Is Nucleoredoxin a Master Regulator of Cellular Redox Homeostasis? Its Implication in Different Pathologies

Proteomic analysis of extracellular vesicles and extracellular vesicle-depleted excretory-secretory products of Toxocara canis and Toxocara cati larval cultures

Toxocara canis and Toxocara cati are parasitic nematodes in the order Ascaridida, which inhabit the small intestines of dogs and cats, respectively, as adults. Although often nonpathogenic as adults, nematodes within this genus are capable of causing widespread disease throughout the host while in a larval stage, during which time larvae migrate throughout the body in a process termed larva migrans. Larvae are also capable of surviving within host tissues in an encysted arrested stage, without immune clearance by the host. The ability of larvae to survive within host tissues during migration and encystment may be attributed to immunomodulatory molecules released by the excretory cells of larvae in excretory-secretory (ES) products. ES products of parasites contain a variety of molecules, including proteins, lipids, and extracellular vesicles (EVs). Toxocara excretory-secretory (TES) products have been studied to some degree, with proteomic analysis of TES proteins described previously; however, investigation of the EVs within TES is lacking, despite the suggested role for these molecules in host interaction and potential immunomodulation. To further characterize the protein cargo within EVs in TES, EVs were isolated from larval cultures of T. canis and T. cati via ultrafiltration, with concurrent collection of EV-depleted TES filtrate for additional study. Isolated EVs and EV-depleted TES from both T. canis and T. cati were submitted for proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). Proteomic identification results revealed 140 proteins across all samples, with 16 shared by all samples, and 76 total proteins shared between T. canis and T. cati, present within EVs and EV-depleted TES. There were 17 proteins shared exclusively by EV samples, and 15 were shared exclusively between EV-depleted TES samples. Many shared proteins were associated with the host immune response. Several proteins were specific to either T. canis or T. cati, highlighting the potential use of these proteins as diagnostic tools in the differentiation of etiologic agents in cases of toxocariasis. The results of this study build upon previously reported proteomic evaluations of TES, contributing new information in regards to newly identified proteins, EV protein cargo within TES, and potential immunomodulatory functions of these proteins.

Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages

The cultivated tomato, Solanum lycopersicum, is highly sensitive to cold stress (CS), resulting in significant losses during cultivation and postharvest fruit storage. Previously, we demonstrated the presence of substantial genetic variation in fruit chilling tolerance in a tomato recombinant inbred line (RIL) population derived from a cross between a chilling-sensitive tomato line and a chilling-tolerant accession of the wild species S. pimpinellifolium. Here, we investigated molecular and biochemical components associated with chilling tolerance in fruit and leaves, using contrasting groups of "chilling tolerant" and "chilling sensitive" RI lines. Transcriptomic analyses were conducted on fruit exposed to CS, and gene expressions and biochemical components were measured in fruit and leaves. The analyses revealed core responding genes specific to either the cold-tolerant or cold-sensitive RI lines, which were differentially regulated in similar fashion in both leaves and fruit within each group. These genes may be used as markers to determine tomato germplasm cold tolerance or sensitivity. This study demonstrated that tomato response to CS in different developmental stages, including seedling and postharvest fruit, might be mediated by common biological/genetic factors. Therefore, genetic selection for cold tolerance during early stages of plant development may lead to lines with greater postharvest fruit chilling tolerance.

Fundamentals of redox regulation in biology

Oxidation-reduction (redox) reactions are central to the existence of life. Reactive species of oxygen, nitrogen and sulfur mediate redox control of a wide range of essential cellular processes. Yet, excessive levels of oxidants are associated with ageing and many diseases, including cardiological and neurodegenerative diseases, and cancer. Hence, maintaining the fine-tuned steady-state balance of reactive species production and removal is essential. Here, we discuss new insights into the dynamic maintenance of redox homeostasis (that is, redox homeodynamics) and the principles underlying biological redox organization, termed the 'redox code'. We survey how redox changes result in stress responses by hormesis mechanisms, and how the lifelong cumulative exposure to environmental agents, termed the 'exposome', is communicated to cells through redox signals. Better understanding of the molecular and cellular basis of redox biology will guide novel redox medicine approaches aimed at preventing and treating diseases associated with disturbed redox regulation.

Lipid Peroxidation-Related Redox Signaling in Osteosarcoma

Oxidative stress and lipid peroxidation play important roles in numerous physiological and pathological processes, while the bioactive products of lipid peroxidation, lipid hydroperoxides and reactive aldehydes, act as important mediators of redox signaling in normal and malignant cells. Many types of cancer, including osteosarcoma, express altered redox signaling pathways. Such redox signaling pathways protect cancer cells from the cytotoxic effects of oxidative stress, thus supporting malignant transformation, and eventually from cytotoxic anticancer therapies associated with oxidative stress. In this review, we aim to explore the status of lipid peroxidation in osteosarcoma and highlight the involvement of lipid peroxidation products in redox signaling pathways, including the involvement of lipid peroxidation in osteosarcoma therapies.

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.

Association of Blood-Based DNA Methylation Markers With Late-Onset Alzheimer Disease: A Potential Diagnostic Approach

BACKGROUND AND OBJECTIVES

There is an urgent need to identify novel noninvasive biomarkers for Alzheimer disease (AD) diagnosis. Recent advances in blood-based measurements of phosphorylated tau (pTau) species are promising but still insufficient to address clinical needs. Epigenetics has been shown to be helpful to better understand AD pathogenesis. Epigenetic biomarkers have been successfully implemented in other medical disciplines, such as oncology. The objective of this study was to explore the diagnostic accuracy of a blood-based DNA methylation marker panel as a noninvasive tool to identify patients with late-onset Alzheimer compared with age-matched controls.

METHODS

A case-control study was performed. Blood DNA methylation levels at 46 cytosine-guanine sites (21 genes selected after a comprehensive literature search) were measured by bisulfite pyrosequencing in patients with "probable AD dementia" following National Institute on Aging and the Alzheimer's Association guidelines (2011) and age-matched and sex-matched controls recruited at Neurology Department-University Hospital of Navarre, Spain, selected by convenience sampling. Plasma pTau181 levels were determined by Simoa technology. Multivariable logistic regression analysis was performed to explore the optimal model to discriminate patients with AD from controls. Furthermore, we performed a stratified analysis by sex.

RESULTS

The final study cohort consisted of 80 patients with AD (age: median [interquartile range] 79 [11] years; 58.8% female) and 100 cognitively healthy controls (age 77 [10] years; 58% female). A panel including DNA methylation levels at NXN, ABCA7, and HOXA3 genes and plasma pTau181 significantly improved (area under the receiver operating characteristic curve 0.93, 95% CI 0.89-0.97) the diagnostic performance of a single pTau181-based model, adjusted for age, sex, and APOE ɛ4 genotype. The sensitivity and specificity of this panel were 83.30% and 90.00%, respectively. After sex-stratified analysis, HOXA3 DNA methylation levels showed consistent association with AD.

DISCUSSION

These results highlight the potential translational value of blood-based DNA methylation biomarkers for noninvasive diagnosis of AD.

REGISTRATION INFORMATION

Research Ethics Committee of the University Hospital of Navarre (PI17/02218).

USF1-mediated ALKBH5 stabilizes FLII mRNA in an m6A-YTHDF2-dependent manner to repress glycolytic activity in prostate adenocarcinoma

Upstream-stimulating factor 1 (USF1) is a ubiquitously expressed transcription factor implicated in multiple cellular processes, including metabolism and proliferation. This study focused on the function of USF1 in glycolysis and the malignant development of prostate adenocarcinoma (PRAD). Bioinformatics predictions suggested that USF1 is poorly expressed in PRAD. The clinical PRAD samples revealed a low level of USF1, which was correlated with an unfavorable prognosis. Artificial upregulation of USF1 significantly repressed glycolytic activity in PRAD cells and reduced cell growth and metastasis in vitro and in vivo. Potential downstream genes of USF1 were probed by integrated bioinformatics analyses. The chromatin immunoprecipitation and luciferase assays indicated that USF1 bound to the α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) promoter for transcription activation. Flightless I (FLII) was identified as the gene showing the highest degree of correlation with ALKBH5. As an m6A demethylase, ALKBH5 enhanced FLII mRNA stability by inducing m6A demethylation in an m6A-YTH N6-methyladenosine RNA-binding protein F2 (YTHDF2)-dependent manner. Either silencing of ALKBH5 or FLII blocked the role of USF1 in PARD cells and restored glycolysis, cell proliferation, and invasion. This study demonstrates that USF1 activates ALKBH5 to stabilize FLII mRNA in an m6A-YTHDF2-dependent manner, thereby repressing glycolysis processes and the progression of PRAD.

Comprehensive Genetic Study of Malignant Cervical Paraganglioma

Malignant middle ear paraganglioma (MEPGL) is an exceedingly rare tumor of the neuroendocrine system. In general, MEPGLs represent as slow growing and hypervascularized benign neoplasms. The genetic basis of MEPGL tumorigenesis has been poorly investigated. We report a case of malignant MEPGL accompanied by the comprehensive genetic analysis of the primary tumor and metastasis. Based on whole-exome sequencing data, the germline pathogenic mutation p.R230H in the SDHB gene, encoding for subunit B of mitochondrial complex II, was found in a patient. Analysis of somatic mutation spectra revealed five novel variants in different genes, including a potentially deleterious variant in UNC13C that was common for the tumor and metastasis. Identified somatic variants clustered into SBS1 and SBS5 mutational signatures. Of note, the primary tumor was characterized by Ki-67 4% and had an elevated mutational load (1.4/Mb); the metastasis' mutational load was about 4.5 times higher (6.4/Mb). In addition, we revealed somatic loss of the wild-type SDHB allele, as well as loss of heterozygosity (LOH) at the 11p locus. Thus, germline mutation in SDHB combined with somatic LOH seem to be drivers that lead to the tumor's initiation and progression. Other somatic changes identified can be additional disease-causing factors. Obtained results expand our understanding of molecular genetic mechanisms associated with the development of this rare tumor.

Nucleoredoxin Plays a Key Role in the Maintenance of Retinal Pigmented Epithelium Differentiation

Nucleoredoxin (Nrx) belongs to the Thioredoxin protein family and functions in redox-mediated signal transduction. It contains the dithiol active site motif Cys-Pro-Pro-Cys and interacts and regulates different proteins in distinct cellular pathways. Nrx was shown to be catalytically active in the insulin assay and recent findings indicate that Nrx functions, in fact, as oxidase. Here, we have analyzed Nrx in the mammalian retina exposed to (perinatal) hypoxia-ischemia/reoxygenation, combining ex vivo and in vitro models. Our data show that Nrx regulates cell differentiation, which is important to (i) increase the number of glial cells and (ii) replenish neurons that are lost following the hypoxic insult. Nrx is essential to maintain cell morphology. These regulatory changes are related to VEGF but do not seem to be linked to the Wnt/β-catenin pathway, which is not affected by Nrx knock-down. In conclusion, our results strongly suggest that hypoxia-ischemia could lead to alterations in the organization of the retina, related to changes in RPE cell differentiation. Nrx may play an essential role in the maintenance of the RPE cell differentiation state via the regulation of VEGF release.