Identification of gene networks and pathways associated with Guillain-Barré syndrome

Interactions Between Extracellular Vesicles and Autophagy in Neuroimmune Disorders

Neuroimmune disorders, such as multiple sclerosis, neuromyelitis optica spectrum disorder, myasthenia gravis, and Guillain-Barré syndrome, are characterized by the dysfunction of both the immune system and the nervous system. Increasing evidence suggests that extracellular vesicles and autophagy are closely associated with the pathogenesis of these disorders. In this review, we summarize the current understanding of the interactions between extracellular vesicles and autophagy in neuroimmune disorders and discuss their potential diagnostic and therapeutic applications. Here we highlight the need for further research to fully understand the mechanisms underlying these disorders, and to develop new diagnostic and therapeutic strategies.

Molecular Responses of the Eukaryotic Cell Line INT407 on the Internalized Campylobacter jejuni-The Other Side of the Coin

Campylobacter jejuni is a zoonotic bacterium with the capacity to invade the epithelial cells during the pathogenic process. Several bacterial factors have been identified to contribute to this process, but our knowledge is still very limited about the response of the host. To reveal the major routes of this response, a whole-transcriptome analysis (WTA) was performed where gene expressions were compared between the 1st and the 3rd hours of internalization in INT407 epithelial cells. From the 41,769 human genes tested, altogether, 19,060 genes were shown through WTA to be influenced to different extents. The genes and regulation factors of transcription (296/1052; 28%), signal transduction (215/1052; 21%), apoptosis (153/1052; 15%), immune responses (97/1052; 9%), transmembrane transport (64/1052; 6%), cell-cell signaling (32/1052; 3%), cell-cell adhesions (29/1052; 3%), and carbohydrate metabolism (28/1052; 3%) were the most affected biological functions. A striking feature of the gene expression of this stage of the internalization process is the activation of both immune functions and apoptosis, which convincingly outlines that the invaded cell faces a choice between death and survival. The seemingly balanced status quo between the invader and the host is the result of a complex process that also affects genes known to be associated with postinfectious pathological conditions. The upregulation of TLR3 (3.79×) and CD36 (2.73×), two general tumor markers, and SERPINEB9 (11.37×), FNDC1 (7.58×), and TACR2 (8.84×), three factors of tumorigenesis, confirms the wider pathological significance of this bacterium.

Biological analysis of the potential pathogenic mechanisms of Infectious COVID-19 and Guillain-Barré syndrome

Background

Guillain-Barré syndrome (GBS) is a medical condition characterized by the immune system of the body attacking the peripheral nerves, including those in the spinal nerve roots, peripheral nerves, and cranial nerves. It can cause limb weakness, abnormal sensations, and facial nerve paralysis. Some studies have reported clinical cases associated with the severe coronavirus disease 2019 (COVID-19) and GBS, but how COVID-19 affects GBS is unclear.

Methods

We utilized bioinformatics techniques to explore the potential genetic connection between COVID-19 and GBS. Differential expression of genes (DEGs) related to COVID-19 and GBS was collected from the Gene Expression Omnibus (GEO) database. By taking the intersection, we obtained shared DEGs for COVID-19 and GBS. Subsequently, we utilized bioinformatics analysis tools to analyze common DEGs, conducting functional enrichment analysis and constructing Protein-protein interaction networks (PPI), Transcription factors (TF) -gene networks, and TF-miRNA networks. Finally, we validated our findings by constructing the Receiver Operating Characteristic (ROC) curves.

Results

This study utilizes bioinformatics tools for the first time to investigate the close genetic relationship between COVID-19 and GBS. CAMP, LTF, DEFA1B, SAMD9, GBP1, DDX60, DEFA4, and OAS3 are identified as the most significant interacting genes between COVID-19 and GBS. In addition, the signaling pathway of NOD-like receptors is believed to be essential in the link between COVID-19 and GBS.

Integrated gene expression profiling and functional enrichment analyses to discover biomarkers and pathways associated with Guillain-Barré syndrome and autism spectrum disorder to identify new therapeutic targets

Guillain-Barré syndrome (GBS) is one of the most prominent and acute immune-mediated peripheral neuropathy, while autism spectrum disorders (ASD) are a group of heterogeneous neurodevelopmental disorders. The complete mechanism regarding the neuropathophysiology of these disorders is still ambiguous. Even after recent breakthroughs in molecular biology, the link between GBS and ASD remains a mystery. Therefore, we have implemented well-established bioinformatic techniques to identify potential biomarkers and drug candidates for GBS and ASD. 17 common differentially expressed genes (DEGs) were identified for these two disorders, which later guided the rest of the research. Common genes identified the protein-protein interaction (PPI) network and pathways associated with both disorders. Based on the PPI network, the constructed hub gene and module analysis network determined two common DEGs, namely CXCL9 and CXCL10, which are vital in predicting the top drug candidates. Furthermore, coregulatory networks of TF-gene and TF-miRNA were built to detect the regulatory biomolecules. Among drug candidates, imatinib had the highest docking and MM-GBSA score with the well-known chemokine receptor CXCR3 and remained stable during the 100 ns molecular dynamics simulation validated by the principal component analysis and the dynamic cross-correlation map. This study predicted the gene-based disease network for GBS and ASD and suggested prospective drug candidates. However, more in-depth research is required for clinical validation.Communicated by Ramaswamy H. Sarma.

Integrated mRNA and microRNA profiling in lung tissue and blood from human silicosis

BACKGROUND

The overwhelming majority of subjects in the current silicosis mRNA and microRNA (miRNA) expression profile are of human blood, lung cells or a rat model, which puts limits on the understanding of silicosis pathogenesis and therapy. To address the limitations, our investigation was focused on differentially expressed mRNA and miRNA profiles in lung tissue from silicosis patients to explore potential biomarker for early detection of silicosis.

METHODS

A transcriptome study was conducted based on lung tissue from 15 silicosis patients and eight normal people, and blood samples from 404 silicosis patients and 177 normal people. Three early stage silicosis, five advanced silicosis and four normal lung tissues were randomly selected for microarray processing and analyze. The differentially expressed mRNAs were further used to conduct Gene Ontology and pathway analyses. Series test of cluster was performed to explore possible changes in differentially expressed mRNA and miRNA expression patterns during the process of silicosis. The blood samples and remaining lung tissues were used in a quantitative real-time PCR (RT-qPCR) (RT-qPCR).

RESULTS

In total, 1417 and 241 differentially expressed mRNAs and miRNAs were identified between lung tissue from silicosis patients and normal people (p < 0.05). However, there was no significant difference in most mRNA or miRNA expression between early stage and advanced stage silicosis lung tissues. RT-qPCR validation results in lung tissues showed expression of four mRNAs (HIF1A, SOCS3, GNAI3 and PTEN) and seven miRNAs was significantly down-regulated compared to those of control group. Nevertheless, PTEN and GNAI3 expression was significantly up-regulated (p < 0.001) in blood samples. The bisulfite sequencing PCR demonstrated that PTEN had significantly decreased the methylation rate in blood samples of silicosis patients.

CONCLUSIONS

PTEN might be a potential biomarker for silicosis as a result of low methylation in the blood.

Extensive cytokine biomarker analysis in serum of Guillain-Barré syndrome patients

Guillain-Barré syndrome (GBS) is an acute idiopathic polyneuropathy which is related to infection and immune mechanism. The exact pathogenesis of the disease is unknown and treatment is limited. Thus, the purpose of the study is to identify biomarkers of GBS serum and elucidate their involvement in the underlying pathogenesis of GBS that could help to treat GBS more accurately. Antibody array technology was used to detect the expression levels of 440 proteins in serum of 5 GBS group and 5 healthy control group. Sixty-seven differentially expressed proteins (DEPs) were identified by antibody array, among which FoLR1, Legumain, ErbB4, IL-1α, MIP-1α and IGF-2 were down-regulated, while 61 proteins were up-regulated. Bioinformatics analysis indicated that most DEPs were associated with leukocytes, among which IL-1α, SDF-1b, B7-1, CD40, CTLA4, IL-9, MIP-1α and CD40L were in the center of protein-protein interaction (PPI) network. Subsequently, the ability of these DEPs to distinguish GBS from healthy control was further evaluated. CD23 was identified by means of Random Forests Analysis (RFA) and verified by enzyme-linked immunosorbent assay (ELISA). The ROC curve result of CD23 respectively displayed that its sensitivity, specificity and AUC were 0.818, 0.800 and 0.824. We speculate that activation of leukocyte proliferation and migration in circulating blood might be associated with inflammatory recruitment of peripheral nerves, leading to the occurrence and development of GBS, but this conclusion still requires deeper confirmation. More importantly, central proteins may play a pivotal role in the pathogenesis of GBS. In addition, we detected IL-1α, IL-9, and CD23 in the serum of GBS patients for the first time, which may be promising biomarkers for the treatment of GBS.

Guillain-Barre Syndrome Secondary to the Use of Dabrafenib and Trametinib for the Treatment of Advanced Thyroid Carcinoma

BRAF V600E mutation in thyroid malignancies is associated with an aggressive phenotype with more rapid tumor growth and higher mortality. V600E is a driver mutation in the BRAF proto-oncogene, where valine (V) is substituted by glutamic acid (E) at amino acid 600. New chemotherapeutic agents targeting the mitogen-activated protein kinase (MAPK) pathway, including direct BRAF inhibitors, have become available and are increasingly used in various advanced thyroid malignancies. These agents are associated with various rare neurological adverse effects. We present a case of Guillain-Barre syndrome (GBS) secondary to dabrafenib and trametinib therapy for the management of anaplastic thyroid carcinoma. A few cases of GBS have been reported previously with the use of these agents in the treatment of melanoma. To our knowledge, this is the first case of GBS with the use of dabrafenib and trametinib for advanced thyroid malignancy. The knowledge of this rare, potentially life-threatening condition is important for clinicians to know, given the increased use of these agents in managing advanced thyroid malignancies.

Downregulation of LKB1/AMPK Signaling in Blood Mononuclear Cells Is Associated with the Severity of Guillain-Barre Syndrome

AMP-activated protein kinase (AMPK) is an intracellular energy sensor that regulates metabolic and immune functions mainly through the inhibition of the mechanistic target of rapamycin (mTOR)-dependent anabolic pathways and the activation of catabolic processes such as autophagy. The AMPK/mTOR signaling pathway and autophagy markers were analyzed by immunoblotting in blood mononuclear cells of 20 healthy control subjects and 23 patients with an acute demyelinating form of Guillain–Barré syndrome (GBS). The activation of the liver kinase B1 (LKB1)/AMPK/Raptor signaling axis was significantly reduced in GBS compared to control subjects. In contrast, the phosphorylated forms of mTOR activator AKT and mTOR substrate 4EBP1, as well as the levels of autophagy markers LC3-II, beclin-1, ATG5, p62/sequestosome 1, and NBR1 were similar between the two groups. The downregulation of LKB1/AMPK signaling, but not the activation status of the AKT/mTOR/4EBP1 pathway or the levels of autophagy markers, correlated with higher clinical activity and worse outcomes of GBS. A retrospective study in a diabetic cohort of GBS patients demonstrated that treatment with AMPK activator metformin was associated with milder GBS compared to insulin/sulphonylurea therapy. In conclusion, the impairment of the LKB1/AMPK pathway might contribute to the development/progression of GBS, thus representing a potential therapeutic target in this immune-mediated peripheral polyneuropathy.

Safety of BRAF+MEK Inhibitor Combinations: Severe Adverse Event Evaluation

Aim: The selective BRAF and MEK inhibitors (BRAFi+MEKi) have substantially improved the survival of melanoma patients with BRAF V600 mutations. However, BRAFi+MEKi can also cause severe or fatal outcomes. We aimed to identify and compare serious adverse events (sAEs) that are significantly associated with BRAFi+MEKi. Methods: In this pharmacovigilance study, we reviewed FDA Adverse Event Reporting System (FAERS) data in order to detect sAE reporting in patients treated with the combination therapies vemurafenib+cobimetinib (V+C), dabrafenib+trametinib (D+T) and encorafenib+binimetinib (E+B). We evaluated the disproportionate reporting of BRAFi+MEKi-associated sAEs. Significant associations were further analyzed to identify combination-specific safety signals among BRAFi+MEKi. Results: From January 2018 through June 2019, we identified 11,721 sAE reports in patients receiving BRAFi+MEKi. Comparison of BRAFi+MEKi combinations demonstrates that skin toxicities, including Stevens–Johnson syndrome, were disproportionally reported using V+C, with an age-adjusted reporting odds ratio (adj. ROR) of 3.4 (95%CI, 2.9–4.0), whereas fever was most significantly associated with D+T treatment with an adj. ROR of 1.9 (95%CI, 1.5–2.4). Significant associations using E+B treatment include peripheral neuropathies (adj. ROR 2.7; 95%CI, 1.2–6.1) and renal disorders (adj. ROR 4.1; 95%CI, 1.3–12.5). Notably, we found an increase in the proportion of Guillain–Barré syndrome reports (adj. ROR 8.5; 95%CI, 2.1–35.0) in patients administered E+B. Conclusion: BRAFi+MEKi combinations share a similar safety profile attributed to class effects, yet concomitantly, these combinations display distinctive effects that can dramatically impact patients’ health. Owing to the limitations of pharmacovigilance studies, some findings warrant further validation. However, the possibility of an increased risk for these events should be considered in patient care.

Inferring immune-associated signatures based on a co-expression network in Guillain-Barré syndrome

Objectives

Guillain‐Barré syndrome (GBS) is a type of acute autoimmune disease, which occurs in peripheral nerves and their roots. There is extensive evidence that suggests many immune‐associated genes have essential roles in GBS. However, the associations between immune genes and GBS have not been sufficiently examined as most previous studies have only focused on individual genes rather than their entire interaction networks.

Materials and methods

In this study, multiple levels of data including immune‐associated genes, GBS‐associated genes, protein‐protein interaction (PPI) networks and gene expression profiles were integrated, and an immune or GBS‐directed neighbour co‐expressed network (IOGDNC network) and a GBS‐directed neighbour co‐expressed network (GDNC network) were constructed.

Results

Our analysis shows the immune‐associated genes are strongly related to GBS‐associated genes whether at the interaction level or gene expression level. Five immune‐associated modules were also identified which could distinguish between GBS and normal samples. In addition, functional analysis indicated that immune‐associated genes are essential in GBS.

Conclusions

Overall, these results highlight a strong relationship between immune‐associated genes and GBS existed and provide a potential role for immune‐associated genes as novel diagnostic and therapeutic biomarkers for GBS.

Integrative metabolomics reveals unique metabolic traits in Guillain-Barré Syndrome and its variants

Guillain-Barré syndrome (GBS) is an acute fatal progressive disease caused by autoimmune mechanism mainly affecting peripheral nervous system. Although the syndrome is clinically sub-classified into several variants, specific biomarker and exact pathomechanism of each subtypes are not well elucidated yet. In current study, integrative metabolomic and lipidomic profiles were acquisitioned from cerebrospinal fluid samples of 86 GBS from three variants and 20 disease controls. And the data were systematically compared to our previous result on inflammatory demyelination disorders of central nervous system (IDDs) and healthy controls. Primary metabolite profiles revealed unique metabolic traits in which 9 and 7 compounds were specifically changed in GBS and IDD, respectively. Next, the biomarker panel with 10 primary metabolites showed a fairly good discrimination power among 3 GBS subtypes, healthy controls, and disease controls (AUCs ranged 0.849-0.999). The robustness of the biomarker panel was vigorously validated by multi-step statistical evaluation. Subsequent lipidomics revealed GBS variant-specific alteration where the significant elevations of lyso-phosphatidylcholines and sphingomyelins were unique to AIDP (acute inflammatory demyelinating polyneuropathy) and AMAN (acute motor axonal neuropathy), respectively. And metabolome-wide multivariate correlation analysis identified potential clinical association between GBS disability scale (Hughes score) and CSF lipids (monoacylglycerols, and sphingomyelins). Finally, Bayesian network analysis of covarianced structures of primary metabolites and lipids proposed metabolic hub and potential biochemical linkage associated with the pathology.

Bioinformatics methodologies for coeliac disease and its comorbidities

Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of gene expression data available in public repositories on CD and less commonly considered comorbidities. Then we developed an innovative pipeline that integrates gene expression, cell-type data and online resources (e.g. a list of comorbidities from the literature), using bioinformatics methods such as gene set enrichment analysis and semantic similarity. Our pipeline is written in R language, available at the following link: http://bioinformatica.isa.cnr.it/COELIAC_DISEASE/SCRIPTS/. We found a list of common differential expressed genes, gene ontology terms and pathways among CD and comorbidities and the closeness among the selected pathologies by means of disease ontology terms. Physicians and other researchers, such as molecular biologists, systems biologists and pharmacologists can use it to analyze pathology in detail, from differential expressed genes to ontologies, performing a comparison with the pathology comorbidities or with other diseases.

Acute motor and sensory axonal neuropathy related to treatment with MEK inhibitors in a patient with advanced melanoma

Approximately one-half of advanced cutaneous melanomas have a V600 mutation in the BRAF gene that activates the mitogen-activated protein kinase pathway. The combination of BRAF plus MEK inhibitors is one of the most effective treatments for these patients. Severe neurological toxicities have been reported in the literature. However, these toxicities are very rare. Here, we present one patient with acute motor and sensory axonal neuropathy, which is a subtype of Guillain-Barre syndrome, secondary to treatment with MEK inhibitors. This side effect had never been described as related to these agents. However, the mitogen-activated protein kinase pathway can be involved in Guillain-Barre syndrome, and awareness of early neurological injury signs is important in patients treated with MEK inhibitors.

Disturbance of Plasma Lipid Metabolic Profile in Guillain-Barre Syndrome

Guillain-Barre Syndrome (GBS) is an inflammatory disease of the peripheral nervous system. Given that plasma metabolic profiles in GBS patients have never been explored, plasma samples of 38 GBS patients, 22 multiple sclerosis (MS) patients, and 40 healthy controls were analyzed by using untargeted and targeted metabolomics analysis. The untargeted analysis showed that levels of a set of plasma lipid metabolites were significantly decreased in GBS patients compared to the controls. Furthermore, the targeted analysis demonstrated that levels of 41 metabolites in GBS patients were significantly changed compared to either the controls or MS patients. A further metabolic analysis showed that 12 of 41 metabolites were significantly lower in classical GBS patients compared to Miller-Fisher syndrome. Among them, each of PCae C34:0, PCae C42:2, PCae C42:3, and SM C24:0 was inversely correlated with Hughes functional grading scale of GBS patients at both nadir and discharge. Receiver operating characteristic curve analysis of combination of three metabolites (PCaa C42:2, PCae C36:0 and SM C24:0) showed a good discrimination between the GBS and the controls (area under curve = 0.86). This study has demonstrated disruption of lipid metabolites in GBS may be potential biomarkers to indicate disease severity and prognosis of GBS.

Genome-wide gene expression analysis of peripheral leukocytes in relation to the male predominance of Guillain-Barre syndrome: differential gene expression between male and female patients

BACKGROUND

Guillain-Barre syndrome (GBS) fulfils most of the clinical features of an autoimmune disease except for its male predominance. No previous studies have evaluated the differential genome-wide expression between male and female GBS patients.

OBJECTIVE

This study sought to identify differences between male and female GBS patients in the gene expression profiles of peripheral leukocytes.

METHODS

We downloaded gene chip data-sets pertaining to peripheral leukocyte samples from GBS patients using the gene expression omnibus (submitted by Chang et al.) and applied hierarchical cluster analysis to detect whether there was a gender difference in genome-wide gene expression levels. Then, we identified the sexually differentially expressed genes using a bioinformatic approach and applied enrichment analysis to the gene ontology and Kyoto Encyclopaedia of Genes and Genomes terms to identify significant pathways related to these genes.

RESULTS

We observed gender stratification among GBS patients. Twenty genes were expressed more highly in male patients and were enriched for functions, such as macrophage differentiation, leukocyte migration, bladder cancer, pathogenic Escherichia coli infection. In female patients, 62 genes were more highly expressed and were enriched for responses to viral infection and defence, retinoic acid-inducible gene I (RIG-I)-like receptors, cytoplasmic DNA sensing. Matrix metalloproteinase 9 (MMP9) seem to play an important role in the male predominance of GBS.

CONCLUSIONS

This study demonstrated gender differences in the genome-wide gene expression of patients with GBS. Bioinformatic approaches offer new means for identifying candidate genes and pathways relevant to the pathophysiology of GBS.

In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases

BACKGROUND

Near universal administration of vaccines mandates intense pharmacovigilance for vaccine safety and a stringently low tolerance for adverse events. Reports of autoimmune diseases (AID) following vaccination have been challenging to evaluate given the high rates of vaccination, background incidence of autoimmunity, and low incidence and variable times for onset of AID after vaccinations. In order to identify biologically plausible pathways to adverse autoimmune events of vaccine-related AID, we used a systems biology approach to create a matrix of innate and adaptive immune mechanisms active in specific diseases, responses to vaccine antigens, adjuvants, preservatives and stabilizers, for the most common vaccine-associated AID found in the Vaccine Adverse Event Reporting System.

RESULTS

This report focuses on Guillain-Barre Syndrome (GBS), Rheumatoid Arthritis (RA), Systemic Lupus Erythematosus (SLE), and Idiopathic (or immune) Thrombocytopenic Purpura (ITP). Multiple curated databases and automated text mining of PubMed literature identified 667 genes associated with RA, 448 with SLE, 49 with ITP and 73 with GBS. While all data sources provided valuable and unique gene associations, text mining using natural language processing (NLP) algorithms provided the most information but required curation to remove incorrect associations. Six genes were associated with all four AIDs. Thirty-three pathways were shared by the four AIDs. Classification of genes into twelve immune system related categories identified more "Th17 T-cell subtype" genes in RA than the other AIDs, and more "Chemokine plus Receptors" genes associated with RA than SLE. Gene networks were visualized and clustered into interconnected modules with specific gene clusters for each AID, including one in RA with ten C-X-C motif chemokines. The intersection of genes associated with GBS, GBS peptide auto-antigens, influenza A infection, and influenza vaccination created a subnetwork of genes that inferred a possible role for the MAPK signaling pathway in influenza vaccine related GBS.

CONCLUSIONS

Results showing unique and common gene sets, pathways, immune system categories and functional clusters of genes in four autoimmune diseases suggest it is possible to develop molecular classifications of autoimmune and inflammatory events. Combining this information with cellular and other disease responses should greatly aid in the assessment of potential immune-mediated adverse events following vaccination.

T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus

Type 2 diabetes mellitus (T2D), affecting >90% of the diabetic patients, is one of the major threats to human health. A comprehensive understanding of the mechanisms of T2D at molecular level is essential to facilitate the related translational research. Here, we introduce a comprehensive and up-to-date knowledgebase for T2D, i.e. T2D@ZJU. T2D@ZJU contains three levels of heterogeneous connections associated with T2D, which is retrieved from pathway databases, protein-protein interaction databases and literature, respectively. In current release, T2D@ZJU contains 1078 T2D related entities such as proteins, protein complexes, drugs and others together with their corresponding relationships, which include 3069 manually curated connections, 14,893 protein-protein interactions and 26,716 relationships identified by text-mining technology. Moreover, T2D@ZJU provides a user-friendly web interface for users to browse and search data. A Cytoscape Web-based interactive network browser is available to visualize the corresponding network relationships between T2D-related entities. The functionality of T2D@ZJU is shown by means of several case studies. Database URL: http://tcm.zju.edu.cn/t2d.