Prognostic significance and expression pattern of glucose related genes in breast cancer: A comprehensive computational biology approach

Breast cancer (BC) is the most common type of malignancy globally and the main reason why women die from tumours. The Warburg effect, a characteristic of tumor, describes how most solid tumour cells acclimatize to their diverse surroundings by relying heavily on aerobic glycolysis for production of energy. In addition to producing key metabolic intermediates that are crucial for the production of macromolecules, which enable cancer cell division, invasiveness, and drug resistance, the transformed energy metabolism also supplies tumor cells with ATP for cellular energy. Here, we evaluated the expression profile, prognostic significance, and clinical relevance of glucose-related genes in BC using a bioinformatic approach. To clarify the significance of glucose-related genes in the development of breast tumours, we also performed a functional enrichment investigation of deregulated genes using the STRING and KEGG portal. The study depicted that of the 61 genes examined, 8 genes had a fold change Collapse

Key Words

• Bioinformatics
• Breast cancer
• Deregulation
• Glucose metabolism
• Prognosis
• Survival analysis
• Warburg effect

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MESH Headings Collapse

Grants Collapse

Affiliation(s)

Bader Alshehri Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Almajmaah 11952, Saudi Arabia

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MicroRNA-765 is upregulated in myelodysplastic syndromes and induces apoptosis via PLP2 inhibition in leukemia cells

Background

Epigenetic studies, particularly research on microRNA (miRNA), have flourished. The abnormal expression of miRNA contributes to the development of hematologic malignancies. miR-765 has been reported to inhibit cell proliferation by downregulating proteolipid protein 2 (PLP2), which causes apoptosis. We investigated miR-765 dysregulation in myelodysplastic syndromes (MDS).

Methods

We compared the expression profiles of miR-765 in 65 patients with MDS and 11 controls. Cell proliferation and apoptosis assays were performed to determine the in vitro effects of miR-765 on leukemia cells transfected with the miR-765 mimic. Reverse transcription quantitative PCR (RT-qPCR) and western blotting were performed to examine the targets of miR-765.

Results

We found that miR-765 levels were upregulated 10.2-fold in patients with MDS compared to controls. In refractory cytopenia with multilineage dysplasia, the percentage of patients with elevated miR-765 levels was significantly higher than in other forms of MDS. Experiments with leukemia cells revealed that transfection with a miR-765 mimic inhibited cell proliferation and induced apoptosis. RT-qPCR and western blotting demonstrated that the target of miR-765 was PLP2.

Conclusion

These findings imply that upregulation of miR-765 induces apoptosis via downregulation of PLP2 and may have a role in MDS pathogenesis.

Implications of Toll-like receptors (TLRs) and their signaling mechanisms in human cancers

Most essential pattern-recognition receptors regulating innate immune functions are toll-like receptors (TLRs). TLRs are characterized by lack of concurrent epithelial markers and are typically identified by their gene expressions. One major mechanism by which TLRs generate their effector functions is by triggering inflammatory responses. Activation of TLRs can impact initiation, advancement, and control of cancers by regulating the inflammatory microenvironment. Several TLRs have been implicated in human cancers and some of them are identified as cancer biomarkers as well; for example, TLRs 2, 3, 5 are expressed more frequently in most cancers. Knowing the upregulation and downregulation of the TLR genes in human cancers will be useful for the development of newer therapeutic targets which can disrupt the pathways associated with such deregulation. We present here the various TLRs and their functions in human lung, gastric, breast, prostate, oral, ovarian, colorectal, cervical, esophageal, bladder and hepatic cancers.

S1P signaling, its interactions and cross-talks with other partners and therapeutic importance in colorectal cancer

Sphingosine-1-Phosphate (S1P) plays an important role in normal physiology, inflammation, initiation and progression of cancer. Deregulation of S1P signaling causes aberrant proliferation, affects survival, leads to angiogenesis and metastasis. Sphingolipid rheostat is crucial for cellular homeostasis. Discrepancy in sphingolipid metabolism is linked to cancer and drug insensitivity. Owing to these diverse functions and being a potent mediator of tumor growth, S1P signaling might be a suitable candidate for anti-tumor therapy or combination therapy. In this review, with a focus on colorectal cancer we have summarized the interacting partners of S1P signaling pathway, its therapeutic approaches along with the contribution of S1P signaling to various cancer hallmarks.

Deregulation of the downstream petroleum industry: An overview of the legal quandaries and proposal for improvement in Nigeria

The study investigates the necessity for deregulation of the downstream petroleum sector to tackles shortfalls and to enhance quantities of petroleum commodities in Nigeria. The objective is to boost proficiency in the industry via governance, statutory transformations and vigorous business competition by learning from other advanced countries' skills to transform and fortify the downstream oil industry laws. The study embraces a conceptual legal approach utilising existing literature to aid a doctrinal legal study technique. The research also utilizes primary and secondary founts of legislations, such as, constitutional and case laws. The finding of the research is the absolute authority of the government in the industry and incongruous valuing of oil commodities which made the industry unappealing to financiers to found private refineries that will ensure adequate supply of petroleum and reasonable profits on their investments owing to excessive regulation of the industry by the government. The study designed a model to halt continuous increment in the fuel price and to ensure efficient downstream petroleum industry. The study concludes with the recommendations, for instance, the necessity of high-tech fusion of policies and encouragements for investment in the downstream to boosts swift enactment of the awaiting Petroleum Industry Governance Bill 2017 and absolute deregulation of the industry to foster private investments and to halt subsidy disbursements being a new fountain of corruption.

Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case

Standard food safety assessments of genetically modified crops require a thorough molecular characterization of the novel DNA as inserted into the plant that is intended for commercialization, as well as a comparison of agronomic and nutritional characteristics of the genetically modified to the non-modified counterpart. These characterization data are used to identify any unintended changes in the inserted DNA or in the modified plant that would require assessment for safety in addition to the assessment of the intended modification. An unusual case of an unintended effect discovered from the molecular characterization of a genetically modified late blight resistant potato developed for growing in Bangladesh and Indonesia is presented here. Not only was a significant portion of the plasmid vector backbone DNA inserted into the plant along with the intended insertion of an R-gene for late blight resistance, but the inserted DNA was split into two separate fragments and inserted into two separate chromosomes. One fragment carries the R-gene and the other fragment carries the NPTII selectable marker gene and the plasmid backbone DNA. The implications of this for the food safety assessment of this late blight resistant potato are considered.

The COVID-19 pandemic as an opportunity to weaken environmental protection in Brazil

This paper examines the effects of the COVID-19 pandemic on environmental protection and legislation in Brazil. We evaluate major legislative actions, environmental fines and deforestation since January 2019. We show that 57 legislative acts aimed at weakening environmental protection in Brazil during the current administration, almost half of which in the seven-month period of the pandemic in Brazil, with September 2020 as the month with the most legislative acts (n = 16). These acts either deregulated or weakened current environmental legislation, with a number of them aimed at dismantling the main federal institutions in charge of environmental protection. We also found a 72% reduction in environmental fines during the pandemic, despite an increase in Amazonian deforestation during this period. We conclude that the current administration is taking advantage of the COVID-19 pandemic to intensify a pattern of weakening environmental protection in Brazil. This has the potential to intensify ongoing loss of biodiversity, greenhouse gas emissions, and the likelihood of other zoonotic disease outbreaks, and inflict substantial harm to traditional and indigenous peoples. We highlight the key role of the scientific community, media and civil society, national and international levels, in order to reverse these harmful actions.

The 2017 deregulation of pharmacies in Italy: Introducing non-pharmacist ownership

Italy is the last European country to adopt policies on the liberalization of pharmacy ownership. In August 2017, the Italian government approved the law n. 124 (annual market and competition law), despite the opposition of some stakeholders. This law extended the ownership of pharmacies to non-pharmacist business partners. Law n. 124 is an important turning point for pharmacists in Italy and could lead to a general reorganization of the Italian pharmaceutical system. As has already happened in several European countries, the removal of barriers to pharmacy ownership incentivizes finance companies and pharmaceutical wholesalers to make significant investments in this sector, leading to the emergence of commercial pharmacy chains. The future of community pharmacies is uncertain and is closely linked to the fate of the current government. However, progressive polarization between independent pharmacies and pharmacies that are part of chains can already be observed.

Regulation of regulators: Role of the complement factor H-related proteins

The complement system, while being an essential and very efficient effector component of innate immunity, may cause damage to the host and result in various inflammatory, autoimmune and infectious diseases or cancer, when it is improperly activated or regulated. Factor H is a serum glycoprotein and the main regulator of the activity of the alternative complement pathway. Factor H, together with its splice variant factor H-like protein 1 (FHL-1), inhibits complement activation at the level of the central complement component C3 and beyond. In humans, there are also five factor H-related (FHR) proteins, whose function is poorly characterized. While data indicate complement inhibiting activity for some of the FHRs, there is increasing evidence that FHRs have an opposite role compared with factor H and FHL-1, namely, they enhance complement activation directly and also by competing with the regulators FH and FHL-1. This review summarizes the current stand and recent data on the roles of factor H family proteins in health and disease, with focus on the function of FHR proteins.

A spatial analysis to evaluate the impact of deregulation policies in the pharmacy sector: Evidence from the case of Navarre

Community pharmacies represent unusual enterprises as their main function is intrinsically related to the provision of healthcare services. Hence, market competition in this sector needs to be regulated, in order to ensure equitable accessibility, efficiency and quality of services. However, recently a general deregulation trend may be observed in Europe. In this paper, we focus on location restrictions, i.e. on demographic and geographic constraints to open new pharmacies, and we evaluate the impact of their relaxation. In particular, we analyze the case of the city of Pamplona (ES), where a striking increase in the number of pharmacies occurred, after the introduction of a new regulatory system in 2000. We evaluate, thanks to an in-depth spatial analysis, the evolution of the system to date and the effects produced on the consumers, in terms of accessibility, and on the competitors, in terms of market shares distribution. By comparing the obtained results with the ones related to the case of a second Spanish city, characterized by more strict restrictions, it emerges that the deregulation risks to produce a limited improvement in terms of accessibility and to exacerbate differences among consumers. Moreover, an increasing number of competitors does not necessarily imply a more equitable distribution of market shares, thus putting at risk the desired effects in terms of cost reduction and service quality improvement.

Individual Comparison of Cholesterol Metabolism in Normal and Tumour Areas in Radical Prostatectomy Specimens from Patients with Prostate Cancer: Results of the CHOMECAP Study

BACKGROUND

Deregulation of cholesterol metabolism represents a hallmark of prostate cancer (PCa) and promotes its development.

OBJECTIVE

To compare cholesterol metabolism on individual paired normal and tumour prostate tissues obtained from patients with PCa.

DESIGN, SETTING, AND PARTICIPANTS

Between 2008 and 2012, normal and tumour paired tissue samples were collected from radical prostatectomy specimens from a cohort of 69 patients treated for localised PCa.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Tumour and normal tissues were subjected to gene analysis, sterol measurement, and immunohistochemistry. The Wilcoxon paired test and Spearman test were applied for comparison and correlation analyses, respectively. Principal component analysis was also carried out to investigate relationships between quantitative variables.

RESULTS AND LIMITATIONS

Overall, cholesterol concentrations were not significantly different between tissue pairs. However, tumour samples were significantly associated with downregulated de novo cholesterol synthesis, but exhibited 54.7% overexpression of SCARB1 that could increase high-density lipoprotein uptake in PCa. Tumour tissues showed different trafficking of available cholesterol, with significantly lower ACAT1, and an altered efflux via APOE. Furthermore, cholesterol metabolism in tumour tissues was characterised by higher accumulation of 7α-hydroxycholesterol (OHC), 7βOHC, and 7-ketosterol, and a lower level of 27OHC.

CONCLUSIONS

Focusing on individually paired prostate tissues, our results highlighted several differences between normal and tumour samples linked to a metabolic shift in cholesterol flux. PCa samples exhibited a specific tissue signature characterised by higher SCARB1 expression, higher accumulation of OHC species, and clear downregulation of de novo cholesterol synthesis.

PATIENT SUMMARY

Comparing normal and tumour tissues from the same prostates, our study identified a set of alterations in prostate cancer samples in terms of their use of cholesterol. These included higher cholesterol uptake, accumulation of oxidised cholesterol derivatives, and autonomous cellular production of cholesterol. Together, these data provide promising clinical targets to fight prostate cancer.

CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production

Background

Anthocyanins are a class of brightly colored, glycosylated flavonoid pigments that imbue their flower and fruit host tissues with hues of predominantly red, orange, purple, and blue. Although all anthocyanins exhibit pH-responsive photochemical changes, distinct structural decorations on the core anthocyanin skeleton also cause dramatic color shifts, in addition to improved stabilities and unique pharmacological properties. In this work, we report for the first time the extension of the reconstituted plant anthocyanin pathway from (+)-catechin to O-methylated anthocyanins in a microbial production system, an effort which requires simultaneous co-option of the endogenous metabolites UDP-glucose and S-adenosyl-l-methionine (SAM or AdoMet).

Results

Anthocyanin O-methyltransferase (AOMT) orthologs from various plant sources were co-expressed in Escherichia coli with Petunia hybrida anthocyanidin synthase (PhANS) and Arabidopsis thaliana anthocyanidin 3-O-glucosyltransferase (At3GT). Vitis vinifera AOMT (VvAOMT1) and fragrant cyclamen ‘Kaori-no-mai’ AOMT (CkmOMT2) were found to be the most effective AOMTs for production of the 3′-O-methylated product peonidin 3-O-glucoside (P3G), attaining the highest titers at 2.4 and 2.7 mg/L, respectively. Following modulation of plasmid copy number and optimization of VvAOMT1 and CkmOMT2 expression conditions, production was further improved to 23 mg/L using VvAOMT1. Finally, CRISPRi was utilized to silence the transcriptional repressor MetJ in order to deregulate the methionine biosynthetic pathway and improve SAM availability for O-methylation of cyanidin 3-O-glucoside (C3G), the biosynthetic precursor to P3G. MetJ repression led to a final titer of 51 mg/L (56 mg/L upon scale-up to shake flask), representing a twofold improvement over the non-targeting CRISPRi control strain and 21-fold improvement overall.

Conclusions

An E. coli strain was engineered for production of the specialty anthocyanin P3G using the abundant and comparatively inexpensive flavonol precursor, (+)-catechin. Furthermore, dCas9-mediated transcriptional repression of metJ alleviated a limiting SAM pool size, enhancing titers of the methylated anthocyanin product. While microbial production of P3G and other O-methylated anthocyanin pigments will likely be valuable to the food industry as natural food and beverage colorants, we expect that the strain constructed here will also prove useful to the ornamental plant industry as a platform for evaluating putative anthocyanin O-methyltransferases in pursuit of bespoke flower pigment compositions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0623-3) contains supplementary material, which is available to authorized users.

coli de novo vanillin biosynthesis pathway

Background

Vanillin is an industrially valuable molecule that can be produced from simple carbon sources in engineered microorganisms such as Saccharomyces cerevisiae and Escherichia coli. In E. coli, de novo production of vanillin was demonstrated previously as a proof of concept. In this study, a series of data-driven experiments were performed in order to better understand limitations associated with biosynthesis of vanillate, which is the immediate precursor to vanillin.

Results

Time-course experiments monitoring production of heterologous metabolites in the E. coli de novo vanillin pathway revealed a bottleneck in conversion of protocatechuate to vanillate. Perturbations in central metabolism intended to increase flux into the heterologous pathway increased average vanillate titers from 132 to 205 mg/L, but protocatechuate remained the dominant heterologous product on a molar basis. SDS-PAGE, in vitro activity measurements, and l-methionine supplementation experiments suggested that the decline in conversion rate was influenced more by limited availability of the co-substrate S-adenosyl-l-methionine (AdoMet or SAM) than by loss of activity of the heterologous O-methyltransferase. The combination of metJ deletion and overexpression of feedback-resistant variants of metA and cysE, which encode enzymes involved in SAM biosynthesis, increased average de novo vanillate titers by an additional 33 % (from 205 to 272 mg/L). An orthogonal strategy intended to improve SAM regeneration through overexpression of native mtn and luxS genes resulted in a 25 % increase in average de novo vanillate titers (from 205 to 256 mg/L). Vanillate production improved further upon supplementation with methionine (as high as 419 ± 58 mg/L), suggesting potential for additional enhancement by increasing SAM availability.

Conclusions

Results from this study demonstrate context dependency of engineered pathways and highlight the limited methylation capacity of E. coli. Unlike in previous efforts to improve SAM or methionine biosynthesis, we pursued two orthogonal strategies that are each aimed at deregulating multiple reactions. Our results increase the working knowledge of SAM biosynthesis engineering and provide a framework for improving titers of metabolic products dependent upon methylation reactions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0459-x) contains supplementary material, which is available to authorized users.

Consumer preferences for over-the-counter drug retailers in the reregulated Swedish pharmacy market

Following a large regulatory reform in 2009, which ended the state's pharmacy monopoly, non-pharmacy retailers in Sweden today sell certain over-the-counter (OTC) drugs. The aim of this study was to investigate consumer preferences regarding OTC drug retailers and the reasons for choosing a pharmacy versus non-pharmacy retailer. We conducted a web survey aimed at Swedish adults. Out of a stratified sample of 4058 persons, 2594 agreed to take part (48% women; mean age: 50.3 years). Questions related to OTC drug use, retailer choice and factors affecting the participants' preferences for OTC drug retailers. Logistic regression was conducted to analyse OTC drug use and reasons for retailer choice in relation to sex, age and education. Nine in ten participants reported OTC drug use in the 6 months prior to the study. For their last OTC purchase, 76% had gone to a pharmacy, 20% to a grocery shop and 4% to a convenience store, gas station or online. Geographic proximity, opening hours and product range were reported as the most important factors in retailer choice. Counselling by trained staff was important to 57% of participants. The end of the state's pharmacy monopoly and the increase in number of pharmacies seem to have impacted more on Swedish consumers' purchase behaviours compared with the deregulation of OTC drug sales.

MicroRNA-194-5p could serve as a diagnostic and prognostic biomarker in myelodysplastic syndromes

Trisomy 8 and trisomy 1q are the most frequent chromosomal abnormalities in Korean patients with myelodysplastic syndrome (MDS). MicroRNA (miRNA) deregulation is involved in the development of hematological malignancies, including MDS, and cancer-associated genomic regions are known to encode miRNAs. The aim of the present study was to investigate the involvement of miRNAs encoded by chromosomes 8 and 1q in MDS. For this, the expression of nine miRNAs encoded by chromosome 8 (miR-30b-5p, miR-30d-5p, miR-101-3p, miR-124-3p, miR-151a-5p, miR-320a, miR-486-5p, miR-596, and miR-875-5p) and three miRNAs encoded by chromosome 1q (miR-29c-3p, miR-194-5p, and miR-214-3p) was compared between 65 MDS patients and 11 controls. We found a significant upregulation of miR-194-5p (5.1-fold, P=0.002) and miR-320a (2.94-fold, P=0.016) in MDS patients compared with controls. The patients with low miR-194-5p expression showed a significantly decreased overall survival (P=0.049). The areas under the miR-194-5p and miR-320a ROC curves were 0.797 (P=0.002) and 0.729 (P=0.016), respectively. Although these findings need to be validated in a larger patient population, our results indicate that miR-194-5p is a candidate diagnostic biomarker for MDS and that low miR-194-5p expression could be associated with poor overall survival for MDS patients.

Clustered airline flight scheduling: Evidence from airline deregulation in Korea

This paper explores the impacts of competition level on airline scheduling in the Korean domestic short-haul routes where a hub-and-spoke system is not the optimal air transport network strategy. The empirical findings using the Korean airline panel data for the period 2006-2010 suggest that competition leads to less differentiated departure flight times as expected from spatial competition theory. Unlike the previous study on the U.S airline industry, the degree of this tendency for less differentiation differs across the type of routes: the Jeju island routes (leisure type) and the inland routes (business type), in the deregulated period. Following the May 2008 Deregulation Act we find an increasingly clustered pattern of airline scheduling in the Jeju island routes where there have been competitive pressures associated with new low cost entrants. This recent evidence would imply that airline carriers strategically schedule departure flight times and allocate flights between routes as competition increases in the deregulated period.

Does deregulation in community pharmacy impact accessibility of medicines, quality of pharmacy services and costs? Evidence from nine European countries

OBJECTIVE

To analyse the impact of deregulation in community pharmacy on accessibility of medicines, quality of pharmacy services and costs.

METHODS

We analysed and compared community pharmacy systems in five rather deregulated countries (England, Ireland, the Netherlands, Norway, Sweden) and four rather regulated countries (Austria, Denmark, Finland, Spain). Data were collected by literature review, a questionnaire survey and interviews.

RESULTS

Following a deregulation, several new pharmacies and dispensaries of Over-the-Counter (OTC) medicines tended to be established, predominantly in urban areas. Unless prevented by regulation, specific stakeholders, e.g. wholesalers, were seen to gain market dominance which limited envisaged competition. There were indications for an increased workload for pharmacists in some deregulated countries. Economic pressure to increase the pharmacy turnover through the sale of OTC medicines and non-pharmaceuticals was observed in deregulated and regulated countries. Prices of OTC medicines were not found to decrease after a deregulation in pharmacy.

CONCLUSIONS

Access to pharmacies usually increases after a deregulation but this is likely to favour urban populations with already good accessibility. Policy-makers are recommended to take action to ensure equitable accessibility and sustainable competition in a more deregulated environment. No association between pharmaceutical expenditure and the extent of regulation/deregulation appears to exist.

Tumor suppressor and hepatocellular carcinoma

A few signaling pathways are driving the growth of hepatocellular carcinoma. Each of these pathways possesses negative regulators. These enzymes, which normally suppress unchecked cell proliferation, are circumvented in the oncogenic process, either the over-activity of oncogenes is sufficient to annihilate the activity of tumor suppressors or tumor suppressors have been rendered ineffective. The loss of several key tumor suppressors has been described in hepatocellular carcinoma. Here, we systematically review the evidence implicating tumor suppressors in the development of hepatocellular carcinoma.