Analysis of ATG4C function in vivo.

ABBREVIATIONS: ATG4 (autophagy related 4 cysteine peptidase); ATG4A (autophagy related 4A cysteine peptidase); ATG4B (autophagy related 4B cysteine peptidase); ATG4C (autophagy related 4C cysteine peptidase); ATG4D (autophagy related 4D cysteine peptidase); Atg8 (autophagy related 8); GABARAP (GABA type A receptor-associated protein); GABARAPL1(GABA type A receptor-associated protein like 1); GABARAPL2 (GABA type A receptor-associated protein like 2); MAP1LC3A/LC3A (microtubule associated protein 1 light chain 3 alpha); MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta); mATG8 (mammalian Atg8); PE (phosphatidylethanolamine); PS (phosphatydylserine); SQSTM1/p62 (sequestosome 1).

Quantitative phosphoproteome analysis of Streptomyces coelicolor by immobilized zirconium (IV) affinity chromatography and mass spectrometry reveals novel regulated protein phosphorylation sites and sequence motifs.

Streptomycetes are multicellular gram-positive bacteria that produce many bioactive compounds, including antibiotics, antitumorals and immunosuppressors. The Streptomyces phosphoproteome remains largely uncharted even though protein phosphorylation at Ser/Thr/Tyr is known to modulate morphological differentiation and specialized metabolic processes. We here expand the S. coelicolor phosphoproteome by optimised immobilized zirconium (IV) affinity chromatography and mass spectrometry to identify phosphoproteins at the vegetative and sporulating stages. We mapped 361 phosphorylation sites (41% pSer, 56.2% pThr, 2.8% pTyr) and discovered four novel Thr phosphorylation motifs ("Kxxxx(pT)xxxxK", "DxE(pT)", "D(pT)" and "Exxxxx(pT)") in 351 phosphopeptides derived from 187 phosphoproteins. We identified 154 novel phosphoproteins, thereby almost doubling the number of experimentally verified Streptomyces phosphoproteins. Novel phosphoproteins included cell division proteins (FtsK, CrgA) and specialized metabolism regulators (ArgR, AfsR, CutR and HrcA) that were differentially phosphorylated in the vegetative and in the antibiotic producing sporulating stages. Phosphoproteins involved in primary metabolism included 27 novel ribosomal proteins that were phosphorylated during the vegetative stage. Phosphorylation of these proteins likely participate in the intricate and incompletely understood regulation of Streptomyces development and secondary metabolism. We conclude that Zr(IV)-IMAC is an efficient and sensitive method to study protein phosphorylation and regulation in bacteria and enhance our understanding of bacterial signalling. SIGNIFICANCE: Two thirds of the secondary metabolites used in clinic, especially antibiotics, were discovered in Streptomyces strains. Antibiotic resistance became one of the major challenges in clinic, and new antibiotics are urgently required in clinic. Next-generation sequencing analyses revealed that streptomycetes harbour many cryptic secondary metabolite pathways, i.e. pathways not expressed in the laboratory. Secondary metabolism is tightly connected with hypha differentiation and sporulation, and understanding Streptomyces differentiation is one of the main challenges in industrial microbiology, in order to activate the expression of cryptic pathways in the laboratory. Protein phosphorylation at Ser/Thr/Tyr modulates development and secondary metabolism, but the Streptomyces phosphoproteome is still largely uncharted. Previous S. coelicolor phosphoproteomic studies used TiO2 affinity enrichment and LC-MS/MS identifying a total of 184 Streptomyces phosphoproteins. Here, we used by first time zirconium (IV) affinity chromatography and mass spectrometry, identifying 186 S. coelicolor phosphoproteins. Most of these phosphoproteins (154) were not identified in previous phosphoproteomic studies using TiO2 affinity enrichment. Thereby we almost doubling the number of experimentally verified Streptomyces phosphoproteins. Zr(IV)-IMAC affinity chromatography also worked in E. coli, allowing the identification of phosphoproteins that were not identified by TiO2 affinity chromatography. We conclude that Zr(IV)-IMAC is an efficient and sensitive method for studies of protein phosphorylation and regulation in bacteria to enhance our understanding of bacterial signalling networks. Moreover, the new Streptomyces phosphoproteins identified will contribute to design further works to understand and modulate Streptomyces secondary metabolism activation.

Post-COVID Complications after Pressure Ulcer Surgery in Patients with Spinal Cord Injury Associate with Creatine Kinase Upregulation in Adipose Tissue.

The risk of complications following surgical procedures is significantly increased in patients with SARS-CoV-2 infection. However, the mechanisms underlying these correlations are not fully known. Spinal cord injury (SCI) patients who underwent reconstructive surgery for pressure ulcers (PUs) before and during the COVID-19 pandemic were included in this study. The patient's postoperative progression was registered, and the subcutaneous white adipose tissue (s-WAT) surrounding the ulcers was analyzed by proteomic and immunohistochemical assays to identify the molecular/cellular signatures of impaired recovery. Patients with SCI and a COVID-19-positive diagnosis showed worse recovery and severe postoperative complications, requiring reintervention. Several proteins were upregulated in the adipose tissue of these patients. Among them, CKMT2 and CKM stood out, and CKM increased for up to 60 days after the COVID-19 diagnosis. Moreover, CKMT2 and CKM were largely found in MGCs within the s-WAT of COVID patients. Some of these proteins presented post-translational modifications and were targeted by autoantibodies in the serum of COVID patients. Overall, our results indicate that CKMT2, CKM, and the presence of MGCs in the adipose tissue surrounding PUs in post-COVID patients could be predictive biomarkers of postsurgical complications. These results suggest that the inflammatory response in adipose tissue may underlie the defective repair seen after surgery.

The Modulation of SCO2730/31 Copper Chaperone/Transporter Orthologue Expression Enhances Secondary Metabolism in Streptomycetes.

Streptomycetes are important biotechnological bacteria that produce several clinically bioactive compounds. They have a complex development, including hyphae differentiation and sporulation. Cytosolic copper is a well-known modulator of differentiation and secondary metabolism. The interruption of the Streptomyces coelicolor SCO2730 (copper chaperone, SCO2730::Tn5062 mutant) blocks SCO2730 and reduces SCO2731 (P-type ATPase copper export) expressions, decreasing copper export and increasing cytosolic copper. This mutation triggers the expression of 13 secondary metabolite clusters, including cryptic pathways, during the whole developmental cycle, skipping the vegetative, non-productive stage. As a proof of concept, here, we tested whether the knockdown of the SCO2730/31 orthologue expression can enhance secondary metabolism in streptomycetes. We created a SCO2730/31 consensus antisense mRNA from the sequences of seven key streptomycetes, which helped to increase the cytosolic copper in S. coelicolor, albeit to a lower level than in the SCO2730::Tn5062 mutant. This antisense mRNA affected the production of at least six secondary metabolites (CDA, 2-methylisoborneol, undecylprodigiosin, tetrahydroxynaphtalene, α-actinorhodin, ε-actinorhodin) in the S. coelicolor, and five (phenanthroviridin, alkylresorcinol, chloramphenicol, pikromycin, jadomycin G) in the S. venezuelae; it also helped to alter the S. albus metabolome. The SCO2730/31 consensus antisense mRNA designed here constitutes a tool for the knockdown of SCO2730/31 expression and for the enhancement of Streptomyces' secondary metabolism.

ATG4D is the main ATG8 delipidating enzyme in mammalian cells and protects against cerebellar neurodegeneration.

Despite the great advances in autophagy research in the last years, the specific functions of the four mammalian Atg4 proteases (ATG4A-D) remain unclear. In yeast, Atg4 mediates both Atg8 proteolytic activation, and its delipidation. However, it is not clear how these two roles are distributed along the members of the ATG4 family of proteases. We show that these two functions are preferentially carried out by distinct ATG4 proteases, being ATG4D the main delipidating enzyme. In mammalian cells, ATG4D loss results in accumulation of membrane-bound forms of mATG8s, increased cellular autophagosome number and reduced autophagosome average size. In mice, ATG4D loss leads to cerebellar neurodegeneration and impaired motor coordination caused by alterations in trafficking/clustering of GABAA receptors. We also show that human gene variants of ATG4D associated with neurodegeneration are not able to fully restore ATG4D deficiency, highlighting the neuroprotective role of ATG4D in mammals.

Sarcopenia, Diet, Physical Activity and Obesity in European Middle-Aged and Older Adults: The LifeAge Study.

The revised European consensus defined sarcopenia as a progressive and generalized skeletal muscle disorder that is associated with an increased likelihood of adverse outcomes including falls, fractures, physical disability and mortality. The aim of this study was to determine the prevalence of sarcopenia and analyse the influence of diet, physical activity (PA) and obesity index as risk factors of each criteria of sarcopenia. A total of 629 European middle-aged and older adults were enrolled in this cross-sectional study. Anthropometrics were assessed. Self-reported PA and adherence to the Mediterranean diet were evaluated with the Global Physical Activity Questionnaire (GPAQ) and Prevention with Mediterranean Diet questionnaire (PREDIMED), respectively. The functional assessment included handgrip strength, lower body muscle strength, gait speed and agility/dynamic balance. Of the participants, 4.84% to 7.33% showed probable sarcopenia. Sarcopenia was confirmed in 1.16% to 2.93% of participants. Severe sarcopenia was shown by 0.86% to 1.49% of participants. Male; age group ≤65 years; lower body mass index (BMI); high levels of vigorous PA; and the consumption of more than one portion per day of red meat, hamburgers, sausages or cold cuts and/or preferential consumption of rabbit, chicken or turkey instead of beef, pork, hamburgers or sausages (OR = 0.126-0.454; all p < 0.013) resulted as protective factors, and more time of sedentary time (OR = 1.608-2.368; p = 0.032-0.041) resulted as a risk factor for some criteria of sarcopenia. In conclusion, age, diet, PA, and obesity can affect the risk of having low muscle strength, low muscle mass or low functional performance, factors connected with sarcopenia.

Missing data imputation and synthetic data simulation through modeling graphical probabilistic dependencies between variables (ModGraProDep): An application to breast cancer survival.

BACKGROUND: Two common issues may arise in certain population-based breast cancer (BC) survival studies: I) missing values in a survivals' predictive variable, such as "Stage" at diagnosis, and II) small sample size due to "imbalance class problem" in certain subsets of patients, demanding data modeling/simulation methods. METHODS: We present a procedure, ModGraProDep, based on graphical modeling (GM) of a dataset to overcome these two issues. The performance of the models derived from ModGraProDep is compared with a set of frequently used classification and machine learning algorithms (Missing Data Problem) and with oversampling algorithms (Synthetic Data Simulation). For the Missing Data Problem we assessed two scenarios: missing completely at random (MCAR) and missing not at random (MNAR). Two validated BC datasets provided by the cancer registries of Girona and Tarragona (northeastern Spain) were used. RESULTS: In both MCAR and MNAR scenarios all models showed poorer prediction performance compared to three GM models: the saturated one (GM.SAT) and two with penalty factors on the partial likelihood (GM.K1 and GM.TEST). However, GM.SAT predictions could lead to non-reliable conclusions in BC survival analysis. Simulation of a "synthetic" dataset derived from GM.SAT could be the worst strategy, but the use of the remaining GMs models could be better than oversampling. CONCLUSION: Our results suggest the use of the GM-procedure presented for one-variable imputation/prediction of missing data and for simulating "synthetic" BC survival datasets. The "synthetic" datasets derived from GMs could be also used in clinical applications of cancer survival data such as predictive risk analysis.

Autophagy couteracts weight gain, lipotoxicity and pancreatic ß-cell death upon hypercaloric pro-diabetic regimens.

In the last years, autophagy has been revealed as an essential pathway for multiple biological processes and physiological functions. As a catabolic route, autophagy regulation by nutrient availability has been evolutionarily conserved from yeast to mammals. On one hand, autophagy induction by starvation is associated with a significant loss in body weight in mice. Here, we demonstrate that both genetic and pharmacological inhibition of the autophagy process compromise weight loss induced by starvation. Moreover, autophagic potential also impacts on weight gain induced by distinct hypercaloric regimens. Atg4b-deficient mice, which show limited autophagic competence, exhibit a major increase in body weight in response to distinct obesity-associated metabolic challenges. This response is characterized by the presence of larger adipocytes in visceral fat tissue, increased hepatic steatosis, as well as reduced glucose tolerance and attenuated insulin responses. Similarly, autophagy-deficient mice are more vulnerable to experimentally induced type-I diabetes, showing an increased susceptibility to acute streptozotocin administration. Notably, pharmacological stimulation of autophagy in wild-type mice by spermidine reduced both weight gain and obesity-associated alterations upon hypercaloric regimens. Altogether, these results indicate that systemic autophagic activity influences the resilience of the organism to weight gain induced by high-calorie diets, as well as to the obesity-associated features of both type-1 and type-2 diabetes.

Mass Spectrometry in Pharmacokinetic Studies of a Synthetic Compound for Spinal Cord Injury Treatment.

The studies of drugs that could constitute a palliative to spinal cord injury (SCI) are a continuous and increasing demand in biomedicine field from developed societies. Recently we described the chemical synthesis and antiglioma activity of synthetic glycosides. A synthetic sulfated glycolipid (here IG20) has shown chemical stability, solubility in polar solvents, and high inhibitory capacity over glioma growth. We have used mass spectrometry (MS) to monitor IG20 (m/z = 550.3) in cells and tissues of the central nervous system (CNS) that are involved in SCI recovery. IG20 was detected by MS in serum and homogenates from CNS tissue of rats, though in the latter a previous deproteinization step was required. The pharmacokinetic parameters of serum clearance at 24 h and half-life at 4 h were determined for synthetic glycoside in the adult rat using MS. A local administration of the drug near of spinal lesion site is proposed.

Does computed tomography prevent inferior alveolar nerve injuries caused by lower third molar removal?

PURPOSE: To verify the utility of computed tomography (CT) in preventing inferior alveolar nerve (IAN) injury owing to lower third molar extraction in close relation to the IAN on orthopantomogram. MATERIALS AND METHODS: A retrospective cohort study design of 150 lower third molar extractions was performed. Patients were divided in 2 groups: the CT group (n = 95) underwent panoramic radiography and mandibular CT and the control group (n = 55) underwent only panoramic radiography. RESULTS: Six extractions (4%) in the control group and 15 (10%) in the CT group resulted in IAN impairment (P > .05). Logistic regression models did not show that undergoing CT decreased the risk of IAN injury from lower third molar extraction. CONCLUSIONS: Patient age and positive radiographic signs (darkening of the root and narrowing of the inferior alveolar canal) were associated with more requests for CT scanning. CT does not seem to significantly decrease the risk of producing IAN injury.

Severe foetal hypertrophic cardiomyopathy evolving to left ventricular non-compaction.

A 29-week-old male foetus was diagnosed by foetal echocardiography with severe hypertrophic cardiomyopathy with systolic dysfunction and generalized oedema, undergoing a Caesarean section at 33 weeks. Mechanical ventilation and milrinone infusion were required during the first week. Systolic function and output parameters improved progressively. Metabolic and infectious screenings were negative. At the follow-up, during the first year of life, hypertrophy regressed, posterior right auricular hypertrophy evolved to a mass with cysts, and left ventricular myocardium developed trabeculations accomplishing non-compaction criteria. Recently, mutations in genes previously implicated in the pathogenesis of hypertrophic cardiomyopathy have been identified in patients with left ventricular non-compaction without hypertrophy. This report suggests that these cardiomyopathies may have a similar genetic origin, and can co-exist in the same patient.

Differential expression of H19 and vitamin D3 upregulated protein 1 as a mechanism of the modulatory effects of high virgin olive oil and high corn oil diets on experimental mammary tumours.

Dietary lipids have a role in the aetiology of breast cancer. We have reported earlier that a high corn oil diet downregulates H19 and vitamin D3 upregulated protein 1 (VDUP1) messenger RNA (mRNA) expression in rat dimethylbenz (alpha) anthracene-induced mammary adenocarcinomas in comparison with the control low-fat diet, this effect being associated with a higher degree of tumour malignancy. This result was compatible with the stimulating effect of this diet. In this study we have investigated the influence of a high extra virgin olive diet on H19 and VDUP1 mRNA and/or protein expression. We have shown earlier that this high-fat diet confers to the tumours a more benign phenotype in accordance with its potential protective effect on mammary cancer. We have also analysed the effects on the mRNA and protein expression of insulin-like growth factor-2 , in close relation with H19, and the expression and activity of the thioredoxin protein, negatively regulated by VDUP1. mRNA and protein expression were analysed by chemiluminescent northern blot and western blot, respectively. Thioredoxin activity was determined by the insulin-reducing assay. The results showed that the high olive oil diet does not change the tumour expression of H19 and VDUP1. Moreover, tumours from the animals fed this diet displayed higher levels of the insulin-like growth factor-2 mRNAs, which are related to a higher rate of degradation or a lower traducibility. Finally, tumour expression and activity levels of thioredoxin-1 protein did not change irrespective of the diet. These results suggest that the differential effects of high olive oil and high corn oil diets on mammary cancer are exerted by means of a different, specific influence on gene expression.

High corn oil and high extra virgin olive oil diets have different effects on the expression of differentiation-related genes in experimental mammary tumors.

Dietary lipids can modify the clinical behavior and morphological features of experimental breast tumors. We previously demonstrated that a high corn oil diet has a tumor-enhancing effect in 7,12-dimethylbenz(alpha)anthracene (DMBA)-induced rat mammary adenocarcinomas, whereas a high olive oil diet acts as a negative modulator of carcinogenesis. In this study, we investigated whether these high fat diets modulate the expression of genes related to differentiation. Rats were induced with DMBA and fed a low fat diet, a high corn oil diet, a high olive oil diet, or both high fat diets. The expression levels of the mammary differentiation biomarkers alpha-casein, beta-casein and transferrin and of beta-actin and its transporter zipcode binding protein 1 (ZBP1) were analyzed by Northern and/or Western blot in the mammary adenocarcinomas. The high fat diets did not induce changes in the expression of caseins, while transferrin expression was increased as a result of the high olive oil diet. beta-actin mRNA levels were higher in the high fat diet groups, though no changes in the protein levels were observed. The expression of ZBP1, a protein reported as having a role in carcinogenesis, was significantly increased by the high corn oil diet. These results suggest that in this model caseins are not good biomarkers of the changes in tumor morphological differentiation conferred by the high fat diets. The modulation of transferrin and ZBP1 expression by the high olive oil and the high corn oil diets could be one of the mechanisms by which such diets have a different influence on mammary carcinogenesis.

Identification of novel differentially expressed genes by the effect of a high-fat n-6 diet in experimental breast cancer.

In previous studies, we demonstrated that high corn oil diets promote the development of 7,12-dimethylbenz(alpha)anthracene (DMBA)-induced mammary tumors. In this study, we have investigated whether modulation of gene expression is one of the mechanisms by which this high-fat diet exerts such effects. Female Sprague-Dawley rats were induced with DMBA and fed normolipidic (3% corn oil) or high-fat (20% corn oil) diet. Screening of genes differentially expressed in adenocarcinomas from the high corn oil diet group compared to the control diet group was performed with cDNA microarrays. The resulting six upregulated and nine downregulated genes were validated by Northern blot and/or reverse transcription (RT)-polymerase chain reaction (PCR). Further investigation in a higher number of adenocarcinomas showed that in the high-fat n-6 diet group, where the tumor phenotype was verified to be more aggressive, the expression of submaxillary gland alpha-2u globulin, vitamin D(3)-upregulated protein 1 (VDUP1), H19, and the unknown function gene that codifies the expressed sequence tag (EST)-Rn.32385 was significantly decreased in comparison with the control group (C). These results, together with the fact that VDUP1, H19, and this globulin have been associated with cell proliferation and differentiation, open a new line of research about how the underexpression of these genes contributes to the stimulating effect of a high corn oil diet on experimental mammary carcinogenesis.

Modulation of EGFR and neu expression by n-6 and n-9 high-fat diets in experimental mammary adenocarcinomas.

In this study we have investigated the influence of dietary mono- and polyunsaturated lipids on 7,12-dimethylbenz(alpha)anthracene (DMBA)-induced mammary tumorigenesis, and the modulation of expression of c-erbB1/EGFR and c-erbB2/neu as a mechanism of this influence. Two series of Sprague-Dawley rats were given a single dose of DMBA. Animals from Series 1 were fed a semi-synthetic low-fat or high-fat corn oil diet, following an initiation-promotion experimental design. Rats from Series 2 were fed low-fat or different high-fat diets (rich in corn oil or rich in olive oil) in the promotion stage of mammary carcinogenesis. High corn oil diet showed clearly a stimulatory effect on experimental breast carcinogenesis, suggesting a role of this kind of lipids on initiation and promotion of mammary tumorigenesis. Moreover, results suggested that olive oil acts as a negative modulator of the experimental breast cancer. On the other hand, two transcripts of EGFR and one neu mRNA were detected by chemiluminescent Northern blot in mammary adenocarcinomas. Analysis of data showed the tendency that high-fat corn oil diet decreases the 2.7 kb mRNA of EGFR, encoding a truncated form of the receptor with no enzimatic activity. High-fat olive oil diet increased EGFR mRNA levels, specially those from 2.7 kb, and decreased the relative abundance of neu mRNA. These data suggest that the modulating effect of dietary lipids on mammary carcinogenesis could result in changes of EGFR and neu mRNA, leading to an increase of EGFR activity by high-fat corn oil diet and a decrease of EGFR and Neu signal transduction pathway by high-fat olive oil diet.