Modulation of tumor plasticity by senescent cells: Deciphering basic mechanisms and survival pathways to unravel therapeutic options.

Senescence is a cellular state in which the cell loses its proliferative capacity, often irreversibly. Physiologically, it occurs due to a limited capacity of cell division associated with telomere shortening, the so-called replicative senescence. It can also be induced early due to DNA damage, oncogenic activation, oxidative stress, or damage to other cellular components (collectively named induced senescence). Tumor cells acquire the ability to bypass replicative senescence, thus ensuring the replicative immortality, a hallmark of cancer. Many anti-cancer therapies, however, can lead tumor cells to induced senescence. Initially, this response leads to a slowdown in tumor growth. However, the longstanding accumulation of senescent cells (SnCs) in tumors can promote neoplastic progression due to the enrichment of numerous molecules and extracellular vesicles that constitutes the senescence-associated secretory phenotype (SASP). Among other effects, SASP can potentiate or unlock the tumor plasticity and phenotypic transitions, another hallmark of cancer. This review discusses how SnCs can fuel mechanisms that underlie cancer plasticity, like cell differentiation, stemness, reprogramming, and epithelial-mesenchymal transition. We also discuss the main molecular mechanisms that make SnCs resistant to cell death, and potential strategies to target SnCs. At the end, we raise open questions and clinically relevant perspectives in the field.

Exposure to coal mining can lead to imbalanced levels of inorganic elements and DNA damage in individuals living near open-pit mining sites.

Coal mining activities are considered harmful to living organisms. These activities release compounds to the environment, such as polycyclic aromatic hydrocarbons (PAHs), metals, and oxides, which can cause oxidative damage to DNA. In this study, we compared the DNA damage and the chemical composition of peripherical blood of 150 individuals exposed to coal mining residues and 120 non-exposed individuals. Analysis of coal particles revealed the presence of elements such as copper (Cu), aluminum (Al), chrome (Cr), silicon (Si) and iron (Fe). The exposed individuals in our study had significant concentrations of Al, sulfur (S), Cr, Fe, and Cu in their blood, as well as hypokalemia. Results from the enzyme-modified comet assay (FPG enzyme) suggest that exposure to coal mining residues caused oxidative DNA damage, particularly purine damage. Furthermore, particles with a diameter of <2.5 µm indicate that direct inhalation could promote these physiological alterations. Finally, a systems biology analysis was performed to investigate the effects of these elements on DNA damage and oxidative stress pathways. Interestingly, Cu, Cr, Fe, and K are key nodes that intensely modulate these pathways. Our results suggest that understanding the imbalance of inorganic elements caused by exposure to coal mining residues is crucial to understanding their effect on human health.

Influence of smoking on oral cells genotoxicity after at-home bleaching using 22% carbamide peroxide: a cohort study.

OBJECTIVE: This study evaluated the influence of smoking on the oral cells genotoxicity before and after at-home bleaching using 22% carbamide peroxide (CP). MATERIALS AND METHODS: This is a prospective observational analytics cohort study which evaluated nonsmokers (NS; n = 24) and smokers (S; n = 16) patients. At-home bleaching was performed using 22% CP gel in individual trays for 1 h per day for 14 days in both groups. Scrapped cells from marginal gums were collected before the bleaching treatment (D0-baseline) and 1 day (D1), 15 days (D15), and 1 month (D30) after its finishing. Cells were stained with Giemsa 10%, and the micronucleus (MN) and metanuclear alterations (MA) were counted by a trained operator in 1000 cells per patient. The collections and data analysis occurred blindly. Data was analyzed by Kruskal-Wallis, Dunn, and Mann-Whitney test (α = 0.05). RESULTS: MN frequency was not influenced by smoking or bleaching. An increase of MA was observed between D0 and D30 for both groups (p < 0.001); however, no statistical difference was found between NS and S (p > 0.05) in the evaluation times. CONCLUSION: Smoking associated with 22% carbamide peroxide gel for at-home bleaching does not show genotoxic potential analyzed by the MN counts. However, a significant increase of MA was found for smokers and nonsmokers. CLINICAL RELEVANCE: Despite of the increase in MA, smoking associated with 22% CP peroxide at-home bleaching showed no important genotoxic potential (MN) for oral cells. Therefore, at-home bleaching treatment is safe for nonsmokers and smokers even with a high carbamide peroxide concentration of 22%.

A molecular strategy to optimize bovine tuberculosis post-mortem diagnosis and the exposure to Mycobacterium tuberculosis variant bovis.

Bovine tuberculosis (bTB) is a zoonotic disease caused by Mycobacterium tuberculosis var. bovis, for which the definitive diagnosis is accomplished by bacterial isolation, which has biosafety issues and requires long time. Thus, diagnostic methods with potential to be faster and more efficient can represent an advance in bTB epidemiological knowledge and decrease exposure to M. tuberculosis var. bovis. This study aimed to validate a molecular test for bTB post-mortem diagnosis, as a strategy to reduce waste in bovine production. A total of 185 tissues from animals of infected herds or with suspected lesions at abattoir were evaluated through bacterial isolation, PCR and histopathology. PCR and histopathology showed sensitivities of 45.1% and 71.2%, respectively, and specificities of 83.3% and 83.0%, respectively, when compared to bacterial isolation. The combination of both tests resulted in enhanced specificity and positive predictive values.Therefore, PCR in conjunction with histopathology may be used as screening, in which concordant results can be considered conclusive, and discordant results may be submitted to bacterial isolation.

Novel frameshift variant of the CFTR gene: S511Lfs*2 from phenotype to molecular predictions.

Cystic fibrosis (CF) is a genetic disease caused by variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. There are over 2,000 different pathogenic and non-pathogenic variants described in association with a broad clinical heterogeneity. In this work, we identified a novel variant S511Lfs*2 in CFTR gene that has not been reported in patients with CF. The patient was a female genotyped with c.1000C>T (legacy name: R334W) variant (pathogenic, CF-causing) and the novel variant (S511Lfs*2). We verified the amino acid sequence, the protein structure, and predicted the pathogenicity employing computational analysis. Our findings showed that S511Lfs*2 is a frameshift variant and suggest that it is associated with severe CF phenotype, as it leads to a lack of CFTR protein synthesis, and consequently the loss of its functional activity.

The most relevant chromosomal abnormalities in the north of Rio Grande do Sul, Brazil: 26 years of cytogenetic analysis.

From 1992 to 2018, cytogenetic analyses were successfully performed to explore the chromosomal abnormalities of 729 patients, who utilised a pioneering counselling service in the city of Passo Fundo in the northern part of the Brazilian state of Rio Grande do Sul. This city is characterised by a large conglomerate of private and public hospitals. A classical cytogenetic analysis and G-banding were performed using the patient samples. Although normal karyotypes were observed for 562 of the cases, 167 individuals evidenced chromosomal alterations. Among those, 110 exhibited numerical alterations (65.86%), 41 demonstrated structural modifications (24.55%) and 16 showed both numerical and structural chromosomal changes (9.58%). This study describes the diversity of the chromosomal alterations in this region, which have not been previously examined. After 26 years of study, the findings are discussed herein in a self-critical form.

Analysis of NTPDase2 in the cell membrane using fluorescence recovery after photobleaching (FRAP).

NTPDase2, a member of the CD39/NTPDase family, is an ecto-nucleotidase anchored to the plasma membrane by two transmembrane domains, with a catalytic site facing the extracellular space and preferentially hydrolyzing nucleoside triphosphates. While NTPDase2 is expressed in many cell types, its unique functionality, mobility and dynamics at the cell membrane remain unexplored. We therefore constructed a recombinant NTPDase2 linked to the yellow fluorescent protein (EYFP) to investigate its dynamics by confocal microscopy. The present study shows that the expression of EYFP-NTPDase2 in different cell lines does not affect its proliferation, migration and adhesion to extracellular matrices (ECM). Moreover, in human embryonic kidney cells 293 (HEK293) grown on collagen type I and fibronectin, EYFP-NTPDase2 fluorescence is greater in free plasma membrane regions than in cell-cell contacts, in comparison with cells grown on other substrates. Differences in the time required for fluorescence recovery after photobleaching (FRAP) in free membrane regions and cell-cell contacts indicate that the mobility of EYFP-NTPDase2 depends on the matrix to which the cells are attached. © 2018 International Society for Advancement of Cytometry.

A Low-Cost and Simple Genetic Screening for Cystic Fibrosis Provided by the Brazilian Public Health System.

Cystic fibrosis newborn screening was implemented in Brazil by the Public Health System in 2012. Because of cost, only 1 mutation was tested - p.Phe508del. We developed a robust low-cost genetic test for screening 11 CFTR gene mutations with potential use in developing countries.

Electrical and Thermal Transport in Coplanar Polycrystalline Graphene-hBN Heterostructures.

We present a theoretical study of electronic and thermal transport in polycrystalline heterostructures combining graphene (G) and hexagonal boron nitride (hBN) grains of varying size and distribution. By increasing the hBN grain density from a few percent to 100%, the system evolves from a good conductor to an insulator, with the mobility dropping by orders of magnitude and the sheet resistance reaching the MΩ regime. The Seebeck coefficient is suppressed above 40% mixing, while the thermal conductivity of polycrystalline hBN is found to be on the order of 30-120 Wm-1 K-1. These results, agreeing with available experimental data, provide guidelines for tuning G-hBN properties in the context of two-dimensional materials engineering. In particular, while we proved that both electrical and thermal properties are largely affected by morphological features (e.g., by the grain size and composition), we find in all cases that nanometer-sized polycrystalline G-hBN heterostructures are not good thermoelectric materials.

Retroviral vectors and transposons for stable gene therapy: advances, current challenges and perspectives.

Gene therapy protocols require robust and long-term gene expression. For two decades, retrovirus family vectors have offered several attractive properties as stable gene-delivery vehicles. These vectors represent a technology with widespread use in basic biology and translational studies that require persistent gene expression for treatment of several monogenic diseases. Immunogenicity and insertional mutagenesis represent the main obstacles to a wider clinical use of these vectors. Efficient and safe non-viral vectors are emerging as a promising alternative and facilitate clinical gene therapy studies. Here, we present an updated review for beginners and expert readers on retro and lentiviruses and the latest generation of transposon vectors (sleeping beauty and piggyBac) used in stable gene transfer and gene therapy clinical trials. We discuss the potential advantages and disadvantages of these systems such as cellular responses (immunogenicity or genome modification of the target cell) following exogenous DNA integration. Additionally, we discuss potential implications of these genome modification tools in gene therapy and other basic and applied science contexts.

Identifying a biomarker network for corticosteroid resistance in asthma from bronchoalveolar lavage samples.

Corticosteroid resistance (CR) is a major barrier to the effective treatment of severe asthma. Hence, a better understanding of the molecular mechanisms involved in this condition is a priority. Network analysis is an emerging strategy to explore this complex heterogeneous disorder at system level to identify a small own network for CR in asthma. Gene expression profile of GSE7368 from bronchoalveolar lavage (BAL) of CR in subjects with asthma was downloaded from the gene expression omnibus (GEO) database and compared to BAL of corticosteroid-sensitive (CS) patients. DEGs were identified by the Limma package in R language. In addition, DEGs were mapped to STRING to acquire protein-protein interaction (PPI) pairs. Topological properties of PPI network were calculated by Centiscape, ClusterOne and BINGO. Subsequently, text-mining tools were applied to design one own cell signalling for CR in asthma. Thirty-five PPI networks were obtained; including a major network consisted of 370 nodes, connected by 777 edges. After topological analysis, a minor PPI network composed by 48 nodes was indentified, which is composed by most relevant nodes of major PPI network. In this subnetwork, several receptors (EGFR, EGR1, ESR2, PGR), transcription factors (MYC, JAK), cytokines (IL8, IL6, IL1B), one chemokine (CXCL1), one kinase (SRC) and one cyclooxygenase (PTGS2) were described to be associated with inflammatory environment and steroid resistance in asthma. We suggest a biomarker network composed by 48 nodes that could be potentially explored with diagnostic or therapeutic use.

Subcellular structure, heterogeneity, and plasticity of senescent cells.

Cellular senescence is a state of permanent growth arrest. It can be triggered by telomere shortening (replicative senescence) or prematurely induced by stresses such as DNA damage, oncogene overactivation, loss of tumor suppressor genes, oxidative stress, tissue factors, and others. Advances in techniques and experimental designs have provided new evidence about the biology of senescent cells (SnCs) and their importance in human health and disease. This review aims to describe the main aspects of SnCs phenotype focusing on alterations in subcellular compartments like plasma membrane, cytoskeleton, organelles, and nuclei. We also discuss the heterogeneity, dynamics, and plasticity of SnCs' phenotype, including the SASP, and pro-survival mechanisms. We advance on the multiple layers of phenotypic heterogeneity of SnCs, such as the heterogeneity between inducers, tissues and within a population of SnCs, discussing the relevance of these aspects to human health and disease. We also raise the main challenges as well alternatives to overcome them. Ultimately, we present open questions and perspectives in understanding the phenotype of SnCs from the perspective of basic and applied questions.

Molecular weight-dependent antitumor effects of prunes-derived type I arabinogalactan on human and murine triple wild-type melanomas.

The regulation of metastasis-related cellular aspects of two structurally similar AGIs from prunes tea infusion, with different molar masses, was studied in vitro against Triple Wild-Type metastatic melanoma (TWM) from murine and human origin. The higher molar mass AGI (AGI-78KDa) induced TWMs cells death and, in murine cell line, it decreased some metastasis-related cellular processes: invasiveness capacity, cell-extracellular matrix interaction, and colonies sizes. The lower molar mass AGI (AGI-12KDa) did not induce cell death but decreased TWMs proliferation rate and, in murine cell line, it decreased cell adhesion and colonies sizes. Both AGIs alter the clonogenic capacity of human cell line. In spite to understand why we saw so many differences between AGIs effects on murine and human cell lines we performed in silico analysis that demonstrated differential gene expression profiles between them. Complementary network topological predictions suggested that AGIs can modulate multiple pathways in a specie-dependent manner, which explain differential results obtained in vitro between cell lines. Our results pointed to therapeutic potential of AGIs from prunes tea against TWMs and showed that molecular weight of AGIs may influence their antitumor effects.

Rifaximin on epigenetics and autophagy in animal model of hepatocellular carcinoma secondary to metabolic-dysfunction associated steatotic liver disease.

BACKGROUND: Prevalence of hepatocellular carcinoma (HCC) is increasing, especially in patients with metabolic dysfunction-associated steatotic liver disease (MASLD). AIM: To investigate rifaximin (RIF) effects on epigenetic/autophagy markers in animals. METHODS: Adult Sprague-Dawley rats were randomly assigned (n = 8, each) and treated from 5-16 wk: Control [standard diet, water plus gavage with vehicle (Veh)], HCC [high-fat choline deficient diet (HFCD), diethylnitrosamine (DEN) in drinking water and Veh gavage], and RIF [HFCD, DEN and RIF (50 mg/kg/d) gavage]. Gene expression of epigenetic/autophagy markers and circulating miRNAs were obtained. RESULTS: All HCC and RIF animals developed metabolic-dysfunction associated steatohepatitis fibrosis, and cirrhosis, but three RIF-group did not develop HCC. Comparing animals who developed HCC with those who did not, miR-122, miR-34a, tubulin alpha-1c (Tuba-1c), metalloproteinases-2 (Mmp2), and metalloproteinases-9 (Mmp9) were significantly higher in the HCC-group. The opposite occurred with Becn1, coactivator associated arginine methyltransferase-1 (Carm1), enhancer of zeste homolog-2 (Ezh2), autophagy-related factor LC3A/B (Map1 Lc3b), and p62/sequestosome-1 (p62/SQSTM1)-protein. Comparing with controls, Map1 Lc3b, Becn1 and Ezh2 were lower in HCC and RIF-groups (P < 0.05). Carm1 was lower in HCC compared to RIF (P < 0.05). Hepatic expression of Mmp9 was higher in HCC in relation to the control; the opposite was observed for p62/Sqstm1 (P < 0.05). Expression of p62/SQSTM1 protein was lower in the RIF-group compared to the control (P = 0.024). There was no difference among groups for Tuba-1c, Aldolase-B, alpha-fetoprotein, and Mmp2 (P > 0.05). miR-122 was higher in HCC, and miR-34a in RIF compared to controls (P < 0.05). miR-26b was lower in HCC compared to RIF, and the inverse was observed for miR-224 (P < 0.05). There was no difference among groups regarding miR-33a, miR-143, miR-155, miR-375 and miR-21 (P > 0.05). CONCLUSION: RIF might have a possible beneficial effect on preventing/delaying liver carcinogenesis through epigenetic modulation in a rat model of MASLD-HCC.

Whole-Exome Sequencing Indicated New Candidate Genes Associated with Unilateral Cryptorchidism in Pigs.

INTRODUCTION: Cryptorchidism is a hereditary anomaly characterized by the incomplete descent of one or both testicles to the scrotum. One of the challenges of this anomaly is that the retained testicle maintains its endocrine function. As a consequence, cryptorchid animals produce hormone-tainted meat in comparison to castrated animals and are likely to be more aggressive. Cryptorchidism can lead to reduced animal welfare outcomes and cause economic losses. Identifying genetic markers for cryptorchidism is an essential step toward mitigating these negative outcomes and may facilitate genome manipulation to reduce the occurrence of cryptorchidism. Attempts to identify such markers have used genome-wide association studies. Using whole-exome sequencing, we aimed to identify single nucleotide polymorphisms (SNPs) in the coding regions of cryptorchid pigs and to characterize functional pathways concerning these SNPs. METHODS: DNA was extracted and sequenced from 5 healthy and 5 cryptorchid animals from the Landrace breed, using the Illumina HiSeq 2500 platform. Data were pre-processed using the SeqyClean tool and further mapped against the swine reference genome (Sus scrofa 11.1) using BWA software. GATK was used to identify polymorphisms (SNPs and InDels), which were annotated using the VEP tool. Network prediction and gene ontology enrichment analysis were conducted using the Cytoscape platform, and STRING software was used for visualization. RESULTS: A total of 63 SNPs were identified across the genes PIGB, CCPG1, COMMD9, LDLRAD3, TRIM44, MYLPF, SEPTIN, ZNF48, TIA1, FAIM2, KRT18, FBP1, FBP2, CTSL, DAPK1, DHX8, GPR179, DEPDC1B, ENSSSCG00000049573, ENSSSCG00000016384, ENSSSCG00000022657, ENSSSCG00000038825, and ENSSSCG00000001229. Using pathway enrichment analyses and network prospection, we have identified the following significant adjusted p value threshold of 0.001 involved with the biological function pathways of estrogen signaling, cytoskeleton organization, and the pentose phosphate pathway. CONCLUSION: Our data suggest the involvement of new SNPs and genes in developing cryptorchidism in pigs. However, further studies are needed to validate our results in a larger cohort population. Variations in the GPR179 gene, with implications at the protein level, may be associated with the appearance of this anomaly in the swine. Finally, we are showing that the estrogen signaling pathway may be involved in the pathophysiological mechanisms of this congenital anomaly as previously reported in GWAS.

pLR: a lentiviral backbone series to stable transduction of bicistronic genes and exchange of promoters.

Gene transfer based on lentiviral vectors allow the integration of exogenous genes into the genome of a target cell, turning these vectors into one of the most used methods for stable transgene expression in mammalian cells, in vitro and in vivo. Currently, there are no lentivectors that allow the cloning of different genes to be regulated by different promoters. Also, there are none that permit the analysis of the expression through an IRES (internal ribosome entry site)-- reporter gene system. In this work, we have generated a series of lentivectors containing: (1) a malleable structure to allow the cloning of different target genes in a multicloning site (mcs); (2) unique site to exchange promoters, and (3) IRES followed by one of two reporter genes: eGFP or DsRed. The series of the produced vectors were named pLR (for lentivirus and RSV promoter) and were fairly efficient with a strong fluorescence of the reporter genes in direct transfection and viral transduction experiments. This being said, the pLR series have been found to be powerful biotechnological tools for stable gene transfer and expression.

Vincristine promotes differential levels of apoptosis, mitotic catastrophe, and senescence depending on the genetic background of glioblastoma cells.

Vincristine (VCR) is a classical chemotherapeutic that has been revisited to treat refractory solid tumors producing encouraging results. VCR binds to tubulin and decreases the rate of microtubule dynamics, thus triggering many cellular responses and behaviors. However, the dynamics of these responses and fates are uncharacterized. This study combined systems biology approaches with acute and long-term in vitro experiments to predict key pathways and mechanisms associated with cell fates during and after VCR treatment. Glioblastoma (GBM) cells were treated with clinically relevant doses of VCR, and interconnected cell fates were explored. A correlation matrix based on experimental cell analysis reported strong negative correlations between cell number, nuclear irregularities, senescence, or apoptosis, depending on the cells' genetic makeup and treatment regimen. P53 would be essential in all analyzed processes according to topological network analysis. Furthermore, despite the high acute sensitivity, both cell lines re-growth in the long term after a single VCR treatment, especially in those populations with high levels of autophagy. These multiple responses may also be triggered in patients' exposed tumors, which should be considered to allow the rational design of VCR protocols, including modulators of the cell fates and pathways mentioned above.

Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients' Samples Reveals Perturbations in Tissue-Specific Pathways.

Cystic fibrosis (CF) is an autosomal recessive disorder, caused by diverse genetic variants for the CF transmembrane conductance regulator (CFTR) protein. Among these, p.Phe508del is the most prevalent variant. The effects of this variant on the physiology of each tissue remains unknown. This study is aimed at predicting cell signaling pathways present in different tissues of fibrocystic patients, homozygous for p.Phe508del. The study involved analysis of two microarray datasets, E-GEOD-15568 and E-MTAB-360 corresponding to the rectal and bronchial epithelium, respectively, obtained from the ArrayExpress repository. Particularly, differentially expressed genes (DEGs) were predicted, protein-protein interaction (PPI) networks were designed, and centrality and functional interaction networks were analyzed. The study reported that p.Phe508del-mutated CFTR-allele in homozygous state influenced the whole gene expression in each tissue differently. Interestingly, gene ontology (GO) term enrichment analysis revealed that only "neutrophil activation" was shared between both tissues; however, nonshared DEGs were grouped into the same GO term. For further verification, functional interaction networks were generated, wherein no shared nodes were reported between these tissues. These results suggested that the p.Phe508del-mutated CFTR-allele in homozygous state promoted tissue-specific pathways in fibrocystic patients. The generated data might further assist in prediction diagnosis to define biomarkers or devising therapeutic strategies.

Diclofenac Administration after Physical Training Blunts Adaptations of Peripheral Systems and Leads to Losses in Exercise Performance: In Vivo and In Silico Analyses.

Recovery in athletes is hampered by soreness and fatigue. Consequently, nonsteroidal anti-inflammatory drugs are used as an effective strategy to maintain high performance. However, impact of these drugs on adaptations induced by training remains unknown. This study assessed the effects of diclofenac administration (10 mg/kg/day) on rats subjected to an exhaustive test, after six weeks of swimming training. Over the course of 10 days, three repeated swimming bouts were performed, and diclofenac or saline were administered once a day. Trained animals exhibited higher muscle citrate synthase and lower plasma creatinine kinase activities as compared to sedentary animals, wherein diclofenac had no impact. Training increased time to exhaustion, however, diclofenac blunted this effect. It also impaired the increase in plasma and liver interleukin-6 levels. The trained group exhibited augmented catalase, glutathione peroxidase, and glutathione reductase activities, and a higher ratio of reduced-to-oxidized glutathione in the liver. However, diclofenac treatment blunted all these effects. Systems biology analysis revealed a close relationship between diclofenac and liver catalase. These results confirmed that regular exercise induces inflammation and oxidative stress, which are crucial for tissue adaptations. Altogether, diclofenac treatment might be helpful in preventing pain and inflammation, but its use severely affects performance and tissue adaptation.