Role of KCNB1 in the prognosis of gliomas and autophagy modulation

Ubiquitin specific peptidase 3: an emerging deubiquitinase that regulates physiology and diseases

Proteins are the keystone for the execution of various life activities, and the maintenance of protein normalization is crucial for organisms. Ubiquitination, as a post-transcriptional modification, is widely present in organisms, and it relies on the sophisticated ubiquitin-proteasome (UPS) system that controls protein quality and modulates protein lifespan. Deubiquitinases (DUBs) counteract ubiquitination and are essential for the maintenance of homeostasis. Ubiquitin specific peptidase 3 (USP3) is a member of the DUBs that has received increasing attention in recent years. USP3 is a novel chromatin modifier that tightly regulates the DNA damage response (DDR) and maintains genome integrity. Meanwhile, USP3 acts as a key regulator of inflammatory vesicles and sustains the normal operation of the innate immune system. In addition, USP3 is aberrantly expressed in a wide range of cancers, such as gastric cancer, glioblastoma and neuroblastoma, implicating that USP3 could be an effective target for targeted therapies. In this review, we retrace all the current researches of USP3, describe the structure of USP3, elucidate its functions in DNA damage, immune and inflammatory responses and the cell cycle, and summarize the important role of USP3 in multiple cancers and diseases.

Pore size and organic carbon of biochar limit the carbon sequestration potential of Bacillus cereus SR

Carbon-fixing functional strain-loaded biochar may have significant potential in carbon sequestration given the global warming situation. The carbon-fixing functional strain Bacillus cereus SR was loaded onto rice straw biochar pyrolyzed at different temperatures with the anticipation of clarifying the carbon sequestration performance of this strain on biochar and the interaction effects with biochar. During the culture period, the content of dissolved organic carbon (DOC), easily oxidizable organic carbon, and microbial biomass carbon in biochar changed. This finding indicated that B. cereus SR utilized organic carbon for survival and enhanced carbon sequestration on biochar to increase organic carbon, manifested by changes in CO2 emissions and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) enzyme activity. Linear regression analysis showed that the strain was likely to consume DOC on 300 °C biochar, although the Rubisco enzyme activity was higher. In contrast, the strain had a higher carbon sequestration potential on 500 °C biochar. Correlation analysis showed that Rubisco enzyme activity was controlled by the physical structure of the biochar. Our results highlight the differences in the survival mode and carbon sequestration potential of B. cereus SR on biochar pyrolyzed at different temperatures.

Non-conducting functions of potassium channels in cancer and neurological disease

Cancer and neurodegenerative disease, albeit fundamental differences, share some common pathogenic mechanisms. Accordingly, both conditions are associated with aberrant cell proliferation and migration. Here, we review the causative role played by potassium (K+) channels, a fundamental class of proteins, in cancer and neurodegenerative disease. The concept that emerges from the review of the literature is that K+ channels can promote the development and progression of cancerous and neurodegenerative pathologies by dysregulating cell proliferation and migration. K+ channels appear to control these cellular functions in ways that not necessarily depend on their conducting properties and that involve the ability to directly or indirectly engage growth and survival signaling pathways. As cancer and neurodegenerative disease represent global health concerns, identifying commonalities may help understand the molecular basis for those devastating conditions and may facilitate the design of new drugs or the repurposing of existing drugs.

Neurons as stromal drivers of nervous system cancer formation and progression

Similar to their pivotal roles in nervous system development, neurons have emerged as critical regulators of cancer initiation, maintenance, and progression. Focusing on nervous system tumors, we describe the normal relationships between neurons and other cell types relevant to normal nerve function, and discuss how disruptions of these interactions promote tumor evolution, focusing on electrical (gap junctions) and chemical (synaptic) coupling, as well as the establishment of new paracrine relationships. We also review how neuron-tumor communication contributes to some of the complications of cancer, including neuropathy, chemobrain, seizures, and pain. Finally, we consider the implications of cancer neuroscience in establishing risk for tumor penetrance and in the design of future anti-tumoral treatments.

Dual transcriptome of Streptococcus mutans and Candida albicans interplay in biofilms

Objective

To assess the interactions between Streptococcus mutans and Candida albicans during cariogenic biofilm formation.

Methods

The S. mutans and C. albicans duo-species biofilms were formed in 1% sucrose to mimic the high caries risk challenges. The biofilm structure was assessed using two-photon laser confocal microscopy. The transcriptome of 48h-biofilms was assessed by RNA-Seq. The expression of S. mutans and C. albicans virulence genes was examined via real-time reverse transcription-polymerase chain reaction.

Results

The morphogenesis of C. albicans-S. mutans duo-species biofilms was significantly altered when comparing to S. mutans or C. albicans single-species biofilm. Duo-species biofilms exhibited unique expression profile with a large number of differentially expressed genes (DEGs), including a higher expression of S. mutans atpD (acid-adaptive), C. albicans CHT2 (fungal cell wall chitin remodeling), and C. albicans SOD3 (cytotoxic oxygen radical destroying) (p < 0.05). KEGG pathway analyses further revealed that the majority of the up-regulated DEGs are related to microbial metabolism. Furthermore, the expressions of S. mutans and C. albicans key virulence genes (gtfB, gtfC, gtfD, ECE1, HWP1, ERG4, CHT2) were associated with sugar availability-related and time-related dynamics.

Conclusion

Cross-kingdom interactions impact S. mutans-C. albicans biofilm formations and dynamic expressions of virulence genes.

Retinoschisin and novel Na/K-ATPase interaction partners Kv2.1 and Kv8.2 define a growing protein complex at the inner segments of mammalian photoreceptors

The RS1 gene on Xp 22.13 encodes retinoschisin which is known to directly interact with the retinal Na/K-ATPase at the photoreceptor inner segments. Pathologic mutations in RS1 cause X-linked juvenile retinoschisis (XLRS), a hereditary retinal dystrophy in young males. To further delineate the retinoschisin-Na/K-ATPase complex, co-immunoprecipitation was performed with porcine and murine retinal lysates targeting the ATP1A3 subunit. This identified the voltage-gated potassium (Kv) channel subunits Kv2.1 and Kv8.2 as direct interaction partners of the retinal Na/K-ATPase. Colocalization of the individual components of the complex was demonstrated at the membrane of photoreceptor inner segments. We further show that retinoschisin-deficiency, a frequent consequence of molecular pathology in XLRS, causes mislocalization of the macromolecular complex during postnatal retinal development with a simultaneous reduction of Kv2.1 and Kv8.2 protein expression, while the level of retinal Na/K-ATPase expression remains unaffected. Patch-clamp analysis revealed no effect of retinoschisin-deficiency on Kv channel mediated potassium ion currents in vitro. Together, our data suggest that Kv2.1 and Kv8.2 together with retinoschisin and the retinal Na/K-ATPase are integral parts of a macromolecular complex at the photoreceptor inner segments. Defective compartmentalization of this complex due to retinoschisin-deficiency may be a crucial step in initial XLRS pathogenesis.

Cysteine-Based Mimic of Arginylation Reproduces Neuroprotective Effects of the Authentic Post-Translational Modification on α-Synuclein

Arginylation is an understudied post-translational modification (PTM) involving the transfer of arginine to aspartate or glutamate sidechains in a protein. Among the targets of this PTM is α-synuclein (αS), a neuronal protein involved in regulating synaptic vesicles. The aggregation of αS is implicated in neurodegenerative diseases, particularly in Parkinson's disease, and arginylation has been found to protect against this pathological process. Arginylated αS has been studied through semisynthesis involving multipart native chemical ligation (NCL), but this can be very labor-intensive with low yields. Here, we present a facile way to introduce a mimic of the arginylation modification into a protein of interest, compatible with orthogonal installation of labels such as fluorophores. We synthesize bromoacetyl arginine and react it with recombinant, site-specific cysteine mutants of αS. We validate the mimic by testing the vesicle binding affinity of mimic-arginylated αS, as well as its aggregation kinetics and monomer incorporation into fibrils, and comparing these results to those of authentically arginylated αS produced through NCL. In cultured neurons, we compare the fibril seeding capabilities of preformed fibrils carrying a small percentage of arginylated αS. We find that, consistent with authentically arginylated αS, mimic-arginylated αS does not perturb the protein's native function but alters aggregation kinetics and monomer incorporation. Both mimic and authentically modified αS suppress aggregation in neuronal cells. Our results provide further insight into the neuroprotective effects of αS arginylation, and our alternative strategy to generate arginylated αS enables the study of this PTM in proteins not accessible through NCL.

Comprehensive Genomic and Epigenomic Analyses on Transcriptomic Regulation in Stomach Adenocarcinoma

Background: DNA methylation (MET)–mediated transcriptomic disturbance and copy number variations (CNVs) exert a significant influence in stimulating the heterogeneous progression of stomach adenocarcinoma (STAD). Nevertheless, the relation of DNA MET with CNVs, together with its impact on tumor occurrence, is still unclear.

Methods: The messenger RNA (mRNA) expression (EXP) profiles, DNA MET, and DNA copy numbers, together with STAD mutation data, were collected from the TCGA official data portal. We employed circular binary segmentation algorithm in “DNAcopy.” library of R package for mapping DNA CNV data at genetic level for all samples based on the segmented CNV data. Stable clusters of samples were recognized using negative matrix factorization cluster analysis based on 50 iterations and the “brunet” method using the MET-correlated (METcor) and CNV-correlated (CNVcor) genes. The R package “iCluster” method was utilized to comprehensively analyze the EXP, MET, and DNA CNV profiles.

Results: A total of 313 STAD samples were isolated for checking DNA copy numbers and MET and for measuring EXP. In accordance with our results, we discovered obvious co-regulation of CNVcor genes and METcor counterparts. Apart from that, these genes were subject to multi-omics integration. Meanwhile, three subtypes of STAD were detected and confirmed based on independent data. Among them, the subtype with increased aggressiveness was related to decreased mutation frequencies of ARID1A, PIK3CA, ZFHX3, SPECC1, OBSCN, KMT2D, FSIP2, ZBTB20, TTN, and RANBP2, together with the abnormal levels of JPH3, KCNB1, and PLCXD3.

Conclusion: According to the results, these aforementioned genes exerted crucial roles in the development of invasive STAD. Our findings on transcriptomic regulation genomically and epigenetically facilitate the understanding of the STAD pathology from different aspects, which help to develop efficient anti-STAD therapy.

Identification of the protective effect of Polygonatum sibiricum polysaccharide on d-galactose-induced brain ageing in mice by the systematic characterization of a circular RNA-associated ceRNA network

CONTEXT

Polygonatum sibiricum polysaccharide (PSP), derived from Polygonatum sibiricum Delar. ex Redoute (Liliaceae), is known to be able to delay the ageing process. However, the specific mechanisms underlying these effects are not clear.

OBJECTIVE

To investigate the mechanisms underlying the effects of PSP treatment on brain ageing by the application of transcriptomic analysis.

MATERIALS AND METHODS

Forty Kunming mice were randomly divided into four groups (control, d-galactose, low-dose PSP, high-dose PSP). Mice were administered d-galactose (50 mg/kg, hypodermic injection) and PSP (200 or 400 mg/kg, intragastric administration) daily for 60 days. Behavioural responses were evaluated with the Morris water maze and the profiles of circRNA, miRNA, and mRNA, in the brains of experimental mice were investigated during the ageing process with and without PSP treatment.

RESULTS

PSP improved cognitive function during brain ageing, as evidenced by a reduced escape latency time (p < 0.05) and an increase in the number of times mice crossed the platform (p < 0.05). A total of 37, 13, and 679, circRNAs, miRNAs, and mRNAs, respectively, were significantly altered by PSP treatment (as evidenced by a fold change ≥2 and p < 0.05). These dysregulated RNAs were closely associated with synaptic activity. PSP regulated regulate nine mRNAs (Slc6a5, Bean1, Ace, Samd4, Olfr679, Olfr372, Dhrs9, Tsc1, Slc12a6), three miRNAs (mmu-miR-5110, mmu-miR-449a-5p, mmu-miR-1981-5p), and two circRNAs (2:29227578|29248878 and 5:106632925|106666845) in the competing endogenous RNA (ceRNA) network.

DISCUSSION AND CONCLUSIONS

Our analyses showed that multiple circRNAs, miRNAs, and mRNAs responded to PSP treatment in mice experiencing brain ageing.

Harnessing polyphenol power by targeting eNOS for vascular diseases

Vascular diseases arise due to vascular endothelium dysfunction in response to several pro-inflammatory stimuli and invading pathogens. Thickening of the vessel wall, formation of atherosclerotic plaques consisting of proliferating smooth muscle cells, macrophages and lymphocytes are the major consequences of impaired endothelium resulting in atherosclerosis, hypercholesterolemia, hypertension, type 2 diabetes mellitus, chronic renal failure and many others. Decreased nitric oxide (NO) bioavailability was found to be associated with anomalous endothelial function because of either its reduced production level by endothelial NO synthase (eNOS) which synthesize this potent endogenous vasodilator from L-arginine or its enhanced breakdown due to severe oxidative stress and eNOS uncoupling. Polyphenols are a group of bioactive compounds having more than 7000 chemical entities present in different cereals, fruits and vegetables. These natural compounds possess many OH groups which are largely responsible for their strong antioxidative, anti-inflammatory antithrombotic and anti-hypersensitive properties. Several flavonoid-derived polyphenols like flavones, isoflavones, flavanones, flavonols and anthocyanidins and non-flavonoid polyphenols like tannins, curcumins and resveratrol have attracted scientific interest for their beneficial effects in preventing endothelial dysfunction. This article will focus on in vitro as well as in vivo and clinical studies evidences of the polyphenols with eNOS modulating activity against vascular disease condition while their molecular mechanism will also be discussed.

A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database

Simple Summary

Glioma patients that present a somatic mutation in the isocitrate dehydrogenase 1 (IDH1) gene have a significantly better prognosis and overall survival than patients with the wild-type genotype. An IDH1 mutation is hypothesized to occur early during cellular transformation and leads to further genetic instability. A genome-wide profiling of glioma patients in the Catalogue of Somatic Mutations in Cancer (COSMIC) database was performed to classify the genetic differences in IDH1-mutant versus IDH1-wildtype patients. This classification will aid in a better understanding of how this specific mutation influences the genetic make-up of glioma and the resulting prognosis. Key differences in co-mutation and gene expression levels were identified that correlate with an improved prognosis.

Abstract

Gliomas are differentiated into two major disease subtypes, astrocytoma or oligodendroglioma, which are then characterized as either IDH (isocitrate dehydrogenase)-wild type or IDH-mutant due to the dramatic differences in prognosis and overall survival. Here, we investigated the genetic background of IDH1-mutant gliomas using the Catalogue of Somatic Mutations in Cancer (COSMIC) database. In astrocytoma patients, we found that IDH1 is often co-mutated with TP53, ATRX, AMBRA1, PREX1, and NOTCH1, but not CHEK2, EGFR, PTEN, or the zinc finger transcription factor ZNF429. The majority of the mutations observed in these genes were further confirmed to be either drivers or pathogenic by the Cancer-Related Analysis of Variants Toolkit (CRAVAT). Gene expression analysis showed down-regulation of DRG2 and MSN expression, both of which promote cell proliferation and invasion. There was also significant over-expression of genes such as NDRG3 and KCNB1 in IDH1-mutant astrocytoma patients. We conclude that IDH1-mutant glioma is characterized by significant genetic changes that could contribute to a better prognosis in glioma patients.

Challenges of applying multicellular tumor spheroids in preclinical phase

The three-dimensional (3D) multicellular tumor spheroids (MCTs) model is becoming an essential tool in cancer research as it expresses an intermediate complexity between 2D monolayer models and in vivo solid tumors. MCTs closely resemble in vivo solid tumors in many aspects, such as the heterogeneous architecture, internal gradients of signaling factors, nutrients, and oxygenation. MCTs have growth kinetics similar to those of in vivo tumors, and the cells in spheroid mimic the physical interaction of the tumors, such as cell-to-cell and cell-to-extracellular matrix interactions. These similarities provide great potential for studying the biological properties of tumors and a promising platform for drug screening and therapeutic efficacy evaluation. However, MCTs are not well adopted as preclinical tools for studying tumor behavior and therapeutic efficacy up to now. In this review, we addressed the challenges with MCTs application and discussed various efforts to overcome the challenges.

Antiviral Potential of Algal Metabolites-A Comprehensive Review

Historically, algae have stimulated significant economic interest particularly as a source of fertilizers, feeds, foods and pharmaceutical precursors. However, there is increasing interest in exploiting algal diversity for their antiviral potential. Here, we present an overview of 50-years of scientific and technological developments in the field of algae antivirals. After bibliometric analysis of 999 scientific references, a survey of 16 clinical trials and analysis of 84 patents, it was possible to identify the dominant algae, molecules and viruses that have been shaping and driving this promising field of research. A description of the most promising discoveries is presented according to molecule class. We observed a diverse range of algae and respective molecules displaying significant antiviral effects against an equally diverse range of viruses. Some natural algae molecules, like carrageenan, cyanovirin or griffithsin, are now considered prime reference molecules for their outstanding antiviral capacity. Crucially, while many algae antiviral applications have already reached successful commercialization, the large spectrum of algae antiviral capacities already identified suggests a strong potential for future expansion of this field.

Reduced Graphene Oxides Modulate the Expression of Cell Receptors and Voltage-Dependent Ion Channel Genes of Glioblastoma Multiforme

The development of nanotechnology based on graphene and its derivatives has aroused great scientific interest because of their unusual properties. Graphene (GN) and its derivatives, such as reduced graphene oxide (rGO), exhibit antitumor effects on glioblastoma multiforme (GBM) cells in vitro. The antitumor activity of rGO with different contents of oxygen-containing functional groups and GN was compared. Using FTIR (fourier transform infrared) analysis, the content of individual functional groups (GN/exfoliation (ExF), rGO/thermal (Term), rGO/ammonium thiosulphate (ATS), and rGO/ thiourea dioxide (TUD)) was determined. Cell membrane damage, as well as changes in the cell membrane potential, was analyzed. Additionally, the gene expression of voltage-dependent ion channels (clcn3, clcn6, cacna1b, cacna1d, nalcn, kcne4, kcnj10, and kcnb1) and extracellular receptors was determined. A reduction in the potential of the U87 glioma cell membrane was observed after treatment with rGO/ATS and rGO/TUD flakes. Moreover, it was also demonstrated that major changes in the expression of voltage-dependent ion channel genes were observed in clcn3, nalcn, and kcne4 after treatment with rGO/ATS and rGO/TUD flakes. Furthermore, the GN/ExF, rGO/ATS, and rGO/TUD flakes significantly reduced the expression of extracellular receptors (uPar, CD105) in U87 glioblastoma cells. In conclusion, the cytotoxic mechanism of rGO flakes may depend on the presence and types of oxygen-containing functional groups, which are more abundant in rGO compared to GN.

Advances in multimodal data fusion in neuroimaging: Overview, challenges, and novel orientation

Multimodal fusion in neuroimaging combines data from multiple imaging modalities to overcome the fundamental limitations of individual modalities. Neuroimaging fusion can achieve higher temporal and spatial resolution, enhance contrast, correct imaging distortions, and bridge physiological and cognitive information. In this study, we analyzed over 450 references from PubMed, Google Scholar, IEEE, ScienceDirect, Web of Science, and various sources published from 1978 to 2020. We provide a review that encompasses (1) an overview of current challenges in multimodal fusion (2) the current medical applications of fusion for specific neurological diseases, (3) strengths and limitations of available imaging modalities, (4) fundamental fusion rules, (5) fusion quality assessment methods, and (6) the applications of fusion for atlas-based segmentation and quantification. Overall, multimodal fusion shows significant benefits in clinical diagnosis and neuroscience research. Widespread education and further research amongst engineers, researchers and clinicians will benefit the field of multimodal neuroimaging.

Continuous moulting by Antarctic krill drives major pulses of carbon export in the north Scotia Sea, Southern Ocean

Antarctic krill play an important role in biogeochemical cycles and can potentially generate high-particulate organic carbon (POC) fluxes to the deep ocean. They also have an unusual trait of moulting continuously throughout their life-cycle. We determine the krill seasonal contribution to POC flux in terms of faecal pellets (FP), exuviae and carcasses from sediment trap samples collected in the Southern Ocean. We found that krill moulting generated an exuviae flux of similar order to that of FP, together accounting for 87% of an annual POC flux (22.8 g m⁻² y⁻¹). Using an inverse modelling approach, we determined the krill population size necessary to generate this flux peaked at 261 g m⁻². This study shows the important role of krill exuviae as a vector for POC flux. Since krill moulting cycle depends on temperature, our results highlight the sensitivity of POC flux to rapid regional environmental change.

Antarctic krill are known to be important to the carbon cycle, but the exact contribution is not known. Here the authors show that krill moulting is a major vector of carbon export in the Southern Ocean, together with krill faecal pellets accounting for almost 90% of annual particulate organic carbon flux.

Western influenced lifestyle and Kv2.1 association as predicted biomarkers for Tunisian colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is the third most diagnosed malignancy worldwide. The global burden is expected to increase along with ongoing westernized behaviors and lifestyle. The etiology of CRC remains elusive and most likely combines environmental and genetic factors. The Kv2.1 potassium channel encoded by KCNB1 plays a collection of roles in malignancy of cancer and may be a key factor of CRC susceptibility. Our study provides baseline association between Tunisian CRC and interactions between KCNB1 variants and lifestyle factors.

METHODS

A case-control study involving 300 CRC patients, and 300 controls was conducted Patients were carefully phenotyped and followed till the end of study. KCNB1 genotyping was confirmed by Sanger sequencing. Bivariate and multivariable logistic regression analyses were used to assess the clinical status, lifestyle and study polymorphisms association with CRC.

RESULTS

We noted significant gender association with CRC occurrence. Moreover, CRC risk increases with high meat and fat consumption, alcohol use and physical activity (PA). Carriage of rs1051296 A/G and both rs11468831 ins/del and del/del genotypes (p < 0.001) were significantly associated with CRC risk. Analysis according to gender reveals correlation of rs1051295 A/G, rs11468831 non ins/ins (p = 0.01) with CRC susceptibility regardless of patients' gender while rs3331 T/C (p = 0.012) was associated with females. Stratification study according to malignancy site; Rectal Cancer (RC) and Colon Cancer (CC), reveals increasing RC risk by gender and high meat and fat consumption, alcohol use and PA. However, additional association with high brine consumption was noted for CC. The rs1051295 A/G (p = 0.01) was associated with RC risk. Increased CC risk was associated with carriage of rs1051295 A/G, rs11168831 (del/del) and (ins/del) genotypes.

CONCLUSION

The risk of CRC increases with modifiable factors by Western influences on Tunisian lifestyle such as alcohol use, high fat consumption and possibly inadequate intake of vegetables. In addition, KCNB1 polymorphisms also markedly influence CRC susceptibility. Our study establishes key elements of a baseline characterization of clinical state, Western influenced lifestyle and KCNB1 variants associated with Tunisian CRC.

Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis

Glioma is the most common brain tumor with high mortality. However, there are still challenges for the timely and accurate diagnosis and effective treatment of the tumor. One hundred and twenty-one samples with grades II, III and IV from the Gene Expression Omnibus database were used to construct gene co-expression networks to identify hub modules closely related to glioma grade, and performed pathway enrichment analysis on genes from significant modules. In gene co-expression network constructed by 2345 differentially expressed genes from 121 gene expression profiles for glioma, we identified the black and blue modules that associated with grading. The module preservation analysis based on 118 samples indicates that the two modules were replicable. Enrichment analysis showed that the extracellular matrix genes were enriched for blue module, while cell division genes were enriched for black module. According to survival analysis, 21 hub genes were significantly up-regulated and one gene was significantly down-regulated. What’s more, IKBIP, SEC24D, and FAM46A are the genes with little attention among the 22 hub genes. In this study, IKBIP, SEC24D, and FAM46A related to glioma were mentioned for the first time to the current knowledge, which might provide a new idea for us to study the disease in the future. IKBIP, SEC24D and FAM46A among the 22 hub genes identified that are related to the malignancy degree of glioma might be used as new biomarkers to improve the diagnosis, treatment and prognosis of glioma.

Ion Channels and Their Role in the Pathophysiology of Gliomas

Malignant gliomas are the most common primary central nervous system tumors and their prognosis is very poor. In recent years, ion channels have been demonstrated to play important roles in tumor pathophysiology such as regulation of gene expression, cell migration, and cell proliferation. In this review, we summarize the current knowledge on the role of ion channels on the development and progression of gliomas. Cell volume changes through the regulation of ion flux, accompanied by water flux, are essential for migration and invasion. Signaling pathways affected by ion channel activity play roles in cell survival and cell proliferation. Moreover, ion channels are involved in glioma-related seizures, sensitivity to chemotherapy, and tumor metabolism. Ion channels are potential targets for the treatment of these lethal tumors. Despite our increased understanding of the contributions of ion channels to glioma biology, this field remains poorly studied. This review summarizes the current literature on this important topic.

Identification and validation of potential novel prognostic biomarkers for patients with glioma based on a gene co-expression network

BACKGROUND

Glioma is widely regarded as one of most lethal and challenging diseases of the nervous system. The aim of this study was to identify novel biomarkers that offer better prognosis prediction for Chinese patients with glioma.

METHODS

By using systematic approaches, the co-expression modules were identified from the Chinese Glioma Genome Atlas (CGGA) database through weighted gene co-expression network analysis and functional enrichment of essential modules of Kyoto Encyclopedia of Genes and Genomes terms. The co-expression modules were validated using The Cancer Genome Atlas database and the protein-protein interaction (PPI) network.

RESULTS

For network construction, 5,374 among 21,494 genes were selected, and an increasing genetic variance was associated with the prognosis of glioma. By using functional enrichment analysis, the involvement of multiple vital processes, including metabolism of fatty acids, was correlated with the patient prognosis. Notably, five hub genes (KCNB1, UST, SOX8, KLHL42, and HDAC4) were identified for these processes. Accordingly, using the Kaplan-Meier method, there was enhanced expression of these genes in patients with significantly lower overall survival rates, especially those from the CGGA database.

CONCLUSIONS

This study not only revealed the essential co-expression gene modules in patients with glioma, but it also unraveled the potential signaling pathways underlying these functional processes.

Ion Channels in Cancer: Orchestrators of Electrical Signaling and Cellular Crosstalk

Ion channels are pore-forming transmembrane proteins that govern ion flux to regulate a myriad of biological processes in development, physiology, and disease. Across various types of cancer, ion channel expression and activity are often dysregulated. We review the contribution of ion channels to multiple stages of tumorigenesis based on data from in vivo model systems. As intertumoral and intratumoral heterogeneities are major obstacles in developing effective therapies, we provide perspectives on how ion channels in tumor cells and their microenvironment represent targetable vulnerabilities in the areas of tumor-stromal cell interactions, cancer neuroscience, and cancer mechanobiology.

KCNB1 gene polymorphisms and related indel as predictor biomarkers of treatment response for colorectal cancer - toward a personalized medicine

The KCNB1 gene variants were differentially associated with cancers. However, their association with colorectal cancer has not yet been explored. We investigated the contribution of the KCNB1 gene variants rs3331, rs1051295, and indel (insertion/deletion) rs11468831 Polymorphism as predictors of the treatment response in colorectal cancer patients. A retrospective study, which involved 291 Tunisian colorectal cancer patients (aged 60.0 ± 13.1 years), who were stratified into responder and non-responder groups, according to TNM stages and their responsiveness to chemotherapy based on fluorouracil. KCNB1 genotyping was performed with amplification-refractory mutation system-polymerase chain reaction, and was confirmed by Sanger sequencing. Sex-specific response was found and colorectal cancer females are less likely to achieve a positive response during the chemotherapy strategy, compared to males. Weight and body mass index, tumor size, and tumor localization are considered as predictive factors to treatment responsiveness. Carriage of rs11468831 Ins allele was significantly associated with successful therapy achievement (p adjusted < 0.001). Stratification of colorectal cancer patients' response according to tumor localization and TNM stages reveals negative association of rs3331 Major allele to treatment response among the patients with advanced cancer stages (subgroup G2). The presence of rs3331 (homozygous minor) C/C genotype was positively associated with decline in carcino-embryonic antigen (p = 0.043) and CA19-9 (p = 0.014) serum levels. On the other hand, the presence of rs1051295 (homozygous minor) A/A genotype was correlated with marked decline in CA19-9 serum levels. KCNB1 haplotype did not reveal any association between haplotypes and treatment response. The results obtained suggest that gender-specific strategies for screening treatment and prevention protocols as well as KCNB1 variants may constitute an effective model for ongoing personalization medicine.

MicroRNAs Associated With Colon Cancer: New Potential Prognostic Markers and Targets for Therapy

MicroRNAs (miRNAs) are a kind of non-coding RNA (ncRNA) that regulate the expression of target genes and play a role in the occurrence and development of cancers. Colon cancer (COAD) is the second most common cause of cancer-related mortality. However, the prognostic value of miRNAs in COAD is still confusing. In this study, we obtain miRNAs and messenger RNAs (mRNAs) expression profiles of COAD from the Cancer Genome Atlas (TCGA) database. After preliminary data screening and preprocessing, we acquire the expression data of 894 miRNAs and 17,019 mRNAs. Then, compared with the normal samples, 39 upregulated miRNAs and 54 downregulated miRNAs are identified by differential expression analysis. Furthermore, we obtain 1,487 upregulated mRNAs and 2,847 downregulated mRNAs. We confirm nine key miRNAs related to the survival rate of COAD patients. Moreover, by using bioinformatics methods, we get 461 common genes from both the target genes of these nine key miRNAs and differentially expressed mRNAs. Through analyzing the protein-protein interaction (PPI) network of these 461 common genes and survival analysis, we confirm five hub genes as promising biomarkers for COAD prognosis. It is worth mentioning that no previous reports have found that PGR and KCNB1 are related to COAD. We expect these key miRNAs and hub genes will provide a new way for the study of COAD.

Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU

Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Therefore, treatments that may be effective in some cases are not effective in others. We previously developed an algorithm for identifying combinations of carcinogenic genes with mutations (multi-hit combinations), which could suggest a likely cause for individual instances of cancer. Most cancers are estimated to require three or more hits. However, the computational complexity of the algorithm scales exponentially with the number of hits, making it impractical for identifying combinations of more than two hits. To identify combinations of greater than two hits, we used a compressed binary matrix representation, and optimized the algorithm for parallel execution on an NVIDIA V100 graphics processing unit (GPU). With these enhancements, the optimized GPU implementation was on average an estimated 12,144 times faster than the original integer matrix based CPU implementation, for the 3-hit algorithm, allowing us to identify 3-hit combinations. The 3-hit combinations identified using a training set were able to differentiate between tumor and normal samples in a separate test set with 90% overall sensitivity and 93% overall specificity. We illustrate how the distribution of mutations in tumor and normal samples in the multi-hit gene combinations can suggest potential driver mutations for further investigation. With experimental validation, these combinations may provide insight into the etiology of cancer and a rational basis for targeted combination therapy.

Unveiled feather microcosm: feather microbiota of passerine birds is closely associated with host species identity and bacteriocin-producing bacteria

The functional relevance of microbiota is a key aspect for understanding host-microbiota interactions. Mammalian skin harbours a complex consortium of beneficial microorganisms known to provide health and immune-boosting advantages. As yet, however, little is known about functional microbial communities on avian feathers, including their co-evolution with the host and factors determining feather microbiota (FM) diversity. Using 16S rRNA profiling, we investigated how host species identity, phylogeny and geographic origin determine FM in free-living passerine birds. Moreover, we estimated the relative abundance of bacteriocin-producing bacteria (BPB) and keratinolytic feather damaging bacteria (FDB) and evaluated the ability of BPB to affect FM diversity and relative abundance of FDB. Host species identity was associated with feather bacterial communities more strongly than host geographic origin. FM functional properties differed in terms of estimated BPB and FDB relative abundance, with both showing interspecific variation. FM diversity was negatively associated with BPB relative abundance across species, whereas BPB and FDB relative abundance was positively correlated. This study provides the first thorough evaluation of antimicrobial peptides-producing bacterial communities inhabiting the feather integument, including their likely potential to mediate niche-competition and to be associated with functional species-specific feather microbiota in avian hosts.

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray

: Breast cancer (BRCA) remains the leading cause of cancer morbidity and mortality worldwide. In the present study, we identified novel biomarkers expressed during estradiol and tamoxifen treatment of BRCA. The microarray dataset of E-MTAB-4975 from Array Express database was downloaded, and the differential expressed genes (DEGs) between estradiol-treated BRCA sample and tamoxifen-treated BRCA sample were identified by limma package. The pathway and gene ontology (GO) enrichment analysis, construction of protein-protein interaction (PPI) network, module analysis, construction of target genes-miRNA interaction network and target genes-transcription factor (TF) interaction network were performed using bioinformatics tools. The expression, prognostic values, and mutation of hub genes were validated by SurvExpress database, cBioPortal, and human protein atlas (HPA) database. A total of 856 genes (421 up-regulated genes and 435 down-regulated genes) were identified in T47D (overexpressing Split Ends (SPEN) + estradiol) samples compared to T47D (overexpressing Split Ends (SPEN) + tamoxifen) samples. Pathway and GO enrichment analysis revealed that the DEGs were mainly enriched in response to lysine degradation II (pipecolate pathway), cholesterol biosynthesis pathway, cell cycle pathway, and response to cytokine pathway. DEGs (MCM2, TCF4, OLR1, HSPA5, MAP1LC3B, SQSTM1, NEU1, HIST1H1B, RAD51, RFC3, MCM10, ISG15, TNFRSF10B, GBP2, IGFBP5, SOD2, DHF and MT1H) , which were significantly up- and down-regulated in estradiol and tamoxifen-treated BRCA samples, were selected as hub genes according to the results of protein-protein interaction (PPI) network, module analysis, target genes-miRNA interaction network and target genes-TF interaction network analysis. The SurvExpress database, cBioPortal, and Human Protein Atlas (HPA) database further confirmed that patients with higher expression levels of these hub genes experienced a shorter overall survival. A comprehensive bioinformatics analysis was performed, and potential therapeutic applications of estradiol and tamoxifen were predicted in BRCA samples. The data may unravel the future molecular mechanisms of BRCA.

Case report: mutation analysis of primary pulmonary lymphoepithelioma-like carcinoma via whole-exome sequencing

Background

Primary pulmonary lymphoepithelioma-like carcinoma (LELC) is a rare tumor subtype accounting for around 0.9% of lung cancers. At present, research on LELC mainly focuses on pathological diagnosis, while the molecular mutation landscape is still unclear.

Case presentation

A 72-year-old female presented a productive cough for three weeks followed by severe symptoms for another week. Respiratory sounds were weak and coarser in the right lung field. F-FDG PET-CTA showed a hypermetabolic mass in the upper lobe of the right lung as well as the enlargement of right hilar and subcarinal lymph nodes. Hematoxylin-eosin staining and immunohistochemistry staining of the biopsy established the diagnosis of primary pulmonary LELC. After thoracoscopic-assisted radical resection of right lung cancer and middle lobe of right lung, the patient’s vital signs were stable without apparent productive cough, chest pain, chest tightness and other subjective discomforts. Furtherwhole exome sequencing of the patient’s tumor tissue and leukocytes (served as a germline mutation control) revealed 613 somatic gene mutations, and of which mutations in PRIM2, KCNB1, CDH1, and ATRX were most likely related to the LELC pathogenesis. The recurrence of gene mutations from various cancers database and a tumor mutation burden (TMB) of 18.7 mutations/mb were revealed as well.

Conclusion

Our findings have illustrated the genomic profile of a primary pulmonary LELC case and provided a positive biomarker that immune checkpoint blockade is potentially effective for this patient in further treatment.

Complex regulatory network allows Myriophyllum aquaticum to thrive under high-concentration ammonia toxicity

Plants easily experience ammonia (NH₄⁺) toxicity, especially aquatic plants. However, a unique wetland plant species, Myriophyllum aquaticum, can survive in livestock wastewater with more than 26 mM NH₄⁺. In this study, the mechanisms of the M. aquaticum response to NH₄⁺ toxicity were analysed with RNA-seq. Preliminary analysis of enzyme activities indicated that key enzymes involved in nitrogen metabolism were activated to assimilate toxic NH₄⁺ into amino acids and proteins. In response to photosystem damage, M. aquaticum seemed to remobilize starch and cellulose for greater carbon and energy supplies to resist NH₄⁺ toxicity. Antioxidative enzyme activity and the secondary metabolite content were significantly elevated for reactive oxygen species removal. Transcriptomic analyses also revealed that genes involved in diverse functions (e.g., nitrogen, carbon and secondary metabolisms) were highly responsive to NH₄⁺ stress. These results suggested that a complex physiological and genetic regulatory network in M. aquaticum contributes to its NH₄⁺ tolerance.

Gas-Generating Nanoplatforms: Material Chemistry, Multifunctionality, and Gas Therapy

The fast advances of theranostic nanomedicine enable the rational design and construction of diverse functional nanoplatforms for versatile biomedical applications, among which gas-generating nanoplatforms (GGNs) have emerged very recently as unique theranostic nanoplatforms for broad gas therapies. Here, the recent developments of the rational design and chemical construction of versatile GGNs for efficient gas therapies by either exogenous physical triggers or endogenous disease-environment responsiveness are reviewed. These gases involve some therapeutic gases that can directly change disease status, such as oxygen (O₂ ), nitric oxide (NO), carbon monoxide (CO), hydrogen (H₂ ), hydrogen sulfide (H₂ S) and sulfur dioxide (SO₂ ), and other gases such as carbon dioxide (CO₂ ), dl-menthol (DLM), and gaseous perfluorocarbon (PFC) for supplementary assistance of the theranostic process. Abundant nanocarriers have been adopted for gas delivery into lesions, including poly(d,l-lactic-co-glycolic acid), micelles, silica/mesoporous silica, organosilica, MnO₂ , graphene, Bi₂ Se₃ , upconversion nanoparticles, CaCO₃ , etc. Especially, these GGNs have been successfully developed for versatile biomedical applications, including diagnostic imaging and therapeutic use. The biosafety issue, challenges faced, and future developments on the rational construction of GGNs are also discussed for further promotion of their clinical translation to benefit patients.

Intramuscular preadipocytes impede differentiation and promote lipid deposition of muscle satellite cells in chickens

Background

Skeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to investigate the effects of IMPA on MSC in chickens and unveil the molecular mechanisms by transcriptome analysis.

Results

Primary MSC and IMPA were isolated from the pectoralis major muscle of 7-day-old chickens. After both cell types reached confluence, MSC were cultured alone or co-cultured with IMPA for 2 or 4 d. MSC treated for 2 d were subjected to RNA-seq. A total of 1653 known differentially expressed genes (DEG) were identified between co-cultured and mono-cultured MSC (|log2 FC| ≥ 1, FDR < 0.01). Based on Gene Ontology analysis, 48 DEG related to muscle development were screened, including the key genes MYOD1, MYOG, PAX7, and TMEM8C. The 44 DEG related to lipid deposition included the key genes CD36, FABP4, ACSBG2, CYP7A1 and PLIN2. Most of the DEG related to muscle development were downregulated in co-cultured MSC, and DEG related to lipid deposition were upregulated. Immunofluorescence of MHC supported IMPA impeding differentiation of MSC, and Oil Red O staining showed concurrent promotion of lipid deposition. Pathway analysis found that several key genes were enriched in JNK/MAPK and PPAR signaling, which may be the key pathways regulating differentiation and lipid deposition in MSC. Additionally, pathways related to cell junctions may also contribute to the effect of IMPA on MSC.

Conclusions

The present study showed that IMPA impeded differentiation of MSC while promoting their lipid deposition. Pathway analysis indicated that IMPA might inhibit differentiation via the JNK/MAPK pathway, and promote lipid deposition via the PPAR pathway. This study supplies insights into the effect of IMPA on MSC, providing new clues on exposing the molecular mechanisms underlying the interplay between skeletal muscle and intramuscular fat in chickens.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5209-5) contains supplementary material, which is available to authorized users.

Insight into selective mechanism of class of I-BRD9 inhibitors toward BRD9 based on molecular dynamics simulations

Recently, bromodomain-containing protein 9 (BRD9), 7 (BRD7), and 4 (BRD4) have been potential targets of anticancer drug design. Molecular dynamic simulations followed by molecular mechanics Poisson-Boltzmann surface area calculation were performed to study the selective mechanism of I-BRD9 inhibitor H1B and its derivatives N1D, TVU, and 5V2 toward BRD9 and BRD4. The rank of our calculated binding free energies agrees with that of the experimental data. The results show that binding free energy of H1B to BRD7 is slightly lower than that of H1B to BRD9, and all four inhibitors bind more tightly to BRD9 than to BRD4. Decomposition of binding free energies into individual residues implies that Ile164 and Asn211 in BRD7 and Ile53 and Asn100 in BRD9 play a significant role in the selectivity of H1B toward BRD7 and BRD9. Besides, several key residues Phe44, Ile53, Asn100, Thr104 in BRD9 and Pro82, Lys91, Asn140, Asp144 in BRD4 that are located in the ZA-loop and BC-loop provide significant contributions to binding selectivity of inhibitors to BRD9 and BRD4. This study is expected to provide important theoretical guidance for rational designs of highly selective inhibitors targeting BRD9 and BRD4.

Identification of a DNA Repair-Related Multigene Signature as a Novel Prognostic Predictor of Glioblastoma

BACKGROUND

Glioblastoma (GBM) is an extremely challenging malignancy to treat. Although temozolomide (TMZ) is a standard treatment regimen, many patients with GBM develop chemoresistance. The aim of this study was to identify a DNA repair-related gene signature to better stratify patients treated with TMZ.

METHODS

We selected 89 cases of primary GBM (pGBM) from the Chinese Glioma Genome Atlas RNA-seq dataset as the training cohort, whereas The Cancer Genome Atlas RNA-seq and Gene Set Enrichment (GSE) 16011 mRNA array sets were used as validation cohorts. Regression analysis and linear risk score assessment were performed to build a DNA repair-related signature. We used Kaplan-Meier analysis to evaluate the predictive value of the signature for overall survival (OS) in the different groups. Multivariate Cox regression analysis was used to determine whether the 5-gene signature could independently predict OS.

RESULTS

Using our 5-gene signature panel of APEX1, APRT, PARP2, PMS2L2, and POLR2L, we divided patients with pGBM into high- and low-risk groups. Patients with a low-risk score were predicted to have favorable survival and greater benefit from TMZ therapy compared with patients from the high-risk group (P < 0.05). Moreover, receiver operating characteristic curves showed that the multigene signature was the most sensitive and specific model for survival prediction (P < 0.05).

CONCLUSIONS

Among patients with pGBM, classification based on a risk score determined using a 5-gene panel indicated different OS and reaction to TMZ. The findings in this study demonstrate that this unique 5-gene signature could be a novel model to predict OS and provide accurate therapy for patients with pGBM.