MMP12 serves as an immune cell-related marker of disease status and prognosis in lung squamous cell carcinoma

Elevated KIF2C Expression Drives Osteosarcoma Progression by Modulating the Wnt/β-Catenin Signaling Pathway and Contributing to an Immunosuppressive Tumor Microenvironment

BACKGROUND

Although kinesin family member 2C (KIF2C) is implicated in various cancers, its role in osteosarcoma (OS) and the associated inflammatory microenvironment remains unclear.

METHODS

Publicly available datasets were analyzed to determine KIF2C expression, diagnostic value, and prognostic relevance in OS. In vitro (proliferation, colony formation, apoptosis, migration, invasion) and in vivo assays assessed its biological functions. KEGG enrichment and GSVA explored underlying pathways. ssGSEA, ESTIMATE algorithms, and single-cell sequencing evaluated the immune context, and molecular docking and molecular dynamics identified potential inhibitory compounds.

RESULTS

KIF2C was significantly overexpressed in OS, effectively distinguishing OS from normal tissues. Elevated KIF2C levels correlated with poor survival outcomes. Silencing KIF2C suppressed OS cell proliferation, migration, invasion, and in vivo tumor growth, while promoting apoptosis; conversely, overexpression of KIF2C had the opposite effect. Mechanistically, co-immunoprecipitation results indicated that KIF2C can bind to β-catenin to regulate the Wnt/β-catenin pathway. Furthermore, high KIF2C expression was associated with an immunosuppressive tumor microenvironment characterized by immune exhaustion. Molecular docking and molecular dynamics suggested butein as a candidate small-molecule inhibitor targeting KIF2C-related oncogenic mechanisms.

CONCLUSION

KIF2C drives OS progression by enhancing Wnt/β-catenin signaling and fostering an immunosuppressive microenvironment. Targeting KIF2C may offer new therapeutic approaches in managing OS.

Kinesin family member 14 expression and its clinical implications in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is the third most common cancer globally, causing over 900000 deaths annually. Risk factors include aging, diet, obesity, sedentary lifestyle, tobacco use, genetic predisposition, and inflammatory bowel disease. Despite current treatments, survival rates for advanced CRC remain low, highlighting the need for better therapeutic strategies.

AIM

To evaluate both the clinical significance and the pathological implications of the Kinesin family member 14 (KIF14) expression within CRC specimens. Additionally, this study aims to investigate the interaction between nitidine chloride (NC) and KIF14, considering their potential as therapeutic targets.

METHODS

The expression of the KIF14 protein in CRC was analyzed using immunohistochemical staining. The integration of multicenter high-throughput data facilitated the calculation of the standardized mean difference (SMD) for KIF14 mRNA levels. The assessment of clinical and pathological impact was enhanced by analyzing combined receiver operating characteristic curves, along with measures of sensitivity, specificity, and likelihood ratios. Additionally, clustered regularly interspaced short palindromic repeats knockout screening for cell growth and single-cell sequencing were employed to validate the significance of KIF14 expression in CRC. Survival analysis established the prognostic value of KIF14 in CRC. The molecular mechanism of NC against CRC was elucidated through whole-genome sequencing and enrichment analysis, and molecular docking was utilized to explore the targeting affinity between NC and KIF14.

RESULTS

KIF14 was highly expressed in 208 CRC patients. Data from 17 platforms involving 2436 CRC samples and 1320 noncancerous colorectal tissue controls indicated that KIF14 expression was significantly higher in CRC samples, with an SMD of 1.92 (95%CI: 1.49-2.35). The area under the curve was 0.94 (95%CI: 0.92-0.96), with a sensitivity of 0.85 (95%CI: 0.78-0.90) and a specificity of 0.90 (95%CI: 0.85-0.93). The positive and negative likelihood ratios were 8.38 (95%CI: 5.39-13.02) and 0.17 (95%CI: 0.11-0.26), respectively. At the single-cell level, significant overexpression of KIF14 was observed in CRC cells (P < 0.001), with 35 CRC cell lines dependent on KIF14 for growth. The K-M plots demonstrated that KIF14 possesses prognostic value in CRC patients within the GSE71187 and GSE103679 datasets (P < 0.05). Binding energy calculations indicated that KIF14 is a potential target for NC (binding energy: 10.3 kcal/mol).

CONCLUSION

KIF14 promotes the growth of CRC cells and acts as an oncogenic factor, potentially serving as a therapeutic target for NC in the treatment of CRC.

Metabolic pathway activation and immune microenvironment features in non-small cell lung cancer: insights from single-cell transcriptomics

Introduction

In this study, we aim to provide a deep understanding of the tumor microenvironment (TME) and its metabolic characteristics in non-small cell lung cancer (NSCLC) through single-cell RNA sequencing (scRNAseq) data obtained from public databases. Given that lung cancer is a leading cause of cancer-related deaths globally and NSCLC accounts for the majority of lung cancer cases, understanding the relationship between TME and metabolic pathways in NSCLC is crucial for developing new treatment strategies.

Methods

Finally, machine learning algorithms were employed to construct a risk signature with strong predictive power across multiple independent cohorts. After quality control, 29,053 cells were retained, and PCA along with UMAP techniques were used to distinguish 13 primary cell subpopulations. Four highly activated metabolic pathways were identified within malignant cell subpopulations, which were further divided into seven distinct subgroups showing significant differences in differentiation potential and metabolic activity. WGCNA was utilized to identify gene modules and hub genes closely associated with these four metabolic pathways.

Results

Our analysis showed that DEGs between tumor and normal tissues were predominantly enriched in immune response and cell adhesion pathways. The comprehensive examination of our model revealed substantial variations in clinical and pathological characteristics, enriched pathways, cancer hallmarks, and immune infiltration scores between high-risk and low-risk groups. Wet lab experiments validated the role of KRT6B in NSCLC, demonstrating that KRT6B expression is elevated and it stimulates the proliferation of cancer cells.

Discussion

These observations not only enhance our understanding of metabolic reprogramming and its biological functions in NSCLC but also provide new perspectives for early detection, prognostic evaluation, and targeted therapy. However, future research should further explore the specific mechanisms of these metabolic pathways and their application potentials in clinical practice.

Overexpression and clinicopathological significance of zinc finger protein 71 in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the most prevalent and aggressive forms of liver cancer, with high morbidity and poor prognosis due to late diagnosis and limited treatment options. Despite advances in understanding its molecular mechanisms, effective biomarkers for early detection and targeted therapy remain scarce. Zinc finger protein 71 (ZNF71), a zinc-finger protein, has been implicated in various cancers, yet its role in HCC remains largely unexplored. This gap in knowledge underscores the need for further investigation into the ZNF71 of potential as a diagnostic or therapeutic target in HCC.

AIM

To explore the expression levels, clinical relevance, and molecular mechanisms of ZNF71 in the progression of HCC.

METHODS

The study evaluated ZNF71 expression in 235 HCC specimens and 13 noncancerous liver tissue samples using immunohistochemistry. High-throughput datasets were employed to assess the differential expression of ZNF71 in HCC and its association with clinical and pathological features. The impact of ZNF71 on HCC cell line growth was examined through clustered regularly interspaced short palindromic repeat knockout screens. Co-expressed genes were identified and analyzed for enrichment using LinkedOmics and Sangerbox 3.0, focusing on significant correlations (P < 0.01, correlation coefficient ≥ 0.3). Furthermore, the relationship between ZNF71 expression and immune cell infiltration was quantified using TIMER2.0.

RESULTS

ZNF71 showed higher expression in HCC tissues vs non-tumorous tissues, with a significant statistical difference (P < 0.05). Data from the UALCAN platform indicated increased ZNF71 levels across early to mid-stage HCC, correlating with disease severity (P < 0.05). High-throughput analysis presented a standardized mean difference in ZNF71 expression of 0.55 (95% confidence interval [CI]: 0.34-0.75). The efficiency of ZNF71 mRNA was evaluated, yielding an area under the curve of 0.78 (95%CI: 0.75-0.82), a sensitivity of 0.63 (95%CI: 0.53-0.72), and a specificity of 0.82 (95%CI: 0.73-0.89). Diagnostic likelihood ratios were positive at 3.61 (95%CI: 2.41-5.41) and negative at 0.45 (95%CI: 0.36-0.56). LinkedOmics analysis identified strong positive correlations of ZNF71 with genes such as ZNF470, ZNF256, and ZNF285. Pathway enrichment analyses highlighted associations with herpes simplex virus type 1 infection, the cell cycle, and DNA replication. Negative correlations involved metabolic pathways, peroxisomes, and fatty acid degradation. TIMER2.0 analysis demonstrated positive correlations of high ZNF71 expression with various immune cell types, including CD4+ T cells, B cells, regulatory T cells, monocytes, macrophages, and myeloid dendritic cells.

CONCLUSION

ZNF71 is significantly upregulated in HCC, correlating with the disease's clinical and pathological stages. It appears to promote HCC progression through mechanisms involving the cell cycle and metabolism and is associated with immune cell infiltration. These findings suggest that ZNF71 could be a novel target for diagnosing and treating HCC.

High expression of stearoyl-coenzyme A desaturase in colorectal cancer oncogenic functions and its potential as a therapeutic target

BACKGROUND

The stearoyl-coenzyme A desaturase (SCD) gene influences colorectal cancer (CRC) pathogenesis, with its expression linked to tumor cell survival and resistance, necessitating further investigation into its role in CRC.

AIM

To explore the clinical and pathological significance of SCD expression in CRC tissues and to evaluate the affinity between nitidine chloride (NC) and SCD as a target.

METHODS

Multi-center high-throughput data related to CRC were integrated to calculate the standardized mean difference of SCD mRNA expression levels. Immunohistochemical staining results, Clustered Regularly Interspaced Short Palindromic Repeats knockout screening results of cell growth, and single-cell sequencing were employed to verify the significance of SCD expression in CRC. The clinical and pathological significance of SCD was assessed using pooled receiver operating characteristic curves, sensitivity, specificity, and likelihood ratios. The molecular mechanism of NC against CRC was clarified using the SwissTarget Prediction and functional enrichment, and molecular docking techniques were utilized to explore the targeting affinity between NC and SCD.

RESULTS

Data from 18 platforms, including 2482 CRC samples and 1334 non-cancerous colorectal tissue controls. SCD expression was significantly upregulated in CRC, with a standardized mean difference of 2.05 [95% confidence interval (CI): 1.69-2.41]. The area under the pooled receiver operating characteristic curve was 0.95 (95%CI: 0.92-0.96), with a sensitivity of 0.86 (95%CI: 0.81-0.90) and a specificity of 0.90 (95%CI: 0.87-0.93). Positive and negative likelihood ratios were 9.02 (95%CI: 6.49-12.51) and 0.15 (95%CI: 0.10-0.22), respectively. High SCD protein expression was noted in 208 CRC patients, significantly associated with vascular invasion (P < 0.001). At the single-cell level, SCD was significantly overexpressed in CRC cells (P < 0.001). A total of 33 CRC cell lines depended on SCD for growth. The potential mechanism of NC against CRC might involve modulation of the cell cycle, positioning SCD as a potential target for NC.

CONCLUSION

SCD promotes CRC cell growth and thus acts as an oncogenic factor, making it a potential therapeutic target for NC in CRC treatment.

Development and validation of an Immune-related Gene-based model for predicting prognosis and immunotherapy outcomes in hepatocellular carcinoma patients

Predicting disease prognosis and the efficacy of immunotherapy presents a significant challenge in the treatment of hepatocellular carcinoma (HCC). By analyzing transcriptome sequencing data from 69 patients and identifying differentially expressed immune genes, a prognostic index named the immune-related gene prognostic index (IRGPI) was established by Lasso-Cox regression. The IRGPI, which consists of six key genes, was found to be a significant predictor of poor prognosis in patients with high IRGPI scores. The model's predictive accuracy was confirmed via receiver operating characteristic (ROC) curve analysis, with area under the curve (AUC) values of 0.85, 0.779, and 0.857 for 1-, 3-, and 5-year survival predictions, respectively. Additionally, patients with high IRGPI scores had increased levels of Treg cells and neutrophils, advanced tumor staging, microvascular invasion grading, and immune checkpoint expression. The IRGPI was also effective in predicting the efficacy of immunotherapy in the IMvigor210 dataset, demonstrating its potential as a valuable tool for assessing patient prognosis and guiding immunotherapy strategies in HCC.

ADAMDEC1 promotes the malignant progression of cholangiocarcinoma by regulating NF-κB signaling pathway

Cholangiocarcinoma (CCA), a highly aggressive form of cancer, is known for its high mortality rate. A Disintegrin and Metalloprotease Domain-like Protein Decysin-1 (ADAMDEC1) can promote the development and metastasis in various tumors by degrading the extracellular matrix. However, its regulatory mechanism in CCA remains unclear. Public databases and clinical tissue samples were used to evaluate whether ADAMDEC1 expression was correlated with the prognosis of CCA. We investigated the expression of ADAMDEC1-related regulatory genes and proteins in CCA and assessed the biological behaviors of CCA cells in vitro through functional experiments. Meanwhile, the interacting proteins of ADAMDEC1 and its involvement in the nuclear factor-kappa B (NF-κB) signaling pathway were screened and verified through bioinformatics analysis. The tumorigenicity of CCA was also assessed in a xenograft nude mouse model. Our results showed that ADAMDEC1 was highly expressed in tumor tissues from CCA patients and was positively correlated with poor prognosis. Interference cell lines targeting ADAMDEC1 in CCA cells were successfully constructed. Knockdown of ADAMDEC1 or MMP12 both affected the biological behaviors of CCA cells, and ADAMDEC1 silencing inhibited tumorigenicity and tumor growth of CCA in vivo. Moreover, ADAMDEC1 interacted with MMP12, modulating its expression and promoting the activation of the NF-κB signaling pathway. Our study uncovered the expression patterns and functional roles of ADAMDEC1 in CCA cells and tissues, highlighting its connection to the NF-κB pathway and MMP12 in the development of CCA. Therefore, ADAMDEC1 may serve as a potential therapeutic target for CCA.

Overexpression of proteasome 26S subunit non-ATPase 6 protein and its clinicopathological significance in intrahepatic cholangiocarcinoma

BACKGROUND

Currently, intrahepatic cholangiocarcinoma (ICC) poses a continuing, significant health challenge, but the relationship has yet to be established between ICC and the proteasome 26S subunit non-ATPase 6 (PSMD6).

AIM

To investigate the protein expression and clinicopathological significance of PSMD6 in ICC.

METHODS

The potential impact of the PSMD6 gene on the growth of ICC cell lines was analyzed using clustered regularly interspaced short palindromic repeat knockout screening technology. Forty-two paired specimens of ICC and adjacent non-cancerous tissues were collected. PSMD6 protein expression was determined by immunohistochemistry. Receiver operating characteristic curve analysis was performed to validate PSMD6 expression level, and its association with ICC patients' various clinicopathological characteristics was investigated.

RESULTS

The PSMD6 gene was found to be essential for the growth of ICC cell lines. PSMD6 protein was significantly overexpressed in ICC tissues (P < 0.001), but showed no significant association with patient age, gender, pathological grade, or tumor-node-metastasis stage (P > 0.05).

CONCLUSION

PSMD6 can promote the growth of ICC cells, thus playing a pro-oncogenic role.

Machine learning for automated classification of lung collagen in a urethane-induced lung injury mouse model

Dysregulation of lung tissue collagen level plays a vital role in understanding how lung diseases progress. However, traditional scoring methods rely on manual histopathological examination introducing subjectivity and inconsistency into the assessment process. These methods are further hampered by inter-observer variability, lack of quantification, and their time-consuming nature. To mitigate these drawbacks, we propose a machine learning-driven framework for automated scoring of lung collagen content. Our study begins with the collection of a lung slide image dataset from adult female mice using second harmonic generation (SHG) microscopy. In our proposed approach, first, we manually extracted features based on the 46 statistical parameters of fibrillar collagen. Subsequently, we pre-processed the images and utilized a pre-trained VGG16 model to uncover hidden features from pre-processed images. We then combined both image and statistical features to train various machine learning and deep neural network models for classification tasks. We employed advanced unsupervised techniques like K-means, principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to conduct thorough image analysis for lung collagen content. Also, the evaluation of the trained models using the collagen data includes both binary and multi-label classification to predict lung cancer in a urethane-induced mouse model. Experimental validation of our proposed approach demonstrates promising results. We obtained an average accuracy of 83% and an area under the receiver operating characteristic curve (ROC AUC) values of 0.96 through the use of a support vector machine (SVM) model for binary categorization tasks. For multi-label classification tasks, to quantify the structural alteration of collagen, we attained an average accuracy of 73% and ROC AUC values of 1.0, 0.38, 0.95, and 0.86 for control, baseline, treatment_1, and treatment_2 groups, respectively. Our findings provide significant potential for enhancing diagnostic accuracy, understanding disease mechanisms, and improving clinical practice using machine learning and deep learning models.

Comprehensive analysis of the clinical significance and molecular mechanism of T-box transcription factor 3 in osteosarcoma

Background: T-box transcription factor 3 (TBX3) has been implicated in various malignant tumors, while its exact involvement in osteosarcoma (OS) remains unknown. Methods: Utilizing microarray data and bulk and single-cell RNA-seq data and qRT-PCR, we compared TBX3 mRNA expression levels in different stages of OS. Diagnostic ability testing and prognosis analysis were conducted to better understand the clinical importance of TBX3. Enrichment analysis was performed using gene groups with biological functions similar to TBX3 in different stages of OS to investigate the potential role of TBX3 in OS progression. In addition, we predicted medications targeted at TBX3 and identified downstream target genes to gain a comprehensive understanding of its therapeutic direction and regulatory mechanism. Results: TBX3 expression was highly upregulated in OS and was predominantly expressed in osteoblastic OS cells, with higher expression levels in metastatic tissues. TBX3 expression appeared somewhat suitable for discriminating between OS and normal samples, as well as different stages of OS. We found that TBX3 increased the malignant development of OS by altering cell cycle and cell adhesion molecules; exisulind and tacrolimus, which are targeted small-molecule medicines, were anticipated to counteract this dysregulation. The expression of CCNA2 could potentially be regulated by TBX3, contributing to OS advancement. Conclusion: TBX3 emerges as a potential biomarker for OS. In-depth research into its underlying molecular processes may offer new perspectives on treating OS.

Tumor-derived KLK8 predicts inferior survival and promotes an immune-suppressive tumor microenvironment in lung squamous cell carcinoma

Lung squamous cell carcinoma (LUSC) is the second most common lung cancer worldwide, leading to millions of deaths annually. Although immunotherapy has expanded the therapeutic choices for LUSC and achieved considerable efficacy in a subset of patients, many patients could not benefit, and resistance was pervasive. Therefore, it is significant to investigate the mechanisms leading to patients' poor response to immunotherapies and explore novel therapeutic targets. Using multiple public LUSC datasets, we found that Kallikrein-8 (KLK8) expression was higher in tumor samples and was correlated with inferior survival. Using a LUSC cohort (n = 190) from our center, we validated the bioinformatic findings about KLK8 and identified high KLK8 expression as an independent risk factor for LUSC. Function enrichment showed that several immune signaling pathways were upregulated in the KLK8 low-expression group and downregulated in the KLK8 high-expression group. For patients with low KLK8 expression, they were with a more active TME, which was both observed in the TCGA database and immune marker immunohistochemistry, and they had extensive positive relations with immune cells with tumor-eliminating functions. This study identified KLK8 as a risk factor in LUSC and illustrated the associations between KLK8 and cancer immunity, suggesting the potentiality of KLK8 as a novel immune target in LUSC.