Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratification (hazard ratio (HR) > 4; log-rank test, p-value < 0.01). Based on independent datasets and seven additional cancers, the diagnostic and prognostic classifiers also had better robustness and stability. The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction. Conclusion The present study provides a comprehensive analysis of ccRCC using multi-omics data. These findings indicated that multi-omics analysis could identify some novel epigenetic factors, which were the most important causes of advanced cancer and poor clinical prognosis. Diagnostic and prognostic biomarkers were identified, which provided a promising avenue to develop effective therapies for ccRCC.
Liu et al. (2020) Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 8:e9654 https://doi.org/10.7717/peerj.9654
Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression
Myostatin (MSTN) is a negative regulator of muscle growth, which restrains the proliferation and differentiation of myoblasts. To understand the role of two mstn genes of Takifugu bimaculatus, the full-length cDNAs of 1131 bp Tbmstn1 and 1,080 bp Tbmstn2 were obtained from the T. bimaculatus’ genomic database, which encodes 376 and 359 amino acids, respectively. The results of qRT-PCR showed that Tbmstn1 was expressed in the eye, kidney, spleen, skeletal muscle, gill, and brain, and the expression level in the skeletal muscle was extremely significantly higher than in other examined tissues. Tbmstn2 was expressed in the skin, skeletal muscle, gill, and brain, and had the highest expression in the skeletal muscle, followed by expression in the brain. Meanwhile, in different stages of embryonic development, the expression of Tbmstn1 started from the gastrula stage. Its expression in the eye-pigment formation stage and hatching stage was significantly higher than that in other stages. The Tbmstn2 was expressed in all examined embryonic stages with different levels, and the highest expression was detected in the eye-pigment formation stage. These results suggested that Tbmstn1 and Tbmstn2 may involve in the development of skeletal muscle, and Tbmstn2 may be related to the formation of nervous system.
Sheng et al. (2020) Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression. PeerJ 8:e9655 https://doi.org/10.7717/peerj.9655
Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians
Background No Arabic or its dialect questionnaire is available to evaluate the anterior knee pain in the Saudi Arabian religious population. This study aims to translate, adapt, and psychometrically validate the Knee Injury and Osteoarthritis Outcome Score (KOOS-PF) Patellofemoral scale in the Arabic language in Saudi Arabic dialect. Method Translation has been done as per standard guidelines. The questionnaire was administered to 95 patients to determine the psychometric properties including on two different occasions, with a 48-hour gap in-between; to ensure that their answers were reliable; 84 patients (88.4% compliance rate) responded for test and retest reliability, ceiling-floor effects, validity and other psychometric criteria. Results Cronbach’s alpha (internal consistency) and test–retest reliability was good and excellent (∞ = 0.81; ICC > 0.95). None of the items showed >30% floor or ceiling effect and the minimal detectable change was within the acceptable range (<30%). The KOOS-PF subscale showed a moderate correlation (−0.568) with pain-visual analog scale for its construct validity. Conclusion The Arabic dialect of KOOS-PFis reliable and valid to be used to evaluate isolated knee pain of patellofemoral origin in Muslim patients in Saudi Arabia.
Ateef (2020) Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians. PeerJ 8:e9323 https://doi.org/10.7717/peerj.9323
Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage
In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic.
Auscavitch et al. (2020) Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ 8:e9523 https://doi.org/10.7717/peerj.9523
Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight
Background Controversy exists on the relationship between iron metabolism and cardiometabolic risk. The aim of this study was to determine if there is a link between dysmetabolic iron and cardiometabolic markers in subjects with excess body weight. Methods Cross-sectional study with fifty participants presenting overweight or obesity and at least another metabolic syndrome factor. Determinations: anthropometry, body composition, blood pressure, lipids, glucose, insulin, leptin, areas under the curve (AUC) for glucose and insulin after an oral glucose tolerance test, hs-C reactive protein (hs-CRP), blood count, ferritin, transferrin, transferrin saturation (TSAT), soluble transferrin receptor (sTfR). Gender-adjusted linear correlations and two independent samples t tests were used. Results Ferritin was positively correlated with insulin-AUC (r = 0.547, p = 0.008) and TSAT was negatively correlated with waist-hip ratio (r = − 0.385, p = 0.008), insulin (r = − 0.551, p < 0.001), and insulin resistance (HOMA-IR, r = − 0.586, p < 0.001). Subjects with TSAT ≤ 20% had higher insulin (p = 0.012) and HOMA-IR (p = 0.003) compared to those with TSAT > 20%. In conclusion, the observed results suggest that iron transport and storage are altered in subjects with overweight/obesity, at the same time that they exhibit the characteristic features of insulin resistance. Nevertheless, this occurs without iron overload or deficiency. These results should be validated in wider cohorts since they suggest that iron transport and storage should be assessed when performing the clinical evaluation of subjects with excess body weight.
Vaquero et al. (2020) Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight. PeerJ 8:e9528 https://doi.org/10.7717/peerj.9528
Heritability of the extra-pair mating behaviour of the pied flycatcher in Western Siberia
Males and females take part in extra-pair copulations in most socially monogamous bird species. The mechanisms leading to the frequent occurrence of extra-pair offspring in socially monogamous couples are strongly debated and unresolved, and they are often difficult to distinguish from one another. Most hypotheses explaining the evolution of extra-pair reproduction suggest selective and adaptive scenarios for their origination and persistence. Is extra-pair paternity a heritable trait? We evaluated the heritability of extra-pair paternity in the pied flycatcher (Ficedula hypoleuca) nesting in Western Siberia. Estimated heritability was low: depending on the model used, the point estimate of the heritability (mode) varied from 0.005 to 0.11, and the bounds of the 95% confidence interval are [0–0.16] in the widest range. Thus, it seems that extra-pair mating behaviour in the pied flycatchers is a plastic phenotypic mating tactic with a small or no genetic component. Our data can help to understand the evolution of extra-pair mating behaviour in socially monogamous species.
Grinkov et al. (2020) Heritability of the extra-pair mating behaviour of the pied flycatcher in Western Siberia. PeerJ 8:e9571 https://doi.org/10.7717/peerj.9571
Functional characterization of the chlorzoxazone 6-hydroxylation activity of human cytochrome P450 2E1 allelic variants in Han Chinese
Backgrounds Cytochrome P450 (P450) 2E1 is one of the primary enzymes responsible for the metabolism of xenobiotics, such as drugs and environmental carcinogens. The genetic polymorphisms of the CYP2E1 gene in promoter and coding regions have been identified previously in the Han Chinese population from four different geographic areas of Mainland China. Methods To investigate whether genetic variants identified in the CYP2E1 coding region affect enzyme function, the enzymes of four single nucleotide polymorphism (SNP) variants in the coding region (novel c.1009C>T, causing p.Arg337X, where X represents the translational stop codon; c.227G>A, causing p.Arg76His; c.517G>A, yielding p.Gly173Ser; and c.1263C>T, presenting the highest allele frequency), two novel alleles (c.[227G>A;1263C>T] and c.[517G>A;1263C>T]), and the wild-type CYP2E1 were heterologously expressed in COS-7 cells and functionally characterized in terms of expression level and chlorzoxazone 6-hydroxylation activity. The impact of the CYP2E1 variant sequence on enzyme activity was predicted with three programs: Polyphen 2, PROVEAN and SIFT. Results The prematurely terminated p.Arg337X variant enzyme was undetectable by western blotting and inactive toward chlorzoxazone 6-hydroxylation. The c.1263C>T and c.[517G>A;1263C>T] variant enzymes exhibited properties similar to those of the wild-type CYP2E1. The CYP2E1 variants c.227G>A and c.[227G>A;1263C>T] displayed significantly reduced enzyme activity relative to that of the wild-type enzyme (decreased by 42.8% and 32.8%, respectively; P < 0.01). The chlorzoxazone 6-hydroxylation activity of the c.517G>A transfectant was increased by 31% compared with the wild-type CYP2E1 enzyme (P < 0.01). Positive correlations were observed between the protein content and enzyme activity for CYP2E1 (P = 0.0005, r2 = 0.8833). The characterization of enzyme function allelic variants in vitro was consistent with the potentially deleterious effect of the amino acid changes as determined by prediction tools. Conclusions These findings indicate that the genetic polymorphisms of CYP2E1, i.e., c.1009C>T (p.Arg337X), c.227G>A (p.Arg76His), and c.517G>A (p.Gly173Ser), could influence the metabolism of CYP2E1 substrates, such as chlorzoxazone.
Wang et al. (2020) Functional characterization of the chlorzoxazone 6-hydroxylation activity of human cytochrome P450 2E1 allelic variants in Han Chinese. PeerJ 8:e9628 https://doi.org/10.7717/peerj.9628
Air quality improvement during triple-lockdown in the coastal city of Kannur, Kerala to combat Covid-19 transmission
The novel SARS-CoV-2 coronavirus that emerged in the city of Wuhan, China, last year has since become the COVID-19 pandemic across all continents. To restrict the spread of the virus pandemic, the Government of India imposed a lockdown from 25 March 2020. In India, Kannur district was identified as the first “hotspot” of virus transmission and a “triple-lockdown” was implemented for a span of twenty days from 20 April 2020. This article highlights the variations of surface O3, NO, NO2, CO, SO2, NH3, VOC’s, PM10, PM2.5 and meteorological parameters at the time of pre-lockdown, lockdown and triple-lockdown days at Kannur town in south India using ground-based analyzers. From pre-lockdown days to triple-lockdown days, surface O3 concentration was found to increase by 22% in this VOC limited environment. NO and NO2 concentrations were decreased by 61% and 71% respectively. The concentration of PM10 and PM2.5 were observed to decline significantly by 61% and 53% respectively. Reduction in PM10 during lockdown and triple-lockdown days enhanced the intensity of solar radiation reaching the lower troposphere, and increased air temperature and reduced the relative humidity. Owing to this, surface O3 production over Kannur was found to have increased during triple-lockdown days. The concentration of CO (67%), VOCs (61%), SO2 (62%) and NH3 (16%) were found to decrease significantly from pre-lockdown days to triple-lockdown days. The air quality index revealed that the air quality at the observational site was clean during the lockdown.
Resmi et al. (2020) Air quality improvement during triple-lockdown in the coastal city of Kannur, Kerala to combat Covid-19 transmission. PeerJ 8:e9642 https://doi.org/10.7717/peerj.9642
DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses
Mollusc shells are an abundant resource that have been long used to predict the structures of ancient ecological communities, examine evolutionary processes, reconstruct paleoenvironmental conditions, track and predict responses to climatic change, and explore the movement of hominids across the globe. Despite the ubiquity of mollusc shell in many environments, it remains relatively unexplored as a substrate for molecular genetic analysis. Here we undertook a series of experiments using the New Zealand endemic greenshell mussel, Perna canaliculus, to explore the utility of fresh, aged, beach-cast and cooked mollusc shell for molecular genetic analyses. We find that reasonable quantities of DNA (0.002–21.48 ng/mg shell) can be derived from aged, beach-cast and cooked mussel shell and that this can routinely provide enough material to undertake PCR analyses of mitochondrial and nuclear gene fragments. Mitochondrial PCR amplification had an average success rate of 96.5% from shell tissue extracted thirteen months after the animal’s death. A success rate of 93.75% was obtained for cooked shells. Amplification of nuclear DNA (chitin synthase gene) was less successful (80% success from fresh shells, decreasing to 10% with time, and 75% from cooked shells). Our results demonstrate the promise of mollusc shell as a substrate for genetic analyses targeting both mitochondrial and nuclear genes.
Ferreira et al. (2020) DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses. PeerJ 8:e9420 https://doi.org/10.7717/peerj.9420
Semantic priming and schizotypal personality: reassessing the link between thought disorder and enhanced spreading of semantic activation
The term schizotypy refers to a group of stable personality traits with attributes similar to symptoms of schizophrenia, usually classified in terms of positive, negative or cognitive disorganization symptoms. The observation of increased spreading of semantic activation in individuals with schizotypal traits has led to the hypothesis that thought disorder, one of the characteristics of cognitive disorganization, stems from semantic disturbances. Nevertheless, it is still not clear under which specific circumstances (i.e., automatic or controlled processing, direct or indirect semantic relation) schizotypy affects semantic priming or whether it does affect it at all. We conducted two semantic priming studies with volunteers varying in schizotypy, one with directly related prime-target pairs and another with indirectly related pairs. Our participants completed a lexical decision task with related and unrelated pairs presented at short (250 ms) and long (750 ms) stimulus onset asynchronies (SOAs). Then, they responded to the brief versions of the Schizotypal Personality Questionnaire and the Oxford-Liverpool Inventory of Feelings and Experiences, both of which include measures of cognitive disorganization. Bayesian mixed-effects models indicated expected effects of SOA and semantic relatedness, as well as an interaction between relatedness and directness (greater priming effects for directly related pairs). Even though our analyses demonstrated good sensitivity, we observed no influence of cognitive disorganization over semantic priming. Our study provides no compelling evidence that schizotypal symptoms, specifically those associated with the cognitive disorganization dimension, are rooted in an increased spreading of semantic activation in priming tasks.
Rodríguez-Ferreiro et al. (2020) Semantic priming and schizotypal personality: reassessing the link between thought disorder and enhanced spreading of semantic activation. PeerJ 8:e9511 https://doi.org/10.7717/peerj.9511