Proteasome subunits mRNA expressions correlate with male BMI: implications for a role in obesity

Analysis of prognostic biomarker models and immune microenvironment in acute myeloid leukemia by integrative bioinformatics

BACKGROUND

Acute myeloid leukemia (AML) is a hematological cancer driven on by aberrant myeloid precursor cell proliferation and differentiation. A prognostic model was created in this study to direct therapeutic care.

METHODS

Differentially expressed genes (DEGs) were investigated using the RNA-seq data from the TCGA-LAML and GTEx. Weighted Gene Coexpression Network Analysis (WGCNA) examines the genes involved in cancer. Find the intersection genes and construct the PPI network to discover hub genes and remove prognosis-related genes. A nomogram was produced for predicting the prognosis of AML patients using the risk prognosis model that was constructed using COX and Lasso regression analysis. GO, KEGG, and ssGSEA analysis were used to look into its biological function. TIDE score predicts immunotherapy response.

RESULTS

Differentially expressed gene analysis revealed 1004 genes, WGCNA analysis revealed 19,575 tumor-related genes, and 941 intersection genes in total. Twelve prognostic genes were found using the PPI network and prognostic analysis. To build a risk rating model, RPS3A and PSMA2 were examined using COX and Lasso regression analysis. The risk score was used to divide the patients into two groups, and Kaplan-Meier analysis indicated that the two groups had different overall survival rates. Univariate and multivariate COX studies demonstrated that risk score is an independent prognostic factor. According to the TIDE study, the immunotherapy response was better in the low-risk group than in the high-risk group.

CONCLUSIONS

We eventually selected out two molecules to construct prediction models that might be used as biomarkers for predicting AML immunotherapy and prognosis.

Upregulated monocyte expression of PLIN2 is associated with early arterial injury in children with overweight/obesity

BACKGROUND AND AIMS

Perilipin 2 (PLIN2) regulates intracellular lipid metabolism in macrophages, and thus, plays a role in atherosclerosis. Aim of the study was to evaluate whether PLIN2 dysregulation is involved in the onset of preclinical atherosclerosis in children with overweight/obesity and to explore dysregulation mechanisms.

METHODS

Sixty-three children with overweight/obesity and 21 normal weight children (controls) of the same age and sex were enrolled. Carotid intima media thickness (cIMT) was evaluated; mRNA expression of PLIN2 and proteasome subunits (PSMD3, PSMC4) was determined by Real Time PCR, and protein expression of PLIN2, LAMP2A and Hsc70 by Western blot analysis; fluorimetric assay was used to measure proteasome chymotrypsin like activity. We performed transient LAMP2A downregulation by siRNA and quantified intracellular lipids in monocytes by Nile Red staining and flow cytometry analysis.

RESULTS

PLIN2 protein levels were significantly higher in children with overweight/obesity and correlated with cIMT after adjusting for confounders. Accordingly, monocytes of children with overweight/obesity showed a higher intracellular amount of lipids compared with controls. mRNA expression of the regulatory subunits PSMC4 and PSMD3 and proteasome activity were lower in children with overweight/obesity, while expression of LAMP2A and Hsc70 proteins, which belong to the chaperone-mediated autophagy (CMA) pathway, was not different, suggesting that PLIN2 dysregulation in monocytes was due to an impairment of proteasome efficiency and was not CMA related.

CONCLUSION

PLIN2 was overexpressed in monocytes of children with overweight/obesity and could contribute to the onset of arteropathy. Our data suggest that proteasome impairment could contribute to PLIN2 overexpression.

Prognostic Value and Molecular Mechanisms of Proteasome 26S Subunit, Non-ATPase Family Genes for Pancreatic Ductal Adenocarcinoma Patients after Pancreaticoduodenectomy

Objective: Pancreatic cancer (PC) is an extremely malignant tumor with similar morbidity and mortality and lack of an effective treatment. This study explored the prognostic value and molecular mechanisms of proteasome 26S subunit, non-ATPase (PSMD) family genes in pancreatic ductal adenocarcinoma (PDAC).Methods: Survival analyses were performed to elucidate the relationship between prognosis and the level of PSMD expression. ROC curves and nomograms were constructed to predict the prognosis. A bioinformatics analysis was used to explore the co-expression and complex interaction networks of PSMDs. The potential mechanisms were further explored via gene set enrichment analysis (GSEA).Results: We find high levels of PSMD6, PSMD9, PSMD11, and PSMD14 expression were significantly associated with a poorer OS. High PSMD6 and PSMD11 expression was associated with a poorer relapse-free survival (RFS). A risk score model was constructed based on prognosis-related genes. The area under ROC curves (AUC) was 53.3%, 59.3%, and 62.9% for 1-, 2-, 3 years, respectively.Conclusion: GSEA revealed that PSMD6 and PSMD11 play a role in PDAC through various biological processes and signaling pathways, including TP53, CDKN2A, MYC pathway, DNA repair, KRAS, cell cycle checkpoint, NIK, NF-κB signaling pathway, and proteasomes. This study demonstrated that PSMD6 and PSMD11 could serve as a potential prognostic and diagnostic biomarkers for patients with early-stage PDAC after pancreaticoduodenectomy.

Differential expression of genes associated with T lymphocytes function in septic patients with hypoxemia challenge

Background

This study aimed to assess gene expression alterations related to T lymphocytes function and explore their potential association with hypoxemia among septic patients.

Methods

This is a retrospective cohort clinical study with laboratory investigations. We studied patients enrolled in sepsis biological specimen bank from Department of Critical Care Medicine, Zhongda Hospital, fulfilling consensus criteria for sepsis without any documented immune comorbidity admitted in ICU within 48 h after onset with whole blood samples drawn within 24 h of admission. Whole genome expression by microarray assay (Human LncRNA Microarray V4.0) was compared in hypoxemia cohort versus without. Differentially expressed (DE) genes with >1 log₂[fold change (FC)] and false discovery rate (FDR) <0.20 that enriched in T cell related biological process entered the adjusted analysis to identify the candidate genes. The correlation analysis within candidate genes or with clinical parameters were performed. We assessed candidate expression ex vivo in co-culture system with RAW246.7 cells and validated genes identified in prior studies of sepsis-ARDS/hypoxemia within our present study.

Results

Septic patients (n=9) with hypoxemic phenotype held higher illness severity, serum lactate and creatine, and incidence of lymphopenia compared with non-hypoxemic group (n=6). Several gene signatures related to apoptosis, inhibitory receptors, T cell immunoreceptor, transcriptions factors, toll-like receptors and cytokine and effector molecules were upregulated in hypoxemic group. Candidate genes were identified after adjustment for age, sex and presence of lymphopenia with significantly negative correlations with partial pressure of O₂ in an arterial blood (PaO₂) and fraction of inspiration O₂ (FiO₂) ratio, among which NLRP3, SOS1, ELF1 and STAT3 held an increasing expression in ex vivo validation while the others, PSMA5, CLEC4D, CD300A, PRKD2 and PSMA2 showed the opposite alteration from those in vivo.

Conclusions

Higher illness severity and incidence of lymphopenia was observed following hypoxemia in sepsis and T cell-related gene signatures were associated with hypoxemia during sepsis.

Profiling Analysis Reveals the Potential Contribution of Peptides to Human Adipocyte Differentiation

PURPOSE

Peptide drugs provide promising regimes in anti-obesity treatment. In order to identify potential bioactive peptides involved in adipogenesis.

EXPERIMENTAL DESIGN

The intracellular peptides between preadipocytes and adipocytes are compared by liquid chromatography/mass spectrometry. The underlying biological function of the identified peptides are evaluated by gene ontology (GO) and pathway analysis of their precursors. To find more potential bioactive peptides, 50 peptide sequences are identified located in the functional domains with the use of the SMART and UniProt databases. Finally, the Open Targets Platform database is used to investigate the precursors related to metabolic diseases.

RESULTS

A total of 181 downregulated peptides and 89 upregulated peptides after differentiation (fold change > 1.5 and p-value < 0.05) are identified. The GO and pathway analysis indicate that these differentially expressed peptides play a role in adipogenesis. A total of 10 putative peptides 6 to 26 amino acids in length are identified that might have bioactive effects in adipogenesis and metabolic diseases.

CONCLUSIONS AND CLINICAL RELEVANCE

On one hand, present preliminary research provides a better understanding of the intracellular peptides during adipocyte differentiation. On the other hand, it lays a foundation for discovering new peptide drugs in anti-obesity treatment.

Genome-wide QTL mapping results for regional DXA body composition and bone mineral density traits in pigs

Abstract. In a previous study, genome-wide mapping of quantitative trait loci (QTL) for five body composition traits, three bone mineral traits and live weight was performed using whole-body dual-energy X-ray absorptiometry (DXA) data. Since QTL for bone mineral traits were rare, the current study aimed to clarify whether the mapping results were influenced by the analysed body regions. Thus, the same material (551 pigs) and methods as in the whole-body QTL mapping study were used. However, for evaluation of the DXA scans, we manually defined two body regions: (i) from the last ribs to the pelvis (A) and (ii) including the pelvis and the hind limbs (P). Since live weight was not affected by the regional analysis, it was omitted from the QTL mapping design. Our results show an overall high consistency of mapping results especially for body composition traits. Two thirds of the initial whole-body QTL are significant for both A and P. Possible causes for the still low number of bone mineral QTL and the lower consistency found for these traits are discussed. For body composition traits, the data presented here show high genome-wide Pearson correlations between mapping results that are based on DXA scans with the time-saving whole-body standard setting and mapping results for DXA data that were obtained by time-consuming manual definition of the regions of interest. However, our results also suggest that whole-body or regional DXA scans might generally be less suitable for mapping of bone mineral traits in pigs. An analysis of single reference bones could be more useful.

Tyrosine hydroxylase is short-term regulated by the ubiquitin-proteasome system in PC12 cells and hypothalamic and brainstem neurons from spontaneously hypertensive rats: possible implications in hypertension

Aberrations in the ubiquitin-proteasome system (UPS) are implicated in the pathogenesis of various diseases. Tyrosine hydroxylase (TH), the rate-limiting enzyme in catecholamines biosynthesis, is involved in hypertension development. In this study we investigated whether UPS regulated TH turnover in PC12 cells and hypothalamic and brainstem neurons from spontaneously hypertensive rats (SHR) and whether this system was impaired in hypertension. PC12 cells were exposed to proteasome or lysosome inhibitors and TH protein level evaluated by Western blot. Lactacystin, a proteasome inhibitor, induced an increase of 86±15% in TH levels after 30 min of incubation, then it started to decrease up to 6 h to reach control levels and finally it rose up to 35.2±8.5% after 24 h. Bafilomycin, a lysosome inhibitor, did not alter TH protein levels during short times, but it increased TH by 92±22% above basal after 6 h treatment. Before degradation proteasome substrates are labeled by conjugation with ubiquitin. Efficacy of proteasome inhibition on TH turnover was evidenced by accumulation of ubiquitinylated TH after 30 min. Further, the inhibition of proteasome increased the quantity of TH phosphorylated at Ser40, which is essential for TH activity, by 2.7±0.3 fold above basal. TH protein level was upregulated in neurons from hypothalami and brainstem of SHR when the proteasome was inhibited during 30 min, supporting that neuronal TH is also short-term regulated by the proteasome. Since the increased TH levels reported in hypertension may result from proteasome dysfunction, we evaluate proteasme activity. Proteasome activity was significantly reduced by 67±4% in hypothalamic and brainstem neurons from SHR while its protein levels did not change. Present findings show that TH is regulated by the UPS. The impairment in proteasome activity observed in SHR neurons may be one of the causes of the increased TH protein levels reported in hypertension.

Transcriptional background of beef marbling - novel genes implicated in intramuscular fat deposition

The purpose of this study was to identify novel marbling-related genes by comparison of the global gene expression in semitendinosus muscle of 15-month-old Limousin (LIM), Holstein-Friesian (HF) and Hereford (HER) bulls. Muscle of LIM was lean with low intramuscular fat (IMF) content (0.53%) unlike the marbled muscles of HER and HF characterized by higher amounts of IMF (1.10 and 0.81%, respectively). The comparison of muscle transcriptional profile between marbled and lean beef revealed significant differences in expression of 144 genes, presumably involved in consecutive stages of adipose tissue development, such as preadipocyte proliferation and differentiation, adipocyte maturation, lipid filling and lipid metabolism leading to increased IMF deposition and marbling development. Correlation coefficients and regression analysis for nine of them (gadd45a, pias3, ccrn4l, diras3, pou5f1, hoxa9, atp2a2 and pim1) validated by real-time qPCR confirmed their moderate-high correlation with IMF% and explained up to 70.5% of the total variability in IMF deposition in the bulls.

Association of obesity with proteasomal gene polymorphisms in children

The aim of this study was to ascertain possible associations between childhood obesity, its anthropometric and clinical parameters, and three loci of proteasomal genes rs2277460 (PSMA6 c.-110C>A), rs1048990 (PSMA6 c.-8C>G), and rs2348071 (PSMA3 c. 543+138G>A) implicated in obesity-related diseases. Obese subjects included 94 otherwise healthy children in Latvia. Loci were genotyped and then analyzed using polymerase chain reactions, with results compared to those of 191 nonobese controls. PSMA3 SNP frequency differences between obese children and controls, while not reaching significance, suggested a trend. These differences, however, proved highly significant (P < 0.002) in the subset of children reporting a family history of obesity. Among obese children denying such history, PSMA6 c.-8C>G SNP differences, while being nonsignificant, likewise suggested a trend in comparison to the nonobese controls. No PSMA6 c.-110C>A SNP differences were detected in the obese group or its subsets. Finally, PSMA3 SNP differences were significantly associated (P < 0.05) with circulating low-density lipoprotein cholesterol (LDL) levels. Our results clearly implicate the PSMA3 gene locus as an obesity risk factor in those Latvian children with a family history of obesity. While being speculative, the clinical results are suggestive of altered circulatory LDL levels playing a possible role in the etiology of obesity in the young.

Conjugated linoleic acid synthesis-related protein proteasome subunit α 5 (PSMA5) is increased by vaccenic acid treatment in goat mammary tissue

This study was conducted to identify proteins associated with the endogenous synthesis of conjugated linoleic acid (CLA) from trans-vaccenic acid (TVA; trans-11 C18:1, a precursor for CLA endogenous synthesis) in mammary tissues. Six lactating goats were divided into 2 groups. One group was given an intravenous bolus injection of TVA (150mg) twice daily over 4 d; the other group received saline injections. Treatment with TVA increased the concentration of cis-9,trans-11 CLA and TVA in goat milk. Additionally, TVA treatment increased the expression of stearoyl-CoA desaturase (SCD) in mammary tissue. Using 2-dimensional gel electrophoresis and electrospray ionization quadrupole time-of-flight mass spectrometry, 3 proteins affected by infusions of TVA were identified. Proteasome (prosome, macropain) subunit α type 5 (PSMA5) was upregulated, whereas peroxiredoxin-1 and translationally controlled tumor protein 1 were downregulated in TVA-treated animals compared with the vehicle-injected controls. Only the effect of TVA on PSMA5 could be confirmed by Western blot analysis. To further explore the regulation of PSMA5 in mammary epithelial cells when TVA is converted into CLA, we used a differentiated bovine mammary epithelial cell line treated with TVA for 6h. Changes in cis-9,trans-11 CLA concentrations and mRNA expression patterns of both SCD and PSMA5 were monitored. The concentration of cis-9,trans-11 CLA increased after TVA treatment. The mRNA expression level of PSMA5 was significantly elevated to 6h, but SCD mRNA expression only increased in 2h after TVA treatment. These results indicate that PSMA5 is highly expressed in goat mammary tissue and bovine mammary epithelial cells when TVA is converted into CLA. Our data suggest that PSMA5 protein is associated with CLA biosynthesis in mammary tissue.

Proteasome alterations during adipose differentiation and aging: links to impaired adipocyte differentiation and development of oxidative stress

Intracellular proteins are degraded by a number of proteases, including the ubiquitin-proteasome pathway (UPP). Impairments in the UPP occur during the aging of a variety of tissues, although little is known in regards to age-related alterations to the UPP during the aging of adipose tissue. The UPP is known to be involved in regulating the differentiation of a variety of cell types, although the potential changes in the UPP during adipose differentiation have not been fully elucidated. How the UPP is altered in aging adipose tissue and adipocyte differentiation and the effects of proteasome inhibition on adipocyte homeostasis and differentiation are critical issues to elucidate experimentally. Adipogenesis continues throughout the life of adipose tissue, with continual differentiation of preadipocytes essential to maintaining tissue function during aging, and UPP alterations in mature adipocytes are likely to directly modulate adipose function during aging. In this study we demonstrate that aging induces alterations in the activity and expression of principal components of the UPP. Additionally, we show that multiple changes in the UPP occur during the differentiation of 3T3-L1 cells into adipocytes. In vitro data link observed UPP alterations to increased levels of oxidative stress and altered adipose biology relevant to both aging and differentiation. Taken together, these data demonstrate that changes in the UPP occur in response to adipose aging and adipogenesis and strongly suggest that proteasome inhibition is sufficient to decrease adipose differentiation, as well as increasing oxidative stress in mature adipocytes, both of which probably promote deleterious effects on adipose aging.

Blood gene expression reveal pathway differences between diet-sensitive and resistant obese subjects prior to caloric restriction

Weight loss in response to caloric restriction displays significant interindividual heterogeneity. To develop early predictors of weight-loss success, we have compared whole-blood gene expression profiles of obese, diet-sensitive vs. obese, diet-resistant subjects prior to the initiation of clinically supervised caloric restriction. Pathway enrichment analysis of gene expression profiles by multiple applications converged on the "oxidative phosphorylation" (OXPHOS) pathway, and to a lesser extent the "proteasome" pathway, as statistically significantly upregulated in obese, diet-sensitive subjects compared to the diet-resistant subjects. The finding of increased OXPHOS is consistent with earlier observations of increased proton leak, increased expression of OXPHOS genes, and increased oxidative muscle fibers in skeletal muscle of obese, diet-sensitive subjects. The current study further highlights the utility of blood as a sentinel tissue reflecting systemic states and provides a potential modality to predict future weight-loss success, relevant to the design of individualized bariatric treatment programs.

Inflammation as death or life signal in diabetic fracture healing

Increased apoptosis of chondrocytes and osteoblasts and prolonged survival of osteoclasts lead to early destruction of callus tissue and impair bone remodeling in fracture healing of diabetic patients. Diabetes is accompanied by an increased inflammatory state, reactive oxygen species (ROS) generation and accumulation of advanced glycation end products (AGEs), a heterogenous group of toxic metabolites that can induce inflammation. Prolonged hyperglycemia and insulin resistance correlate with increased apoptosis rate and, accordingly, the proapoptotic role of several inflammatory mediators, ROS and AGEs has been also documented. In this review we summarize the most recent reports supporting the idea that inflammatory signaling increases chondrocyte and osteoblast death and prolongs osteoclast survival, resulting in impaired bone regeneration in diabetes. Antagonising inflammatory signal pathways and solution of inflammation may deserve greater attention in the management of diabetic fracture healing.

Proteasome activity correlates with male BMI and contributes to the differentiation of adipocyte in hADSC

We have previously reported that 26S proteasome subunit mRNA expressions correlate with male body mass index (BMI). In this study, to investigate whether proteasome activities are correlated with BMI, we recruited 61 healthy young Japanese male subjects, measured proteasome activities in their plasma, and correlated them with their BMI and various metabolic factors. We found that among three different proteasome activities, chymotrypsin-like activity in plasma was positively correlated with BMI in healthy Japanese male subjects. Furthermore, we analyzed proteasome activity in vitro during the differentiation of human adipose-derived stem cell (hADSC) into mature adipocytes. In the early stage of differentiation, proteasome activity was at its highest level, and proteasome inhibitor could inhibit hADSC adipocyte differentiation. Our findings suggest that proteasome is an important controlling factor for the development of obesity and adipogenesis.