Integrative Analysis of Biomarkers and Mechanisms in Adamantinomatous Craniopharyngioma

Causal inference of inflammatory proteins in infertility: a Mendelian randomization study

Background

Infertility affects 8-12% of couples globally, manifesting as a complex reproductive disorder with varied causes, negatively impacting emotional, physical, and social well-being. Inflammation is implicated in many diseases, including male and female infertility.

Methods

This study employed Mendelian randomization (MR) with two-sample, bidirectional, and mediation approaches to explore the relationship between circulating inflammatory proteins and infertility. Causal analysis was conducted using inverse variance-weighted (IVW) and MR-Egger regression, supplemented by enrichment analysis, protein-protein interaction (PPI) network exploration, and drug signature analysis.

Results

Our findings identified a significant positive correlation between C-X-C motif chemokine 6 (CXCL6) and male infertility, positioning CXCL6 as a potential therapeutic target or biomarker. No causal links were detected between circulating inflammatory proteins and female infertility post-FDR adjustment. Minor mediation effects were observed for metabolites such as androstenediol monosulfate, arachidonoylcholine, and serum phosphate to glycerol ratio. Cytokine-related pathways emerged as significant in both male and female infertility. Gene-drug interaction analysis highlighted the need for further investigation of pioglitazone in treating female infertility.

Conclusion

This study establishes a potentially causal relationship between CXCL6 and male infertility, suggesting its potential as a drug target or molecular biomarker. The integrative approach combining causal inference with molecular pathway and drug interaction analysis opens new avenues for understanding and treating infertility.

Ferroptosis-related biomarkers for adamantinomatous craniopharyngioma treatment: conclusions from machine learning techniques

Introduction

Adamantinomatous craniopharyngioma (ACP) is difficult to cure completely and prone to recurrence after surgery. Ferroptosis as an iron-dependent programmed cell death, may be a critical process in ACP. The study aimed to screen diagnostic markers related to ferroptosis in ACP to improve diagnostic accuracy.

Methods

Gene expression profiles of ACP were obtained from the gene expression omnibus (GEO) database. Limma package was used to analyze the differently expressed genes (DEGs). The intersection of DEGs and ferroptosis-related factors was obtained as differently expressed ferroptosis-related genes (DEFRGs). Enrichment analysis was processed, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), disease ontology (DO), gene set enrichment analysis (GSEA), and Gene Set Variation Analysis (GSVA) analysis. Machine learning algorithms were undertaken for screening diagnostic markers associated with ferroptosis in ACP. The levels of DEFRGs were verified in ACP patients. A nomogram was drawn to predict the relationship between key DEFRG expression and risk of disease. The disease groups were then clustered by consensus clustering analysis.

Results

DEGs were screened between ACP and normal samples. Ferroptosis-related factors were obtained from the FerrDb V2 and GeneCard databases. The correlation between DEFRGs and ferroptosis markers was also confirmed. A total of 6 overlapped DEFRGs were obtained. Based on the results of the nomogram, CASP8, KRT16, KRT19, and TP63 were the protective factors of the risk of disease, while GOT1 and TFAP2C were the risk factors. According to screened DEFRGs, the consensus clustering matrix was differentiated, and the number of clusters was stable. CASP8, KRT16, KRT19, and TP63, were upregulated in ACP patients, while GOT1 was downregulated. CASP8, KRT16, KRT19, TP63, CASP8, and GOT1 affect multiple ferroptosis marker genes. The combination of these genes might be the biomarker for ACP diagnosis via participating ferroptosis process.

Discussion

Ferroptosis-related genes, including CASP8, KRT16, KRT19, TP63, and GOT1 were the potential markers for ACP, which lays the theoretical foundation for ACP diagnosis.

Gender-specific microbial signatures in saliva: Unveiling the association between the oral microbiome and the pathogenesis of glioma

The intricate interplay between the human oral microbiome and systemic health is increasingly being recognized, particularly in the context of central nervous system pathologies such as glioblastoma. In this study, we aimed to elucidate gender-specific differences in the salivary microbiome of glioma patients by utilizing 16S rRNA sequencing data from publicly available salivary microbiome datasets. We conducted comprehensive bioinformatics analysis, encompassing quality control, noise reduction, species classification, and microbial community composition analysis at various taxonomic levels. Machine learning algorithms were employed to identify microbial signatures associated with glioma. When compared to healthy controls, our analysis revealed distinct differences in the salivary microbiota of glioma patients. Notably, the genera Leptotrichia and Atopobium exhibited significant variations in abundance between genders. Leptotrichia was prevalent in healthy females but exhibited a reduced abundance in female glioma patients. In contrast, Atopobium was more abundant in male glioma patients. These findings suggest that hormonal influences might play a role in shaping the salivary microbiome and its association with glioma. We utilized a combination of LASSO-logistic regression and random forest models for feature selection, and identified key microbial features that differentiated glioma patients from healthy controls. We developed a diagnostic model with high predictive accuracy and area under the curve and principal component analysis metrics confirmed its robustness. The analysis of microbial markers, including Atopobium and Leptotrichia, highlighted the potential of the salivary microbiota as a non-invasive biomarker for the diagnosis and prognosis of glioma. Our findings highlight significant gender-specific disparities in the salivary microbiome of patients with glioma, offering new insights into the pathogenesis of glioma and paving the way for innovative diagnostic and therapeutic strategies. The use of saliva as a diagnostic fluid, given its ease of collection and non-invasive nature, holds immense promise for monitoring systemic health and the trajectory of disease. Future research should focus on investigating the underlying mechanisms by which the salivary microbiome influences the development of glioma and identifying potential microbiome-targeted therapies to enhance the management of glioma.

Proteomics study of primary and recurrent adamantinomatous craniopharyngiomas

BACKGROUND

Adamantinomatous craniopharyngiomas (ACPs) are rare benign epithelial tumours with high recurrence and poor prognosis. Biological differences between recurrent and primary ACPs that may be associated with disease recurrence and treatment have yet to be evaluated at the proteomic level. In this study, we aimed to determine the proteomic profiles of paired recurrent and primary ACP, gain biological insight into ACP recurrence, and identify potential targets for ACP treatment.

METHOD

Patients with ACP (n = 15) or Rathke's cleft cyst (RCC; n = 7) who underwent surgery at Sanbo Brain Hospital, Capital Medical University, Beijing, China and received pathological confirmation of ACP or RCC were enrolled in this study. We conducted a proteomic analysis to investigate the characteristics of primary ACP, paired recurrent ACP, and RCC. Western blotting was used to validate our proteomic results and assess the expression of key tumour-associated proteins in recurrent and primary ACPs. Flow cytometry was performed to evaluate the exhaustion of tumour-infiltrating lymphocytes (TILs) in primary and recurrent ACP tissue samples. Immunohistochemical staining for CD3 and PD-L1 was conducted to determine differences in T-cell infiltration and the expression of immunosuppressive molecules between paired primary and recurrent ACP samples.

RESULTS

The bioinformatics analysis showed that proteins differentially expressed between recurrent and primary ACPs were significantly associated with extracellular matrix organisation and interleukin signalling. Cathepsin K, which was upregulated in recurrent ACP compared with that in primary ACP, may play a role in ACP recurrence. High infiltration of T cells and exhaustion of TILs were revealed by the flow cytometry analysis of ACP.

CONCLUSIONS

This study provides a preliminary description of the proteomic differences between primary ACP, recurrent ACP, and RCC. Our findings serve as a resource for craniopharyngioma researchers and may ultimately expand existing knowledge of recurrent ACP and benefit clinical practice.

First evidence of anti-VEGF efficacy in an adult case of adamantinomatous craniopharyngioma: Case report and illustrative review

BACKGROUND

Craniopharyngioma (CP) is a neurosurgical challenge, due to location and to the substantial risk of morbidity associated with surgical resection. Recent advances in molecular research have identified a mutation signature in papillary craniopharyngiomas: BRAF V600E. This has led to targeted therapy, yielding positive results. Despite numerous studies of the pathophysiology of adamantinomatous craniopharyngioma, treatment options for molecular-based therapy are still lacking. The objective of our study was to provide an illustrative review of the literature on possible molecular targets in adamantinomatous craniopharyngioma and to report the case of a patient harboring an adamantinomatous craniopharyngioma deemed unsuitable for surgical resection, in which an anti-VEGF antibody was used to achieve tumor control.

CASE REPORT

An 84-year-old-man was referred to our department with a history of visual loss caused by recurrent infundibular adamantinomatous craniopharyngioma. A first surgical attempt to reduce the cystic portion of the tumor compressing the optic pathway failed. Due to rapid worsening of visual function, adjuvant therapy with bevacizumab was initiated before radiotherapy.

RESULTS

Neuroradiological and ophthalmological follow-up showed a decrease in tumor volume and improvement in visual function as early as 6 weeks after commencing therapy. These results were confirmed 3 months after commencement of chemotherapy. Radiotherapy was scheduled for long-term tumor control.

CONCLUSIONS

To the best of our knowledge, our case is the first in the literature in which targeted therapy using anti-VEGF was successfully used as a single agent to treat adamantinomatous craniopharyngioma, with favorable outcome in terms of tumor shrinkage and clinical improvement. These preliminary results may open new perspectives for the management of adamantinomatous craniopharyngioma. Validation of this approach requires additional clinical evidence.

Protein expression of S100A2 reveals it association with patient prognosis and immune infiltration profile in colorectal cancer

PURPOSE

Colorectal cancer (CRC) is the third most diagnosed cancer worldwide. Despite a well-established knowledge of tumour development, biomarkers to predict patient outcomes are still required. S100 calcium-binding protein A2 (S100A2) has been purposed as a potential marker in many types of cancer, however, the prognostic value of S100A2 in CRC is rarely reported.

MATERIAL AND METHODS

In this study, immunohistochemistry (IHC) was performed to identify the prognostic role of S100A2 protein expression in the tumour core of the tissue microarrays (TMAs) in colorectal cancer patients (n=787). Bulk RNA transcriptomic data was used to identify significant genes compared between low and high cytoplasmic S100A2 groups. Multiplex immunofluorescence (mIF) was performed to further study and confirm the immune infiltration in tumours with low and high cytoplasmic S100A2.

RESULTS

Low cytoplasmic protein expression of S100A2 in the tumour core was associated with poor survival (HR 0.539, 95%CI 0.394-0.737, P<0.001) and other adverse tumour phenotypes. RNA transcriptomic analysis showed a gene significantly associated with the low cytoplasmic S100A2 group (AKT3, TAGLN, MYLK, FGD6 and ETFDH), which correlated with tumour development and progression. GSEA analysis identifies the enriched anti-tumour and immune activity group of genes in high cytoplasmic S100A2. Additionally, mIF staining showed that high CD3+FOXP3+ and CD163+ inversely associated with low cytoplasmic S100A2 (P<0.001, P=0.009 respectively).

CONCLUSION

Our finding demonstrates a prognostic value of S100A2 together with the correlation with immune infiltration in CRC.

Identification of PANoptosis-relevant subgroups to evaluate the prognosis and immune landscape of patients with liver hepatocellular carcinoma

Liver hepatocellular carcinoma (LIHC) is one of the most common malignant tumors, which is difficult to be diagnosed at an early stage due to its poor prognosis. Despite the fact that PANoptosis is important in the occurrence and development of tumors, no bioinformatic explanation related to PANoptosis in LIHC can be found. A bioinformatics analysis on the data of LIHC patients in TCGA database was carried out on the basis of previously identified PANoptosis-related genes (PRGs). LIHC patients were divided into two PRG clusters whose gene characteristics of differentially expressed genes (DEGs) were discussed. According to DEGs, the patients were further divided into two DEG clusters, and prognostic-related DEGs (PRDEGs) were applied to risk score calculation, the latter of which turned out to be practical in identifying the relationship among risk score, patient prognosis, and immune landscape. The results suggested that PRGs and relevant clusters were bound up with the survival and immunity of patients. Moreover, the prognostic value based on two PRDEGs was evaluated, the risk scoring model was constructed, and the nomogram model for predicting the survival rate of patients was further developed. Therefore, it was found that the prognosis of the high-risk subgroup was poor. Additionally, three factors, namely, the abundance of immune cells, the expression of immune checkpoints, and immunotherapy and chemotherapy were considered to be associated with the risk score. RT-qPCR results indicated higher positive expression of CD8A and CXCL6 in both LIHC tissues and most human liver cancer cell lines. In summary, the results suggested that PANoptosis was bound up with LIHC-related survival and immunity. Two PRDEGs were identified as potential markers. Thus, the understanding of PANoptosis in LIHC was enriched, with some strategies provided for the clinical therapy of LIHC.

Pathological Diagnosis of Adult Craniopharyngioma on MR Images: An Automated End-to-End Approach Based on Deep Neural Networks Requiring No Manual Segmentation

PURPOSE

The goal of this study was to develop end-to-end convolutional neural network (CNN) models that can noninvasively discriminate papillary craniopharyngioma (PCP) from adamantinomatous craniopharyngioma (ACP) on MR images requiring no manual segmentation.

MATERIALS AND METHODS

A total of 97 patients diagnosed with ACP or PCP were included. Pretreatment contrast-enhanced T1-weighted images were collected and used as the input of the CNNs. Six models were established based on six networks, including VGG16, ResNet18, ResNet50, ResNet101, DenseNet121, and DenseNet169. The area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity were used to assess the performances of these deep neural networks. A five-fold cross-validation was applied to evaluate the performances of the models.

RESULTS

The six networks yielded feasible performances, with area under the receiver operating characteristic curves (AUCs) of at least 0.78 for classification. The model based on Resnet50 achieved the highest AUC of 0.838 ± 0.062, with an accuracy of 0.757 ± 0.052, a sensitivity of 0.608 ± 0.198, and a specificity of 0.845 ± 0.034, respectively. Moreover, the results also indicated that the CNN method had a competitive performance compared to the radiomics-based method, which required manual segmentation for feature extraction and further feature selection.

CONCLUSIONS

MRI-based deep neural networks can noninvasively differentiate ACP from PCP to facilitate the personalized assessment of craniopharyngiomas.

Applications of machine learning in tumor-associated macrophages

Evaluation of tumor-host interaction and intratumoral heterogeneity in the tumor microenvironment (TME) is gaining increasing attention in modern cancer therapies because it can reveal unique information about the tumor status. As tumor-associated macrophages (TAMs) are the major immune cells infiltrating in TME, a better understanding of TAMs could help us further elucidate the cellular and molecular mechanisms responsible for cancer development. However, the high-dimensional and heterogeneous data in biology limit the extensive integrative analysis of cancer research. Machine learning algorithms are particularly suitable for oncology data analysis due to their flexibility and scalability to analyze diverse data types and strong computation power to learn underlying patterns from massive data sets. With the application of machine learning in analyzing TME, especially TAM’s traceable status, we could better understand the role of TAMs in tumor biology. Furthermore, we envision that the promotion of machine learning in this field could revolutionize tumor diagnosis, treatment stratification, and survival predictions in cancer research. In this article, we described key terms and concepts of machine learning, reviewed the applications of common methods in TAMs, and highlighted the challenges and future direction for TAMs in machine learning.

The Challenging Management of Craniopharyngiomas in Adults: Time for a Reappraisal?

Simple Summary

Craniopharyngiomas (CPs) currently represent one of the most challenging diseases to deal with in the group of skull base tumors. Due to their location near, within, or surrounding the pituitary gland and stalk, CPs can be revealed by pituitary tumor syndrome and/or symptoms of hormonal deficiencies. Furthermore, surgery, which represents the first-line therapy, almost always results in hypopituitarism, diabetes insipidus and, in the case of hypothalamic involvement by the tumor, the occurrence of hypothalamic syndrome. The latter is characterized by intractable weight gain associated with severe morbid obesity, memory impairment, attention deficit, reduced impulse control and, eventually, increased risk of cardiovascular and metabolic disorders. Recent progress made in the understanding of the molecular pathways involved in CPs tumorigenesis paves the way for promising alternative therapeutic approaches and diagnostic procedures. Taken together, they lay the groundwork for new paradigms in the management of CPs in adults.

Abstract

Craniopharyngiomas (CPs) are rare tumors of the skull base, developing near the pituitary gland and hypothalamus and responsible for severe hormonal deficiencies and an overall increase in mortality rate. While surgery and radiotherapy represent the recommended first-line therapies for CPs, a new paradigm for treatment is currently emerging, as a consequence of accumulated knowledge concerning the molecular mechanisms involved in tumor growth, paving the way for anticipated use of targeted therapies. Significant clinical and basic research conducted in the field of CPs will undoubtedly constitute a real step forward for a better understanding of the behavior of these tumors and prevent associated complications. In this review, our aim is to summarize the multiple steps in the management of CPs in adults and emphasize the most recent studies that will contribute to advancing the diagnostic and therapeutic algorithms.

Influence of S100A2 in Human Diseases

S100 proteins are a family of low-molecular-weight proteins characterized by two calcium-binding sites with a helix-loop-helix (“EF-hand-type”) domain. The S100 family of proteins is distributed across various organs and can interact with diverse molecules. Among the proteins of the S100 family, S100 calcium-binding protein A2 (S100A2) has been identified in mammary epithelial cells, glands, lungs, kidneys, and prostate gland, exhibiting various physiological and pathological actions in human disorders, such as inflammatory diseases and malignant tumors. In this review, we introduce basic knowledge regarding S100A2 regulatory mechanisms. Although S100A2 is a tumor suppressor, we describe the various influences of S100A2 on cancer and inflammatory diseases.