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1.
RNA ; 2024 May 22.
Article in English | MEDLINE | ID: mdl-38777382

ABSTRACT

The long noncoding RNA TERRA is transcribed from telomeres in virtually all eukaryotes with linear chromosomes. In humans, TERRA transcription is driven in part by promoters comprising CpG dinucleotide-rich repeats of 29 base pairs (29 bp repeats), believed to be present in half of the subtelomeres. Thus far, TERRA expression has been analyzed mainly using molecular biology-based approaches that only generate partial and somehow biased results. Here, we present a novel experimental pipeline to study human TERRA based on long read sequencing (TERRA ONTseq). By applying TERRA ONTseq to different cell lines, we show that the vast majority of human telomeres produce TERRA and that the cellular levels of TERRA transcripts varies according to their chromosomes of origin. Using TERRA ONTseq, we also identified regions containing TERRA transcription start sites (TSSs) in more than half of human subtelomeres. TERRA TSS regions are generally found immediately downstream of 29 bp repeat-related sequences, which appear to be more widespread than previously estimated. Finally, we isolated a novel TERRA promoter from the highly expressed subtelomere of the long arm of chromosome 7. With the development of TERRA ONTseq, we provide a refined picture of human TERRA biogenesis and expression and we equip the scientific community with an invaluable tool for future studies.

2.
Small ; 20(28): e2311526, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38396215

ABSTRACT

Counterfeit products and data vulnerability present significant challenges in contemporary society. Hence, various methods and technologies are explored for anticounterfeiting encoding, with luminescent tracers, particularly luminescent carbon dots (CDs), emerging as a notable solution. CDs offer promising contributions to product security, environmental sustainability, and the circular economy. This critical review aims to highlight the luminescence responsiveness of CDs to physical and chemical stimuli, achieved through nanoengineering their chemical structure. The discussion will delve into the various tunable luminescence mechanisms and decay times of CDs, investigating preferential excitations such as up-conversion, delayed fluorescence, fluorescence, room temperature phosphorescence, persistent luminescence, energy and charge transfer, as well as photo-chemical interactions. These insights are crucial for advancing anticounterfeiting solutions. Following this exploration, a systematic review will focus on the research of luminescent CDs' smart encoding applications, encompassing anticounterfeiting, product tracing, quality certification, and information encryption. Finally, the review will address key challenges in implementing CDs-based technology, providing specific insights into strategies aimed at maximizing their stability and efficacy in anticounterfeiting encoding applications.

3.
Article in English | MEDLINE | ID: mdl-38648778

ABSTRACT

OBJECTIVES: To compare proliferative (PLN) and membranous (MLN) lupus nephritis (LN) regarding clinical and laboratory presentation and long-term outcomes; To investigate predictors of progression to chronic kidney disease (CKD). METHODS: Multicentre observational study, with retrospective analysis of a prospective cohort, using data from the Rheumatic Diseases Portuguese Registry-Reuma.pt. Patients with biopsy-proven PLN, MLN and mixed LN were included. Cox regression survival analysis was used to investigate predictors of CKD. RESULTS: 260 patients were included. Median follow-up was 8 years (IQR 11; minimum 1, maximum 35 years). MLN patients presented with significantly lower serum creatinine (0.70 (IQR 0.20; minimum 0.50, maximum 1.30) mg/dl vs 0.80 (IQR 0.31; minimum 0.26, maximum 2.60) in PLN, p= 0.003). Proteinuria levels did not differ between groups (p= 0.641). Levels of complement were reduced in PLN but nearly normal in MLN patients, and there were fewer patients with positive anti-dsDNA antibodies in the MLN group (p< 0.001). One year after the beginning of treatment, 62% of the patients achieved EULAR/ERA-EDTA complete response, with further 5% achieving partial response. Patients with lower proteinuria at diagnosis were more likely to achieve a complete renal response at one year, however, proteinuria at diagnosis or at one year did not predict long term CKD. Estimated glomerular filtration rate (eGFR) ≤75 mL/min/1.73 m2 at one year was the strongest predictor of progression to CKD (HR 23 [95% CI 8-62], p< 0.001). Other possible predictors included the use of azathioprine for induction of remission, older age at diagnosis and male sex. CONCLUSION: Proteinuria levels did not predict LN histologic class in our cohort. eGFR cutoff of 75 mL/min/1.73 m2 after one year of treatment was strongly predictive of progression to CKD.

4.
Haematologica ; 109(4): 1171-1183, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-37646663

ABSTRACT

The transcription factor MYC is a well-described oncogene with an important role in lymphomagenesis, but its significance for clinical outcome in mantle cell lymphoma (MCL) remains to be determined. We performed an investigation of the expression of MYC protein in a cohort of 251 MCL patients complemented by analyses of structural aberrations and mRNA, in a sub-cohort of patients. Fourteen percent (n=35) of patients showed high MYC protein expression with >20% positive cells (MYChigh), among whom only one translocation was identified, and 86% (n=216) of patients showed low MYC protein expression. Low copy number gains of MYC were detected in ten patients, but with no correlation to MYC protein levels. However, MYC mRNA levels correlated significantly to MYC protein levels with a R2 value of 0.76. Patients with a MYChigh tumor had both an independent inferior overall survival and an inferior progression-free survival (hazard ratio [HR]=2.03, 95% confidence interval [95% CI]: 1.2-3.4 and HR=2.2, 95% CI: 1.04-4.6, respectively) when adjusted for additional high-risk features. Patients with MYChigh tumors also tended to have additional high-risk features and to be older at diagnosis. A subgroup of 13 patients had concomitant MYChigh expression and TP53/p53 alterations and a substantially increased risk of progression (HR=16.9, 95% CI: 7.4-38.3) and death (HR=7.8, 95% CI: 4.4-14.1) with an average overall survival of only 0.9 years. In summary, we found that at diagnosis a subset of MCL patients (14%) overexpressed MYC protein, and had a poor prognosis but that MYC rearrangements were rare. Tumors with concurrent MYC overexpression and TP53/p53 alterations pinpointed MCL patients with a dismal prognosis with a median overall survival of less than 3 years. We propose that MYC needs to be assessed beyond the current high-risk factors in MCL in order to identify cases in need of alternative treatment.


Subject(s)
Lymphoma, Mantle-Cell , Adult , Humans , Cell Proliferation , Lymphoma, Mantle-Cell/diagnosis , Lymphoma, Mantle-Cell/genetics , Prognosis , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , RNA, Messenger , Translocation, Genetic , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
5.
Cell Mol Life Sci ; 80(11): 342, 2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37904059

ABSTRACT

Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.


Subject(s)
Arsenic , Metalloids , Neurodegenerative Diseases , Humans , Arsenic/toxicity , Antimony/toxicity , Neurodegenerative Diseases/chemically induced , DNA Damage
6.
J Biol Chem ; 298(12): 102680, 2022 12.
Article in English | MEDLINE | ID: mdl-36356902

ABSTRACT

The poisonous metalloid arsenite induces widespread misfolding and aggregation of nascent proteins in vivo, and this mode of toxic action might underlie its suspected role in the pathology of certain protein misfolding diseases. Evolutionarily conserved protein quality-control systems protect cells against arsenite-mediated proteotoxicity, and herein, we systematically assessed the contribution of the ubiquitin-proteasome system, the autophagy-vacuole pathway, and chaperone-mediated disaggregation to the clearance of arsenite-induced protein aggregates in Saccharomyces cerevisiae. We show that the ubiquitin-proteasome system is the main pathway that clears aggregates formed during arsenite stress and that cells depend on this pathway for optimal growth. The autophagy-vacuole pathway and chaperone-mediated disaggregation both contribute to clearance, but their roles appear less prominent than the ubiquitin-proteasome system. Our in vitro assays with purified components of the yeast disaggregating machinery demonstrated that chaperone binding to aggregates formed in the presence of arsenite is impaired. Hsp104 and Hsp70 chaperone activity was unaffected by arsenite, suggesting that this metalloid influences aggregate structure, making them less accessible for chaperone-mediated disaggregation. We further show that the defect in chaperone-mediated refolding of a model protein was abrogated in a cysteine-free version of the substrate, suggesting that arsenite directly modifies cysteines in non-native target proteins. In conclusion, our study sheds novel light on the differential contributions of protein quality-control systems to aggregate clearance and cell proliferation and extends our understanding of how these systems operate during arsenite stress.


Subject(s)
Arsenites , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/metabolism , Proteasome Endopeptidase Complex/metabolism , Protein Aggregates , Arsenites/pharmacology , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Molecular Chaperones/metabolism , HSP70 Heat-Shock Proteins/metabolism , Ubiquitin/metabolism , Autophagy , Heat-Shock Proteins/metabolism
7.
J Cell Sci ; 134(11)2021 06 01.
Article in English | MEDLINE | ID: mdl-34085697

ABSTRACT

The toxic metalloid arsenic causes widespread misfolding and aggregation of cellular proteins. How these protein aggregates are formed in vivo, the mechanisms by which they affect cells and how cells prevent their accumulation is not fully understood. To find components involved in these processes, we performed a genome-wide imaging screen and identified Saccharomyces cerevisiae deletion mutants with either enhanced or reduced protein aggregation levels during arsenite exposure. We show that many of the identified factors are crucial to safeguard protein homeostasis (proteostasis) and to protect cells against arsenite toxicity. The hits were enriched for various functions including protein biosynthesis and transcription, and dedicated follow-up experiments highlight the importance of accurate transcriptional and translational control for mitigating protein aggregation and toxicity during arsenite stress. Some of the hits are associated with pathological conditions, suggesting that arsenite-induced protein aggregation may affect disease processes. The broad network of cellular systems that impinge on proteostasis during arsenic stress identified in this current study provides a valuable resource and a framework for further elucidation of the mechanistic details of metalloid toxicity and pathogenesis. This article has an associated First Person interview with the first authors of the paper.


Subject(s)
Arsenic , Arsenites , Saccharomyces cerevisiae Proteins , Arsenites/toxicity , Protein Aggregates , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics
8.
Development ; 147(3)2020 02 04.
Article in English | MEDLINE | ID: mdl-31969325

ABSTRACT

Axon ensheathment is fundamental for fast impulse conduction and the normal physiological functioning of the nervous system. Defects in axonal insulation lead to debilitating conditions, but, despite its importance, the molecular players responsible are poorly defined. Here, we identify RalA GTPase as a key player in axon ensheathment in Drosophila larval peripheral nerves. We demonstrate through genetic analysis that RalA action through the exocyst complex is required in wrapping glial cells to regulate their growth and development. We suggest that the RalA-exocyst pathway controls the targeting of secretory vesicles for membrane growth or for the secretion of a wrapping glia-derived factor that itself regulates growth. In summary, our findings provide a new molecular understanding of the process by which axons are ensheathed in vivo, a process that is crucial for normal neuronal function.


Subject(s)
Axons/metabolism , Drosophila Proteins/metabolism , Drosophila melanogaster/metabolism , Monomeric GTP-Binding Proteins/metabolism , Myelin Sheath/metabolism , Peripheral Nerves/metabolism , Vesicular Transport Proteins/metabolism , Animals , Animals, Genetically Modified , Axon Fasciculation/genetics , Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Larva/metabolism , Locomotion/genetics , Monomeric GTP-Binding Proteins/genetics , Mutation , Neuroglia/metabolism , RNA Interference
9.
Haematologica ; 108(4): 1092-1104, 2023 04 01.
Article in English | MEDLINE | ID: mdl-36519324

ABSTRACT

The variable outcome to standard immunochemotherapy for mantle cell lymphoma (MCL) patients is a clinical challenge. Established risk factors, including high MCL International Prognostic Index (MIPI), high proliferation (Ki-67), non-classic (blastoid/pleomorphic) morphology, and mutated TP53, only partly identify patients in need of alternative treatment. Deepened understanding of biological factors that influence time to progression and relapse would allow for an improved stratification, and identification of novel targets for high-risk patients. We performed gene expression analyses to identify pathways and genes associated with outcome in a cohort of homogeneously treated patients. In addition to deregulated proliferation, we show that thermogenesis, fatty acid degradation and oxidative phosphorylation are altered in patients with poor survival, and that high expression of carnitine palmitoyltransferase 1A (CPT1A), an enzyme involved in fatty acid degradation, can specifically identify high-risk patients independent of the established high-risk factors. We suggest that complementary investigations of metabolism may increase the accuracy of patient stratification and that immunohistochemistry- based assessment of CPT1A can contribute to defining high-risk MCL.


Subject(s)
Lymphoma, Mantle-Cell , Adult , Humans , Lymphoma, Mantle-Cell/drug therapy , Lymphoma, Mantle-Cell/genetics , Carnitine O-Palmitoyltransferase/genetics , Risk Assessment , Prognosis , Neoplasm Recurrence, Local , Immunologic Factors/therapeutic use , Fatty Acids/therapeutic use
10.
J Clin Rheumatol ; 29(4): e32-e39, 2023 Jun 01.
Article in English | MEDLINE | ID: mdl-36870085

ABSTRACT

BACKGROUND: In systemic sclerosis (SSc), high-resolution computed tomography (HRCT) of the chest is the standard criterion for the diagnosis of interstitial lung disease (ILD). However, recent evidence suggests that lung ultrasound (LUS) can also detect ILD, without radiation exposure. Thus, our goal was to perform a systematic review, aiming to clarify the role of LUS in the detection of ILD in SSc. METHODS: A systematic review was carried out in PubMed and EMBASE (PROSPERO register number CRD42022293132), to identify studies that compared LUS with HRCT in the detection of ILD in patients with SSc. Risk of bias was assessed with the QUADAS-2 () tool. RESULTS: Three hundred seventy-five publications were identified. After screening, 13 were included in the final analysis. No study presented high risk of bias. Lung ultrasound protocol was highly heterogeneous between authors, specifically concerning transducer, intercostal spaces evaluated, exclusion criteria, and definition of positive LUS. Most authors evaluated the presence of B-lines as a surrogate of ILD, with only 4 focusing on pleural changes. A positive correlation between LUS findings and ILD detected by HRCT was reported. Results also revealed high sensitivity (74.3%-100%) but variable specificity (16%-99%). Positive predictive value varied between 16% and 95.1%, and negative predictive value between 51.7% and 100%. CONCLUSION: Lung ultrasound is sensitive in the detection of ILD, but specificity must be optimized. The value of pleural evaluation also requires further investigation. Moreover, a consensus is needed to define a uniform LUS protocol to implement in future investigations.


Subject(s)
Lung Diseases, Interstitial , Scleroderma, Systemic , Humans , Lung/diagnostic imaging , Lung Diseases, Interstitial/diagnostic imaging , Lung Diseases, Interstitial/etiology , Tomography, X-Ray Computed/methods , Predictive Value of Tests , Scleroderma, Systemic/diagnostic imaging
11.
PLoS Comput Biol ; 17(3): e1008704, 2021 03.
Article in English | MEDLINE | ID: mdl-33684125

ABSTRACT

Acrylic acid is a value-added chemical used in industry to produce diapers, coatings, paints, and adhesives, among many others. Due to its economic importance, there is currently a need for new and sustainable ways to synthesise it. Recently, the focus has been laid in the use of Escherichia coli to express the full bio-based pathway using 3-hydroxypropionate as an intermediary through three distinct pathways (glycerol, malonyl-CoA, and ß-alanine). Hence, the goals of this work were to use COPASI software to assess which of the three pathways has a higher potential for industrial-scale production, from either glucose or glycerol, and identify potential targets to improve the biosynthetic pathways yields. When compared to the available literature, the models developed during this work successfully predict the production of 3-hydroxypropionate, using glycerol as carbon source in the glycerol pathway, and using glucose as a carbon source in the malonyl-CoA and ß-alanine pathways. Finally, this work allowed to identify four potential over-expression targets (glycerol-3-phosphate dehydrogenase (G3pD), acetyl-CoA carboxylase (AccC), aspartate aminotransferase (AspAT), and aspartate carboxylase (AspC)) that should, theoretically, result in higher AA yields.


Subject(s)
Acrylates/metabolism , Carbon/metabolism , Escherichia coli/metabolism , Models, Biological , Biosynthetic Pathways , Glucose/metabolism , Glycerol/metabolism , Lactic Acid/analogs & derivatives , Lactic Acid/metabolism , Metabolic Engineering
12.
Appl Microbiol Biotechnol ; 106(12): 4617-4626, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35739346

ABSTRACT

Zymomonas mobilis ZM4 is an attractive host for the development of microbial cell factories to synthesize high-value compounds, including prebiotics. In this study, a straightforward process to produce fructooligosaccharides (FOS) from sucrose was established. To control the relative FOS composition, recombinant Z. mobilis strains secreting a native levansucrase (encoded by sacB) or a mutated ß-fructofuranosidase (Ffase-Leu196) from Schwanniomyces occidentalis were constructed. Both strains were able to produce a FOS mixture with high concentration of 6-kestose. The best results were obtained with Z. mobilis ZM4 pB1-sacB that was able to produce 73.4 ± 1.6 g L-1 of FOS, with a productivity of 1.53 ± 0.03 g L-1 h-1 and a yield of 0.31 ± 0.03 gFOS gsucrose-1. This is the first report on the FOS production using a mutant Z. mobilis ZM4 strain in a one-step process. KEY POINTS: • Zymomonas mobilis was engineered to produce FOS in a one-step fermentation process. • Mutant strains produced FOS mixtures with high concentration of 6-kestose. • A new route to produce tailor-made FOS mixtures was presented.


Subject(s)
Zymomonas , Ethanol , Fermentation , Oligosaccharides , Sucrose , Zymomonas/genetics
13.
Molecules ; 27(21)2022 Oct 25.
Article in English | MEDLINE | ID: mdl-36364054

ABSTRACT

Coumarins and furanocoumarins are plant secondary metabolites with known biological activities. As they are present in low amounts in plants, their heterologous production emerged as a more sustainable and efficient approach to plant extraction. Although coumarins biosynthesis has been positively established, furanocoumarin biosynthesis has been far more challenging. This study aims to evaluate if Escherichia coli could be a suitable host for furanocoumarin biosynthesis. The biosynthetic pathway for coumarins biosynthesis in E. coli was effectively constructed, leading to the production of umbelliferone, esculetin and scopoletin (128.7, 17.6, and 15.7 µM, respectively, from tyrosine). However, it was not possible to complete the pathway with the enzymes that ultimately lead to furanocoumarins production. Prenyltransferase, psoralen synthase, and marmesin synthase did not show any activity when expressed in E. coli. Several strategies were tested to improve the enzymes solubility and activity with no success, including removing potential N-terminal transit peptides and expression of cytochrome P450 reductases, chaperones and/or enzymes to increase dimethylallylpyrophosphate availability. Considering the results herein obtained, E. coli does not seem to be an appropriate host to express these enzymes. However, new alternative microbial enzymes may be a suitable option for reconstituting the furanocoumarins pathway in E. coli. Nevertheless, until further microbial enzymes are identified, Saccharomyces cerevisiae may be considered a preferred host as it has already been proven to successfully express some of these plant enzymes.


Subject(s)
Furocoumarins , Furocoumarins/chemistry , Escherichia coli/metabolism , Coumarins/metabolism , Scopoletin/metabolism , Plants/metabolism
14.
Molecules ; 27(16)2022 Aug 15.
Article in English | MEDLINE | ID: mdl-36014439

ABSTRACT

Ensuring a sustainable supply of food for the world's fast growing population is a major challenge in today's economy, as modern lifestyle and increasing consumer concern with maintaining a balanced and nutritious diet is an important challenge for the agricultural sector worldwide. This market niche for healthier products, especially fruits and vegetables, has increased their production, consequently resulting in increased amounts of agri-food surplus, waste, and loss (SWL) generated during crop production, transportation, storage, and processing. Although many of these materials are not utilized, negatively affecting the environmental, economic, and social segments, they are a rich source of valuable compounds that could be used for different purposes, thus preventing the losses of natural resources and boosting a circular economy. This review aimed to give insights on the efficient management of agri-food SWL, considering conventional and emerging recovery and reuse techniques. Particularly, we explored and summarized the chemical composition of three worldwide cultivated and consumed vegetables (carrots, broccoli and lettuce) and evaluate the potential of their residues as a sustainable alternative for extracting value-added ingredients for the development of new biodynamic products.


Subject(s)
Fruit , Vegetables , Agriculture , Crop Production , Diet , Fruit/chemistry
15.
Nat Prod Rep ; 38(5): 869-879, 2021 05 26.
Article in English | MEDLINE | ID: mdl-33174568

ABSTRACT

Covering: up to October 2020 Furanocoumarins are plant secondary metabolites used to treat several skin disorders, such as psoriasis and vitiligo, and also with other potential therapeutic activities. Furanocoumarins are extracted from plants where they accumulate in low amounts over long growth periods. In addition, their extraction and purification are difficult in an environmentally unfriendly and expensive process. Hence, new sustainable and greener production schemes able to overcome such limitations ought to be developed. While the heterologous production of simple coumarins has been demonstrated, the biosynthesis of more complex furanocoumarins remains greatly unexplored. Although several important steps of the pathway have been elucidated in the last decade, the complete pathway has not been completely unravelled. In this paper, we review the natural conversion of amino acids into furanocoumarins, as well as the heterologous expression of each enzyme of the pathway. We also explore the challenges that need to be addressed so that their heterologous production can become a viable alternative.


Subject(s)
Furocoumarins/biosynthesis , Plants/metabolism , Molecular Structure , Phytochemicals/biosynthesis , Secondary Metabolism
16.
Br J Haematol ; 193(3): 520-531, 2021 05.
Article in English | MEDLINE | ID: mdl-33686666

ABSTRACT

We characterised patients with mantle cell lymphoma (MCL) with poor prognosis based on differences in immune infiltration. Different expressions of the tumour cell markers Cyclin D1 and sex-determining region Y-box transcription factor 11 (SOX11), and the immune markers cluster of differentiation 3 (CD3), CD4, CD8, CD25, forkhead box protein P3 (FoxP3), T-box transcription factor TBX21 (T-bet), programmed cell death protein 1 (PD-1), programmed-death ligand 1 (PD-L1) and CD163 were investigated for all-cause mortality in 282 patients with MCL and time-to-progression (TTP) in 106 clinical trial patients. With increasing age, a significantly lower infiltration of CD3+ T lymphocytes was seen. T-cell infiltration was independent of cellular tumour antigen p53 (p53) expression, Ki-67, morphology and frequency of tumour cells. The all-cause mortality was higher in patients with PD-L1-expression above cut-off [hazard ratio (HR) 1·97, 95% confidence interval (CI) 1·18-3·25, adjusted for sex and MCL International Prognostic Index (MIPI)] and a higher frequency of CD163+ cells (continuously, HR 1·51, 95% CI 1·03-2·23, adjusting for age, sex, morphology, Ki-67 and p53). In patients treated within the Nordic Lymphoma Group MCL2/3 trials, TTP was shorter in patients with a higher frequency of FoxP3+ cells (HR 3·22, 95% CI 1·40-7·43) and CD163+ cells (HR 6·09, 95% CI 1·84-20·21), independent of sex and MIPI. When combined a higher frequency of CD163+ macrophages and PD-L1+ cells or high CD163+ macrophages and FoxP3+ regulatory T cells indicated worse outcome independent of established risk factors. The T-cell infiltrate was in turn independent of molecular characteristics of the malignant cells and decreased with age.


Subject(s)
Aging/metabolism , Antigens, CD/biosynthesis , Antigens, Differentiation, Myelomonocytic/biosynthesis , B7-H1 Antigen/biosynthesis , Forkhead Transcription Factors/biosynthesis , Lymphoma, Mantle-Cell , Neoplasm Proteins/biosynthesis , Receptors, Cell Surface/biosynthesis , Aged , Female , Humans , Lymphoma, Mantle-Cell/metabolism , Lymphoma, Mantle-Cell/mortality , Male , Middle Aged , Risk Factors
17.
Biochem Soc Trans ; 49(2): 843-854, 2021 04 30.
Article in English | MEDLINE | ID: mdl-33704376

ABSTRACT

Aberrant cell surface glycosylation signatures are currently known to actively drive the neoplastic transformation of healthy cells. By disrupting the homeostatic functions of their protein carriers, cancer-associated glycans mechanistically underpin several molecular hallmarks of human malignancy. Furthermore, such aberrant glycan structures play key roles in the acquisition of molecular resistance to targeted therapeutic agents, which compromises their clinical efficacy, by modulating tumour cell aggressiveness and supporting the establishment of an immunosuppressive microenvironment. Recent advances in the study of the tumour cell glycoproteome have unravelled previously elusive molecular mechanisms of therapeutic resistance, guided the rational design of novel personalized therapeutic strategies, and may further improve the clinical performance of currently approved anti-cancer targeted agents. In this review, we highlight the impact of glycosylation in cancer targeted therapy, with particular focus on receptor tyrosine kinase-targeted therapy, immune checkpoints blockade therapy, and current developments on therapeutic strategies directed to glycan-binding proteins and other innovative glycan therapeutic strategies.


Subject(s)
Glycoproteins/metabolism , Neoplasms/metabolism , Polysaccharides/metabolism , Proteome/metabolism , Proteomics/methods , Proteostasis , Animals , Antineoplastic Agents/therapeutic use , Drug Resistance, Neoplasm , Glycosylation , Humans , Neoplasms/drug therapy , Neoplasms/pathology
18.
Appl Microbiol Biotechnol ; 105(23): 8881-8893, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34724083

ABSTRACT

The world economy is currently moving towards more sustainable approaches. Lignocellulosic biomass has been widely used as a substitute for fossil sources since it is considered a low-cost bio-renewable resource due to its abundance and continuous production. Compost habitats presenting high content of lignocellulosic biomass are considered a promising source of robust lignocellulose-degrading enzymes. Recently, several novel biocatalysts from different environments have been identified using metagenomic techniques. A key point of the metagenomics studies is the extraction and purification of nucleic acids. Nevertheless, the isolation of high molecular weight DNA from soil-like samples, such as compost, with the required quality for metagenomic approaches remains technically challenging, mainly due to the complex composition of the samples and the presence of contaminants like humic substances. In this work, a rapid and cost-effective protocol for metagenomic DNA extraction from compost samples composed of lignocellulosic residues and containing high content of humic substances was developed. The metagenomic DNA was considered as representative of the global environment and presented high quality (> 99% of humic acids effectively removed) and sufficient quantity (10.5-13.8 µg g-1 of compost) for downstream applications, namely functional metagenomic studies. The protocol takes about 4 h of bench work, and it can be performed using standard molecular biology equipment and reagents available in the laboratory. KEY POINTS/HIGHLIGHTS: • Metagenomic DNA was successfully extracted from compost samples rich in humic acids • The improved protocol was established by optimizing the cell lysis method and buffer • Complete removal of humic acids was achieved through the use of activated charcoal • The suitability of the DNA was proven by the construction of a metagenomic library.


Subject(s)
Composting , Metagenomics , DNA/genetics , Humic Substances/analysis , Lignin , Soil
19.
Int J Mol Sci ; 22(21)2021 Oct 24.
Article in English | MEDLINE | ID: mdl-34768886

ABSTRACT

Exposure to heavy metals, including arsenic and cadmium, is associated with neurodegenerative disorders such as Parkinson's disease. However, the mechanistic details of how these metals contribute to pathogenesis are not well understood. To search for underlying mechanisms involving α-synuclein, the protein that forms amyloids in Parkinson's disease, we here assessed the effects of arsenic and cadmium on α-synuclein amyloid formation in vitro and in Saccharomyces cerevisiae (budding yeast) cells. Atomic force microscopy experiments with acetylated human α-synuclein demonstrated that amyloid fibers formed in the presence of the metals have a different fiber pitch compared to those formed without metals. Both metal ions become incorporated into the amyloid fibers, and cadmium also accelerated the nucleation step in the amyloid formation process, likely via binding to intermediate species. Fluorescence microscopy analyses of yeast cells expressing fluorescently tagged α-synuclein demonstrated that arsenic and cadmium affected the distribution of α-synuclein aggregates within the cells, reduced aggregate clearance, and aggravated α-synuclein toxicity. Taken together, our in vitro data demonstrate that interactions between these two metals and α-synuclein modulate the resulting amyloid fiber structures, which, in turn, might relate to the observed effects in the yeast cells. Whilst our study advances our understanding of how these metals affect α-synuclein biophysics, further in vitro characterization as well as human cell studies are desired to fully appreciate their role in the progression of Parkinson's disease.


Subject(s)
Metals, Heavy/toxicity , Neurodegenerative Diseases , alpha-Synuclein/metabolism , Amyloid/metabolism , Arsenites/toxicity , Cadmium/toxicity , Cell Line/metabolism , Neurodegenerative Diseases/etiology , Neurodegenerative Diseases/metabolism , Parkinson Disease/etiology , Parkinson Disease/metabolism , Saccharomyces cerevisiae/metabolism , alpha-Synuclein/drug effects
20.
Molecules ; 26(7)2021 Mar 26.
Article in English | MEDLINE | ID: mdl-33810432

ABSTRACT

Ruscus aculeatus L. is a subshrub used in traditional medicine in different parts of the world, namely in Europe and the Iberian Peninsula. According to reported folk knowledge, the aerial parts are mainly used as diuretics and the underground organs are used for the treatment of disorders of the urinary system and as a laxative. In this work, the aerial part and the roots and rhizomes of R. aculeatus were chemically characterized with regard to the content of phenolic compounds and bioactive properties. Aqueous (infusions and decoctions) preparations and hydroethanolic extracts from the two mentioned parts of the plant were prepared. Nine phenolic compounds were detected in all the extracts. Apigenin-C-hexoside-C-pentoside isomer II was the major compound in aqueous extracts and, in the hydroethanolic extract was quercetin-O-deoxyhexoside-hexoside followed by apigenin-C-hexoside-C-pentoside isomer II. All extracts revealed antioxidant activity and potential to inhibit some of the assayed bacteria; aqueous extracts of the aerial part and infusions of roots and rhizomes did not show cytotoxic effects on a non-tumor primary cell culture. This preliminary study provides suggestions of the biological potential associated with the empirical uses and knowledge of this species, in particular its bioactivities.


Subject(s)
Phenols , Plant Components, Aerial , Plant Extracts , Plant Roots , Ruscus/chemistry , Animals , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacology , Antioxidants/chemistry , Antioxidants/pharmacology , Bacteria/drug effects , Cell Line, Tumor , Hepatocytes , Humans , Mice , Phenols/chemistry , Phenols/pharmacology , Plant Components, Aerial/chemistry , Plant Extracts/chemistry , Plant Extracts/pharmacology , Plant Roots/chemistry , Primary Cell Culture , RAW 264.7 Cells , Sheep , Swine
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