Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens

For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.

Project SATURN- a real-world evidence data collaboration with existing European datasets in Osteogenesis Imperfecta to support future therapies

Regulatory marketing authorisation is not enough to ensure patient access to new medicinal products. Health Technology Assessment bodies may require data on effectiveness, relative effectiveness, and cost-effectiveness. Healthcare systems may require data on clinical utility, savings, and budget impact. Furthermore, the exact requirements of these bodies vary country by country and sometimes even region to region, resulting in a patchwork of different data requirements to achieve effective, reimbursed patient access to new therapies. In addition, clinicians require data to make informed clinical management decisions. This requirement is of key importance in rare diseases where there is often limited data and clinical experience at the time of regulatory approval.This paper describes an innovative initiative that is called Project SATURN: Systematic Accumulation of Treatment practices and Utilization, Real world evidence, and Natural history data for the rare disease Osteogenesis Imperfecta. The objective of this project is to generate a common core dataset by utilising existing data sources to meet the needs of the various stakeholders and avoiding fragmentation through multiple approaches (e.g., a series of individual national requests/approaches, and unconnected with the regulators' potential requirements). It is expected that such an approach will reduce the time for patient access to life-changing medications. Whilst Project SATURN applies to Osteogenesis Imperfecta, it is anticipated that the principles could also be applied to other rare diseases and reduce the time for patient access to new medications.

Equitable inclusion of diverse populations in oncology clinical trials: deterrents and drivers

The burden of cancer exerts a disproportionate impact across different regions and population subsets. Disease-specific attributes, coupled with genetic and socioeconomic factors, significantly influence cancer treatment outcomes. Precision oncology promises the development of safe and effective options for specific ethnic phenotypes and clinicodemographic profiles. Currently, clinical trials are concentrated in resource-rich geographies with younger, healthier, white, educated, and empowered populations. Vulnerable and marginalized people are often deprived of opportunities to participate in clinical trials. Despite consistent endeavors by regulators, industry, and other stakeholders, factors including diversity in trial regulations and patient and provider-related cultural, logistic, and operational barriers limit the inclusiveness of clinical trials. Understanding and addressing these constraints by collaborative actions involving regulatory initiatives, industry, patient advocacy groups, community engagement in a culturally sensitive manner, and designing and promoting decentralized clinical trials are vital to establishing a clinical research ecosystem that promotes equity in the representation of population subgroups.

A comprehensive review of m6A research in cervical cancer

Cervical cancer (CC) remains one of the most common malignancies among women worldwide, posing a serious threat to women's health. N6-methyladenosine (m6A) modification, as the most abundant type of RNA methylation modification, and has been found to play a crucial role in various cancers. Current research suggests a close association between RNA m6A modification and the occurrence and progression of CC, encompassing disruptions in m6A levels and its regulatory machinery. This review summarizes the current status of m6A modification research in CC, explores the mechanisms underlying m6A levels and regulators (methyltransferases, demethylases, reader proteins) in CC and examines the application of small-molecule inhibitors of m6A regulators in disease treatment. The findings provide new insights into the future treatment of CC.

LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria

Actinobacteria undergo a complex multicellular life cycle and produce a wide range of specialized metabolites, including the majority of the antibiotics. These biological processes are controlled by intricate regulatory pathways, and to better understand how they are controlled we need to augment our insights into the transcription factor binding sites. Here, we present LogoMotif (https://logomotif.bioinformatics.nl), an open-source database for characterized and predicted transcription factor binding sites in Actinobacteria, along with their cognate position weight matrices and hidden Markov models. Genome-wide predictions of binding site locations in Streptomyces model organisms are supplied and visualized in interactive regulatory networks. In the web interface, users can freely access, download and investigate the underlying data. With this curated collection of actinobacterial regulatory interactions, LogoMotif serves as a basis for binding site predictions, thus providing users with clues on how to elicit the expression of genes of interest and guide genome mining efforts.

Fluoropolymers as Unique and Irreplaceable Materials: Challenges and Future Trends in These Specific Per or Poly-Fluoroalkyl Substances

In contrast to some low-molar-mass per- and polyfluoroalkyl substances (PFASs), which are well established to be toxic, persistent, bioaccumulative, and mobile, fluoropolymers (FPs) are water-insoluble, safe, bioinert, and durable. These niche high-performance polymers fulfil the 13 polymer-of-low-concern (PLC) criteria in their recommended conditions of use. In addition, more recent innovations (e.g., the use of non-fluorinated surfactants in aqueous radical (co)polymerization of fluoroalkenes) from industrial manufacturers of FPs are highlighted. This review also aims to show how these specialty polymers endowed with outstanding properties are essential (even irreplaceable, since hydrocarbon polymer alternatives used in similar conditions fail) for our daily life (electronics, energy, optics, internet of things, transportation, etc.) and constitute a special family separate from other "conventional" C1-C10 PFASs found everywhere on Earth and its oceans. Furthermore, some information reports on their recycling (e.g., the unzipping depolymerization of polytetrafluoroethylene, PTFE, into TFE), end-of-life FPs, and their risk assessment, circular economy, and regulations. Various studies are devoted to environments involving FPs, though they present a niche volume (with a yearly production of 330,300 t) compared to all plastics (with 460 million t). Complementary to other reviews on PFASs, which lack of such above data, this review presents both fundamental and applied strategies as evidenced by major FP producers.

Single-cell RNA sequencing identifies critical transcription factors of tumor cell invasion induced by hypoxia microenvironment in glioblastoma

Rationale: Glioblastoma (GBM) is an aggressive malignant primary brain cancer with poor survival. Hypoxia is a hallmark of GBM, which promotes tumor cells spreading (invasion) into the healthy brain tissue. Methods: To better elucidate the influence of hypoxia on GBM invasion, we proposed a data-driven modeling framework for predicting cellular hypoxia (CHPF) by integrating single cell transcriptome profiling and hypoxia gene signatures. Results: We characterized the hypoxia status landscape of GBM cells and observed that hypoxic cells were only present in the tumor core. Then, by investigating the cell-cell communication between immune cells and tumor cells, we discovered significant interaction between macrophages and tumor cells in hypoxic microenvironment. Notably, we dissected the functional heterogeneity of tumor cells and identified a hypoxic subpopulation that had highly invasive potential. By constructing cell status specific gene regulatory networks, we further identified 14 critical regulators of tumor invasion induced by hypoxic microenvironment. Finally, we confirmed that knocking down two critical regulators CEBPD and FOSL1 could reduce the invasive ability of GBM under hypoxic conditions. Additionally, we revealed the therapeutic effect of Axitinib and Entinostat through the mice model. Conclusion: Our work revealed the critical regulators in hypoxic subpopulation with high invasive potential in GBM, which may have practical implications for clinical targeted-hypoxia cancer drug therapy.

Advances in the study of regulators of ferroptosis in head and neck squamous cell carcinoma (Review)

Head and neck squamous cell carcinoma (HNSCC), a common malignancy of the head and neck, is associated with a rapid progression, a high mortality rate and unsatisfactory curative effects. The treatment efficacy is unsatisfactory due to chemotherapeutic drug resistance, the lack of ideal therapeutic agents, as well as the absence of clinical prognostic models. Thus, the identification of novel potential therapeutic targets for its diagnosis and treatment is vital. Ferroptosis is an iron‑dependent regulatory cell death mode different from traditional cell death modes, such as apoptosis and autophagy, and has notable therapeutic potential in cancer treatment. The study of ferroptosis in HNSCC is expected to solve this bottleneck problem. In the present review, the findings, characteristics and regulatory mechanisms of ferroptosis are summarized, with emphasis on the factors and drugs that regulate ferroptosis in HNSCC, in order to provide theoretical basis for the targeted therapy of ferroptosis in HNSCC.

Emerging Role of Ferroptosis in Diabetic Kidney Disease: Molecular Mechanisms and Therapeutic Opportunities

Diabetic kidney disease (DKD) is one of the most common and severe microvascular complications of diabetes mellitus (DM), and has become the leading cause of end-stage renal disease (ESRD) worldwide. Although the exact pathogenic mechanism of DKD is still unclear, programmed cell death has been demonstrated to participate in the occurrence and development of diabetic kidney injury, including ferroptosis. Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, has been identified to play a vital role in the development and therapeutic responses of a variety of kidney diseases, such as acute kidney injury (AKI), renal cell carcinoma and DKD. In the past two years, ferroptosis has been well investigated in DKD patients and animal models, but the specific mechanisms and therapeutic effects have not been fully revealed. Herein, we reviewed the regulatory mechanisms of ferroptosis, summarized the recent findings associated with the involvement of ferroptosis in DKD, and discussed the potential of ferroptosis as a promising target for DKD treatment, thereby providing a valuable reference for basic study and clinical therapy of DKD.

Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations

Splice-modulating antisense oligonucleotides (ASOs) offer treatment options for rare neurological diseases, including those with very rare mutations, where patient-specific, individualized ASOs have to be developed. Inspired by the development of milasen, the 1 Mutation 1 Medicine (1M1M) and Dutch Center for RNA Therapeutics (DCRT) aim to develop patient-specific ASOs and treat eligible patients within Europe and the Netherlands, respectively. Treatment will be provided under a named patient setting. Our initiatives benefited from regulatory advice from the European Medicines Agency (EMA) with regard to preclinical proof-of-concept studies, safety studies, compounding and measuring benefit and safety in treated patients. We here outline the most important considerations from these interactions and how we implemented this advice into our plan to develop and treat eligible patients within Europe.

Trends and recent progresses of selenium nanoparticles as novel autophagy regulators for therapeutic development

Autophagy, one of the major intracellular degradation systems, plays an important role in maintaining normal cellular physiological functions and protecting organisms from different diseases. Selenium (Se), an essential trace element, is involved in many metabolic regulatory signaling events and plays a key role in human health. In recent years, selenium nanoparticles (Se NPs) have attracted increasing attentions in biomedical field due to their low toxicity, high bioavailability and high bioactivity. Taking the advantage of their advanced biological activities, Se NPs can be used alone as potential therapeutic agents, or combine with other agents and served as carriers for the development of novel therapeutics. More interestingly, Se NPs have been widely reported to affect autophagy signaling, which therefor allow Se NPs to be used as potential therapeutic agents against different diseases. Here, this review suggested the relationships between Se and autophagy, followed by the trends and recent progresses of Se NPs for autophagy regulation in different diseased conditions. More importantly, this work discussed the roles and potential mechanisms of Se NPs in autophagy regulating, which might enhance our understanding about how Se NPs regulate autophagy for potential disease treatment. This work is expected to promote the potential application of Se NPs as novel autophagy regulators, which might benefit the development of novel autophagy associated therapeutics.

The Role of Superoxide Dismutase 1 in Amyotrophic Lateral Sclerosis: Identification of Signaling Pathways, Regulators, Molecular Interaction Networks, and Biological Functions through Bioinformatics

Mutations in superoxide dismutase 1 (SOD1) result in misfolding and aggregation of the protein, causing neurodegenerative amyotrophic lateral sclerosis (ALS). In recent years, several new SOD1 variants that trigger ALS have been identified, making it increasingly crucial to understand the SOD1 toxicity pathway in ALS. Here we used an integrated bioinformatics approach, including the Ingenuity Pathway Analysis (IPA) tool to analyze signaling pathways, regulators, functions, and network molecules of SOD1 with an emphasis on ALS. IPA toxicity analysis of SOD1 identified superoxide radicals' degradation, apelin adipocyte, ALS, NRF2-mediated oxidative stress response, and sirtuin signaling as the key signaling pathways, while the toxicity of SOD1 is exerted via mitochondrial swelling and oxidative stress. IPA listed CNR1, APLN, BTG2, MAPK, DRAP1, NFE2L2, SNCA, and CG as the upstream regulators of SOD1. IPA further revealed that mutation in SOD1 results in hereditary disorders, including ALS. The exploration of the relationship between SOD1 and ALS using IPA unveiled SOD1-ALS pathway molecules. The gene ontology (GO) analysis of SOD1-ALS pathway molecules with ShinyGO reaffirmed that SOD1 toxicity results in ALS and neurodegeneration. The GO analysis further identified enriched biological processes, molecular functions, and cellular components for SOD1-ALS pathway molecules. The construction of a protein-protein interaction network of SOD1-ALS pathway molecules using STRING and further analysis of that network with Cytoscape identified ACTB followed by TP53, IL6, CASP3, SOD1, IL1B, APP, APOE, and VEGFA as the major network hubs. Taken together, our study provides insight into the molecular underpinning of SOD1's toxicity in ALS.

A CRISPR/Cas9-mediated screen identifies determinants of early plasma cell differentiation

Introduction

The differentiation of B cells into antibody-secreting plasma cells depends on cell division-coupled, epigenetic and other cellular processes that are incompletely understood.

Methods

We have developed a CRISPR/Cas9-based screen that models an early stage of T cell-dependent plasma cell differentiation and measures B cell survival or proliferation versus the formation of CD138+ plasmablasts. Here, we refined and extended this screen to more than 500 candidate genes that are highly expressed in plasma cells.

Results

Among known genes whose deletion preferentially or mostly affected plasmablast formation were the transcription factors Prdm1 (BLIMP1), Irf4 and Pou2af1 (OBF-1), and the Ern1 gene encoding IRE1a, while deletion of XBP1, the transcriptional master regulator that specifies the expansion of the secretory program in plasma cells, had no effect. Defective plasmablast formation caused by Ern1 deletion could not be rescued by the active, spliced form of XBP1 whose processing is dependent on and downstream of IRE1a, suggesting that in early plasma cell differentiation IRE1a acts independently of XBP1. Moreover, we newly identified several genes involved in NF-kB signaling (Nfkbia), vesicle trafficking (Arf4, Preb) and epigenetic regulators that form part of the NuRD complex (Hdac1, Mta2, Mbd2) to be required for plasmablast formation. Deletion of ARF4, a small GTPase required for COPI vesicle formation, impaired plasmablast formation and blocked antibody secretion. After Hdac1 deletion plasmablast differentiation was consistently reduced by about 50%, while deletion of the closely related Hdac2 gene had no effect. Hdac1 knock-out led to strongly perturbed protein expression of antagonistic transcription factors that govern plasma cell versus B cell identity (by decreasing IRF4 and BLIMP1 and increasing BACH2 and PAX5).

Discussion

Taken together, our results highlight specific and non-redundant roles for Ern1, Arf4 and Hdac1 in the early steps of plasma cell differentiation.

Ferroptosis: A new insight for treatment of acute kidney injury

Acute kidney injury (AKI), one of the most prevalent clinical diseases with a high incidence rate worldwide, is characterized by a rapid deterioration of renal function and further triggers the accumulation of metabolic waste and toxins, leading to complications and dysfunction of other organs. Multiple pathogenic factors, such as rhabdomyolysis, infection, nephrotoxic medications, and ischemia-reperfusion injury, contribute to the onset and progression of AKI. However, the detailed mechanism remains unclear. Ferroptosis, a recently identified mechanism of nonapoptotic cell death, is iron-dependent and caused by lipid peroxide accumulation in cells. A variety of studies have demonstrated that ferroptosis plays a significant role in AKI development, in contrast to other forms of cell death, such as apoptosis, necroptosis, and pyroptosis. In this review, we systemically summarized the definition, primary biochemical mechanisms, key regulators and associated pharmacological research progress of ferroptosis in AKI. We further discussed its therapeutic potential for the prevention of AKI, in the hope of providing a useful reference for further basic and clinical studies.

Strengthening the Interface of Evidence-Based Decision Making Across European Regulators and Health Technology Assessment Bodies

OBJECTIVES

Access to medicines in Europe depends on a benefit-risk decision taken by regulators and a relative effectiveness assessment performed by health technology assessment bodies (HTABs) to inform, as one element, a reimbursement decision. Although various similarities in evidence needs exist, understanding of their needs is currently suboptimal and therefore the evidence generated does not always meet their needs. Subsequently, delays in decision making can be expected, negatively affecting access. To overcome this, this study reviewed the evidentiary needs of European regulators and HTABs at European level and analyzed how their collaboration can further facilitate optimal evidence generation plans, evidence use, and evidence presentation.

METHODS

Through systematic literature review, expert interviews, and pairwise comparison of assessment reports by the European Medicines Agency and European network for health technology assessment, respective clinical evidence requirements and impact of product-specific collaboration between European Medicines Agency and HTABs were established.

RESULTS

Clinical evidence needs are quite similar but differences exist in comparator choice, preferred efficacy endpoints, and target population. Results of the impact of collaboration to date were mixed: preapproval joint advice procedures were successful and highly valued by all stakeholders; information exchange at the time of regulatory decision is coming together, yet the European Public Assessment Report can be further optimized; and collaboration on postlicensing evidence generation requirements shows potential but needs solidifying.

CONCLUSIONS

These findings demonstrate the potential to further improve the evidence utilization across stakeholders to avoid duplication and streamline decision making, to ultimately improve access to medicines for European patients.

Regulation of the rhythmic diversity of daily photoreceptor outer segment phagocytosis in vivo

Outer segment phagocytosis (OSP) is a highly-regulated, biological process wherein photoreceptor outer segment (OS) tips are cyclically phagocytosed by the adjacent retinal pigment epithelium (RPE) cells. Often an overlooked retinal process, rhythmic OSP ensures the maintenance of healthy photoreceptors and vision. Daily, the photoreceptors renew OS at their base and the most distal, and likely oldest, OS tips, are phagocytosed by the RPE, preventing the accumulation of photo-oxidative compounds by breaking down phagocytosed OS tips and recycling useful components to the photoreceptors. Light changes often coincide with an escalation of OSP and within hours the phagosomes formed in each RPE cell are resolved. In the last two decades, individual molecular regulators were elucidated. Some of the molecular machinery used by RPE cells for OSP is highly similar to mechanisms used by other phagocytic cells for the clearance of apoptotic cells. Consequently, in the RPE, many molecular regulators of retinal phagocytosis have been elucidated. However, there is still a knowledge gap regarding the key regulators of physiological OSP in vivo between endogenous photoreceptors and the RPE. Understanding the regulation of OSP is of significant clinical interest as age-related macular degeneration (AMD) and inherited retinal diseases (IRD) are linked with altered OSP. Here, we review the in vivo timing of OSP peaks in selected species and focus on the reported in vivo environmental and molecular regulators of OSP.

Non-Coding RNAs as Novel Regulators of Neuroinflammation in Alzheimer's Disease

Alzheimer’s disease (AD) is one of the most common causes of dementia. Although significant breakthroughs have been made in understanding the progression and pathogenesis of AD, it remains a worldwide problem and a significant public health burden. Thus, more efficient diagnostic and therapeutic strategies are urgently required. The latest research studies have revealed that neuroinflammation is crucial in the pathogenesis of AD. Non-coding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNA-derived small RNAs (tsRNAs), have been strongly associated with AD-induced neuroinflammation. Furthermore, several ongoing pre-clinical studies are currently investigating ncRNA as disease biomarkers and therapeutic interventions to provide new perspectives for AD diagnosis and treatment. In this review, the role of different types of ncRNAs in neuroinflammation during AD are summarized in order to improve our understanding of AD etiology and aid in the translation of basic research into clinical practice.

Molecular Regulation of Arbuscular Mycorrhizal Symbiosis

Plant-microorganism interactions at the rhizosphere level have a major impact on plant growth and plant tolerance and/or resistance to biotic and abiotic stresses. Of particular importance for forestry and agricultural systems is the cooperative and mutualistic interaction between plant roots and arbuscular mycorrhizal (AM) fungi from the phylum Glomeromycotina, since about 80% of terrestrial plant species can form AM symbiosis. The interaction is tightly regulated by both partners at the cellular, molecular and genetic levels, and it is highly dependent on environmental and biological variables. Recent studies have shown how fungal signals and their corresponding host plant receptor-mediated signalling regulate AM symbiosis. Host-generated symbiotic responses have been characterized and the molecular mechanisms enabling the regulation of fungal colonization and symbiosis functionality have been investigated. This review summarizes these and other recent relevant findings focusing on the molecular players and the signalling that regulate AM symbiosis. Future progress and knowledge about the underlying mechanisms for AM symbiosis regulation will be useful to facilitate agro-biotechnological procedures to improve AM colonization and/or efficiency.

Ferroptosis and Acute Kidney Injury (AKI): Molecular Mechanisms and Therapeutic Potentials

Acute kidney injury (AKI), a common and serious clinical kidney syndrome with high incidence and mortality, is caused by multiple pathogenic factors, such as ischemia, nephrotoxic drugs, oxidative stress, inflammation, and urinary tract obstruction. Cell death, which is divided into several types, is critical for normal growth and development and maintaining dynamic balance. Ferroptosis, an iron-dependent nonapoptotic type of cell death, is characterized by iron overload, reactive oxygen species accumulation, and lipid peroxidation. Recently, growing evidence demonstrated the important role of ferroptosis in the development of various kidney diseases, including renal clear cell carcinoma, diabetic nephropathy, and AKI. However, the exact mechanism of ferroptosis participating in the initiation and progression of AKI has not been fully revealed. Herein, we aim to systematically discuss the definition of ferroptosis, the associated mechanisms and key regulators, and pharmacological progress and summarize the most recent discoveries about the role and mechanism of ferroptosis in AKI development. We further conclude its potential therapeutic strategies in AKI.

A review of stakeholder recommendations for defining fit-for-purpose real-world evidence algorithms

Aim: The credibility and value of real-world evidence (RWE) are either supported or undermined by the algorithms (i.e., operational definitions) used. Methods: We conducted a targeted evidence review of key RWE decision makers' published recommendations on RWE algorithms through April 2021. Stakeholders were regulatory bodies, other governmental agencies and payer organizations. Results: Our review identified recommended criteria: relevance, validity, reliability, responsiveness, transparency and replicability, safety, feasibility and quality process. Stakeholders routinely recommended accuracy measures, subgroups evaluation and specific considerations for assessing exposures and covariates and the underlying real-world data (RWD) quality. Conclusion: The importance of stakeholder guidance on fit-for-purpose RWE algorithms is growing. We highlight gaps that future guidance and stakeholder recommendations could address.

Τelomerase inhibitors and activators in aging and cancer: A systematic review

The main aim of the present systematic review was to summarize the most frequently used telomerase regulators with an impact on aging and cancer that are referred to in in vitro and in vivo studies. For this purpose, a systematic review of the available literature on telomerase regulators referred to in articles from PubMed and Scopus libraries published from 2002 to 2021 and in accordance with PRISMA 2020 criteria, was conducted. Articles were included if they met the following criteria: They referred to telomerase modulators in aging and in cancer and were in vitro and/or in vivo studies, while studies that did not provide sufficient data or studies not written in English were excluded. In the present systematic review, 54 publications were included, of which 29 were full-text published studies, 11 were full-text reviews, 10 structure-based design studies and 4 abstracts are reported in this review. Telomerase regulators were then categorized as synthetic direct telomerase inhibitors, synthetic indirect telomerase inhibitors, synthetic telomerase activators, natural direct telomerase activators, natural telomerase inhibitors and natural indirect telomerase activators, according to their origin and their activity. On the whole, as demonstrated herein, telomerase regulators appear to be promising treatment agents in various age-related diseases. However, further in vivo and in vitro studies need to be performed in order to clarify the potentiality of telomerase as a therapeutic target.

The Regulators Associated With N6-Methyladenosine in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma Reveal New Clinical and Prognostic Markers

N6-methyladenosine (m⁶A) methylation is of significant importance in the initiation and progression of tumors, but how specific genes take effect in different lung cancers still needs to be explored. The aim of this study is to analyze the correlation between the m⁶A RNA methylation regulators and the occurrence and development of lung cancer. The data of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were obtained through the TCGA database. We systematically analyzed the related pathological characteristics and prognostic factors by applying univariate and multivariate Cox regression, as well as LASSO Cox regression. Some of 23 m⁶A regulators are identified as having high expression in lung cancer. In addition, risk score has been shown to be an independent prognostic factor in lung cancer. Our research not only fully reveals that m⁶A regulators and clinical pathological characteristics are potentially useful with respect to survival and prognosis in different lung tumors but also can lay a theoretical root for the treatment for lung cancer—notably, to point out a new direction for the development of treatment.

In Silico Prediction of Steroids and Triterpenoids as Potential Regulators of Lipid Metabolism

This review focuses on a rare group of steroids and triterpenoids that share common properties as regulators of lipid metabolism. This group of compounds is divided by the type of chemical structure, and they represent: aromatic steroids, steroid phosphate esters, highly oxygenated steroids such as steroid endoperoxides and hydroperoxides, α,β-epoxy steroids, and secosteroids. In addition, subgroups of carbon-bridged steroids, neo steroids, miscellaneous steroids, as well as synthetic steroids containing heteroatoms S (epithio steroids), Se (selena steroids), Te (tellura steroids), and At (astatosteroids) were presented. Natural steroids and triterpenoids have been found and identified from various sources such as marine sponges, soft corals, starfish, and other marine invertebrates. In addition, this group of rare lipids is found in fungi, fungal endophytes, and plants. The pharmacological profile of the presented steroids and triterpenoids was determined using the well-known computer program PASS, which is currently available online for all interested scientists and pharmacologists and is currently used by research teams from more than 130 countries of the world. Our attention has been focused on the biological activities of steroids and triterpenoids associated with the regulation of cholesterol metabolism and related processes such as anti-hyperlipoproteinemic activity, as well as the treatment of atherosclerosis, lipoprotein disorders, or inhibitors of cholesterol synthesis. In addition, individual steroids and triterpenoids were identified that demonstrated rare or unique biological activities such as treating neurodegenerative diseases, Alzheimer's, and Parkinson's diseases with a high degree of certainty over 95 percent. For individual steroids or triterpenoids or a group of compounds, 3D drawings of their predicted biological activities are presented.

Levels of lymphocyte-associated regulators of complement system CD55 and CD59 are changed in schizophrenia patients

OBJECTIVE

Although pathological mechanisms of schizophrenia are unknown, evidence in the literature suggests that the immune system might be involved in the pathogenesis. Complement is an important part of the immune system and it has been suggested to play role in the pathogenesis of schizophrenia. We aimed to investigate the potential involvement of the complement system in schizophrenia by the determination of peripheral concentrations of certain complement proteins and their regulators in patients.

METHODS

Plasma concentrations of complement C3, C4, and C1 inhibitory protein were measured by chemiluminescence in 41 schizophrenia patients and 39 healthy controls. Expression of CD55, CD59, and CD46 proteins on peripheral blood mononuclear cells were determined by flow cytometry in the same groups.

RESULTS

Frequencies of peripheral immune cells expressing CD55 were determined to be significantly higher in schizophrenia patients than in healthy people (p = 0.020). Frequencies of peripheral immune cells expressing CD59 was determined to be significantly higher in healthy people than in schizophrenia patients (p = 0.012). The expression level of CD55 per cell was measured to be significantly elevated in patients compared to healthy controls (p = 0.026).

CONCLUSIONS

Our data clearly demonstrate an elevated complement activity in schizophrenia and points to a possible complement association in the pathogenesis.Key pointsIncreased the expression level, and frequency of CD55 in schizophrenia patients.Decreased frequency of CD59 in schizophrenia patients.No difference in the expression level of CD59; the expression level, and frequency of CD46; frequency of complement C3, C4, and C1 inhibitory protein.

m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer

Objective: Increasing evidence highlights the roles of N⁶-methyladenosine (m⁶A) and its regulators in oncogenesis. Herein, this study observed the associations of m⁶A regulators with breast cancer. Methods: RNA-seq profiles of breast cancer were retrieved from the Cancer Genome Atlas (TCGA) database. The expression of m⁶A regulators was analyzed in tumor and normal tissues. Their expression correlations were analyzed by Spearson test. Overall survival (OS) analysis of these regulators was then presented. Gene set enrichment analysis (GSEA) was performed in high and low YTHDF1 expression groups. The correlations of YTHDF1 expression with immune cells and tumor mutation burden (TMB) were calculated in breast cancer samples. Somatic variation was assessed in high and low YTHDF1 expression groups. Results: Most of m⁶A regulators were abnormally expressed in breast cancer compared to normal tissues. At the mRNA levels, there were closely relationships between them. Among them, YTHDF1 up-regulation was significantly related to undesirable prognosis (p = 0.025). GSEA results showed that high YTHDF1 expression was associated with cancer-related pathways. Furthermore, YTHDF1 expression was significantly correlated with T cells CD4 memory activated, NK cells activated, monocytes, and macrophages. There were higher TMB scores in YTHDF1 up-regulation group than its down-regulation group. Missense mutation and non-sense mutation were the most frequent mutation types. Conclusion: Our findings suggested that dysregulated m⁶A regulator YTHDF1 was predictive of survival outcomes as well as response to immunotherapy of breast cancer, and were closely related to immune microenvironment.

[Research progress on natural cannabinoid receptor type 2( CB2R)regulators and their effects on bone metabolism]

Cannabinoid receptor type 2( CB2 R),a member of the G protein-coupled receptor( GPCR) superfamily,has a variety of biological activities,such as regulating pain response,resisting inflammation and fibrosis,and mediating bone metabolism. Some CB2 R regulators exhibit a good regulatory effect on bone metabolism. Cannabinoids in Cannabis sativa can cause psychoactive effects despite various pharmacological actions they exerted by targeting CB2 R. Therefore,it is of great significance to discover CB2 R regulators in non-Cannabis plants for finding new lead compounds without psychoactive effects and elucidating the action mechanism of plant drugs. The present study clarifies the discovery,structure,and physiological functions of CB2 R,especially its regulatory effects on bone metabolism,summarized CB2 R regulators extracted from non-Cannabis plants,and systematically analyzes the regulatory effects of CB2 R regulators on bone metabolism in animals,osteoblasts,and osteoclasts,to provide a scientific basis for the discovery of new CB2 R regulators and the development of anti-osteoporotic drugs.

[Improvement of natural product production in Streptomyces by manipulating pathway-specific regulators]

Streptomyces are major sources of bioactive natural products. Genome sequencing reveals that Streptomyces have great biosynthetic potential, with an average of 20-40 biosynthetic gene clusters each strain. However, most natural products from Streptomyces are produced in low yields under regular laboratory cultivation conditions, which hamper their further study and drug development. The production of natural products in Streptomyces is controlled by the intricate regulation mechanisms. Manipulation of the regulatory systems that govern secondary metabolite production will strongly facilitate the discovery and development of natural products of Streptomyces origin. In this review, we summarize progresses in pathway-specific regulators from Streptomyces in the last five years and highlight their role in improving the yields of corresponding natural products.

Vertical integration methods for gene expression data analysis

Gene expression data have played an essential role in many biomedical studies. When the number of genes is large and sample size is limited, there is a 'lack of information' problem, leading to low-quality findings. To tackle this problem, both horizontal and vertical data integrations have been developed, where vertical integration methods collectively analyze data on gene expressions as well as their regulators (such as mutations, DNA methylation and miRNAs). In this article, we conduct a selective review of vertical data integration methods for gene expression data. The reviewed methods cover both marginal and joint analysis and supervised and unsupervised analysis. The main goal is to provide a sketch of the vertical data integration paradigm without digging into too many technical details. We also briefly discuss potential pitfalls, directions for future developments and application notes.

Multiple Myeloma Bone Disease: Implication of MicroRNAs in Its Molecular Background

Multiple myeloma (MM) is a common hematological malignancy arising from terminally differentiated plasma cells. In the majority of cases, symptomatic disease is characterized by the presence of bone disease. Multiple myeloma bone disease (MMBD) is a result of an imbalance in the bone-remodeling process that leads to increased osteoclast activity and decreased osteoblast activity. The molecular background of MMBD appears intriguingly complex, as several signaling pathways and cell-to-cell interactions are implicated in the pathophysiology of MMBD. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate the expression of their target mRNAs. Numerous miRNAs have been witnessed to be involved in cancer and hematological malignancies and their role has been characterized either as oncogenic or oncosuppressive. Recently, scientific research turned towards miRNAs as regulators of MMBD. Scientific data support that miRNAs finely regulate the majority of the signaling pathways implicated in MMBD. In this review, we provide concise information regarding the molecular pathways with a significant role in MMBD and the miRNAs implicated in their regulation. Moreover, we discuss their utility as molecular biomarkers and highlight the putative usage of miRNAs as novel molecular targets for targeted therapy in MMBD.

Regulators of commensal and pathogenic life-styles of an opportunistic fungus-Candida albicans

The yeast Candida albicans is primarily a commensal of humans that colonizes the mucosal surfaces of the gastrointestinal and genital tracts. Yet, C. albicans can under certain circumstances undergo a shift from commensalism to pathogenicity. This transition is governed by fungal factors such as morphological transitions, environmental cues for instance relationships with gut microbiota and the host immune system. C. albicans utilizes distinct sets of regulatory programs to colonize or infect its host and to evade the host defense systems. Moreover, an orchestrated iron acquisition mechanism operates to adapt to specific niches with variable iron availability. Studies on regulatory networks and morphogenesis of these two distinct modes of C. albicans growth, suggest that both yeast and hyphal forms exist in both growth patterns and the regulatory circuits are inter-connected. Here, we summarize current knowledge about C. albicans commensal-to-pathogen shift, its regulatory elements and their contribution to human disease.

Identification and Validation of the N6-Methyladenosine RNA Methylation Regulator YTHDF1 as a Novel Prognostic Marker and Potential Target for Hepatocellular Carcinoma

Purpose: N6-methyladenosine (m⁶A) RNA methylation has been implicated in various malignancies. This study aimed to identify the m⁶A methylation regulator-based prognostic signature for hepatocellular carcinoma (HCC) as well as provide candidate targets for HCC treatment.

Methods: The least absolute shrinkage and selection operator (LASSO) analyses were performed to identify a risk signature in The Cancer Genome Atlas (TCGA) datasets. The risk signature was further validated in International Cancer Genome Consortium (ICGC) and Pan-Cancer Analysis of Whole Genomes (PCAWG) datasets. Following transfection of short hairpin RNA (shRNA) targeting YTHDF1, the biological activities of HCC cells were evaluated by Cell Counting Kit-8 (CCK-8), wound-healing, Transwell, flow cytometry, and xenograft tumor assays, respectively. The potential mechanisms mediated by YTHDF1 were predicted by overrepresentation enrichment analysis (ORA)/gene set enrichment analysis (GSEA) and validated by Western blotting.

Results: Overexpression of m⁶A RNA methylation regulators was correlated with malignant clinicopathological characteristics of HCC patients. The Cox regression and LASSO analyses identified a risk signature with five m⁶A methylation regulators (KIAA1429, ZC3H13, YTHDF1, YTHDF2, and METTL3). In accordance with HCC cases in TCGA, the prognostic value of risk signature was also determined in ICGC and PCAWG datasets. Following analyzing the expression and clinical implications in TCGA and Gene Expression Omnibus (GEO), YTHDF1 was chosen for further experimental validation. Knockdown of YTHDF1 significantly inhibited the proliferation, migration, and invasion of HCC cells, as well as enhanced the apoptosis in vitro. Moreover, silencing YTHDF1 repressed the growth of xenograft tumors in vivo. Mechanism investigation indicated that YTHDF1 might promote the aggressive phenotypes by facilitating epithelial–mesenchymal transition (EMT) and activating AKT/glycogen synthase kinase (GSK)-3β/β-catenin signaling.

Conclusion: The current study identified a robust risk signature consisting of m⁶A RNA methylation regulators for HCC prognosis. In addition, YTHDF1 was a potential molecular target for HCC treatment.

[Spatial-temporal Variations and the Regulators of Nitrate Status in Shallow Groundwater of the Typical Mountainous Agricultural Watershed in the Upper Reaches of the Yangtze River]

Shallow groundwater is the main drinking water supply for the mountainous area in the upper reaches of the Yangtze River, while its quality is often degraded by nitrate (NO₃^--N) pollution due to intensive agricultural production activities. In the present study, we selected a mountainous agricultural watershed in the upper reaches of the Yangtze River to investigate the land use, management, and hydrogeological conditions, aiming to clarify the spatial-temporal variations in NO₃^--N concentration of shallow groundwater, thereby exploring the key regulators. The results showed that the NO₃^--N concentrations of the groundwater ranged from 0.40 to 12.51 mg ·L^-1in the study area, and the exceeding ratio was nearly 30%. On an average, NO₃^--N concentrations for the wet season were higher than that for the dry season, indicating great variations in NO₃^--N concentration across different seasons. In addition, the spatial variations of NO₃^--N concentration in groundwater were also significant among different sub-catchment, which was mainly due to variations in the groundwater table depth and land uses. Furthermore, the significant correlations between the NO₃^--N concentrations and concentrations of Cl^-, NH₄⁺-N, DOC, and SO₄^2- in the shallow groundwater were also explored in this study, suggesting that the NO₃^--N concentrations were likely to depend on the chemical factors of the shallow groundwater in the study area. Overall, our current study highlights that the characterization of spatial-temporal variations of NO₃^--N status in shallow groundwater and illustration of key regulators are essential to mitigate NO₃^--N pollution and prevent quality degradation of shallow groundwater in mountainous rural areas of the upper Yangtze River watershed.

B7-H3 Immune Checkpoint Protein in Human Cancer

B7-H3 belongs to the B7 family of immune checkpoint proteins, which are important regulators of the adaptive immune response and emerging key players in human cancer. B7-H3 is a transmembrane protein expressed on the surface of tumor cells, antigen presenting cells, natural killer cells, tumor endothelial cells, but can also be present in intra- and extracellular vesicles. Additionally, B7-H3 may be present as a circulating soluble isoform in serum and other body fluids. B7-H3 is overexpressed in a variety of tumor types, in correlation with poor prognosis. B7-H3 is a promising new immunotherapy target for anti-cancer immune response, as well as a potential biomarker. Besides its immunoregulatory role, B7-H3 has intrinsic pro-tumorigenic activities related to enhanced cell proliferation, migration, invasion, angiogenesis, metastatic capacity and anti-cancer drug resistance. B7-H3 has also been found to regulate key metabolic enzymes, promoting the high glycolytic capacity of cancer cells. B7-H3 receptors are still not identified, and little is known about the molecular mechanisms underlying B7-H3 functions. Here, we review the current knowledge on the involvement of B7-H3 in human cancer.

Integrated Datasets of Proteomic and Metabolomic Biomarkers to Predict Its Impacts on Comorbidities of Type 2 Diabetes Mellitus

OBJECTIVE

The objective of the current study is to accomplish a relative exploration of the biological roles of differentially dysregulated genes (DRGs) in type 2 diabetes mellitus (T2DM). The study aimed to determine the impact of these DRGs on the biological pathways and networks that are related to the associated disorders and complications in T2DM and to predict its role as prospective biomarkers.

METHODS

Datasets obtained from metabolomic and proteomic profiling were used for investigation of the differential expression of the genes. A subset of DRGs was integrated into IPA software to explore its biological pathways, related diseases, and their regulation in T2DM. Upon entry into the IPA, only 94 of the DRGs were recognizable, mapped, and matched within the database.

RESULTS

The study identified networks that explore the dysregulation of several functions; cell components such as degranulation of cells; molecular transport process and metabolism of cellular proteins; and inflammatory responses. Top disorders associated with DRGs in T2DM are related to organ injuries such as renal damage, connective tissue disorders, and acute inflammatory disorders. Upstream regulator analysis predicted the role of several transcription factors of interest, such as STAT3 and HIF alpha, as well as many kinases such as JAK kinases, which affects the gene expression of the dataset in T2DM. Interleukin 6 (IL6) is the top regulator of the DRGs, followed by leptin (LEP). Monitoring the dysregulation of the coupled expression of the following biomarkers (TNF, IL6, LEP, AGT, APOE, F2, SPP1, and INS) highlights that they could be used as potential prognostic biomarkers.

CONCLUSION

The integration of data obtained by advanced metabolomic and proteomic technologies has made it probable to advantage in understanding the role of these biomarkers in the identification of significant biological processes, pathways, and regulators that are associated with T2DM and its comorbidities.

Deciphering the Mounting Complexity of the p53 Regulatory Network in Correlation to Long Non-Coding RNAs (lncRNAs) in Ovarian Cancer

Amongst the various gynecological malignancies affecting female health globally, ovarian cancer is one of the predominant and lethal among all. The identification and functional characterization of long non-coding RNAs (lncRNAs) are made possible with the advent of RNA-seq and the advancement of computational logarithm in understanding human disease biology. LncRNAs can interact with deoxyribonucleic acid (DNA), ribonucleic acid (RNA), proteins and their combinations. Moreover, lncRNAs regulate orchestra of diverse functions including chromatin organization and transcriptional and post-transcriptional regulation. LncRNAs have conferred their critical role in key biological processes in human cancer including tumor initiation, proliferation, cell cycle, apoptosis, necroptosis, autophagy, and metastasis. The interwoven function of tumor-suppressor protein p53-linked lncRNAs in the ovarian cancer paradigm is of paramount importance. Several lncRNAs operate as p53 regulators or effectors and modulates a diverse array of functions either by participating in various signaling cascades or via interaction with different proteins. This review highlights the recent progress made in the identification of p53 associated lncRNAs while elucidating their molecular mechanisms behind the altered expression in ovarian cancer tumorigenesis. Moreover, the development of novel clinical and therapeutic strategies for targeting lncRNAs in human cancers harbors great promise.

Identification of Functional Transcriptional Binding Sites within Chicken Abcg2 Gene Promoter and Screening Its Regulators

Breast cancer resistance protein (BCRP), an ATP-binding cassette (ABC) half transporter encoded by the Abcg2 gene, is reported to influence the pharmacokinetics of substrate drugs during clinical therapy. The aim of this study was to clarify the mechanisms that regulate the transcription of the chicken Abcg2 gene through cloning and characterization of its promoter region. Results showed that the Abcg2 gene is transcribed by a TATA-less promoter with several putative Sp1 sites upstream from two putative CpG islands. A luciferase reporter assay conducted both in chicken leghorn male hepatoma (LMH) cells and chicken primary hepatocytes mapped a basal promoter to nucleotides -110 to +30, which is responsible for the constitutive expression of Abcg2. The 5'-region upstream of the basal promoter was characterized by both positive and negative regulatory domains. Further, using the cell-based reporter gene assay combined with RT-PCR and drug accumulation analysis, we found that four xenobiotics, daidzein, clotrimazole, ivermectin, and lipopolysaccharide (LPS), influence the expression and function of BCRP through significant regulation of the Abcg2 gene promoter. Interaction sites with the Abcg2 gene promoter of these four selected regulators were clarified by progressive deletions and mutation assays. This study shed some light on the regulatory mechanisms involved in chicken Abcg2 gene expression and the results may have far-reaching significance regarding the usage and development of veterinary drugs.

[Adaptation of elderly Petersburgers to the situation of the coronavirus pandemic.]

The elderly's adaptation to the situation of coronavirus pandemic is described in the paper from the standpoint of a holistic approach. This includes the interaction between the elderly person, the social environment in which he/she is included in one form or another, and the regulators of this interaction. The purpose of the research was to identify the degree of main actors' readiness to achieve the required balance of an elderly person's interests in self-preservation and the requirements of the coronavirus environment In Saint-Petersburg. The typology of the elderly according to their adaptation to the conditions of the pandemic is presented. It was found that a significant part of the elderly did not sufficiently adapt to the conditions of self-preservation, therefore, technologies for teaching the elderly to rational behavior, optimization of the social and city environment, and improvement of their regulators are needed.

ETph: enhancers and their targets in pig and human database

Enhancers, as the genomic non-coding sequences, play a key role in the activation of gene expression. They have been widely identified in the human genome. Pig is an important biomedical model for human health. Few studies have been performed to explore the enhancers in the pig genome. The human enhancer information may be useful to identify enhancers in the pig genome. In addition, the genetic background of pig traits could be useful to annotate human enhancers and diseases. Thus, in order to further study enhancers and their potential roles in human and pig, we developed a public database, ETph (Enhancers and their Targets in pig and human). ETph integrates the information on human enhancers, pig putative enhancers, target genes, pig QTL terms, human diseases, GO terms and the KEGG pathway. A total of 25 182 enhancers were identified in the pig genome using the human homology sequence information. Among them, 6232 high-confidence enhancers were used to build the ETph. ETph provides a convenient platform to search, browse and download data. Moreover, a web-based analytical tool was designed to visualize networks and topology graphs among pig putative enhancers, target genes, pig QTL traits and human diseases. ETph might provide a useful tool for researchers to investigate the genetic background of pig traits and human diseases. ETph is freely accessible at http://klab.sjtu.edu.cn/enhancer/.

Perspectives on the draft ICH-M10 guidance: an interview with John Kadavil

Biography Dr Kadavil received his bachelor's degree in biochemistry from the University of Maryland, Baltimore County. He then received his PhD in molecular pharmacology and experimental therapeutics from the University of Maryland, Baltimore, School of Medicine. Following his PhD, he joined the US FDA as a pharmacologist. He first worked in the Office of Scientific Investigations - Division of Bioequivalence & Good Laboratory Practice under the Office of Compliance at CDER. During his 8 years at the Office of Scientific Investigations, he conducted foreign and domestic bioanalytical and clinical inspections for bioequivalence, bioavailability, pharmacokinetic and GLP studies. In 2011, he joined the Division of Human Food Safety at CVM as a pharmacologist, where he conducted reviews of residue chemistry studies and directed method trials. In 2014, he returned to CDER to become the team lead for the Collaboration, Risk Evaluation and Surveillance Team under the Office of Study Integrity and Surveillance. In September 2018, he became the Deputy Director for the Division of Generic Drug Bioequivalence Evaluation in Office of Study Integrity and Surveillance. This interview was conducted by Sankeetha Nadarajah, Managing Commissioning Editor of Bioanalysis, at the AAPS ICH-M10 Public Consultation Workshop (MD, USA).

Upstream regulators of phosphoinositide 3-kinase and their role in diseases

Phosphoinositide 3-kinase (PI3K), a crucial signaling molecule, is regulated by various upstream regulators. Traditionally, receptor tyrosine kinases and G protein-coupled receptor are regarded as its principle upstream regulators; however, recent reports have indicated that spleen tyrosine kinase, β-arrestin2, Janus kinase, and RAS can also perform this role. Dysregulation of PI3K is common in the progression of various diseases, including, but not limited to, tumors, Alzheimer's disease, Parkinson's disease, rheumatoid arthritis, and acute myelogenous leukemia. The aim of this review is to provide a perspective on PI3K-related diseases examining both the classical and nonclassical upstream regulators of PI3K in detail.

MicroRNAs: Crucial Regulators of Stress

Background

Signaling pathways including gene silencing, cellular differentiation, homeostasis, development and apoptosis are regulated and controlled by a wide range of miRNAs.

Objective

Due to their potential binding sites in human-protein coding genes, many studies have also linked their altered expressions in various cancer types making them tumor suppressors agents.

Methods

Moreover, each miRNA is predicted to have many mRNA targets indicating their extensive regulatory role in cell survival and developmental processes. Nowadays, diagnosis of early cancer stage development is now dependent on variable miRNA expression levels as potential oncogenic biomarkers in validating and targeting microRNAs for cancer therapy.

Results

As the majority of miRNA, transcripts are derived from RNA polymerase II-directed transcription, stress response could result on a general reduction in the abundance of these transcripts. Over expression of various microRNAs have lead to B cell malignancy, potentiated KrasG12D-induced lung tumorigenesis, chronic lymphocytic leukemia, lymphoproliferative disease and autoimmunity.

Conclusion

Altered miRNA expressions could have a significant impact on the abundance of proteins, making them attractive candidates as biomarkers for cancer detection and important regulators of apoptosis.

Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer

The lung metastasis of breast cancer involves complicated regulatory changes driven by chromatin remodelling. However, the epigenetic reprogramming and regulatory mechanisms in lung metastasis of breast cancer remain unclear. Here, we generated and analysed genome‐wide profiles of multiple histone modifications (H3K4me3, H3K27ac, H3K27me3, H3K4me1 and H3K9me3), as well as transcriptome data in lung‐metastatic and non‐lung‐metastatic breast cancer cells. Our results showed that the expression changes were correlated with the enrichment of specific histone modifications in promoters and enhancers. Promoter and enhancer reprogramming regulated gene expression in a synergetic way, and involved in multiple important biological processes and pathways. In addition, lots of gained super‐enhancers were identified in lung‐metastatic cells. We also identified master regulators driving differential gene expression during lung metastasis of breast cancer. We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover, regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. Functional studies motivated by our data analyses uncovered an important role of LMO4 in regulating metastasis. This study provided comprehensive insights into regulatory mechanisms, as well as potential prognostic markers for lung metastasis of breast cancer.

Non-muscle Myosin II: Role in Microbial Infection and Its Potential as a Therapeutic Target

Currently, the major measures of preventing and controlling microbial infection are vaccinations and drugs. However, the appearance of drug resistance microbial mounts is main obstacle in current anti-microbial therapy. One of the most ubiquitous actin-binding proteins, non-muscle myosin II (NM II) plays a crucial role in a wide range of cellular physiological activities in mammals, including cell adhesion, migration, and division. Nowadays, growing evidence indicates that aberrant expression or activity of NM II can be detected in many diseases caused by microbes, including viruses and bacteria. Furthermore, an important role for NM II in the infection of some microbes is verified. Importantly, modulating the expression of NM II with small hairpin RNA (shRNA) or the activity of it by inhibitors can affect microbial-triggered phenotypes. Therefore, NM II holds the promise to be a potential target for inhibiting the infection of microbes and even treating microbial-triggered discords. In spite of these, a comprehensive view on the functions of NM II in microbial infection and the regulators which have an impact on the roles of NM II in this context, is still lacking. In this review, we summarize our current knowledge on the roles of NM II in microbial-triggered discords and provide broad insights into its regulators. In addition, the existing challenge of investigating the multiple roles of NM II in microbial infection and developing NM II inhibitors for treating these microbial-triggered discords, are also discussed.

Steering Coacervation by a Pair of Broad-Spectrum Regulators

Coacervation is liquid-liquid phase separation ubiquitous in industrial applications and cellular biology. Inspired by cellular manipulation of coacervate droplets such as P granules, we report here a regulatory strategy to manipulate synthetic coacervation in a spatiotemporally controllable manner. Two oppositely charged small molecules are shown to phase separate into coacervate droplets in water as a result of electrostatic attraction, hydrophobic effect, and entropy. We identify a down regulator, β-cyclodextrin, to disrupt the hydrophobic effect, thus dissolving the droplets, and an up regulator, amylase, to decompose β-cyclodextrin, thus restoring the droplets. The regulation kinetics is followed in real time on a single-droplet level, revealing diffusion-limited dissolution and reaction-limited condensation, respectively, taking ∼4 s and 2-3 min. Versatility of this strategy to manipulate the coacervation is demonstrated in two aspects: spatially distributed coacervation in virtue of amylase-grafted hydrogel frameworks and coacervate transportation across membranes and hydrogel networks via a disassemble-to-pass strategy. The current regulatory pairs and strategies are anticipated to be general for a wide variety of synthetic self-assembly systems.

Transcripts and tumors: regulatory and metabolic programming during biotrophic phytopathogenesis

Biotrophic fungal pathogens of plants must sense and adapt to the host environment to complete their life cycles. Recent transcriptome studies of the infection of maize by the biotrophic pathogen Ustilago maydis are providing molecular insights into an ordered program of changes in gene expression and the deployment of effectors as well as key features of nutrient acquisition. In particular, the transcriptome data provide a deeper appreciation of the complexity of the transcription factor network that controls the biotrophic program of invasion, proliferation, and sporulation. Additionally, transcriptome analysis during tumor formation, a key late stage in the life cycle, revealed features of the remodeling of host and pathogen metabolism that may support the formation of tremendous numbers of spores. Transcriptome studies are also appearing for other smut species during interactions with their hosts, thereby providing opportunities for comparative approaches to understand biotrophic adaptation.

Circular RNAs as novel biomarkers with regulatory potency in human diseases

Circular RNAs (circRNAs) are a large class of noncoding RNAs characterized with closed loop structures without 3′ and 5′ polar ends. They can roughly be divided into exonic circRNAs, exon–intron circRNAs and circular intronic RNAs. CircRNAs are characterized with stability, prevalence, specificity and conservation, which arouse great interest in circRNAs as disease biomarkers. Their abilities to sponge to miRNAs, cis-regulate parent genes, bind to proteins and encode proteins endow circRNAs a critical role of regulation in eukaryotic cells. This concise review focuses on circRNAs as functional biomarkers and therapeutic targets in both tumor and nontumorous diseases.

Although they were discovered in 1970s, circular RNAs (circRNAs) have attracted great interest only relatively recently. Instead of genome ‘junk matters’, circRNAs are now considered as promising biomarkers and treatment targets. CircRNAs are involved in numerous cancer-related and noncancer diseases, such as lung cancer, gastric cancer, cardiovascular diseases, diabetes mellitus and so on. This review outlines the classification, characterization and function of circRNAs, with a specific focus on recent studies concerning the role of circRNAs in human diseases.

The problems of increasing transparency on uncertainty

Public regulators (such as European Food Safety Authority, European Medicines Agency, and European Centre for Disease Prevention and Control) are placing increasing demands on scientists to make uncertainties about their evidence transparent to the public. The stated goal is utilitarian, to inform and empower the public and ensure the accountability of policy and decision-making around the use of scientific evidence. However, it is questionable what constitutes uncertainty around the evidence on any given topic, and, while the goal is laudable, we argue the drive to increase transparency on uncertainty of the scientific process specifically does more harm than good, and may not serve the interests of those intended. While highlighting some of the practical implications of making uncertainties transparent using current guidelines, the aim is to discuss what could be done to make it worthwhile for both public and scientists.