extraction from food, as well as biotransformation of nutrients.

Scope of the review

This review provides an overview of the role of the gut microbiota in the physiological and metabolic alterations observed in two body weight dysregulation-related disorders, namely obesity and cachexia. Second, we assess the available evidence for different strategies, including caloric restriction, intermittent fasting, ketogenic diet, bariatric surgery, probiotics, prebiotics, synbiotics, high-fibre diet, and fermented foods – effects on body weight and gut microbiota composition. This approach was used to give insights into the possible link between body weight control and gut microbiota configuration.

Major conclusions

Despite extensive associations between body weight and gut microbiota composition, limited success could be achieved in the translation of microbiota-related interventions for body weight control in humans. Manipulation of the gut microbiota alone is insufficient to alter body weight and future research is needed with a combination of strategies to enhance the effects of lifestyle interventions.

•

The gut microbiota is involved in the control of nutrient availability, appetite, and body weight.

•

Both obesity and cachexia are associated with altered gut microbiota.

•

Specific dietary and surgical approaches positively impact body weight and gut microbiota.

•

Manipulation of the gut microbiota alone is insufficient to alter body weight in humans.

The bacterial quorum sensing molecule, 2-heptyl-3-hydroxy-4-quinolone (PQS), inhibits signal transduction mechanisms in brain tissue and is behaviorally active in mice

Interkingdom communication between bacteria and host organisms is one of the most interesting research topics in biology. Quorum sensing molecules produced by Gram-negative bacteria, such as acylated homoserine lactones and quinolones, have been shown to interact with host cell receptors, stimulating innate immunity and bacterial clearance. To our knowledge, there is no evidence that these molecules influence CNS function. Here, we have found that low micromolar concentrations of the Pseudomonas aeruginosa quorum sensing autoinducer, 2-heptyl-3-hydroxy-4-quinolone (PQS), inhibited polyphosphoinositide hydrolysis in mouse brain slices, whereas four selected acylated homoserine lactones were inactive. PQS also inhibited forskolin-stimulated cAMP formation in brain slices. We therefore focused on PQS in our study. Biochemical effects of PQS were not mediated by the bitter taste receptors, T2R4 and T2R16. Interestingly, submicromolar concentrations of PQS could be detected in the serum and brain tissue of adult mice under normal conditions. Levels increased in five selected brain regions after single i.p. injection of PQS (10 mg/kg), peaked after 15 min, and returned back to normal between 1 and 4 h. Systemically administered PQS reduced spontaneous locomotor activity, increased the immobility time in the forced swim test, and largely attenuated motor response to the psychostimulant, methamphetamine. These findings offer the first demonstration that a quorum sensing molecule specifically produced by Pseudomonas aeruginosa is centrally active and influences cell signaling and behavior. Quorum sensing autoinducers might represent new interkingdom signaling molecules between ecological communities of commensal, symbiotic, and pathogenic microorganisms and the host CNS.

PapRIV, a BV-2 microglial cell activating quorum sensing peptide

Quorum sensing peptides (QSPs) are bacterial peptides produced by Gram-positive bacteria to communicate with their peers in a cell-density dependent manner. These peptides do not only act as interbacterial communication signals, but can also have effects on the host. Compelling evidence demonstrates the presence of a gut-brain axis and more specifically, the role of the gut microbiota in microglial functioning. The aim of this study is to investigate microglial activating properties of a selected QSP (PapRIV) which is produced by Bacillus cereus species. PapRIV showed in vitro activating properties of BV-2 microglia cells and was able to cross the in vitro Caco-2 cell model and reach the brain. In vivo peptide presence was also demonstrated in mouse plasma. The peptide caused induction of IL-6, TNFα and ROS expression and increased the fraction of ameboid BV-2 microglia cells in an NF-κB dependent manner. Different metabolites were identified in serum, of which the main metabolite still remained active. PapRIV is thus able to cross the gastro-intestinal tract and the blood–brain barrier and shows in vitro activating properties in BV-2 microglia cells, hereby indicating a potential role of this quorum sensing peptide in gut-brain interaction.

Roflupram, a novel phosphodiesterase 4 inhibitor, inhibits lipopolysaccharide-induced neuroinflammatory responses through activation of the AMPK/Sirt1 pathway

Roflupram (ROF) is a novel phosphodiesterase 4 inhibitor. We previously found that ROF suppressed the production of pro-inflammatory factors in microglial cells; however, the underlying mechanisms are largely unknown. The present study aimed to elucidate the underlying molecular mechanisms of the anti-neuroinflammatory effects of ROF in lipopolysaccharide (LPS)-activated microglial cells and LPS-challenged mice. Treatment with ROF suppressed LPS-induced expression of interleukin (IL)-6 and tumor necrosis factor (TNF)-α in BV-2 microglia cell line. Immunofluorescence and Western blotting analysis showed that ROF significantly inhibited the activation of microglia, as evidenced by decreased expression of ionized calcium binding adaptor molecule-1 (Iba1). Similar results were obtained in primary cultured microglial cells. ROF induced the phosphorylation of AMP-activated protein kinase (AMPK) and the expression of Sirtuin 1 (Sirt1). Interestingly, the AMPK inhibitor, compound C, blocked the role of ROF in both the phosphorylation of AMPK and the expression of Sirt1 in BV-2 cells stimulated with LPS. More importantly, the Sirt1 inhibitor, EX527, abolished the inhibitory role of ROF on the production of pro-inflammatory factors, and reactivated BV-2 cells. In mice challenged with LPS, ROF improved cognition and decreased the levels of IL-6 and TNF-α in both the cortex and hippocampus. In contrast, EX527 weakened the effects of ROF on cognitive enhancement and reduction of pro-inflammatory factors in the cortex and hippocampus. Furthermore, EX527 blocked the inhibitory role of ROF in the activation of microglial cells in both the hippocampus and cortex. Taken together, our results indicated that ROF attenuated LPS-induced neuroinflammatory responses in microglia, and the AMPK/Sirt1 pathway is essential for the anti-inflammatory effects of ROF.

Dual-Target Peptide-Modified Erythrocyte Membrane-Enveloped PLGA Nanoparticles for the Treatment of Glioma

Penetration of the blood–brain barrier (BBB) and the blood–brain tumor barrier (BBTB) remains a significant challenge for the delivery of drugs in the treatment of glioma. Therefore, the development of targeted preparations with the ability to penetrate the BBB and BBTB, and target gliomas, is an important approach if we are to improve the efficacy of glioma treatment. In the current study, an active targeting preparation based on PLGA nanoparticles coated with erythrocyte membranes (RBCNPs) and dual-modified with ^DWSW and NGR peptide ligands (^DWSW/NGR-RBCNPs). Euphorbia factor L1 (EFL1) extracted from euphorbiae semen was used as the model drug. The final nanoparticles were characterized by in vivo and in vitro tests. In vitro results showed that EFL1-loaded ^DWSW/NGR-RBCNPs were taken up by cells and had the ability to penetrate the BBB and BBTB and produce cytotoxic effects. Furthermore, in vivo studies in mice showed that when injected intravenously, these specialized NPs could enter the brain, target tumor tissue, and significantly extend life span. The results showed that dual-targeting EFL1-loaded ^DWSW/NGR-RBCNPs have significant potential as a nanotherapeutic tool for the treatment of brain glioma.

Dialog between skin and its microbiota: Emergence of "Cutaneous Bacterial Endocrinology"

Microbial endocrinology is studying the response of microorganisms to hormones and neurohormones and the microbiota production of hormones-like molecules. Until now, it was mainly applied to the gut and revealed that the intestinal microbiota should be considered as a real organ in constant and bilateral interactions with the whole human body. The skin harbours the second most abundant microbiome and contains an abundance of nerve terminals and capillaries, which in addition to keratinocytes, fibroblasts, melanocytes, dendritic cells and endothelial cells, release a huge diversity of hormones and neurohormones. In the present review, we will examine recent experimental data showing that, in skin, molecules such as substance P, calcitonin gene-related peptide, natriuretic peptides and catecholamines can directly affect the physiology and virulence of common skin-associated bacteria. Conversely, bacteria are able to synthesize and release compounds including histamine, glutamate and γ-aminobutyric acid or peptides showing partial homology with neurohormones such as α-melanocyte-stimulating hormone (αMSH). The more surprising is that some viruses can also encode neurohormones mimicking proteins. Taken together, these elements demonstrate that there is also a cutaneous microbial endocrinology and this emerging concept will certainly have important consequences in dermatology.

Influence of Blood Collection Methods and Long-Term Plasma Storage on Quorum-Sensing Peptide Stability

Finding adequate biomarkers for rapid and accurate disease detection, prognosis, and therapy is increasingly important. Quorum-sensing peptides are herein a new emerging group, produced by bacteria, fungi, protozoa, and viruses, with blood being the most straightforward sample type to detect/quantitate them. However, detailed information about suitable blood sample collection methods and storage conditions for measuring these quorum-sensing peptides hampers further clinical research and development. Here, we first tested the time-dependent stability of a set of chemically diverse quorum-sensing peptides, spiked in blood at different temperatures (4, 21, and 37 °C) in four different ethylenediamine tetraacetic acid (EDTA)-containing plasma tubes (with different protein-stabilizing additives) over a period of up to 7.5 h. Next, we determined the storage stability of these quorum-sensing peptides in plasma at different temperatures (4, -35, and -80 °C). UPLC/MS-MS was used to selectively detect and quantify the spiked quorum-sensing peptides. The results of this study indicate that a cost-effective tube, designed for traditional proteomics and stored at 4 °C, is the preferred collection condition when quorum-sensing peptides need to be detected/quantified in human plasma. When the tubes are handled at room temperature (21 °C), a more specialized tube is required. Long-term storage of plasma samples, even under low-temperature conditions (-80 °C), indicates rapid degradation of certain quorum-sensing peptides.

Sinomenine inhibits amyloid beta-induced astrocyte activation and protects neurons against indirect toxicity

Amyloid beta is a major constituent of the plaques found in the brains of patients suffering from Alzheimer’s disease (AD). A growing body of research work suggests that neuroinflammation plays important roles in the development of AD. Thus, considerable efforts are directed towards identification of compounds that can reduce or inhibit neuroinflammation. Here, we show that sinomenine, a compound present in a Chinese medicinal plant, Sinomenium acutum, inhibits oligomeric amyloid beta-induced production of reactive oxygen species (ROS), nitric oxide (NO) and inflammation-related molecules from astrocytic cells. The conditioned medium from oligomeric amyloid beta-treated astrocytic cells induces cell death in the hippocampal neuronal cells. Importantly, sinomenine inhibits this cell death. In addition, this compound has inhibitory effects on the production of ROS, NO and inflammation-related factors from oligomeric amyloid-beta treated human astrocytes. Finally, the conditioned medium from oligomeric amyloid beta-treated human astrocytes induces cell death in the primary culture of human neurons, which is inhibited by sinomenine. Thus, sinomenine inhibits amyloid beta-induced production of toxic factors from astrocytes, and confers protection to hippocampal neuronal cells as well as human neurons against indirect toxicity. The results suggest that this compound could provide beneficial effects in AD and other neurodegenerative conditions by reducing inflammation and neuronal cell death.

WITHDRAWN: This article has been withdrawn

This article has been withdrawn at the request of the author for administrative reasons. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

Microbiota: a novel regulator of pain

Among the various regulators of the nervous system, the gut microbiota has been recently described to have the potential to modulate neuronal cells activation. While bacteria-derived products can induce aversive responses and influence pain perception, recent work suggests that "abnormal" microbiota is associated with neurological diseases such as Alzheimer's, Parkinson's disease or autism spectrum disorder (ASD). Here we review how the gut microbiota modulates afferent sensory neurons function and pain, highlighting the role of the microbiota/gut/brain axis in the control of behaviors and neurological diseases. We outline the changes in gut microbiota, known as dysbiosis, and their influence on painful gastrointestinal disorders. Furthermore, both direct host/microbiota interaction that implicates activation of "pain-sensing" neurons by metabolites, or indirect communication via immune activation is discussed. Finally, treatment options targeting the gut microbiota, including pre- or probiotics, will be proposed. Further studies on microbiota/nervous system interaction should lead to the identification of novel microbial ligands and host receptor-targeted drugs, which could ultimately improve chronic pain management and well-being.

The Potential Role of Quorum Sensing in Clonal Growth and Subsequent Expansion of Bone Marrow Stromal Cell Strains in Culture

Clonal development (clonogenicity) is an inherent property of a subset of postnatal bone marrow (BM) adherent stromal mesenchymal stem cells (MSCs) from which a multipotent progeny develops in culture. Our data suggest that clonogenicity and BM-MSC expansion are two distinct biological events. This hypothesis is based on the following observations: (1) the beginning of clonal growth is a property strictly dependent on serum and independent of the social context, (2) the expansion of individual clone is influenced by events deriving from a social context during initial growth, (3) clonogenic cells grown in a social context in presence of serum can emancipate themselves to generate a secondary different progeny, and (4) the ability of socially generated clones to develop an inherent potential for further growth suggests that quorum sensing may operate in BM-MSC cultures and determine the potential growth of clonal strains.