Comprehensive Analysis of the Association between Human Diseases and Water Pollutants

mRNA expression insights: Unraveling the relationship between COPD and lung cancer

BACKGROUND

Lung cancer is a prevalent form of cancer worldwide. A possible link between lung cancer and chronic obstructive pulmonary disease (COPD) has been suggested by recent studies. The objective of our research was to analyze the mRNA expression patterns in both situations, with a specific emphasis on their biological functions and the pathways they are linked to.

METHOD

Data on COPD mRNA expression was collected from the NCBI-GEO database, while information regarding lung cancer mRNA was acquired from The Cancer Genome Atlas database. To examine the association of COPD-related scores in lung cancer patients, we utilized the ssGSEA algorithm for single sample gene set enrichment analysis. The possible routes were examined through the utilization of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Risk models were developed using Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. Moreover, a GSEA was performed to investigate significant pathways among various risk groups.

RESULT

After identifying 17 genes that were differentially expressed and linked to COPD, we found that they met the criteria of having a false discovery rate < 0.05 and an absolute log2 fold change > 0.585. By utilizing the ssGSEA algorithm, it became possible to classify individuals with lung cancer into two distinct groups based on their COPD status. Consequently, a seven-gene risk model was developed specifically for these patients. The risk score was determined by applying the given formula: risk score = AC022784.1 × 0.0423737993775888 + CRISP3 × 0.0415322046890524 + MELTF × 0.0661848418476596 + MT2P1 × 0.111843227536117 + FAM83A-AS1 × 0.045295939710361 + ZNF506 × -0.309489953363417 + ITGA6 × 0.01813978449589. The risk model associated with COPD showed a notable connection with different immune cells found in the lung cancer sample, including macrophages of M0/M1/M2 types, hematopoietic stem cells, mast cells, NK T cells and regulatory T cells. Overexpression of crucial genes was seen to enhance cell proliferation and invasive potential in the lung cancer sample. In the lung cancer sample, it was observed that an increase in ZNF506 expression enhanced both cell proliferation and invasion.

CONCLUSION

In conclusion, this study effectively examines the potential correlation between COPD and lung cancer. A prognostic model based on seven COPD-associated genes demonstrated robust predictive potential in the lung cancer sample. Our analysis offers comprehensive insights for lung cancer patients.

Relationship between potentially toxic elements and macrophyte communities in the Sava river

Freshwater ecosystems are at significant risk of contamination by potentially toxic elements (PTEs) due to their high inherent toxicity, their persistence in the environment and their tendency to bioaccumulate in sediments and living organisms. We investigated aquatic macrophyte communities and the concentrations of As, Cu, Cd, Cr, Pb, Zn, Ni and Fe in water and sediment samples to identify a pollution pattern along the Sava River and to investigate the potential impact of these PTEs on the diversity and structure of macrophyte communities. The study, which covered 945 km of the Sava River, showed a downstream increase in sediment concentrations of the analyzed elements. Both species richness and alpha diversity of macrophyte communities also generally increase downstream. Ordinary and partial Mantel tests indicate that macrophyte communities are significantly correlated with sediment chemistry, but only weakly correlated with water chemistry. In the lowland regions (downstream), beta diversity decreases successively, which can be attributed to an increasing similarity of environmental conditions at downstream sites. Species richness is relatively low at sites with low concentrations of Cr, Cd, Fe, and Cu in the sediment. However, species richness increases to a certain extent with increasing element concentrations; as element concentrations increase further, species richness decreases, probably as a result of increased toxicity. Some species that are generally more tolerant to high concentrations of PTEs are: Ceratophyllum demersum, Iris pseudacorus, Najas marina, Butomus umbellatus, Vallisneria spiralis, Potamogeton gramineus and Bolboschoenus maritimus maritimus. Potamogeton perfoliatus and the moss species Cinclidotus fontinaloides and Fontinalis antipyretica have narrow ecological amplitudes in relation to the concentrations of PTEs in the sediment.

Integrative analysis of triphenyl phosphate: contextual interpretation of bladder cancer cohort

In recent years, organophosphate ester flame retardants (OPFRs) have emerged as preferred alternatives to brominated flame retardants (BFRs) in materials such as building supplies, textiles, and furnishings. Simultaneously, a notable surge in bladder cancer incidences has been observed globally, particularly in developed nations, placing it as the 10th most prevalent cancer type. Among the extensive OPFRs, the linkage between triphenyl phosphate (TPP) and bladder cancer remains inadequately investigated. Hence, our study endeavors to elucidate this potential association. We sourced transcriptome profiles and TPP-related data from The Cancer Genome Atlas and Comparative Toxicogenomics databases. Using the ssGSEA algorithm, we established TPP-correlated scores within the bladder cancer cohort. Differentially expressed analysis enabled us to identify key genes in bladder cancer patients. We utilized the LASSO regression analysis, along with univariate and multivariate COX regression analyses to construct a prognostic prediction model. To uncover critical pathways involving key genes, we employed GSEA and GSVA enrichment analyses. Molecular docking analysis was performed to determine the binding capability between TPP and proteins. Our findings reveal that the TPP-centric risk model offers valuable prediction for bladder cancer cohorts. Furthermore, the reliability of this TPP-influenced risk model was verified through ROC curve analysis and survival studies. Intriguingly, TPP exposure appears to bolster the proliferation and invasiveness of bladder cancer cells. This study furnishes new insights into the possible benefits of minimizing TPP exposure for hindering bladder cancer progression.

Investigating the role of LncRNA PSMG3-AS1 in gastric cancer: implications for prognosis and therapeutic intervention

LncRNAs are widely linked to the complex development of gastric cancer, which is acknowledged worldwide as the third highest contributor to cancer-related deaths and the fifth most common form of cancer. The primary focus of this study is to examine the role of LncRNA PSMG3-AS1 in a group of individuals with gastric cancer. The results of our study indicate that PSMG3-AS1 is highly expressed in over 20 different types of cancer. Significantly, there was a clear association found between the expression of PSMG3-AS1 and a multitude of TMB and MSI tumors. PSMG3-AS1 exhibited significant upregulation in gastric cancer patients compared to healthy individuals within the gastric cancer cohort. The prognosis of gastric cancer patients is intrinsically associated with PSMG3-AS1, as confirmed by survival analysis and ROC curves. Furthermore, we created a disruption vector based on LncRNA PSMG3-AS1 and introduced it into AGS and MKN-45 cells, which are human gastric cancer cells. Significant decreases in the expression of the PSMG3-AS1 gene were noticed in both intervention groups compared to the NC group, reflecting the protein level expressions. Significantly, the proliferative and invasive capabilities of MKN-45 and AGS cells were notably reduced following transfection with PSMG3-AS1 siRNA. The results of our study indicate that disruption of the LncRNA PSMG3-AS1 gene may impact the CAV1/miR-451a signaling pathway, thereby leading to a reduction in the ability of gastric cancer cells to multiply and invade.

Environmental explanation of prostate cancer progression based on the comprehensive analysis of perfluorinated compounds

Perfluorinated compounds (PFCs) are man-made chemicals used in the manufacture of many products with water and dirt repellent properties. Many diseases have been proved to be related to the exposure of PFCs, including breast fibroadenoma, hepatocellular carcinoma, breast cancer and leydig cell adenoma. However, whether the PFCs promote the progression of prostate cancer remains unclear. In this work, through comprehensive bioinformatics analysis, we discovered the correlation between the prostate cancer and five PFCs using Comparative Toxicogenomics Database (CTD), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. In addition, further analysis showed that several PFCs-related genes demonstrated strong prognostic value for prostate cancer patients. The survival analysis and receiver operating characteristic (ROC) curves revealed that PFCs-related genes based prognostic model held great predictive value for the prognosis of prostate cancer, which could potentially serve as an independent risk factor in the future. In vitro experiments verified the promotive role of perfluorooctanoic acid (PFOA) and perfluorononanoic acid (PFNA) in the growth of prostate cancer cells. This study provided novel insights into understanding the role of PFCs in prostate cancer and brought attention to the environmental association with cancer risks and progression.

The role of tumor-associated macrophages in glioma cohort: through both traditional RNA sequencing and single cell RNA sequencing

Gliomas are the leading cause in more than 50% of malignant brain tumor cases. Prognoses, recurrences, and mortality are usually poor for gliomas that have malignant features. In gliomas, there are four grades, with grade IV gliomas known as glioblastomas (GBM). Currently, the primary methods employed for glioma treatment include surgical removal, followed by chemotherapy after the operation, and targeted therapy. However, the outcomes of these treatments are unsatisfactory. Gliomas have a high number of tumor-associated macrophages (TAM), which consist of brain microglia and macrophages, making them the predominant cell group in the tumor microenvironment (TME). The glioma cohort was analyzed using single-cell RNA sequencing to quantify the genes related to TAMs in this study. Furthermore, the ssGSEA analysis was utilized to assess the TAM-associated score in the glioma group. In the glioma cohort, we have successfully developed a prognostic model consisting of 12 genes, which is derived from the TAM-associated genes. The glioma cohort demonstrated the predictive significance of the TAM-based risk model through survival analysis and time-dependent ROC curve. Furthermore, the correlation analysis revealed the significance of the TAM-based risk model in the application of immunotherapy for individuals diagnosed with GBM. Ultimately, the additional examination unveiled the prognostic significance of PTX3 in the glioma group, establishing it as the utmost valuable prognostic indicator in patients with GBM. The PCR assay revealed the PTX3 is significantly up-regulated in GBM cohort. Additionally, the assessment of cell growth further confirms the involvement of PTX3 in the GBM group. The analysis of cell proliferation showed that the increased expression of PTX3 enhanced the ability of glioma cells to proliferate. The prognosis of glioblastomas and glioma is influenced by the proliferation of tumor-associated macrophages.

The identification of tumor antigens and immune subtypes based on the development of immunotherapies targeting head and neck squamous cell carcinomas resulting from periodontal disease

Among cancer treatments, immunotherapy is considered a promising strategy. Nonetheless, only a small number of individuals with head and neck squamous cell carcinoma exhibit positive responses to immunotherapy. This study aims to discover possible antigens for head and neck squamous cell carcinoma, create an mRNA vaccine for this type of cancer, investigate the connection between head and neck squamous cell carcinoma and periodontal disease, and determine the immune subtype of cells affected by head and neck squamous cell carcinoma. To ascertain gene expression profiles and clinical data corresponding to them, an examination was carried out on the TCGA database. Antigen-presenting cells were detected using TIMER. Targeting six immune-related genes (CXCL5, ADM, FGF9, AIMP1, STC1, and CDKN2A) in individuals diagnosed with head and neck squamous cell carcinoma has shown promising results in immunotherapy triggered by periodontal disease. These genes have been linked to improved prognosis and increased immune cell infiltration. Additionally, CXCL5, ADM, FGF9, AIMP1, STC1, and CDKN2A exhibited potential as antigens in the creation of an mRNA vaccine. A nomogram model containing ADM expression and tumor stage was constructed for clinical practice. To summarize, ADM shows potential as a candidate biomarker for predicting the prognosis, molecular features, and immune characteristics of head and neck squamous cell carcinoma cells. Our results, obtained through real-time PCR analysis, showed a significant upregulation of ADM in the SCC-25 cell line compared to the NOK-SI cell line. This suggests that ADM might be implicated in the pathogenesis of HNSC, highlighting the potential of ADM as a target in HNSC treatment. However, further research is needed to elucidate the functional role of ADM in HNSC. Our findings provide a basis for the further exploration of the molecular mechanisms underlying HNSC and could help develop novel therapeutic strategies.

Bibliometric analysis of the association between drinking water pollution and bladder cancer

Background

Bladder cancer has become an increasingly intractable health problem worldwide. Long-term drinking water pollution is known to promote its occurrence. This study aimed to analyze the research status, hot spots, and future trends of drinking water pollution and bladder cancer through extensive bibliometric examination to provide reference data for better prevention and management of bladder cancer.

Methods

The Scopus database developed by Elsevier was browsed for articles that met the predefined criteria using the search terms related to drinking water and bladder cancer. Included articles were further evaluated by year of publication, subject category, institution, article type, source journal, authors, co-authorship networks, and text mining of titles by R software packages tm, ggplot2 and VOSviewer software.

Results

In total, 687 articles were selected after a comprehensive literature search by the Scopus database, including 491 research articles, 98 review articles, 26 conference papers, 23 letters and 49 other documents. The total number of articles published showed an upward trend. The United States has the largest number of published articles (345 articles), institutions (7/10) and funding sponsors (top 5). The journal with the most publications was Environmental Health Perspectives, with 46 published. The highest number of citations up to 2330 times for a single article published in 2007 on the journal of Mutation Research. Professor Cantor K.P. was the highest number of publications with 35 articles and Smith A.H. was the most cited author with the number of citations reaching 6987 times overall and 225 times per article. The most frequent keywords excluding the search subject were "arsenic", "chlorination", "trihalomethane", and "disease agents".

Conclusion

This study is the first systematic bibliometric study of the literature publications on drinking water pollution and bladder cancer. It offers an overall and intuitive understanding of this topic in the past few years, and points out a clear direction research hotspots and reveals the trends for further in-depth study in future.

Damage Effects of Bisphenol A against Sepsis Induced Acute Lung Injury

In addition to oxidative damage, sepsis can cause multiple organ dysfunction and poses a life-threatening threat. In addition to severe tissue damage, hypotension, and multiple organ failure, sepsis can cause high morbidity and mortality. It is the lungs that are most vulnerable in abdominal sepsis, with impaired oxygen and nutrient exchange occurring in the pulmonary microcirculation. However, the etiology of sepsis and the link between sepsis and lung injury has not been elucidated. In this work, by exploring the data from the GEO and CTD database, a gene association study was conducted to determine whether sepsis-induced lung injury is caused by BPA. Further analysis demonstrated that MMP9, CEBPA, CYP1B1, CTSD, FKBP5, DGAT2, HP, TIMP2, ARG1 and MGST1 may play an important role in sepsis-induced lung injury. Finally, the single-cell RNA sequence demonstrated that CEBPA is mainly enriched in lung epithelial cells and epithelial cells, whereas CYP1B1 is closely related to basal cells, macrophages, and interstitial cells. In order to maintain lung function, epithelial and alveolar macrophages as well as other lung cells are important. When the lung epithelium is activated for a prolonged period of time, barrier function may be compromised and tissue damage may result, aggravating the lung injury. By using the animal model, we successfully simulated the model of sepsis lung injury. The HE staining demonstrated the rats with BPA-treated septic lung injury showed more alveolar structure to be disordered, pulmonary interstitial edema to be evident, and red blood cells as well as inflammatory cells. For PCR assay, the results demonstrated that the expression level of CEBPA is higher in the lung samples with sepsis compared with the normal samples of the lung. In order to evaluate the expression level of CEBPA and CYP1B1 in lung tissue, we then performed the PCR assay. For CYP1B1, the results demonstrated that the expression level of CYP1B1 in lung samples with sepsis is lower than in normal lung samples. In total, BPA may be a potential contributing factor to sepsis-induced lung injury.

Melatonin inhibited the progression of gastric cancer induced by Bisphenol S via regulating the estrogen receptor 1

In recent years, Bisphenol S (BPS) has increasingly been used as an alternative to Bisphenol A (BPA) in food, paper, and personal care products. It is imperative to clarify the relationship between BPS and tumors in order to treat and prevent diseases. This study discovered a new method for predicting tumor correlations between BPS interactive genes. According to analyses conducted by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, interactive genes were primarily found in gastric cancer. Based on gene-targeted prediction and molecular docking, BPS appears to exert potential gastric cancer-causing effects through estrogen receptor 1 (ESR1). In addition, gastric cancer patients' prognosis could be accurately predicted by a bisphenol-based prognostic prediction model. Subsequently, the proliferation and migration abilities of gastric cancer cells were further demonstrated to be significantly enhanced by BPS. Similarly, molecular docking analysis revealed that melatonin is also highly correlated with gastric cancer and BPS. In cell proliferation and migration assays, melatonin and BPS exposure inhibited the invasion abilities of gastric cancer cells compared to BPS-exposure. Our research provided a new direction for the exploration the correlation between cancer and environmental toxicity.

Single-cell RNA sequencing and traditional RNA sequencing reveals the role of cancer-associated fibroblasts in oral squamous cell carcinoma cohort

Chronic inflammation of the alveolar bones and connective tissues supporting teeth causes periodontal disease, one of the most prevalent infectious diseases in humans. It was previously reported that oral cancer was the sixth most common cancer in the world, followed by squamous cell carcinoma. Periodontal disease has been linked to an increased risk for oral cancer in some studies, and these studies have found a positive relationship between oral cancer and periodontal disease. In this work, we aimed to explore the potential correlation between oral squamous cell carcinoma (OSCC) and Periodontal disease. The single-cell RNA sequence analysis was applied to explore the genes that were closely associated with cancer-associated fibroblasts (CAFs). the head and neck squamous cell carcinoma. The Single sample Gene Set Enrichment Analysis (ssGSEA) algorithm was applied to explore the scores of CAFs. Subsequently, the differentially expressed analysis was applied to explore the CAFs-related genes that play a key role in the OSCC cohort. The LASSO regression analysis and the COX regression analysis were applied to construct the CAFs-based periodontal disease-related risk model. In addition, the correlation analysis was used to explore the correlation between the risk model and clinical features, immune-related cells, and immune-related genes. By using the single-cell RNA sequence analysis, we successfully obtained the biomarkers for the CAFs. Finally, we successfully obtained a six-CAFs-related genes risk model. The ROC curve and survival analysis revealed that the risk model showed good predictive value in OSCC patients. Our analysis successfully provided a new direction for the treatment and prognosis of OSCC patients.