Multiple correlations of mRNA expression and protein abundance in human cytokine profile

Novel biomarkers and interferon signature in secondary progressive multiple sclerosis

Multiple sclerosis (MS) exhibits poor immune regulation and subnormal interferon (IFN-β) signaling. Secondary Progressive MS displays waning exacerbations, relentless neurodegeneration, and diminished benefit of therapy. We find dysregulated serum protein balance (Th1/Th2) and excessive gene expression in Relapsing-Remitting MS vs. healthy controls (8700 differentially-expressed genes, DEG) and intermediate levels in SPMS (3900 DEG). Olfactory receptor genes (chemosensing), and WNT/ß-catenin (anti-inflammatory, repair) and metallothionein (anti-oxidant) gene pathways, have less expression in SPMS than RRMS. IFN-β treatment decreased pro-inflammatory and increased metallothionein gene expression in SPMS. These gene expression biomarkers suggest new targets for immune regulation and brain repair in this neurodegenerative disease.

Adaptive and innate immune responses in multiple sclerosis with anti-CD20 therapy: Gene expression and protein profiles

Background

Anti-CD20 is a highly effective therapy for multiple sclerosis (MS), a disease with multiple abnormalities in function of B and T cells and innate immune cells. Anti-CD20 therapy depletes B cells, which alters antibody production and has diverse effects on B cell immunity. These changes potentially affect immunity beyond B cells in MS.

Objective

Determine if anti-CD20 therapy effects non-B cell, as well as B cell, gene expression, and serum protein levels.

Methods

Samples were collected from 10 healthy controls and from clinically stable relapsing-remitting MS - 10 untreated, 9 interferon-β-treated, and 15 ocrelizumab-treated patients were studied before, and 2  weeks and 6  months after, the first anti-CD20 infusion. Peripheral blood mononuclear cells (PBMC) were analyzed with sensitive, 135,000-transcript RNA expression microarrays, using stringent criteria. Gene expression was compared to 43 MS-relevant serum immune and neurotrophic proteins, using multiplex protein assays.

Results

Anti-CD20 therapy reduced expression of 413 total genes and 185 B-cell-regulated genes at 2  weeks vs. pre-therapy. Expression of 19 (15%) of these B cell genes returned toward baseline by 6  months, including genes for the B cell activation protein, CD79A, and for immunoglobulin A, D, and G heavy chains. Expression pathways for Th17 and CD4 regulatory T-cell (Treg) development, differentiation, and proliferation also quieted. In contrast, expression increased in Th1 and myeloid cell antiviral, pro-inflammatory, and toll-like receptor (TLR) gene pathways.

Conclusion

These findings have clinical implications. B cell gene expression diminishes 2  weeks after anti-CD20 antibody infusion, but begins to rebound by 6  months. This suggests that the optimum time for vaccination is soon before reinfusion of anti-CD20 therapy. In addition, at 6  months, there is enhanced Th1 cell gene expression and induction of innate immune response genes and TLR expression, which can enhance anti-viral and anti-tumor immunity. This may compensate for diminished B cell gene expression after therapy. These data suggest that anti-CD20 therapy has dynamic effect on B cells and causes a compensatory rise in Th1 and myeloid immunity.

Gene dysregulation in acute HIV-1 infection – early transcriptomic analysis reveals the crucial biological functions affected

Introduction

Transcriptomic analyses from early human immunodeficiency virus (HIV) infection have the potential to reveal how HIV causes widespread and lasting damage to biological functions, especially in the immune system. Previous studies have been limited by difficulties in obtaining early specimens.

Methods

A hospital symptom-based screening approach was applied in a rural Mozambican setting to enrol patients with suspected acute HIV infection (Fiebig stage I-IV). Blood samples were collected from all those recruited, so that acute cases and contemporaneously recruited, uninfected controls were included. PBMC were isolated and sequenced using RNA-seq. Sample cellular composition was estimated from gene expression data. Differential gene expression analysis was completed, and correlations were determined between viral load and differential gene expression. Biological implications were examined using Cytoscape, gene set enrichment analysis, and enrichment mapping.

Results

Twenty-nine HIV infected subjects one month from presentation and 46 uninfected controls were included in this study. Subjects with acute HIV infection demonstrated profound gene dysregulation, with 6131 (almost 13% of the genome mapped in this study) significantly differentially expressed. Viral load was correlated with 1.6% of dysregulated genes, in particular, highly upregulated genes involved in key cell cycle functions, were correlated with viremia. The most profoundly upregulated biological functions related to cell cycle regulation, in particular, CDCA7 may drive aberrant cell division, promoted by overexpressed E2F family proteins. Also upregulated were DNA repair and replication, microtubule and spindle organization, and immune activation and response. The interferome of acute HIV was characterized by broad activation of interferon-stimulated genes with antiviral functions, most notably IFI27 and OTOF. BCL2 downregulation alongside upregulation of several apoptotic trigger genes and downstream effectors may contribute to cycle arrest and apoptosis. Transmembrane protein 155 (TMEM155) was consistently highly overexpressed during acute infection, with roles hitherto unknown.

Discussion

Our study contributes to a better understanding of the mechanisms of early HIV-induced immune damage. These findings have the potential to lead to new earlier interventions that improve outcomes.

Prolonged Interferon-Stimulated Gene and Protein Signatures in Multiple Sclerosis Induced by PEGylated IFN-β-1a Compared to Non-PEGylated IFN-β-1a

Interferon (IFN)-β-1a (Avonex) and longer half-life, polyethylene glycol-conjugated IFN-β-1a (PEG-IFN-β-1a, Plegridy), may generate different molecular responses. We identified different short-term and long-term in vivo global RNA signatures of IFN-stimulated genes in multiple sclerosis (MS) peripheral blood mononuclear cells and in selected paired serum immune proteins. At 6 h, non-PEGylated IFN-β-1a injection upregulated expression of 136 genes and PEG-IFN-β-1a upregulated 85. At 24 h, induction was maximal; IFN-β-1a upregulated 476 genes and PEG-IFN-β-1a now upregulated 598. Long-term PEG-IFN-β-1a therapy increased expression of antiviral and immune-regulatory genes (IFIH1, TLR8, IRF5, TNFSF10 [TRAIL], STAT3, JAK2, IL15, and RB1) and IFN signaling pathways (IFNB1, IFNA2, IFNG, IRF7), but downregulated expression of inflammatory genes (TNF, IL1B, and SMAD7). Long-term PEG-IFN-β-1a induced longer and stronger expression of Th1, Th2, Th17, chemokine, and antiviral proteins than long-term IFN-β-1a. Long-term therapy also primed the immune system, evoking higher gene and protein induction after IFN reinjection at 7 months than at 1 month of PEG-IFN-β-1a treatment. Both forms of IFN-β balanced correlations of expression among these genes and proteins, with positive correlations between Th1 and Th2 families, quelling the "cytokine storm" of untreated MS. Both IFNs induced long-term, potentially beneficial, molecular effects on immune and possibly neuroprotective pathways in MS.

Inflammation-related transcripts define "high" and "low" subgroups of individuals with schizophrenia and bipolar disorder in the midbrain

Dopamine dysregulation in schizophrenia may be associated with midbrain inflammation. Previously, we found elevated levels of pro-inflammatory cytokine mRNAs in the post-mortem midbrain of people with schizophrenia (46%) but not from unaffected controls (0%) using a brain cohort from Sydney, Australia. Here, we measured cytokine mRNAs and proteins in the midbrain in the Stanley Medical Research Institute (SMRI) array cohort (N = 105). We tested if the proportions of individuals with schizophrenia and with high inflammation can be replicated, and if individuals with bipolar disorder with elevated midbrain cytokines can be identified. mRNA levels of 7 immune transcripts from post-mortem midbrain tissue were measured via RT-PCR and two-step recursive clustering analysis was performed using 4 immune transcripts to define "high and low" inflammatory subgroups. The clustering predictors used were identical to our earlier midbrain study, and included: IL1B, IL6, TNF, and SERPINA3 mRNA levels. 46% of schizophrenia cases (16/35 SCZ), 6% of controls (2/33 CTRL), and 29% of bipolar disorder cases (10/35 BPD) were identified as belonging to the high inflammation (HI) subgroups [χ² (2) = 13.54, p < 0.001]. When comparing inflammatory subgroups, all four mRNAs were significantly increased in SCZ-HI and BPD-HI compared to low inflammation controls (CTRL-LI) (p < 0.05). Additionally, protein levels of IL-1β, IL-6, and IL-18 were elevated in SCZ-HI and BPD-HI compared to all other low inflammatory subgroups (all p < 0.05). Surprisingly, TNF-α protein levels were unchanged according to subgroups. In conclusion, we determined that almost half of the individuals with schizophrenia were defined as having high inflammation in the midbrain, replicating our previous findings. Further, we detected close to one-third of those with bipolar disorder to be classified as having high inflammation. Elevations in some pro-inflammatory cytokine mRNAs (IL-1β and IL-6) were also found at the protein level, whereas TNF mRNA and protein levels were not concordant.

Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

Background

Silicosis is a systemic disease characterized by persistent inflammation and incurable pulmonary fibrosis. Although great effort has been made to understand the pathogenesis of the disease, molecular mechanism underlying silicosis is not fully elucidated. This study was aimed to explore proteomic and transcriptomic changes in rat model of silicosis.

Methods

Twenty male Wistar rats were randomly divided into two groups with 10 rats in each group. Rats in the model group were intratracheally instilled with 50 mg/mL silicon dioxide (1 mL per rat) and rats in the control group were treated with 1.0 mL saline (1 mL per rat). Twenty-eight days later, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the altered genes and proteins. The integrated analysis was performed between transcriptome and proteome. The data were further verified by RT-qPCR and parallel reaction monitoring (PRM).

Results

In total, 1769 differentially expressed genes (DEGs) and 650 differentially expressed proteins (DEPs) were identified between the silicosis model and control groups. The integrated analysis showed 250 DEPs were correlated to the corresponding DEGs (cor-DEPs-DEGs), which were mainly enriched in phagosome, leukocyte transendothelial migration, complement and coagulation cascades and cellular adhesion molecule (CAM). These pathways are interrelated and converged at common points to produce an effect. GM2a, CHI3L1, LCN2 and GNAI1 are involved in the extracellular matrix (ECM) and inflammation contributing to fibrosis.

Conclusion

Our comprehensive transcriptome and proteome data provide new insights into the mechanisms of silicosis and helpful information for more targeted prevention and treatment of silicosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-021-01807-w.

Neuroprotective modulation of microglia effector functions following priming with interleukin 4 and 13: current limitations in understanding their mode-of-action

In recent years the long-standing theory of microglia's properties for dual polarization towards a pro- or anti-inflammatory phenotype has been deeply challenged. Furthermore, the elucidation of microglia ontogenesis exposed intrinsic differences between microglia and peripheral myeloid cells, thereby further underscoring the need to re-evaluate microglia-specific activation behavior, especially within an inflamed central nervous system (CNS) environment. This review critically summarizes recent literature on the in vitro and in vivo response of murine microglia to the immune-modulatory cytokines interleukin 4 (IL4) and interleukin 13 (IL13), i.e. those driving the so-called anti-inflammatory phenotype. Here we highlight several pivotal factors that may influence experimental outcome and/or interpretation of in vitro and in vivo studies evaluating microglia's phenotypical and functional properties upon IL4/IL13 treatment. Finally, the current therapeutic relevance of IL4/IL13-induced microglia activation in both acute and chronic CNS disorders is discussed.

Cytokine mRNA and protein expression by cell cultures of epithelial ovarian cancer-Methodological considerations on the choice of analytical method for cytokine analyses

PROBLEM

To get a comprehensive picture of cytokine expression in health and disease is difficult, cytokines are transiently and locally expressed, and protein analyses are burdened by biological modifications, technical issues, and sensitivity to handling of samples. Thus, alternative methods, based on molecular techniques for cytokine mRNA analyses, are often used. We compared cytokine mRNA and protein expression to evaluate whether cytokine mRNA profiles can be used instead of protein analyses.

METHOD OF STUDY

In kinetic experiments, cytokine mRNA and protein expression of IL-1β, IL-6, IL-8, TNF-α, and TNF-β/LTA were studied using real-time RT-qPCR and Luminex^® microarrays in the ovarian cancer cell lines OVCAR-3, SKOV-3 and the T-cell line Jurkat, after activation of transcription by thermal stress. In addition, we analyzed IL-6 and IL-8 mRNA and protein in a small number of ovarian cancer patients.

RESULTS

Ovarian cancer cells can express cytokines on both mRNA and protein level, with 1-4 hours' time delay between the mRNA and protein peak and a negative Spearman correlation. The mRNA and protein expression in patient samples was poorly correlated, reflecting previous studies.

CONCLUSION

Cytokine mRNA and protein expression levels show diverging results, depending on the material analyzed and the method used. Considering the high sensitivity and reproducibility of real-time RT-qPCR, we suggest that cytokine mRNA profiles could be used as a proxy for protein expression for some specific purposes, such as comparisons between different patient groups, and in defining mechanistic pathways involved in the pathogenesis of cancer and other pathological conditions.

In-depth transcriptomic and proteomic analyses of the hippocampus and cortex in a rat model after cerebral ischemic injury and repair by Shuxuetong (SXT) injection

BACKGROUND

There is a lack of systematic descriptions and characterization of strokes and their effects in both the cerebral hippocampus and cortex. Shuxuetong (SXT) injection was reported to have good therapeutic effects in the clinic; therefore, it was selected as a drug intervention method for cerebral ischemia repair in rat models. The aim of this study was to understand the features of molecules and pathways and to reveal key processes of SXT repair.

MATERIALS AND METHODS

Evaluation of neurological deficit and infarct volume measurement was used to estimate the pharmacological effects of SXT injection on Ischemia-reperfusion(I/R) model rats. LC-MS/MS and RNA-Seq analysis were used to analyze the proteins and mRNA expression in the cerebral hippocampus and cortex 6 h and 24 h after ischemic injury and repair. A label-free approach (IBAQ) for proteomics analysis and FPKM based on gene read count for transcriptomics analysis were used to quantify the differences among the three experimental groups (Sham, Model and SXT-treated groups). Transcriptomics and proteomics analyses were verified by RT-qPCR and western blotting.

RESULTS

By combining LC-MS/MS and RNA-Seq, eight larger datasets (two time points and two tissues) were confidently identified in more than three biological replicates. An average of 4500 unique proteins and 8200 protein-coding genes were confidently identified. By combining the subcellular localization, hierarchical clustering, pathway enrichment analysis in the injury and repair phase, six core proteins and related genes that were significantly expressed were verified as candidates for cerebral ischemic injury by western blotting and quantitative real-time PCR. Meanwhile, the results indicated that there was better expression in the 6 h group by significant proteomics analysis during the development and progression of cerebral ischemia. Two primary co-enriched pathways, the PI3K-AKT and MAPK signaling pathways, and six related core candidates may play key roles in molecular mechanisms related to cerebral ischemic injury and repair by SXT injection.

CONCLUSION

Our data not only identified six core candidates and two key signaling pathways for cerebral ischemic injury and verification but also provided evidence for the explanation, prevention and treatment of cerebral ischemia by SXT injection. The results of the present study provide evidence for the explanation, prevention and treatment of cerebral ischemia by SXT injection.

Multiple protein and mRNA expression correlations in the rat cerebral cortex after ischemic injury and repair due to buchang naoxintong jiaonang (BNJ) intervention

Stroke is the one of the most common causes of death worldwide. Systematic description and characterization of the types of stroke and the effects induced in the cerebral cortex have not been performed so far. Here, we analyzed the protein and mRNA expression in the cerebral cortex12 h after ischemic injury and repair. Drug intervention using Buchang Naoxintong Jiaonang (BNJ), which has been reported to have good clinical therapeutic effects, was selected for our study of cerebral ischemic repair in rat models. Two powerful techniques can be merged in a single study to examine and yield new perspectives in physiology and pathophysiology. Combining LC-MS/MS and DNA microarray analyses of the rat cerebral cortex confidently identified two large datasets in more than three biological replicates. Quantitative approaches were then used to quantify the differences among the four experimental groups the naive, sham, middle cerebral artery occlusion MCAO and MCAO + BNJ groups by a label-free proteomics approach and a Cy5-labeled microarray approach. In brief, 3217 unique proteins and 24,300 unique gene symbols were confidently identified. Bioinformatics analysis revealed that of these unique proteins and gene symbols, 269 proteins and 632 gene symbols were identified to be differentially expressed. The results of subcellular localization, hierarchical clustering, and pathway enrichment analyses were combined with the results of the injury and repair phase analyses, and twelve proteins and twenty-seven gene symbols were significantly differentially expressed and were identified as potential candidates for cerebral ischemic injury involvement; all the candidates were verified by western blot and quantitative real-time PCR analysis. The primary enriched MAPK signaling pathway may play a key role in the molecular mechanisms related to cerebral ischemic injury. The observations of the present study help to illuminate the regulatory mechanism of cerebral ischemic injury and repair due to BNJ intervention.

Viral Mimetic-Induced Inflammation Abolishes Q-Pathway, but Not S-Pathway, Respiratory Motor Plasticity in Adult Rats

Inflammation arises from diverse stimuli eliciting distinct inflammatory profiles, yet little is known about the effects of different inflammatory stimuli on respiratory motor plasticity. Respiratory motor plasticity is a key feature of the neural control of breathing and commonly studied in the form of phrenic long-term facilitation (pLTF). At least two distinct pathways can evoke pLTF with differential sensitivities to bacterial-induced inflammation. The Q-pathway is abolished by bacterial-induced inflammation, while the S-pathway is inflammation-resistant. Since viral-induced inflammation is common and elicits distinct temporal inflammatory gene profiles compared to bacterial inflammation, we tested the hypothesis that inflammation induced by a viral mimetic (polyinosinic:polycytidylic acid, polyIC) would abolish Q-pathway-evoked pLTF, but not S-pathway-evoked pLTF. Further, we hypothesized Q-pathway impairment would occur later relative to bacterial-induced inflammation. PolyIC (750 μg/kg, i.p.) transiently increased inflammatory genes in the cervical spinal cord (3 h), but did not alter medullary and splenic inflammatory gene expression, suggesting region specific inflammation after polyIC. Dose-response experiments revealed 750 μg/kg polyIC (i.p.) was sufficient to abolish Q-pathway-evoked pLTF at 24 h (17 ± 15% change from baseline, n = 5, p > 0.05). However, polyIC (750 μg/kg, i.p.) at 3 h was not sufficient to abolish Q-pathway-evoked pLTF (67 ± 21%, n = 5, p < 0.0001), suggesting a unique temporal impairment of pLTF after viral-mimetic-induced systemic inflammation. A non-steroidal anti-inflammatory (ketoprofen, 12.5 mg/kg, i.p., 3 h) restored Q-pathway-evoked pLTF (64 ± 24%, n = 5, p < 0.0001), confirming the role of inflammatory signaling in pLTF impairment. On the contrary, S-pathway-evoked pLTF was unaffected by polyIC-induced inflammation (750 μg/kg, i.p., 24 h; 72 ± 25%, n = 5, p < 0.0001) and was not different from saline controls (65 ± 32%, n = 4, p = 0.6291). Thus, the inflammatory-impairment of Q-pathway-evoked pLTF is generalizable between distinct inflammatory stimuli, but differs temporally. On the contrary, S-pathway-evoked pLTF is inflammation-resistant. Therefore, in situations where respiratory motor plasticity may be used as a tool to improve motor function, strategies targeting S-pathway-evoked plasticity may facilitate therapeutic outcomes.

Broad blocking of MDR efflux pumps by acetylshikonin and acetoxyisovalerylshikonin to generate hypersensitive phenotype of malignant carcinoma cells

Cytotoxic activities of acetylshikonin and acetoxyisovalerylshikonin alone and in combination with chemotherapeutic agents against parental and drug resistant cell lines were determined using the MTT assay. Effects of Shikonin derivatives on BCRP, MDR1 and MRP transcript and protein levels were relatively measured. Finally, accumulation and efflux kinetics were conducted. The results revealed cell- and concentration-dependency of the cell cytotoxicity. Acetylshikonin and acetoxyisovalerylshikonin transiently made the mRNA ocean turbulent, but FACS analyses using fluorescent-labeled antibodies showed no significant change in the MDR-protein levels. Functional kinetics revealed significant block of MDR1, BCRP and MRP transporter in the presence of shikonin derivatives. Maximum accumulation fold changes was quantified to be 4.4 and consequently, acetoxyisovalerylshikonin pretreated EPG85.257RDB cells was chemosensitized to daunorubicin tension 3.1-fold. Although, the MDR blockage was reported to follow time- and cell-dependent patterns, MDR1, BCRP and MRP2 responses to the shikonins are concentration-independent. These data suggest uncompetitive transporter blockage behavior of these agents. The results indicated that shikonin derivatives stimulate uptake and reduce efflux of chemotherapeutic agents in the malignant cancer cells, suggesting that chemotherapy in combination with shikonin compounds may be beneficial to cancer cells that overexpress multidrug resistance transporters.

Annexin A2 as a target endothelial cell membrane autoantigen in Behçet's disease

Cell membrane proteins are believed to play a critical role in the pathogenesis of autoimmune diseases. However, few membrane autoantigens have been linked with Behçet's disease. Here, a cell-chip was performed to identify autoantibody target cells, and the suspected autoantigens were detected using immunoblotting. The amino acid sequences of the detected proteins were determined using LC-MALDI-TOF/TOF. Putative proteins were recombinantly expressed and purified, and a corresponding ELISA was developed and clinically validated using real clinical samples. It was found that a 36-kDa membrane protein--annexin A2--was detected in approximately one-third of the patients' blood circulation. The immunohistochemistry results showed that annexin A2 was highly expressed in vascular endothelial cells. Moreover, vascular involvement was significantly higher in the anti-annexin A2 antibody-positive group versus the anti-annexin A2 antibody-negative group among all the clinical samples analyzed, indicating that annexin A2 is a novel endothelial cell membrane antigen involved in Behçet's disease.

Identification of heat shock protein 27 as a novel autoantigen of Behçet's disease

OBJECTIVE

The aim of this study was to identify candidate pathogenic autoantigens of Behçet's disease (BD) in pathogen-stimulated target cells.

METHODS

First, three cell lines were used as target cells to screen autoantibody. Second, selected target cells were simulated with pathogens. Third, western blotting was used for detecting the auto-antigens in cell extracts. Next, immunoprecipitation was performed and the amino-acid sequences of target antigens were analyzed by LC-MALDI-TOF/TOF. Then, the potential target antigen was expressed, purified, and immunologically confirmed. And finally, an ELISA kit was developed and clinically validated through the assessments of 456 clinical samples with BD.

RESULTS

One antigen with a molecular weight of approximately 27-kDa was identified as heat shock protein 27 (HSP27). The reactivity of serum IgG against recombinant human HSP27 was detected in 52 of 91 BD patients (57%), 66 of 92 rheumatoid arthritis (RA) patients (72%), 32 of 90 Sjogren syndrome (SS) patients (36%), 22 of 92 systemic lupus erythematosus (SLE) patients (24%) and 0 of 91 healthy controls (HC). The reactivity of BD serum IgG antibodies against HSP27 was significantly higher than SLE (P<0.0001) SS (P<0.0001) and HC (P<0.0001).

CONCLUSIONS

This study identified HSP27 as a candidate endothelial cell autoantigen of BD, which is interesting and probably worth further exploration.