Evolutionary divergence and functions of the human interleukin (IL) gene family

Humanized zebrafish enhance human hematopoietic stem cell survival and promote acute myeloid leukemia clonal diversity

Xenograft models are invaluable tools in establishing the current paradigms of hematopoiesis and leukemogenesis. The zebrafish has emerged as a robust alternative xenograft model but, like mice, lack specific cytokines that mimic the microenvironment found in human patients. To address this critical gap, we generated the first humanized zebrafish that express human hematopoietic-specific cytokines (GM-CSF, SCF, and SDF1α). Termed GSS fish, these zebrafish promote survival, self-renewal and multilineage differentiation of human hematopoietic stem and progenitor cells and result in enhanced proliferation and hematopoietic niche-specific homing of primary human leukemia cells. Using error-corrected RNA sequencing, we determined that patient-derived leukemias transplanted into GSS zebrafish exhibit broader clonal representation compared to transplants into control hosts. GSS zebrafish incorporating error-corrected RNA sequencing establish a new standard for zebrafish xenotransplantation that more accurately recapitulates the human context, providing a more representative cost-effective preclinical model system for evaluating personalized response-based treatment in leukemia and therapies to expand human hematopoietic stem and progenitor cells in the transplant setting.

Integrative omics analyses uncover the mechanism underlying the immunotoxicity of perfluorooctanesulfonate in human lymphocytes

Perfluorooctanesulfonate (PFOS) is a man-made chemical widely used in industrial products. Due to its high persistence, PFOS has been detected in most animal species including the human population, wild animals, and aquatic organisms. Both cross-sectional studies and laboratory animal studies have shown hepatotoxicity, renal toxicity, and reproductive toxicity caused by PFOS exposure. Recently, a limited number of PFOS studies have raised concerns about its potential immune system effects. However, the molecular mechanism underlying the immunotoxicity of PFOS remains unknown. In this study, we used primary human lymphocytes as a model, together with integrative omics analyses, including the transcriptome and lipidome, and bioinformatics analysis, to resolve the immune toxicity effects of PFOS. Our results demonstrated that PFOS could alter the production of interleukins in human lymphocytes. Additionally, PFOS exposure could dysregulate clusters of genes and lipids that play important roles in immune functions, such as lymphocyte differentiation, inflammatory response, and immune response. The findings of this study offer novel insight into the molecular mechanisms underlying the immunotoxicity of PFOS, and open the potential of using the identified PFOS-responsive genes and lipids as biomarkers for risk assessment.

Microbiota, Immune System and Autism Spectrum Disorders: An Integrative Model towards Novel Treatment Options

BACKGROUND

Autism Spectrum Disorder (ASD) is a condition strongly associated with genetic predisposition and familial aggregation. Among ASD patients, different levels of symptoms severity are detectable, while the presence of intermediate autism phenotypes in close relatives of ASD probands is also known in literature. Recently, increasing attention has been paid to environmental factors that might play a role in modulating the relationship between genomic risk and development and severity of ASD. Within this framework, an increasing body of evidence has stressed a possible role of both gut microbiota and inflammation in the pathophysiology of neurodevelopment. The aim of this paper is to review findings about the link between microbiota dysbiosis, inflammation and ASD.

METHODS

Articles ranging from 1990 to 2018 were identified on PUBMED and Google Scholar databases, with keyword combinations as: microbiota, immune system, inflammation, ASD, autism, broad autism phenotype, adult.

RESULTS

Recent evidence suggests that microbiota alterations, immune system and neurodevelopment may be deeply intertwined, shaping each other during early life. However, results from both animal models and human samples are still heterogeneous, while few studies focused on adult patients and ASD intermediate phenotypes.

CONCLUSION

A better understanding of these pathways, within an integrative framework between central and peripheral systems, might not only shed more light on neural basis of ASD symptoms, clarifying brain pathophysiology, but it may also allow to develop new therapeutic strategies for these disorders, still poorly responsive to available treatments.

Macromolecular biomarkers of chronic obstructive pulmonary disease in exhaled breath condensate

Biomarkers provide important diagnostic and prognostic information on heterogeneous diseases such as chronic obstructive pulmonary disease (COPD). However, finding a suitable specimen for clinical analysis of biomarkers for COPD is challenging. Exhaled breath condensate (EBC) sampling is noninvasive, rapid, cost-effective and easily repeatable. EBC sampling has also provided recent progress in the identification of biological macromolecules, such as lipids, proteins and DNA in EBC samples, which has increased its utility for clinical scientists. In this article, we review applications involving EBC sampling for the analysis of COPD biomarkers and discuss its future potential.

Oxidized cell-free DNA as a stress-signaling factor activating the chronic inflammatory process in patients with autism spectrum disorders

BACKGROUND

Autism spectrum disorders (ASD) are known to be associated with an inflammatory process related to immune system dysfunction. This study's aim was to investigate the role of cell-free DNA in chronic inflammatory process in ASD patients.

METHODS

The study included 133 ASD patients and 27 healthy controls. Sixty-two ASD patients were demonstrated to have mild-to-moderate disease severity (group I) and 71 individuals to have severe ASD (group II). Plasma cell-free (cf) DNA characteristics, plasma cytokine concentrations, expression of the genes for NFкB1 transcription factor and pro-inflammatory cytokines TNFα, IL-1β and IL-8 in peripheral blood lymphocytes (PBL) of ASD patients, and unaffected controls were investigated. Additionally, in vitro experiments with oxidized DNA supplementation to PBL cultures derived from ASD patients and healthy controls were performed.

RESULTS

The data indicates that ASD patients have demonstrated increased cfDNA concentration in their circulation. cfDNA of patients with severe ASD has been characterized by a high abundance of oxidative modification. Furthermore, ASD patients of both groups have shown elevated plasma cytokine (IL-1β, IL-8, IL-17A) levels and heightened expression of genes for NFкB1 nuclear factor and pro-inflammatory cytokines TNFα, IL-1β, and IL-8 in PBL. In vitro experiments have shown that NF-κB/cytokine mRNA expression profiles of ASD patient PBL treated with oxidized DNA fragments were significantly different from those of healthy controls.

CONCLUSIONS

It may be proposed that oxidized cfDNA plays a role of stress-signaling factor activating the chronic inflammatory process in patients with ASD.

Computational investigation on the effects of pharmaceutical polymers on the structure and dynamics of interleukin2 in heat stress

Application of proteinous drugs can be associated with difficulties during both in storage/transportation and in the body when they are used. However, using pharmaceutical carbohydrates that are widely employed in drug delivery systems, besides the drug can be protected, these systems leading to gradually release the drug over time, or deliver it to the target cell. Using a combination of molecular modeling and simulation techniques, in this study the effects of five carbohydrate polymers of Chitosan, Alginate, Cyclodextrin, Hyaluronic acid and Pectin on structure and dynamics of interleukin2 protein at 298 K and 343 K, are investigated. Data achieved using molecular modeling methods showed that when the temperature rises, the protein stability decreases. Among different polymers, Chitosan and Cyclodextrin have shown to be able to protect protein against the negative effects of high temperatures in comparison with other polymers which suggests that the use of Cyclodextrin biopolymer for the preparation of pharmaceutical formulations of interleukin2 can be the best possible choice among other polymers investigated in this research.Communicated by Ramaswamy H. Sarma.

The cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system

In 2019-2020 a new coronavirus named SARS-CoV-2 was identified as the causative agent of a several acute respiratory infection named COVID-19, which is causing a worldwide pandemic. There are still many unresolved questions regarding the pathogenesis of this disease and especially the reasons underlying the extremely different clinical course, ranging from asymptomatic forms to severe manifestations, including the Acute Respiratory Distress Syndrome (ARDS). SARS-CoV-2 showed phylogenetic similarities to both SARS-CoV and MERS-CoV viruses, and some of the clinical features are shared between COVID-19 and previously identified beta-coronavirus infections. Available evidence indicate that the so called "cytokine storm" an uncontrolled over-production of soluble markers of inflammation which, in turn, sustain an aberrant systemic inflammatory response, is a major responsible for the occurrence of ARDS. Chemokines are low molecular weight proteins with powerful chemoattractant activity which play a role in the immune cell recruitment during inflammation. This review will be aimed at providing an overview of the current knowledge on the involvement of the chemokine/chemokine-receptor system in the cytokine storm related to SARS-CoV-2 infection. Basic and clinical evidences obtained from previous SARS and MERS epidemics and available data from COVID-19 will be taken into account.

Angiogenesis in Breast Cancer Progression, Diagnosis, and Treatment

Angiogenesis is a significant event in a wide range of healthy and diseased conditions. This process frequently involves vasodilation and an increase in vascular permeability. Numerous players referred to as angiogenic factors, work in tandem to facilitate the outgrowth of endothelial cells (EC) and the consequent vascularity. Conversely, angiogenic factors could also feature in pathological conditions. Angiogenesis is a critical factor in the development of tumors and metastases in numerous cancers. An increased level of angiogenesis is associated with decreased survival in breast cancer patients. Therefore, a good understanding of the angiogenic mechanism holds a promise of providing effective treatments for breast cancer progression, thereby enhancing patients' survival. Disrupting the initiation and progression of this process by targeting angiogenic factors such as vascular endothelial growth factor (Vegf)-one of the most potent member of the VEGF family- or by targeting transcription factors, such as Hypoxia-Inducible Factors (HIFs) that act as angiogenic regulators, have been considered potential treatment options for several types of cancers. The objective of this review is to highlight the mechanism of angiogenesis in diseases, specifically its role in the progression of malignancy in breast cancer, as well as to highlight the undergoing research in the development of angiogenesis-targeting therapies.

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life

BACKGROUND

Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions.

RESULTS

In this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals.

CONCLUSIONS

Our results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.

Exercise as an anti-inflammatory therapy for cancer cachexia: a focus on interleukin-6 regulation

Cancer cachexia is a complicated disorder of extreme, progressive skeletal muscle wasting. It is directed by metabolic alterations and systemic inflammation dysregulation. Numerous studies have demonstrated that increased systemic inflammation promotes this type of cachexia and have suggested that cytokines are implicated in the skeletal muscle loss. Exercise is firmly established as an anti-inflammatory therapy that can attenuate or even reverse the process of muscle wasting in cancer cachexia. The interleukin IL-6 is generally considered to be a key player in the development of the microenvironment of malignancy; it promotes tumor growth and metastasis by acting as a bridge between chronic inflammation and cancerous tissue and it also induces skeletal muscle atrophy and protein breakdown. Paradoxically, a beneficial role for IL-6 has also been identified recently, and that is its status as a “founding member” of the myokine class of proteins. Skeletal muscle is an important source of circulating IL-6 in people who participate in exercise training. IL-6 acts as an anti-inflammatory myokine by inhibiting TNFα and improving glucose uptake through the stimulation of AMPK signaling. This review discusses the action of IL-6 in skeletal muscle tissue dysfunction and the role of IL-6 as an “exercise factor” that modulates the immune system. This review also sheds light on the main considerations related to the treatment of muscle wasting in cancer cachexia.

Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in zebrafish gonads

There is crosstalk between the immune and reproductive systems in which sexual dimorphism is a common pattern in vertebrates. In recent years, epigenetics has emerged as a way to study the molecular mechanisms involved in gonadal development, those responsible for integrating environmental information that contribute to assigning a specific sexual phenotype (either an ovary or a testis). The knowledge of epigenetic mechanisms in certain molecular processes allows the development of epigenetic markers. In fish gonads, the existence of reproduction-immune system interactions is known, although the epigenetic mechanisms involved are far from clear. Here, we used the zebrafish (Danio rerio) as a model to study the DNA methylation patterns in gonads of two well-known innate immune genes: IL1β and Casp9. DNA methylation levels were studied by a candidate gene approach at single nucleotide resolution and gene expression analyses were also carried out. Results showed that there was clear sexual dimorphism in the DNA methylation levels of the two immune genes studied, being significantly higher in the testes when compared to the ovaries. In summary, and although further research is needed, this paper presents sexual dimorphic methylation patterns of two immune-related genes, thus sex-biased differences in methylation profiles should considered when analyzing immune responses in fish. Data showed here can help to develop epimarkers with forthcoming applications in livestock and fish farming production, for example, in immune fish diseases or sexual control programs as epigenetic molecular tools to predict environmental pressure in the gonads.

Comparisons of lung and gluteus transcriptome profiles between yaks at different ages

The yak, Bos grunniens, is the only large mammal in the Qinghai-Tibet Plateau and has been bred to provide meat, milk, and transportation. Previous studies indicate that the immune system contributes to the yak's adaptation to high-altitude environments. In order to further investigate changes in immune function during yak development, we compared the transcriptome profiles of gluteus and lung tissues among yaks at 6, 30, 60, and 90 months of age. Analyses of significantly differentially expressed genes (DEGs) in lung tissues revealed that immune function was more activated at 6-months and less activated at 90-months than in the 30 and 60-month-old animals. DEG exploration in gluteal tissues revealed that immune functions were more highly activated at both 6 and 90-months, compared with 30 and 60-months. Immune system activation in the muscle and lung tissues of 30-month-old yaks may increase their resistance to infections, while decreased may be due to aging. Furthermore, the higher immune activation status in the gluteal tissues in 90-month-old yaks could be due to muscle injury and subsequent regeneration, which is supported by the fact that 5 unigenes related with muscle injury and 3 related to muscle regeneration displayed greater expression levels at 90-months than at 30 and 60-months. Overall, the present study highlights the important role of the immune system in yak development, which will facilitate future investigations.

Transmissible Cancers and Immune Downregulation in Tasmanian Devil (Sacrophilus harrisii) and Canine Populations

Known as devil facial tumor disease (DFTD) and canine transmissible venereal tumor (CTVT), transmissible cancer occurs in both Tasmanian devil and canine populations, respectively. Both malignancies show remarkable ability to be transmitted as allografts into subsequent hosts. How DFTD and CTVT avoid detection by immunocompetent hosts is of particular interest, given that these malignancies are rarely seen in other species in nature. Both of these transmissible cancers can downregulate the host immune system, enabling proliferation. DFTD is characterized by epigenetic modifications to the DNA promoter regions of β₂microglobulin, transporters associated with antigen processing 1 and 2, MHC I, and MHC II-crucial proteins required in the detection and surveillance of foreign material. Downregulation during DFTD may be achieved by altering the activity of histone deacetylases. DFTD has caused widespread destruction of devil populations, placing the species on the brink of extinction. CTVT demonstrates a proliferative phase, during which the tumor evades immune detection, allowing it to proliferate, and a regressive phase when hosts mount an effective immune response. Alteration of TGFβ signaling in CTVT likely impedes the antigen-processing capabilities of canine hosts in addition to hindering the ability of natural killer cells to detect immune system downregulation. Immunosuppressive cytokines such as CXCL7 may contribute to a favorable microenvironment that supports the proliferation of CTVT. When viewed from an evolutionary paradigm, both DFTD and CTVT may conform to a model of host-parasite coevolution. Furthermore, various genetic features, such as genetically active transposons in CTVT and chromosomal rearrangements in DFTD, play important roles in promoting the survival of these disease agents. Understanding the mode of transmission for these transmissible cancers may shed light on mechanisms for human malignancies and reveal opportunities for treatment in the future.

Aqueous humor IL-8, IL-10, and VEGF levels in Fuchs' uveitis syndrome and Behçet's uveitis

PURPOSE

This study investigated the levels of interleukin (IL)-8, IL-10, and vascular endothelial growth factor (VEGF) in the aqueous humor (AqH) of patients with Behçet's uveitis (BU) and Fuchs' uveitis syndrome (FUS) during an inactive period and compared these levels with those in the AqH of noninflammatory healthy control subjects.

METHODS

This prospective and case-control study included 33 patients (16 patients with BU and 17 patients with FUS) and 35 control subjects. IL-8, IL-10, and VEGF levels in the AqH were quantified by performing sandwich enzyme-linked immunosorbent assay. Kruskal-Wallis test was used to compare the cytokine levels in the different groups, and statistical significance was set at p < 0.05.

RESULTS

IL-8 levels were significantly higher in the AqH of patients with BU and FUS than in the AqH of control subjects (p < 0.001 and p < 0.001, respectively). IL-10 levels were significantly lower in the AqH of patients with BU than in the AqH of patients with FUS and of control subjects (p = 0.001 and p < 0.001, respectively). Although VEGF levels were higher in the AqH of patients with FUS than in the AqH of patients with BU and of control subjects, the difference was significant only between patients with FUS and control subjects (p < 0.001).

CONCLUSIONS

We observed a significant decrease in IL-10 levels in the AqH of patients with BU and a significant increase in VEGF levels in the AqH of patients with FUS compared to controls. IL-8 and VEGF levels showed no significant difference among uveitis patients.

Muscle Damage in Different Approaches in Total Hip Arthroplasty According to Serum Markers

Background:

Total Hip Arthroplasty (THA) is the final treatment of end-stage hip osteoarthritis. Nowadays, THA has become very common, cost- effective and one of the most successful orthopaedic procedures. Recently, surgeons have shifted their interest to approaches according to Minimally Invasive Surgery (MIS). These approaches are either modifications of conventional approaches or they are designed from the beginning as MIS approaches. Muscle damage and soft tissue damage are issues that concern researchers who perform studies on THA.

Objective:

The aim of this study is to review the literature concerning studies by comparing different approaches using serum and inflammatory markers for muscle and soft tissue damage.

Methods:

We searched the PubMed database in the English language systematically for clinical studies or reviews, comparing muscle damage according to serum markers between two or more approaches in primary total arthroplasty.

Results:

In total, twenty-one studies were included in this review. Although the results are controversial, it seems that MIS approaches in most of the studies were related to lower levels of inflammation markers contrasting with conventional approaches. Nevertheless, this difference in muscle damage is not correlated with a difference in functional scores or other perioperative data and clinical outcomes in all studies.

Conclusion:

The existing literature does not lead to a safe consensus about the superiority of any approach. Therefore, there is still a need for further research with well-designed studies.

Development of the hematopoietic system: Role of inflammatory factors

Hematopoietic stem cells (HSCs) have two defining features, multipotency and self-renewal, both of which are tightly controlled by cell autonomous programs and environmental factors throughout the lifetime of an organism. During development, HSCs are born in the aorta-gonad-mesonephros region, and migrate to distinct hematopoietic organs such as the placenta, fetal liver and spleen, continuously self-renewing and expanding to reach a homeostatic number. HSCs ultimately seed the bone marrow around the time of birth and become dormant to sustain lifelong hematopoiesis. In this review, we will summarize the recent findings on the role of inflammatory factors regulating HSC development, that is, emergence, trafficking and differentiation. An understanding of HSC kinetics during developmental processes will provide useful knowledge on HSC behavior under physiological and pathophysiological conditions. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Environmental Control of Stem Cells.

Computational Evolution of Threonine-Rich β-Hairpin Peptides Mimicking Specificity and Affinity of Antibodies

The development of recognition molecules with antibody-like properties is of great value to the biotechnological and bioanalytical communities. The recognition molecules presented here are peptides with a strong tendency to form β-hairpin structures, stabilized by alternate threonines, which are located at one face of the peptide. Amino acids at the other face of the peptide are available for interaction with the target molecule. Using this scaffold, we demonstrate that recognition molecules can efficiently be designed in silico toward four structurally unrelated proteins, GFP, IL-1β, IL-2, and IL-6. On solid support, 10 different antibody-mimetic recognition molecules were synthesized. They displayed high affinity and no cross-reactivity, as observed by fluorescence microscopy. Stabilized variants were readily obtained by incorporation of azido acids and propargylglycine followed by cyclization via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. As this new class of antibody mimics can be designed toward essentially any protein, the concept is believed to be useful to a wide range of technologies. Here, their use in protein separation and in the detection of proteins in a sandwich-type assay is demonstrated.

IL-26, a Cytokine With Roles in Extracellular DNA-Induced Inflammation and Microbial Defense

Interleukin 26 (IL-26) is the most recently identified member of the IL-20 cytokine subfamily, and is a novel mediator of inflammation overexpressed in activated or transformed T cells. Novel properties have recently been assigned to IL-26, owing to its non-conventional cationic, and amphipathic features. IL-26 binds to DNA released from damaged cells and, as a carrier molecule for extracellular DNA, links DNA to inflammation. This observation suggests that IL-26 may act both as a driver and an effector of inflammation, leading to the establishment of a deleterious amplification loop and, ultimately, sustained inflammation. Thus, IL-26 emerges as an important mediator in local immunity/inflammation. The dysregulated expression and extracellular DNA carrier capacity of IL-26 may have profound consequences for the chronicity of inflammation. IL-26 also exhibits direct antimicrobial properties. This review summarizes recent advances on the biology of IL-26 and discusses its roles as a novel kinocidin.

Interplay between heat shock proteins, inflammation and cancer: a potential cancer therapeutic target

The historical relationship between cancer and inflammation has long been evaluated, and dates back to the early work of Virchow (1863), where he hypothesised that chronic inflammation as a direct cause of tissue injury and infection, could actually promote tissue proliferation. At that period in time however, the exact mechanisms that mediated this relationship were little understood. Subsequent studies have since then demonstrated that chronic inflammation plays significant roles in microenvironments, mostly in the progression of tumours, probably, through over-secretion of proinflammatory cytokines and other immune-killing apparatus such as reactive oxygen species (ROS) which cause damage to normal cells leading to DNA damage and increased cellular mutation rates. Recently, the identification of DNA lesion 5-chlorocytosine (5-CIC) created by hypochlorous acid (HOCl) secreted to nullify or kill infectious agents and toll-like receptor 4 (TLR4)-mediated chronic inflammation in the human gut, has become the latest evidence linking inflammation directly to cancer. The key to cellular survival and adaptation under unfavourable or pathological conditions is the expression of heat shock proteins (HSPs) also called molecular chaperones. These proteins play essential roles in DNA repair processes by maintaining membrane integrity, orderliness and stability of client proteins that play prominent roles in DNA repair mechanisms. More so, HSPs have also been shown to modulate the effects of pro-inflammatory/apoptotic cytokines through the inhibition of cascades leading to the generation of ROS-mediated DNA damage, while promoting the DNA repair mechanism, thus playing prominent roles in various stages of DNA repair and cancer progression. Hence, studies targeting HSPs and their inhibitors in inflammation, DNA damage, and repair, could improve current cancer therapeutic efficiency. Here the focus will be on the relationship between HSPs, inflammation and cancer, as well as roles of HSPs in DNA damage response (DDR).

Gene polymorphisms in the interleukins gene and the risk of acute pancreatitis: A meta-analysis

Single nucleotide polymorphisms (SNPs) within the interleukins (IL) gene may affect the risk of acute pancreatitis. Many epidemiological studies have reported an association between the IL gene and acute pancreatitis risk, but the results remain inconsistent. Given the controversial available data, we carried out a meta-analysis to systematically evaluate and clarify the association between IL gene polymorphisms and AP. A systematic search of studies for this association was obtained from the PubMed, EMBASE, Web of Science and Chinese National Knowledge Infrastructure (CNKI) databases until June 1, 2017. We also searched the references of the included studies to identify additional studies. Odds ratios (ORs) with 95% confidence intervals (95% CIs) were used to pool the effect size. Stata12.0 was used for whole statistical analysis. Fifteen studies that contained 3371 AP cases and 3506 controls were included in final combination. Overall, a significant association was found between the IL-8-251 T/A (rs4073) polymorphism, the IL-10-1082 A/G (rs1800896) polymorphism and the AP risk in four genetic models (homozygote model, recessive model, dominant model, allele model). Meanwhile, individuals with IL-1β+3954 C/T (rs1143634, (homozygote model, recessive model)), IL-1β -511 C/T (rs16944, (dominant model)) and IL-6-634C/G (rs1800796, (allele model)) polymorphism were associated with an increased risk of AP. No evidence of an association was found between IL and 10-592 C/A (rs1800872) and IL-10-819 C/T (rs1800871) polymorphism and AP risk.

Optogenetics-induced activation of glutamate receptors improves memory function in mice with Alzheimer's disease

Optogenetics is a combination of optics and genetics technology that can be used to activate or inhibit specific cells in tissues. It has been used to treat Parkinson’s disease, epilepsy and neurological diseases, but rarely Alzheimer’s disease. Adeno-associated virus carrying the CaMK promoter driving the optogenetic channelrhodopsin-2 (CHR2) gene (or without the CHR2 gene, as control) was injected into the bilateral dentate gyri, followed by repeated intrahippocampal injections of soluble low-molecular-weight amyloid-β1–42 peptide (Aβ_1–42). Subsequently, the region was stimulated with a 473 nm laser (1–3 ms, 10 Hz, 5 minutes). The novel object recognition test was conducted to test memory function in mice. Immunohistochemical staining was performed to analyze the numbers of NeuN and synapsin Ia/b-positive cells in the hippocampus. Western blot assay was carried out to analyze the expression levels of glial fibrillary acidic protein, NeuN, synapsin Ia/b, metabotropic glutamate receptor-1a (mGluR-1a), mGluR-5, N-methyl-D-aspartate receptor subunit NR1, glutamate receptor 2, interleukin-1β, interleukin-6 and interleukin-10. Optogenetic stimulation improved working and short-term memory in mice with Alzheimer’s disease. This neuroprotective effect was associated with increased expression of NR1, glutamate receptor 2 and mGluR-5 in the hippocampus, and decreased expression of glial fibrillary acidic protein and interleukin-6. Our results show that optogenetics can be used to regulate the neuronal-glial network to ameliorate memory functions in mice with Alzheimer’s disease. The study was approved by the Animal Resources Committee of Jinan University, China (approval No. LL-KT-2011134) on February 28, 2011.

Oral lichen-planus-associated fibroblasts acquire myofibroblast characteristics and secrete pro-inflammatory cytokines in response to Porphyromonas gingivalis lipopolysaccharide stimulation

Background

Oral lichen planus (OLP) is a chronic inflammatory oral mucosal disease in which comprehensive inflammation-related cytokines are involved. These cytokines are commonly produced by immune cells and specific nonimmune cells including keratinocytes, endothelial cells and fibroblasts. This raises the question of whether fibroblasts in OLP lesions contribute to the inflammatory process upon inflammatory simulation.

Methods

Primary cultured Oral lichen-planus-associated fibroblasts (OLP AFs, n = 5) and normal buccal mucosal fibroblasts (NFs, n = 5) were examined by immunohistochemistry, Western blotting and reverse transcription-polymerase chain reactions (RT-PCR). Various inflammatory mediators were evaluated with a multiplex assay. Differences among groups were assessed using a Student’s test or repeated measures one-way ANOVA, as appropriate.

Results

OLP AFs express significantly higher levels of α-smooth muscle actin (α-SMA) than NFs, indicating the presence of myofibroblasts. Myofibroblasts secrete Interleukin (IL)-6, IL-8, and tumor necrosis factor-α (TNF-α) in response to Porphyromonas gingivalis lipopolysaccharide (pg. LPS).

Conclusion

OLP AFs demonstrated α-SMA expression and secreted pro-inflammatory cytokines in response to pg. LPS stimulation.

Electronic supplementary material

The online version of this article (10.1186/s12903-018-0656-6) contains supplementary material, which is available to authorized users.

Cytokines and radiation-induced pulmonary injuries

Radiation therapy is one of the most common treatment strategies for thorax malignancies. One of the considerable limitations of this therapy is its toxicity to normal tissue. The lung is the major dose-limiting organ for radiotherapy. That is because ionizing radiation produces reactive oxygen species that induce lesions, and not only is tumor tissue damaged, but overwhelming inflammatory lung damage can occur in the alveolar epithelium and capillary endothelium. This damage may result in radiation-induced pneumonitis and/or fibrosis. While describing the lung response to irradiation generally, the main focus of this review is on cytokines and their roles and functions within the individual stages. We discuss the relationship between radiation and cytokines and their direct and indirect effects on the formation and development of radiation injuries. Although this topic has been intensively studied and discussed for years, we still do not completely understand the roles of cytokines. Experimental data on cytokine involvement are fragmented across a large number of experimental studies; hence, the need for this review of the current knowledge. Cytokines are considered not only as molecular factors involved in the signaling network in pathological processes, but also for their diagnostic potential. A concentrated effort has been made to identify the significant immune system proteins showing positive correlation between serum levels and tissue damages. Elucidating the correlations between the extent and nature of radiation-induced pulmonary injuries and the levels of one or more key cytokines that initiate and control those damages may improve the efficacy of radiotherapy in cancer treatment and ultimately the well-being of patients.

Bioinformatics analysis to identify key genes and pathways influencing synovial inflammation in osteoarthritis

Osteoarthritis (OA) is a chronic arthropathy that occurs in the middle-aged and elderly population. The present study aimed to identify gene signature differences between synovial cells from OA synovial membrane with and without inflammation, and to explain the potential mechanisms involved. The differentially expressed genes (DEGs) between 12 synovial membrane with inflammation and 12 synovial membrane without inflammation from the dataset GSE46750 were identified using the Gene Expression Omnibus 2R. The DEGs were subjected to enrichment analysis, protein-protein interaction (PPI) analysis and module analysis. The analysis results were compared with text-mining results. A total of 174 DEGs were identified. Gene Ontology enrichment results demonstrated that functional molecules encoded by the DEGs primarily had extracellular location, molecular functions predominantly involving ‘chemokine activity’ and ‘cytokine activity’, and were associated with biological processes, including ‘inflammatory response’ and ‘immune response’. The Kyoto Encyclopedia of Genes and Genomes results demonstrated that DEGS may function through pathways associated with ‘rheumatoid arthritis’, ‘chemokine signaling pathway’, ‘complement and coagulation cascades’, ‘TNF signaling pathway’, ‘intestinal immune networks for IgA production’, ‘cytokine-cytokine receptor interaction’, ‘allograft rejection’, ‘Toll-like receptor signaling pathway’ and ‘antigen processing and presentation’. The top 10 hub genes [interleukin (IL)6, IL8, matrix metallopeptidase (MMP)9, colony stimulating factor 1 receptor, FOS proto-oncogene, AP1 transcription factor subunit, insulin-like growth factor 1, TYRO protein tyrosine kinase binding protein, MMP3, cluster of differentiation (CD)14 and CD163] and four gene modules were identified from the PPI network using Cytoscape. In addition, text-mining was used to identify the commonly used drugs and their targets for the treatment of OA. It was initially verified whether the results of the present study were useful for the study of OA treatment targets and pathways. The present study provided insight for the molecular mechanisms of OA synovitis. The hub genes and associated pathways derived from analysis may be targets for OA treatment. IL8 and MMP9, which were validated by text-mining, may be used as molecular targets for the OA treatment, while other hub genes require further validation.

Interleukin-1β signaling in osteoarthritis - chondrocytes in focus

Osteoarthritis (OA) can be regarded as a chronic, painful and degenerative disease that affects all tissues of a joint and one of the major endpoints being loss of articular cartilage. In most cases, OA is associated with a variable degree of synovial inflammation. A variety of different cell types including chondrocytes, synovial fibroblasts, adipocytes, osteoblasts and osteoclasts as well as stem and immune cells are involved in catabolic and inflammatory processes but also in attempts to counteract the cartilage loss. At the molecular level, these changes are regulated by a complex network of proteolytic enzymes, chemokines and cytokines (for review: [1]). Here, interleukin-1 signaling (IL-1) plays a central role and its effects on the different cell types involved in OA are discussed in this review with a special focus on the chondrocyte.

The Relationship between Fatigue and Cytokine Levels in Patients with Acute Myeloid Leukemia

Background: Cancer-related fatigue (CRF) is a very prominent complaint and disabling symptom in cancer patients probably influenced by endogenous cytokines. But, the published data on this subject are limited. We explored the relationship of cytokines such as tumor necrosis factor (TNF-α) and interleukin-6 (IL-6) with fatigue in patients with AML. Materials and Methods: This study was performed on 45 patients (25 men, 20 women) with newly diagnosed AML. We examined fatigue in these patients with validated questionnaire. Simultaneously, blood samples were obtained for quantitative measurement of IL-6 and TNF-α. Results: Our results showed a positive correlation between fatigue and circulating levels of IL-6 (P=0.004, R=0.416). Conclusion: Many patients with AML experienced severe fatigue before the onset of treatment, which is not related to their hemoglobin (Hb) levels. Cytokine levels may be beneficial markers in resistance to fatigue, but further studies are needed before considering targeted therapies as a treatment for CRF.

Molecular recognition of IL-8, IL-10, IL-12, and IL-15 in biological fluids using phthalocyanine-based stochastic sensors

Two stochastic sensors based on the modification of graphite paste with the complexes formed by phthalocyanine (PhCN) with Ni and Cu were designed and used for molecular recognition of IL-8, IL-10, IL-12, and IL-15. The four interleukins were recognized according to their signatures-called t_off (qualitative parameter) from the diagrams obtained after measurements. The limit of determination for IL-8 was 1 × 10^-4μg mL^-1 when both stochastic sensors were used; for IL-10, the determination limit was 4.5 × 10^-4μg mL^-1 for the Ni complex-based sensor, and 4.5 × 10^-7μg mL^-1 for the Cu complex-based sensor, respectively; for IL-12, the determination limit was 5 × 10^-4μg mL^-1 for the Ni complex-based sensor, and 5 × 10^-7μg mL^-1 for the Cu complex-based sensor, respectively; while for IL-15, the determination limit was 5 × 10^-5μg/mL for the Ni complex-based sensor, and 5 × 10^-5μg/mL for the Cu complex-based sensor, respectively. The stochastic method used was validated using the following biological fluids: nasal lavage, saliva, serum, and whole blood. Graphical abstract ᅟ.

Physical Exercise-Induced Myokines and Muscle-Adipose Tissue Crosstalk: A Review of Current Knowledge and the Implications for Health and Metabolic Diseases

Physical exercise has beneficial effects on metabolic diseases, and a combined therapeutic regimen of regular exercise and pharmaceutical treatment is often recommended for their clinical management. However, the mechanisms by which exercise produces these beneficial effects are not fully understood. Myokines, a group of skeletal muscle (SkM) derived peptides may play an important part in this process. Myokines are produced, expressed and released by muscle fibers under contraction and exert both local and pleiotropic effects. Myokines such as IL-6, IL-10, and IL-1ra released during physical exercise mediate its health benefits. Just as exercise seems to promote the myokine response, physical inactivity seems to impair it, and could be a mechanism to explain the association between sedentary behavior and many chronic diseases. Myokines help configure the immune-metabolic factor interface and the health promoting effects of physical exercise through the release of humoral factors capable of interacting with other tissues, mainly adipose tissue (AT). AT itself secretes proinflammatory cytokines (adipokines) as a result of physical inactivity and it is well recognized that AT inflammation can lead to the development of metabolic diseases, such as type 2 diabetes mellitus (T2DM) and atherosclerosis. On the other hand, the browning phenotype of AT has been suggested to be one of the mechanisms through which physical exercise improves body composition in overweight/obese individuals. Although, many cytokines are involved in the crosstalk between SkM and AT, in respect of these effects, it is IL-6, IL-15, irisin, and myostatin which seem to have the decisive role in this “conversation” between AT and SkM. This review article proposes to bring together the latest “state of the art” knowledge regarding Myokines and muscle-adipose tissue crosstalk. Furthermore, it is intended to particularly focus on the immune-metabolic changes from AT directly mediated by myokines.

The link between immunity, autoimmunity and endometriosis: a literature update

Endometriosis (EMS), an estrogen-dependent inflammatory disorder affects approximately 5-10% of the general female population of reproductive age and 20-90% of women with pelvic pain and infertility. Many immunological factors are known to contribute significantly to the pathogenesis and pathophysiology of EMS, and both chronic local inflammation and autoantibodies in EMS shares many similarities with autoimmune diseases (AD). However, the autoimmune etiology in EMS remains controversial, and its evidence on autoimmune basis may be limited. Here we aim to review the current understanding between autoimmunity and EMS to provide important knowledge to develop future potential immunomodulatory therapy for the treatment of EMS.

In silico mutational analysis and identification of stability centers in human interleukin-4

Interleukin-4 (IL-4) is a multifunctional cytokine that plays a critical role in apoptosis, differentiation and proliferation. The intensity of IL4 response depends upon binding to its receptor, IL-4R. The therapeutic efficiency of interleukins can be increased by generating structural mutants having greater stability. In the present work, attempts were made to increase the stability of human IL-4 using in-silico site directed mutagenesis. Different orthologous sequences of IL4 from Pan troglodytes, Aotusnigriceps, Macacamulatta, Papiohamadryas, Chlorocebusaethiops, Vicugnapacos, Susscrofa and Homo sapiens were aligned using Clustal Omega that revealed the conserved and non-conserved positions. For each non-conserved position, possible favorable and stabilizing mutations were found using CUPSAT with predicted ΔΔG (kcal/mol). The one with highest ΔΔG (kcal/mol) among all possible mutations, for each non-conserved position was selected and introduced manually in human IL-4 sequence resulting in multiple mutants of IL-4. Mutant proteins were modeled using structure of IL4 (PDB ID: 2B8U) as a template by SWISS MODEL. The mutants A49L and Q106T were identified to have stability centre using SCide. Molecular dynamics and docking analysis also confirmed the mutants stability and binding respectively. Mutants A49L and Q106T had -7.580079 kcal/mol and -39.418124 kcal/mol respectively lesser energy value than the wild type IL4. The result suggested that, the stability of human IL-4 has been increased by mutation.

Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis

Background

Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date.

Methods

In this work, taking M. tuberculosis H37Rv (MTB) that is co-evolving with its human host as an example, we propose a general computational framework that exploits the known bacterial pathogen protein interaction networks in STRING database to predict pathogen-host protein interactions and their signaling cross-talks. In this framework, significant interlogs are derived from the known pathogen protein interaction networks to train a predictive l₂-regularized logistic regression model.

Results

The computational results show that the proposed method achieves excellent performance of cross validation as well as low predicted positive rates on the less significant interlogs and non-interlogs, indicating a low risk of false discovery. We further conduct gene ontology (GO) and pathway enrichment analyses of the predicted pathogen-host protein interaction networks, which potentially provides insights into the machinery that M. tuberculosis H37Rv targets human genes and signaling pathways. In addition, we analyse the pathogen-host protein interactions related to drug resistance, inhibition of which potentially provides an alternative solution to M. tuberculosis H37Rv drug resistance.

Conclusions

The proposed machine learning framework has been verified effective for predicting bacteria-host protein interactions via known bacterial protein interaction networks. For a vast majority of bacterial pathogens that lacks experimental studies of bacteria-host protein interactions, this framework is supposed to achieve a general-purpose applicability. The predicted protein interaction networks between M. tuberculosis H37Rv and Homo sapiens, provided in the Additional files, promise to gain applications in the two fields: (1) providing an alternative solution to drug resistance; (2) revealing the patterns that M. tuberculosis H37Rv genes target human immune signaling pathways.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4873-9) contains supplementary material, which is available to authorized users.

Networks of blood proteins in the neuroimmunology of schizophrenia

Levels of certain circulating cytokines and related immune system molecules are consistently altered in schizophrenia and related disorders. In addition to absolute analyte levels, we sought analytes in correlation networks that could be prognostic. We analyzed baseline blood plasma samples with a Luminex platform from 72 subjects meeting criteria for a psychosis clinical high-risk syndrome; 32 subjects converted to a diagnosis of psychotic disorder within two years while 40 other subjects did not. Another comparison group included 35 unaffected subjects. Assays of 141 analytes passed early quality control. We then used an unweighted co-expression network analysis to identify highly correlated modules in each group. Overall, there was a striking loss of network complexity going from unaffected subjects to nonconverters and thence to converters (applying standard, graph-theoretic metrics). Graph differences were largely driven by proteins regulating tissue remodeling (e.g. blood-brain barrier). In more detail, certain sets of antithetical proteins were highly correlated in unaffected subjects (e.g. SERPINE1 vs MMP9), as expected in homeostasis. However, for particular protein pairs this trend was reversed in converters (e.g. SERPINE1 vs TIMP1, being synthetical inhibitors of remodeling of extracellular matrix and vasculature). Thus, some correlation signals strongly predict impending conversion to a psychotic disorder and directly suggest pharmaceutical targets.

Inflammation and Neuro-Immune Dysregulations in Autism Spectrum Disorders

Autism Spectrum Disorder (ASD) is characterized by persistent deficits in social communication and interaction and restricted-repetitive patterns of behavior, interests, or activities. Strong inflammation states are associated with ASD. This inflammatory condition is often linked to immune system dysfunction. Several cell types are enrolled to trigger and sustain these processes. Neuro-inflammation and neuro-immune abnormalities have now been established in ASD as key factors in its development and maintenance. In this review, we will explore inflammatory conditions, dysfunctions in neuro-immune cross-talk, and immune system treatments in ASD management.

Nearly neutral evolution in IFNL3 gene retains the immune function to detect and clear the viral infection in HCV

IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed. The codon evolution result suggests that nearly neutral mutation is the key pattern in shaping the IFNL3 evolution. The results were validated by subjecting the human IFNL3 protein variants to that of the native through a molecular dynamics simulation study. The molecular dynamics simulation clearly depicts the negative impact on the reported variants in human IFNL3 protein. However, these detrimental mutations (R157Q and R157W) were shown to be negatively selected in the evolutionary study of the mammals. Hence, the variation revealed a mild impact on the IFNL3 function and may be removed from the population through negative selection due to its high functional constraints. In a nutshell, our study may contribute the overall evidence in phylotyping and structural transformation that takes place in the non-synonymous substitutions of IFNL3 protein. Substantially, our obtained theoretical knowledge will lay the path to extend the experimental validation in HCV clearance.

Pruritus: Progress toward Pathogenesis and Treatment

Pruritus, the most common cutaneous symptom, is widely seen in many skin complaints. It is an uncomfortable feeling on the skin and sometimes impairs patients' quality of life. At present, the specific mechanism of pruritus still remains unclear. Antihistamines, which are usually used to relieve pruritus, ineffectively work in some patients with itching. Recent evidence has suggested that, apart from histamine, many mediators and signaling pathways are involved in the pathogenesis of pruritus. Various therapeutic options for itching correspondingly have been developed. In this review, we summarize the updated pathogenesis and therapeutic strategies for pruritus.

IL-13/STAT6 signaling plays a critical role in the epithelial-mesenchymal transition of colorectal cancer cells

Colorectal cancer (CRC) is one of the most common causes of cancer-related death worldwide due to the distant metastases. Compelling evidence has reported that epithelial-mesenchymal transition (EMT) is involved in promoting cancer invasion and metastasis. However, the precise molecular events that initiate this complex EMT process remain poorly understood. Here, we showed that the pleiotropic cytokine interleukin-13 (IL-13) could induce an aggressive phenotype displaying EMT by enhancing the expression of EMT-promoting factor ZEB1. Importantly, STAT6 signaling inhibitor and STAT6 knockdown significantly reversed IL-13-induced EMT and ZEB1 induction in CRC cells, whereas ectopic STAT6 expression in STAT6^null CRC cell line markedly promoted EMT in the present of IL-13. ChIP-PCR and Luciferase assays revealed that activated STAT6 directly bound to the promoter of ZEB1. Otherwise, we found IL-13 also up-regulated the stem cell markers (nanog, CD44, CD133 and CD166) and promoted cell migration and invasion through STAT6 pathway. We also found that siRNA-mediated knockdown of IL-13Rα1 could reverse IL-13-induced ZEB1 and EMT changes by preventing STAT6 signaling. Finally, we demonstrated positive correlation between IL-13Rα1 and ZEB1 at mRNA levels in human CRC samples. Taken together, our findings first demonstrated that IL-13/IL-13Rα1/STAT6/ZEB1 pathway plays a critical role in promoting EMT and aggressiveness of CRC.

Interleukins and their signaling pathways in the Reactome biological pathway database

BACKGROUND

There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete stylized representations that assume the reader is an expert and familiar with the established details of the process, which are consequently not fully explained. Pathway representations in publications frequently do not represent a complete, detailed, and unambiguous description of the molecules involved; their precise posttranslational state; or a full account of the molecular events they undergo while participating in a process. Although this might be sufficient to be interpreted by an expert reader, the lack of detail makes such pathways less useful and difficult to understand for anyone unfamiliar with the area and of limited use as the basis for computational models.

OBJECTIVE

Reactome was established as a freely accessible knowledge base of human biological pathways. It is manually populated with interconnected molecular events that fully detail the molecular participants linked to published experimental data and background material by using a formal and open data structure that facilitates computational reuse. These data are accessible on a Web site in the form of pathway diagrams that have descriptive summaries and annotations and as downloadable data sets in several formats that can be reused with other computational tools. The entire database and all supporting software can be downloaded and reused under a Creative Commons license.

METHODS

Pathways are authored by expert biologists who work with Reactome curators and editorial staff to represent the consensus in the field. Pathways are represented as interactive diagrams that include as much molecular detail as possible and are linked to literature citations that contain supporting experimental details. All newly created events undergo a peer-review process before they are added to the database and made available on the associated Web site. New content is added quarterly.

RESULTS

The 63rd release of Reactome in December 2017 contains 10,996 human proteins participating in 11,426 events in 2,179 pathways. In addition, analytic tools allow data set submission for the identification and visualization of pathway enrichment and representation of expression profiles as an overlay on Reactome pathways. Protein-protein and compound-protein interactions from several sources, including custom user data sets, can be added to extend pathways. Pathway diagrams and analytic result displays can be downloaded as editable images, human-readable reports, and files in several standard formats that are suitable for computational reuse. Reactome content is available programmatically through a REpresentational State Transfer (REST)-based content service and as a Neo4J graph database. Signaling pathways for IL-1 to IL-38 are hierarchically classified within the pathway "signaling by interleukins." The classification used is largely derived from Akdis et al.

CONCLUSION

The addition to Reactome of a complete set of the known human interleukins, their receptors, and established signaling pathways linked to annotations of relevant aspects of immune function provides a significant computationally accessible resource of information about this important family. This information can be extended easily as new discoveries become accepted as the consensus in the field. A key aim for the future is to increase coverage of gene expression changes induced by interleukin signaling.

MicroRNA expression profiling of intestinal mucosa tissue predicts multiple crucial regulatory molecules and signaling pathways for gut barrier dysfunction of AIDS patients

Human immunodeficiency virus‑1 (HIV‑1) infection severely damages the gut‑associated lymphoid tissue (GALT), the immune system and the gut barrier, which leads to accelerating the disease progression for patients with acquired immune deficiency syndrome (AIDS). Dysregulation of microRNAs (miRNAs) may contribute to this process. However, few studies have investigated the importance of miRNAs in AIDS pathogenesis and progression. The whole miRNA profile of patients with HIV infection from southwest P.R. China and the mode of interaction between HIV‑1 and miRNAs remains to be elucidated. Colon mucosal samples were collected from HIV+ patients and HIV‑ healthy individuals, miRNAs were isolated and subjected to array hybridization in the present study. A total of 476 human and virus‑derived microRNAs were significantly altered in the HIV+ group when compared with the control group (P<0.05), which may be involved in the progression to AIDS. Target genes of the significantly altered miRNAs were predicted using the TargetScan, miRbase and miRanda databases and the 10 shared target genes of upregulated miRNAs and the 391 target genes of downregulated miRNAs were selected. As only 10 target genes were predicted for upregulated miRNAs, subsequent GO and KEGG pathway analyses were focused on the 391 target genes of the downregulated miRNAs. The findings of the present study identified a series of crucial pathways, including cell‑extracellular matrix interaction and chemokine regulation, which indicated close affinity with CD4+ T cell activation. These pathways, involving genes such as integrin α5, led to a gut barrier dysfunction of patients with HIV. Important miRNAs include hsa‑miRNA‑32‑5p, hsa‑miRNA‑195‑5p, hsa‑miRNA‑20b‑5p, hsa‑miRNA‑590‑5p. The expression levels of the miRNAs and their target genes were confirmed using RT‑qPCR. Taking into previous observations, the findings of the present study identified the importance of miRNAs for regulating gut barrier dysfunction via multiple regulatory molecules and signaling pathways, which elucidated the underlying molecular mechanism of gut barrier dysfunction in patients with HIV.

Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia

Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species. We find that the immune gene complement in bandicoot is often conserved with respect to other marsupials; however, the diversity of expressed transcripts in several key families, such as major histocompatibility complex, T cell receptor μ and natural killer cell receptors, appears greater in the bandicoot than other Australian marsupials, including devil and koala. This transcriptome is an important first step for future studies of bandicoots and the bilby, allowing for population level analysis and construction of bandicoot-specific immunological reagents and assays. Such studies will be critical to understanding the immunology and physiology of Peramelemorphia and to inform the conservation of these unique marsupials.

The cargo protein MAP17 (PDZK1IP1) regulates the immune microenvironment

Inflammation is a complex defensive response activated after various harmful stimuli allowing the clearance of damaged cells and initiating healing and regenerative processes. Chronic, or pathological, inflammation is also one of the causes of neoplastic transformation and cancer development. MAP17 is a cargo protein that transports membrane proteins from the endoplasmic reticulum. Therefore, its overexpression may be linked to an excess of membrane proteins that may be recognized as an unwanted signal, triggering local inflammation. Therefore, we analyzed whether its overexpression is related to an inflammatory phenotype. In this work, we found a correlation between MAP17 expression and inflammatory phenotype in tumors and in other inflammatory diseases such as Crohn's disease, Barrett's esophagus, COPD or psoriasis. MAP17 expression correlated also with the markers of inflammation HLAs, BBS10, HERC2, ADNP and PYCARD. Furthermore, we found that MAP17 expression directly regulates NFAT2 and IL-6 activation, inducing the differentiation of monocytes to dendritic cells and suggesting a causal role of MAP17 in inflammation. Immunohistochemistry confirms local inflammation, mainly CD45⁺ cells, at the site of expression of MAP17, at least in tumors, Crohn's and psoriasis. Therefore, our data indicates that the overexpression of the protein MAP17 plays important role in diseases involving chronic inflammation.

Effect of lipopolysaccharide on the expression of inflammatory mRNAs and microRNAs in the mouse oviduct

Infection with Gram-negative bacteria is a major cause of aberrant inflammation in the oviduct; consequences can include tubal-based infertility and/or ectopic pregnancy. Understanding the inflammatory response is necessary for the development of novel treatment options that counter inflammation-induced infertility. The aim of the present study was to determine the effect of intraperitoneal (i.p.) administration of Escherichia coli-derived lipopolysaccharide (LPS) on the acute expression of inflammatory mRNAs and microRNAs (miRNAs) in the oviduct. On the day of oestrus, 6- to 8-week-old CD1 mice were injected i.p. with 0, 2 or 10µg LPS in 100μL phosphate-buffered saline. Mice were killed 24h later and the oviducts collected for gene expression analyses. The effect of treatment on the expression of mRNAs and miRNAs was evaluated by one-way analysis of variance (ANOVA), with treatment means of differentially expressed (P<0.05) transcripts separated using Scheffé's test. LPS treatment affected 49 of 179 targeted inflammatory mRNAs and 51 of 578 miRNAs (P<0.05). The identity of differentially expressed miRNAs predicted as regulators of chemokine and interleukin ligand mRNAs was then extracted using the microRNA.org database. The results of the present study indicate that systemic treatment with LPS induces a robust inflammatory response in the oviducts of mice, and identify key mRNAs and putative miRNAs modulating this effect.

Identification and characterization of an interleukin-16-like gene from pacific white shrimp Litopenaeus vannamei

Interleukins are a group of cytokines that play essential roles in immune regulation. Almost all interleukin genes are only found in vertebrates. In this study, an interleukin-16-like gene (LvIL-16L) was identified from Pacific white shrimp, Litopenaeus vannamei. LvIL-16L was predicted to encode a precursor (pro-LvIL-16L) with 1378 amino acids, sharing similarities with predicted pro-IL-16-like proteins from insects. The C-terminus of pro-LvIL-16L protein contained two PDZ domains homologous to the mature IL-16 cytokine of vertebrates. In tissues, LvIL-16L could be processed into a ∼36 kDa mature peptide through a caspase-3 cleavage site, which was verified by in vitro site mutation analysis and in vivo RNA interference (RNAi) experiments. The LvIL-16L mRNA could be detected in all the analyzed tissues and the expression of LvIL-16L was significantly up-regulated after immune stimulation. Using RNAi strategy, the role of LvIL-16L in immune responses was initially investigated. Interestingly, knockdown of LvIL-16L could significantly increase the mortality of the Vibro parahaemolyticus infected shrimps but reduce that of the WSSV infected shrimps, suggesting that LvIL-16L could have opposite effects on the antiviral and antibacterial immune responses in shrimp. To our knowledge, this is the first study of an IL-16-like gene in invertebrates, which could help to elucidate interleukin evolution and regulatory mechanisms of shrimp immune responses.

Ultrasensitive SERS immunoassay based on diatom biosilica for detection of interleukins in blood plasma

An ultrasensitive surface-enhanced Raman scattering (SERS) immunoassay based on diatom biosilica with integrated gold nanoparticles (AuNPs) for the detection of interleukin 8 (IL-8) in blood plasma has been developed. The SERS sensing originates from unique features of the diatom frustules, which are capable of enhancing the localized surface-plasmon resonance of metal nanostructures. The SERS immune tags ware fabricated by functionalizing 70-nm Au nanoparticles with DTNB (i.e., 5,5′-dithiobis(2-nitrobenzoic acid)), which acted as a Raman reporter molecule, as well as the specific antibodies. These DTNB-labeled immune-AuNPs can form a sandwich structure with IL-8 antigens (infection marker) and the antibodies immobilized on the biosilica material. Our method showed an improved IL-8 detection limit in comparison to standard ELISA methods. The current detection limit for IL-8 using a conventional ELISA test is about 15.6 pg mL⁻¹. The lower detection limit for IL-8 in blood plasma was estimated to be 6.2 pg mL⁻¹. To the best of our knowledge, this is the first report on the recognition of IL-8 in human samples using a SERS-based method. This method clearly possesses high sensitivity to clinically relevant interleukin concentrations in body fluids. The average relative standard deviation of this method is less than 8%, which is sufficient for analytical analysis and comparable to those of classical ELISA methods. This SERS immunoassay also exhibits high biological specificity for the detection of IL-8 antigens. The established SERS immunoassay offers a valuable platform for the ultrasensitive and highly specific detection of immune biomarkers in a clinical setting for medical diagnostics.

Graphical Abstract

Frontiers in Drug Research and Development for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is idiopathic, lifelong, immune-mediated diseases, for which curative therapies are not yet available. In the last 15 years, the introduction of monoclonal antibodies targeting tumor necrosis factor-α, a cytokine playing a key role in bowel inflammation, has revolutionized treatment paradigms for IBD. Despite their proven long-term efficacy, however, many patients do not respond or progressively lose response to these drugs. Major advances of knowledge in immunology and pathophysiology of intestinal inflammatory processes have made possible the identification of new molecular targets for drugs, thus opening several new potential therapeutic opportunities for IBD. The abnormal response of intestinal immunity to unknown antigens leads to the activation of T helper lymphocytes and triggers the inflammatory cascade. Sphingosine 1-phosphate receptor agonists negatively modulate the egress of lymphocytes, inducted by antigen-presenting cells, from secondary lymphoid tissues to intestinal wall. Leukocyte adhesion inhibitors (both anti-integrin and anti-Mucosal Vascular Addressin Cell Adhesion Molecule 1) interfere with the tissue homing processes. Activated T helper lymphocytes increase the levels of pro-inflammatory cytokines, such as interleukin 12, 23, and 6, offering several potential pharmacological interventions. The Janus kinases, intracellular enzymes mediating the transduction of several cytokine signals, are other explored targets for treating immune-mediated diseases. Finally, the impact of modulating Smad7 pathway, which is responsible for the down-regulation of the immunosuppressive cytokine transforming growth factor-β signaling, is currently under investigation. The purpose of this review is to discuss the most promising molecules in late-stage clinical development, with a special emphasis on pharmacological properties.