Vimentin promotes glioma progression and maintains glioma cell resistance to oxidative phosphorylation inhibition

AmiCa: Atlas of miRNA-gene correlations in cancer

The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.

Serum nutritional predictive biomarkers and risk assessment for anastomotic leakage after laparoscopic surgery in rectal cancer patients

BACKGROUND

Anastomotic leakage (AL) is one of the severest complications after laparoscopic surgery for middle/low rectal cancer, significantly impacting patient outcomes. Identifying reliable predictive factors for AL remains a clinical challenge. Serum nutritional biomarkers have been implicated in surgical outcomes but are underexplored as predictive tools for AL in this setting. Our study hypothesizes that preoperative serum levels of prealbumin (PA), albumin (ALB), and transferrin (TRF), along with surgical factors, can accurately predict AL risk.

AIM

To determine the predictive value of preoperative serum nutritional biomarkers for rectal cancer AL following laparoscopic surgery.

METHODS

In the retrospective cohort study carried out at a tertiary cancer center, we examined 560 individuals who underwent laparoscopic procedures for rectal cancer from 2018 to 2022. Preoperative serum levels of PA, ALB, and TRF were measured. We employed multivariate logistic regression to determine the independent risk factors for AL, and a predictive model was constructed and evaluated using receiver operating characteristic curve analysis.

RESULTS

AL occurred in 11.96% of cases, affecting 67 out of 560 patients. Multivariate analysis identified PA, ALB, and TRF as the independent risk factor, each with an odds ratio of 2.621 [95% confidence interval (CI): 1.582-3.812, P = 0.012], 3.982 (95%CI: 1.927-4.887, P = 0.024), and 2.109 (95%CI: 1.162-2.981, P = 0.031), respectively. Tumor location (< 7 cm from anal verge) and intraoperative bleeding ≥ 300 mL also increased AL risk. The predictive model demonstrated an excellent accuracy, achieving an area under the receiver operating characteristic curve of 0.942, a sensitivity of 0.844, and a specificity of 0.922, demonstrating an excellent ability to discriminate.

CONCLUSION

Preoperative serum nutritional biomarkers, combined with surgical factors, reliably predict anastomotic leakage risk after rectal cancer surgery, highlighting their importance in preoperative assessment.

Elevated BEAN1 expression correlates with poor prognosis, immune evasion, and chemotherapy resistance in rectal adenocarcinoma

BACKGROUND

The BEAN1 gene, primarily studied in neurodegenerative diseases, has been scarcely studied in the context of cancers. Our research examines BEAN1 expression specifically in rectal adenocarcinoma (READ) and its association with prognosis, immune evasion, and chemotherapy resistance.

METHODS

Data from TCGA and GEO were analyzed to assess BEAN1 levels across various cancer types, with particular emphasis on READ. Functional enrichment, immune infiltration, and treatment response analyses were conducted, followed by validation using patient tissue samples.

RESULTS

READ tissues exhibited a marked increase in BEAN1 expression compared to normal tissues. Elevated BEAN1 levels were associated with reduced overall survival and increased immune suppression, characterized by elevated M2 macrophage infiltration and reduced CD8+ T cell presence. BEAN1 expression was also linked to higher immune checkpoint genes expression and resistance to immune checkpoint inhibitors and 5-fluorouracil.

CONCLUSION

This research offers initial evidence that BEAN1 is linked to unfavorable prognosis, immune escape, and resistance to chemotherapy in READ. BEAN1 appears to be a promising new biomarker and potential therapeutic target, warranting further investigation into its potential clinical applications in improving treatment outcomes for READ patients.

The role of KLF5 in gut microbiota and lung adenocarcinoma: unveiling programmed cell death pathways and prognostic biomarkers

Lung adenocarcinoma (LUAD) is the most important subtype of lung cancer. It is well known that the gut microbiome plays an important role in the pathophysiology of various diseases, including cancer, but little research has been done on the intestinal microbiome associated with LUAD. Utilizing bioinformatics tools and data analysis, we identified novel potential prognostic biomarkers for LUAD. To integrate differentially expressed genes and clinical significance modules, we used a weighted correlation network analysis system. According to the Peryton database and the gutMGene database, the composition and structure of gut microbiota in LUAD patients differed from those in healthy individuals. LUAD was associated with 150 gut microbiota and 767 gut microbiota targets, with Krüppel-like factor 5 (KLF5) being the most closely related. KLF5 was associated with immune status and correlated well with the prognosis of LUAD patients. The identification of KLF5 as a potential prognostic biomarker suggests its utility in improving risk stratification and guiding personalized treatment strategies for LUAD patients. Altogether, KLF5 could be a potential prognostic biomarker in LUAD.

Epithelial-Mesenchymal Transition Related Score Functions as a Predictive Tool for Immunotherapy and Candidate Drugs in Glioma

Gliomas are aggressive CNS tumors where the epithelial-mesenchymal transition (EMT) is crucial for prognosis. We developed an EMT-based score predicting overall survival (OS) and conducted pathway analyses, revealing functions such as cell proliferation and immune response in glioma progression. The EMT score, correlated with immune functions and cell infiltration, shows potential as an immune response indicator. We identified two promising compounds, BIX02189 and QL-XI-92, as potential glioma treatments based on candidate gene analysis.

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations

Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of transcriptomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Such platforms can help bridge the gap between computational and wet lab scientists through user-friendly web-based interfaces needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.

Inflammatory loop involving Staphylococcus aureus, IL-36γ, and cathepsin S drives immunity disorders in familial acne inversa keratinocytes

Acne inversa (AI) is an inflammatory skin disease associated with nicastrin (NCSTN) mutations. Despite the dysregulated bacterial-host immune interactions being an essential event in AI, the interaction between bacteria and keratinocytes in AI pathophysiology remains unclear. In this study, the NCSTN gene was suppressed using short hairpin RNA in HaCaT cells. Using RNA sequencing, real-time polymerase chain reaction, and western blotting, the expression of IL-36 cytokines was analyzed. The impact of Staphylococcus aureus on AI keratinocyte inflammation and underlying regulatory molecules was investigated by exposing the HaCaT cells to S. aureus. By stimulating NCSTN knockdown HaCaT cells with IFN-γ, the expression and regulatory mechanism of Cathepsin S (Cat S), an IL-36γ cleavage and activating protease, were investigated. After NCSTN knockdown, the IL-36α expression increased, and the IL-36Ra expression was downregulated. NCSTN/MEK/ERK impairment-induced Krüppel-like factor 4 (KLF4) up-regulation in concert with S. aureus-induced nuclear factor kappa B elevation acts synergistically to promote IL-36γ production with the subsequent IL-8 activation in HaCaT cells. NCSTN/MEK/ERK impairment was also observed in familial AI lesions. IFN-γ-induced Cat S in keratinocytes was enhanced after NCSTN knockdown. The expression of IFN-II pathway molecules was significantly upregulated in both NCSTN knockdown HaCaT cells and familial AI lesions. The Cat S expression was significantly elevated in the patient's AI lesions. Our findings suggested a synergistic relationship between S. aureus and NCSTN/MAPK/KLF4 axis in IL-36γ-induced familial AI keratinocytes.

Characteristics of immune cells and causal relationship with chondromalacia: A two-sample, bidirectional mendelian randomization study

Chondromalacia, characterized by the softening of cartilage, is a prevalent condition affecting joint health with complex etiology. The immune system's role in its pathogenesis has been implicated but remains to be fully elucidated. To address a critical knowledge gap, we conducted a two-sample Mendelian randomization analysis of 731 immune cell phenotypes, assessing parameters like fluorescence, cell count, and morphology. After sensitivity and pleiotropy checks, and applying a false discovery rate correction, our study linked 17 phenotypes to chondromalacia (p < .05). Among them, seven immune cell phenotypes were found to have a protective effect against chondromalacia (IVW: p < .05, OR <1), while 10 were considered risk factors (IVW:p < .05, OR >1). Despite the constraints of sample size and possible genetic differences among populations, our research has identified a notable genetic correlation between specific immune cell indicators and chondromalacia. This breakthrough sheds light on the pathophysiological mechanisms of the condition. The identification of protective and risk-associated immune cell phenotypes provides a foundation for further exploration of immunological mechanisms in chondromalacia and may pave the way for targeted interventions. Future research is warranted to validate these findings and explore their clinical implications.

Single-cell transcriptomics reveals heterogeneity in esophageal squamous epithelial cells and constructs models for predicting patient prognosis and immunotherapy

Background

Esophageal squamous cell carcinoma (ESCC), characterized by its high invasiveness and malignant potential, has long been a formidable challenge in terms of treatment.

Methods

A variety of advanced analytical techniques are employed, including single-cell RNA sequencing (scRNA-seq), cell trajectory inference, transcription factor regulatory network analysis, GSVA enrichment analysis, mutation profile construction, and the inference of potential immunotherapeutic drugs. The purpose is to conduct a more comprehensive exploration of the heterogeneity among malignant squamous epithelial cell subgroups within the ESCC microenvironment and establish a model for predicting the prognosis and immunotherapy outcomes of ESCC patients.

Results

An analysis was conducted through scRNA-seq, and three Cluster of malignant epithelial cells were identified using the infer CNV method. Cluster 0 was found to exhibit high invasiveness, whereas Cluster 1 displayed prominent characteristics associated with epithelial-mesenchymal transition. Confirmation of these findings was provided through cell trajectory analysis, which positioned Cluster 0 at the initiation stage of development and Cluster 1 at the final developmental stage. The abundance of Cluster 0-2 groups in TCGA-LUAD samples was assessed using ssGSEA and subsequently categorized into high and low-expression groups. Notably, it was observed that Cluster 0-1 had a significant impact on survival (p<0.05). Furthermore, GSVA enrichment analysis demonstrated heightened activity in hallmark pathways for Cluster 0, whereas Cluster 1 exhibited notable enrichment in pathways related to cell proliferation. It is noteworthy that a prognostic model was established utilizing feature genes from Cluster 0-1, employing the Lasso and stepwise regression methods. The results revealed that in TCGA and GSE53624 cohorts, the low-risk group demonstrated significantly higher overall survival and increased levels of immune infiltration. An examination of four external immunotherapy cohorts unveiled that the low-risk group exhibited improved immunotherapeutic efficacy. Additionally, more meaningful treatment options were identified for the low-risk group.

Conclusion

The findings revealed distinct interactions between malignant epithelial cells of ESCC and subgroups within the tumor microenvironment. Two cell clusters, strongly linked to survival, were pinpointed, and a signature was formulated. This signature is expected to play a crucial role in identifying and advancing precision medicine approaches for the treatment of ESCC.

Unexplained Causes of Glioma-Associated Epilepsies: A Review of Theories and an Area for Research

Approximately 30% of glioma patients are able to survive beyond one year postdiagnosis. And this short time is often overshadowed by glioma-associated epilepsy. This condition severely impairs the patient's quality of life and causes great suffering. The genetic, molecular and cellular mechanisms underlying tumour development and epileptogenesis remain incompletely understood, leading to numerous unanswered questions. The various types of gliomas, namely glioblastoma, astrocytoma and oligodendroglioma, demonstrate distinct seizure susceptibility and disease progression patterns. Patterns have been identified in the presence of IDH mutations and epilepsy, with tumour location in cortical regions, particularly the frontal lobe, showing a more frequent association with seizures. Altered expression of TP53, MGMT and VIM is frequently detected in tumour cells from individuals with epilepsy associated with glioma. However, understanding the pathogenesis of these modifications poses a challenge. Moreover, hypoxic effects induced by glioma and associated with the HIF-1a factor may have a significant impact on epileptogenesis, potentially resulting in epileptiform activity within neuronal networks. We additionally hypothesise about how the tumour may affect the functioning of neuronal ion channels and contribute to disruptions in the blood-brain barrier resulting in spontaneous depolarisations.