COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression
Background Colorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression. Methods Using the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. The candidate biomarkers were also examined for constructing a prognostic model based on survival analysis. Results Among the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN3, GABRD, and LPAR1, was sufficient to optimize a RandomForest model that achieved > 98% balanced accuracy (and performant recall) of cancer vs. normal on external validation. Design of an optimal multivariate model based on survival analysis yielded a prognostic panel of three stage-IV salient genes, namely HOTAIR, GABRD, and DKK1. Based on the above sparse signatures, we have developed COADREADx, a web-server for potentially assisting colorectal cancer screening and patient risk stratification. COADREADx provides uncertainty measures for its predictions and needs clinical validation. It has been deployed for experimental non-commercial use at: https://apalanialab.shinyapps.io/coadreadx/.
Palaniappan et al. (2024) COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression. PeerJ 12:e18347 https://doi.org/10.7717/peerj.18347
The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures
Background Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ) but not ${\mathrm{NO}}_{2}^{-}$ NO 2 − to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$ NO 3 − to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Furthermore, ${\mathrm{NO}}_{3}^{-}$ NO 3 − is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Methods Both strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$ NO 3 − , or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − / ${\mathrm{NO}}_{2}^{-}$ NO 2 − transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. Results The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$ NO 3 − . These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − than those in both strains cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Since NnrS senses NO, these results suggest that strain GP59 reduced ${\mathrm{NO}}_{3}^{-}$ NO 3 − to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to ${\mathrm{NO}}_{3}^{-}$ NO 3 − by flavohemoproteins (NO dioxygenase; Hmp), explaining why ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction is not observed in strain GP59 cultured under oxic conditions. Conclusions Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.
Lestin et al. (2024) The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures. PeerJ 12:e18361 https://doi.org/10.7717/peerj.18361
Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis
Objective This study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis. Methods Single-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment. Results Two subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration. Conclusion The study revealed the heterogeneity of TECs in HCC and their potential roles in tumor progression, offering new perspectives and potential therapeutic targets for HCC molecular mechanisms. The findings emphasize the importance of further exploring TECs heterogeneity for understanding HCC pathogenesis and developing personalized treatment strategies.
Sun et al. (2024) Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis. PeerJ 12:e18362 https://doi.org/10.7717/peerj.18362
Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index
Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000–2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran’s Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000–2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000–2020 period, with a relatively stable overall spatial distribution. Areas with high–high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low–low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could directly enhance meltwater runoff from glaciers in the basin, thereby resulting in short-term improvement in the basin EEQ. Furthermore, rapid urbanization from 2015 to 2020 resulted in a decrease in the average RSEI value of the Tarim River Basin by 0.1 over this period, consequently, the EEQ level decreased slightly. Briefly, the EEQ in the Tarim River Basin showed an overall increasing trend from 2000 to 2020, further demonstrating the effectiveness of a series of implemented ecological restoration measures in the Tarim River Basin over this period.
Environmental Contamination and Remediation
Spatial and Geographic Information Science
Tang et al. (2024) Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index. PeerJ 12:e18368 https://doi.org/10.7717/peerj.18368
Development of a welfare assessment tool for tourist camp elephants in Asia
Background Approximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps. Methods Using direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (e.g., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0–2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests. Results The initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (n = 5), Environment (n = 14), Health (n = 10), and Behavior and Mental State (n = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfaction. The final tool consisted of 42 questions related to 36 measures, including 18 animal-based and 18 resource-based measures within the Nutrition (n = 5), Environment (n = 11), Health (n = 10), and Behavior and Mental State (n = 10) domains. Intraclass correlation coefficients (ICC) for inter-rater reliability (0.78–0.90, p < 0.05) and test-retest (0.77–0.91, p < 0.05) analyses conducted at two camps showed good agreement. Conclusions This new assessment tool (EWAT) is a context-specific, holistic method designed to offer a practical means of conducting individual and institutional-level assessments of elephant welfare in tourist camps. It is based on the Five Domains Model using reliable and validated animal- and resource-based measures, data collection through direct observation and interviews, and a numerical scoring system. The tool includes several criteria applicable to tourist rather than zoo venues to make it more relevant to the challenges faced by working elephants in Asia.
Ghimire et al. (2024) Development of a welfare assessment tool for tourist camp elephants in Asia. PeerJ 12:e18370 https://doi.org/10.7717/peerj.18370
Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part
Background Occupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a “service gap”. Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site. Methods This study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part. Results The results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences according to affected site or age group. This study revealed age- and body part-related relationships with chronic musculoskeletal pain in middle-aged patients and highlighted healthcare service gaps in its management in Japan.
Oka et al. (2024) Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part. PeerJ 12:e18389 https://doi.org/10.7717/peerj.18389
The impact of maternal serum biomarkers on maternal and neonatal outcomes in twin pregnancies: a retrospective cohort study conducted at a tertiary hospital
Background Prior prediction models used for screening preeclampsia (PE) in twin pregnancies were found to be inadequate. In singleton pregnancies, various maternal biomarkers have been shown to be correlated with negative pregnancy outcomes. However, the impact of these biomarkers in twin pregnancies remained uncertain. Methods A retrospective cohort study was carried out on 736 twin pregnancies at a tertiary hospital in Hangzhou, China. Multivariable logistic models were employed to examine the association between levels of serological markers and the likelihood of adverse pregnancy outcomes. The final logistic model was formulated as a user-friendly nomogram. The primary outcome assessed was the occurrence of PE. Results were presented as odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Results The prevalence of PE in the study was 10.3%. When comparing women diagnosed with PE to those without, it was evident that the former group experienced a significantly higher risk of unfavorable maternal and neonatal outcomes. A multivariable logistic regression analysis revealed notable associations between various factors including maternal age, parity, gestational weight gain, a family history of hypertension, as well as levels of cholesterol, albumin, and creatinine and the risk of developing PE, with a significance level of P < 0.05. The concordance index for the constructed nomogram was determined to be 0.792 (95% CI: [0.739–0.844]). Furthermore, an increment of 1 * 1012/L in red blood cell (RBC) count was associated with more than a two-fold increase in the odds of experiencing adverse maternal outcomes (OR 2.247, 95% CI: [1.229–4.107]). However, no significant correlations were identified between any of the examined variables and neonatal outcomes. Conclusions In this study, we developed a user-friendly predictive model that achieves notable detection rates by incorporating maternal serum biomarker levels alongside maternal characteristics and medical history. Our findings indicate that the probability of adverse maternal outcomes increases with elevated levels of RBCs. Obstetricians should consider intensifying surveillance for these women in clinical practice.
Wu et al. (2024) The impact of maternal serum biomarkers on maternal and neonatal outcomes in twin pregnancies: a retrospective cohort study conducted at a tertiary hospital. PeerJ 12:e18415 https://doi.org/10.7717/peerj.18415
Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma
Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an in vitro study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies.
Worasilchai et al. (2024) Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma. PeerJ 12:e18421 https://doi.org/10.7717/peerj.18421
Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls
In mammals, the patella is the biggest sesamoid bone of the skeleton and is of crucial importance in posture and locomotion, ensuring the role of a pulley for leg extensors while protecting and stabilizing the knee joint. Despite its central biomechanical role, the relation between the shape of the patella and functional factors, such as body mass or locomotor habit, in the light of evolutionary legacy are poorly known. Here, we propose a morphofunctional investigation of the shape variation of the patella among modern rhinoceroses and more generally among perissodactyls, this order of ungulates displaying a broad range of body plan, body mass and locomotor habits, to understand how the shape of this sesamoid bone varies between species and relatively to these functional factors. Our investigation, relying on three dimensional geometric morphometrics and comparative analyses, reveals that, within Rhinocerotidae and between the three perissodactyl families, the shape of the patella strongly follows the phylogenetic affinities rather than variations in body mass. The patellar shape is more conservative than initially expected both within and between rhinoceroses, equids and tapirs. The development of a medial angle, engendering a strong mediolateral asymmetry of the patella, appears convergent in rhinoceroses and equids, while tapirs retain a symmetric bone close to the plesiomorphic condition of the order. This asymmetric patella is likely associated with the presence of a “knee locking” mechanism in both equids and rhinos. The emergence of this condition may be related to a shared locomotor habit (transverse gallop) in both groups. Our investigation underlines unexcepted evolutionary constraints on the shape of a sesamoid bone usually considered as mostly driven by functional factors.
Mallet et al. (2024) Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls. PeerJ 12:e18067 https://doi.org/10.7717/peerj.18067
Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions
Background Plant growth and development can be greatly impacted by drought stress. Suitable plant growth promoting rhizobacteria (PGPR) or biochar (BC) application has been shown to alleviate drought stress for plants. However, their co-application has not been extensively explored in this regard. Methods We isolated bacterial strains from rhizospheric soils of plants from arid soils and characterized them for plant growth promoting characteristics like IAA production and phosphate solubilization as well as for drought tolerance. Three bacterial strains or so called PGPRs, identified as Bacillus thuringiensis, Bacillus tropicus, and Bacillus paramycoides based on their 16S rRNA, were screened for further experiments. Wheat was grown on normal, where soil moisture was maintained at 75% of water holding capacity (WHC), and induced-drought (25% WHC) stressed soil in pots. PGPRs were applied alone or in combination with a biochar derived from pyrolysis of tree wood. Results Drought stress substantially inhibited wheat growth. However, biochar addition under stressed conditions significantly improved the wheat growth and productivity. Briefly, it increased straw yield by 25%, 100-grain weight by 15% and grain yield by 10% compared to the control. Moreover, co-application of biochar with PGPRs B. thuringiensis, B. tropicus and B. paramycoides further enhanced straw yield by 37–41%, 100-grain weight by 30–36%, and grain yield by 22–22.57%, respectively. The co-application also enhanced soil quality by increasing plant-available phosphorus by 4–31%, microbial biomass by 33–45%, and soil K+/Na+ ratio by 41–44%. Conclusion Co-application of PGPRs and biochar alleviated plant drought stress by improving nutrient availability and absorption. Acting as a nutrient reservoir, biochar worked alongside PGPRs, who solubilized nutrients from the former and promoted wheat growth. We recommend that the co-application of suitable PGPRs and biochar is a better technology to produce wheat under drought conditions than using these enhancers separately.
Malik et al. (2024) Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions. PeerJ 12:e18171 https://doi.org/10.7717/peerj.18171