Influence of the polymorphism of the DUSP14 gene on the expression of immune-related genes and development of pulmonary tuberculosis

Substantiate a read-across hypothesis by using transcriptome data-A case study on volatile diketones

This case study explores the applicability of transcriptome data to characterize a common mechanism of action within groups of short-chain aliphatic α-, β-, and γ-diketones. Human reference in vivo data indicate that the α-diketone diacetyl induces bronchiolitis obliterans in workers involved in the preparation of microwave popcorn. The other three α-diketones induced inflammatory responses in preclinical in vivo animal studies, whereas beta and gamma diketones in addition caused neuronal effects. We investigated early transcriptional responses in primary human bronchiolar (PBEC) cell cultures after 24 h and 72 h of air-liquid exposure. Differentially expressed genes (DEGs) were assessed based on transcriptome data generated with the EUToxRisk gene panel of Temp-O-Seq^®. For each individual substance, genes were identified displaying a consistent differential expression across dose and exposure duration. The log fold change values of the DEG profiles indicate that α- and β-diketones are more active compared to γ-diketones. α-diketones in particular showed a highly concordant expression pattern, which may serve as a first indication of the shared mode of action. In order to gain a better mechanistic understanding, the resultant DEGs were submitted to a pathway analysis using ConsensusPathDB. The four α-diketones showed very similar results with regard to the number of activated and shared pathways. Overall, the number of signaling pathways decreased from α-to β-to γ-diketones. Additionally, we reconstructed networks of genes that interact with one another and are associated with different adverse outcomes such as fibrosis, inflammation or apoptosis using the TRANSPATH-database. Transcription factor enrichment and upstream analyses with the geneXplain platform revealed highly interacting gene products (called master regulators, MRs) per case study compound. The mapping of the resultant MRs on the reconstructed networks, visualized similar gene regulation with regard to fibrosis, inflammation and apoptosis. This analysis showed that transcriptome data can strengthen the similarity assessment of compounds, which is of particular importance, e.g., in read-across approaches. It is one important step towards grouping of compounds based on biological profiles.

Offense and Defense in Granulomatous Inflammation Disease

Granulomatous inflammation (GI) diseases are a group of chronic inflammation disorders characterized by focal collections of multinucleated giant cells, epithelioid cells and macrophages, with or without necrosis. GI diseases are closely related to microbes, especially virulent intracellular bacterial infections are important factors in the progression of these diseases. They employ a range of strategies to survive the stresses imposed upon them and persist in host cells, becoming the initiator of the fighting. Microbe-host communication is essential to maintain functions of a healthy host, so defense capacity of hosts is another influence factor, which is thought to combine to determine the result of the fighting. With the development of gene research technology, many human genetic loci were identified to be involved in GI diseases susceptibility, providing more insights into and knowledge about GI diseases. The current review aims to provide an update on the most recent progress in the identification and characterization of bacteria in GI diseases in a variety of organ systems and clinical conditions, and examine the invasion and escape mechanisms of pathogens that have been demonstrated in previous studies, we also review the existing data on the predictive factors of the host, mainly on genetic findings. These strategies may improve our understanding of the mechanisms underlying GI diseases, and open new avenues for the study of the associated conditions in the future.

The MAPK dual specific phosphatase (DUSP) proteins: A versatile wrestler in T cell functionality

The functional state of T cells is diverse and under dynamic control for adapting to the changes of microenvironment. Reversible protein phosphorylation represents an important post-translational modification that not only involves in the immediate early response of T cells, but also affects their functionality in the long run. Perturbation of global phosphorylation profile and/or phosphorylation of specific signaling nodes result in aberrant T cell activity. Dual specific phosphatases (DUSPs), which target MAPKs and beyond, have increasingly been emerged as a versatile regulator in T cell biology. Herein in this mini review, we sought to summarize and discuss the impact of DUSP proteins on the regulation of effector T cell activity, T cell polarization, regulatory T cell development and T cell senescence/exhaustion. Given the distinctive engagement of each DUSP member under various disease settings such as chronic infection, autoimmune disorders, cancer and age-related diseases, DUSP proteins likely hold the promise to become a druggable target other than the existing therapeutics that are predominantly by manipulating protein kinase activity.

Eriocitrin attenuates ischemia reperfusion-induced oxidative stress and inflammation in rats with acute kidney injury by regulating the dual-specificity phosphatase 14 (DUSP14)-mediated Nrf2 and nuclear factor-κB (NF-κB) pathways

Background

Ischemia reperfusion (IR)-induced acute kidney injury (AKI) is accompanied by increased inflammatory response and oxidative stress. Eriocitrin is a flavonoid that is mainly derived from lemon or citrate juice. It exhibits various pharmacological effects and is known to have antioxidant and anti-steatotic benefits. However, research on the effect of eriocitrin against IR-induced oxidative stress and inflammation in AKI is limited.

Methods

In this study, an OGD/R of HK-2 cell in vitro and rat model of AKI in vivo were constructed. Then the cell or rats were treated with eriocitrin at different doses (60, 30, 10 mg/kg). The levels of apoptotic were detected by flow cytometry. Inflammatory and oxidative stress factors in supernatant in vitro and tissue in vivo. Meanwhile, Western blot was used to detect the change of dual-specificity phosphatase 14 (DUSP14), Nrf2 and nuclear factor-κB (NF-κB).

Results

Eriocitrin attenuated apoptosis of the human renal tubular epithelial cell line HK-2 mediated by oxygen glucose deprivation/reperfusion via the repression of inflammation and oxidative stress in a dose-dependent manner. Eriocitrin also enhanced the levels of dual-specificity phosphatase 14 (DUSP14) and Nrf2, and decreased NF-κB phosphorylation. Furthermore, the in vivo experiments indicated that eriocitrin dose-dependently alleviated IR-induced AKI and apoptosis in rats. By elevating DUSP14, eriocitrin promoted the expression of Nrf2 and inactivated NF-κB, thereby downregulating inflammation and oxidative stress. Moreover, inhibiting DUSP14 expression with protein tyrosine phosphatase (PTP) inhibitor IV reversed the kidney-protective effects of Eriocitrin.

Conclusions

Eriocitrin protected IR-induced AKI by attenuating oxidative stress and inflammation via elevating DUSP14, thereby providing a theoretical basis for the treatment of IR-induced AKI.

CLEC4E (Mincle) genetic variation associates with pulmonary tuberculosis in Guinea-Bissau (West Africa)

Tuberculosis (TB) is the leading cause of death from a single infectious agent. According to the WHO, 85% of cases in 2018 were pulmonary tuberculosis (PTB), making it the most prevalent form of the disease. Although the bacillus responsible for disease, Mycobacterium tuberculosis (MTB), is estimated to infect 1.7 billion people worldwide, only a small portion of those infected (5-10%) will transition into active TB. Because such a small fraction of infected people develop active disease, we hypothesized that underlying host genetic variation associates with developing active pulmonary disease. Variation in CLEC4E has been of interest in previous association studies showing either no effect or protection from PTB. For our study we assessed 60 SNPs in 11 immune genes, including CLEC4E, using a case-control study from Guinea-Bissau. The 289 cases and 322 controls differed in age, sex, and ethnicity all of which were included in adjusted models. Initial association analysis with unadjusted logistic regression revealed putative association with seven SNPs (p < 0.05). All SNPs were then assessed in an adjusted model. Of the six SNPs that remained significant, three of them were assigned to the CLEC4E gene (rs12302046, rs10841847, and rs11046143). Of these, only rs10841847 passed FDR adjustment for multiple testing. Adjusted regression analyses showed that the minor allele at rs10841847 associated with higher risk of developing PTB (OR = 1.55, CI = 1.22-1.96, p-value = 0.00036). Based on these initial association tests, CLEC4E seemed to be the predictor of interest for PTB risk in this population. Haplotype analysis (2-SNP and 3-SNP windows) showed that minor alleles in segments including rs10841847 were the only ones to pass the threshold of global significance, compared to other haplotypes (p-value < 0.05). Linkage disequilibrium patterns showed that rs12302046 is in high LD with rs10841847 (r2 = 0.67), and all other SNPs lost significance when adjusted for rs10841847 effects. These findings indicate that rs10841847 in CLEC4E is the single best predictor of pulmonary tuberculosis risk in our study population. These results provide evidence for the hypothesis that genetic variation of CLEC4E influences risk to TB in Guinea-Bissau.

Activation of Dusp14 protects against osteoclast generation and bone loss by regulating AMPKα-dependent manner

Osteoporosis is a progressive systematic skeletal disorder featured by decreased bone and enhanced risk of fracture due to an uncoupling of bone resorption. Chronic inflammatory response plays an essential role in osteoporosis progression. Unfortunately, the pathogenesis that contributes to osteoporosis still remains unclear. Dual-specificity phosphatase 14 (Dusp14, also known as MKP6) is a MAP kinase phosphatase, and has important roles in regulating various cellular processes. In the study, we attempted to explore the effects of Dusp14 on osteoporosis development. The results indicated that Dusp14 expression was decreased during osteoclast differentiation and that Dusp14 over-expression markedly alleviated osteoclast generation regulated by macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL). In M-CSF/RANKL-treated bone marrow-derived cells (BMMs), promoting Dusp14 expression significantly alleviated inflammation and apoptosis by suppressing nuclear factor (NF)-κB and Caspase-3 signaling pathways, respectively. Furthermore, AMP-activated protein kinase (AMPK)-α activation was markedly increased by Dusp14 over-expression in M-CSF/RANKL-incubated BMMs. Importantly, we found that AMPKα blockage obviously abolished the role of Dusp14 in preventing osteoclasts differentiation at least partly via elevating M-CSF/RANKL-elicited inflammation and apoptosis. In vivo, magnesium silicate-induced inflammatory osteoporosis was obviously alleviated in Dusp14 transgenic (TG) mice. Taken together, we defined Dusp14 as an important molecular switch resulting in osteoporosis through an AMPKα-dependent manner.

Clinical relevance of the lnc-HNF1B-3:1 genetic polymorphisms in Western Chinese tuberculosis patients

Background

Tuberculosis remains a global public health problem. Genetic polymorphisms may affect the susceptibility, clinical characteristics, and adverse drug reactions of patients with TB. The present study aimed to examine the association of single nucleotide polymorphisms of lncRNA‐HNF1B‐3:1 with the clinical manifestation of TB in a Western Chinese population.

Method

A total of 526 tuberculosis patients and 561 healthy subjects were recruited in Western China. The correlation between lnc‐HNF1B‐3:1 polymorphism and tuberculosis susceptibility was investigated. Moreover, the influence on adverse drug reactions following treatment was explored. A total of 7 SNPs within the lnc‐HNF1B‐3:1 locus was genotyped by the improved multiplex ligation detection reaction method.

Results

No significant associations were noted between TB susceptibility and the presence of all 7 SNPs of the lnc‐HNF1B‐3:1 as determined by single‐locus analysis (All P > .05). The AA genotype of rs12939622 (in the dominant model) and the AA genotype of rs4262994 (in the recessive model) caused increased susceptibility of the subjects to fever (P < .001 and P = .008, respectively). The Rs2542670 G allele was associated with increased risk of thrombocytopenia, leukopenia, and chronic kidney damage following drug administration (P = .007, .029, .003, respectively).

Conclusion

The present study reported for the first time that the rs12939622, rs4262994 and rs2542670 genotypes in lnc‐HNF1B‐3:1 locus may influence the clinical manifestations of tuberculosis.

Dual-Specificity Phosphatases in Immunity and Infection: An Update

Kinase activation and phosphorylation cascades are key to initiate immune cell activation in response to recognition of antigen and sensing of microbial danger. However, for balanced and controlled immune responses, the intensity and duration of phospho-signaling has to be regulated. The dual-specificity phosphatase (DUSP) gene family has many members that are differentially expressed in resting and activated immune cells. Here, we review the progress made in the field of DUSP gene function in regulation of the immune system during the last decade. Studies in knockout mice have confirmed the essential functions of several DUSP-MAPK phosphatases (DUSP-MKP) in controlling inflammatory and anti-microbial immune responses and support the concept that individual DUSP-MKP shape and determine the outcome of innate immune responses due to context-dependent expression and selective inhibition of different mitogen-activated protein kinases (MAPK). In addition to the canonical DUSP-MKP, several small-size atypical DUSP proteins regulate immune cells and are therefore also reviewed here. Unexpected and complex findings in DUSP knockout mice pose new questions regarding cell type-specific and redundant functions. Another emerging question concerns the interaction of DUSP-MKP with non-MAPK binding partners and substrate proteins. Finally, the pharmacological targeting of DUSPs is desirable to modulate immune and inflammatory responses.

The role of human host genetics in tuberculosis resistance

INTRODUCTION

Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.

Human genetic factors in tuberculosis: an update

Tuberculosis (TB) is a major threat to human health, especially in many developing countries. Human genetic variability has been recognised to be of great relevance in host responses to Mycobacterium tuberculosis infection and in regulating both the establishment and the progression of the disease. An increasing number of candidate gene and genome-wide association studies (GWAS) have focused on human genetic factors contributing to susceptibility or resistance to TB. To update previous reviews on human genetic factors in TB we searched the MEDLINE database and PubMed for articles from 1 January 2014 through 31 March 2017 and reviewed the role of human genetic variability in TB. Search terms applied in various combinations were 'tuberculosis', 'human genetics', 'candidate gene studies', 'genome-wide association studies' and 'Mycobacterium tuberculosis'. Articles in English retrieved and relevant references cited in these articles were reviewed. Abstracts and reports from meetings were also included. This review provides a recent summary of associations of polymorphisms of human genes with susceptibility/resistance to TB.

Quality by design (QbD) approach of pharmacogenomics in drug designing and formulation development for optimization of drug delivery systems

Conventional approaches of drug discovery are very complex, costly and time consuming. But after the completion of human genome project, applications of pharmacogenomics in this area completely revolutionize the drug discovery and development process to produce a quality by design (QbD) approach based products. The applications of two areas of pharmacogenomics i.e. structural and functional pharmacogenomics excel the drug discovery process by employing genomic data in drug target identification and evaluation, lead optimization via high throughput screening, evaluation of drug metabolizing enzymes, drug transporters and drug receptors using computer aided technique and bioinformatics library data base. Pharmacogenomics also provides an important and reliable basis for evaluation and optimization of the dosage forms as well as repositioning of failed drugs for the treatment of new disease. Various dosage forms of category of drugs such as anticancer drugs, vaccines, gene and DNA delivery systems and immunological agents can be easily evaluated based on the genetic markers of the related disease. The effect of different formulation polymers on pharmacokinetic and pharmacodynamic properties of drugs can be assessed easily and therefore it plays an important role in formulation optimization. However, current applications of pharmacogenomics in drug discovery and formulation optimization are very limited because of costly and non accessible techniques for everyone, but in future, with the advancement in the technology; the application of genomic data in drug discovery will provide us with innovative, safer and more efficacious medicines.