Overexpression of semaphorin 3A in patients with urothelial cancer

Role of semaphorins, neuropilins and plexins in cancer progression

Progress in understanding nervous system-cancer interconnections has emphasized the functional role of semaphorins (SEMAs) and their receptors, neuropilins (NRPs) and plexins (PLXNs), in cancer progression. SEMAs are a conserved and extensive family of broadly expressed soluble and membrane-associated proteins that were first described as regulators of axon guidance and neural and vascular development. However, recent advances have shown that they can have a dual role in cancer progression, acting either as tumor promoters or suppressors. SEMAs effects result from their interaction with specific co-receptors/receptors NRPs/PLXNs, that have also been described to play a role in cancer progression. They can influence both cancer cells and tumor microenvironment components modulating various aspects of tumorigenesis such as oncogenesis, tumor growth, invasion and metastatic spread or treatment resistance. In this review we focus on the role of these axon guidance signals and their receptors and co-receptors in various aspects of cancer. Furthermore, we also highlight their potential application as novel approaches for cancer treatment in the future.

The Role of Semaphorin 6D (Sema6D) in Non-Muscle-Invasive Bladder Cancer-A Preliminary Study on Human Plasma and Urine

The incidence of bladder cancer worldwide in the last three decades has been increasing in both men and women. So far, there is no established non-invasive bladder cancer biomarker in daily clinical practice. Semaphorin 6D (sema6D) is a transmembrane protein that belongs to the class VI semaphorins. The aim of this study was to evaluate for the first time the potential role of sema6D in bladder cancer. The study group consisted of 40 patients with non-muscle-invasive bladder cancer (NMIBC) and the control group of 20 patients without malignancies. There was a statistically significantly higher urinary sema6D concentration in patients than controls (p < 0.05) but no significant difference in plasma 6D. There were no statistically significant differences in urinary or plasma concentration of sema6D between low- or high-grade cancer and according to the tumor stage in TNM classification. There was a statistically significant negative correlation between plasma sema6D and age of patients (R = -0.6; p = 0.019). Plasma sema6D does not seem to be useful in the clinical practice at this point. However, the urinary sema6D concentration could potentially serve as a marker of NMIBC used for diagnostic purposes, monitoring, and early relapse detection or the assessment of the treatment efficacy. Urinary sema6D is probably not associated with the grading or staging of NMIBC, so it cannot be used for the prediction of disease prognosis.

Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data

MOTIVATION

Unraveling the transcriptional programs that control how cells divide, differentiate, and respond to their environments requires a precise understanding of transcription factors' (TFs) DNA-binding activities. Calling cards (CC) technology uses transposons to capture transient TF binding events at one instant in time and then read them out at a later time. This methodology can also be used to simultaneously measure TF binding and mRNA expression from single-cell CC and to record and integrate TF binding events across time in any cell type of interest without the need for purification. Despite these advantages, there has been a lack of dedicated bioinformatics tools for the detailed analysis of CC data.

RESULTS

We introduce Pycallingcards, a comprehensive Python module specifically designed for the analysis of single-cell and bulk CC data across multiple species. Pycallingcards introduces two innovative peak callers, CCcaller and MACCs, enhancing the accuracy and speed of pinpointing TF binding sites from CC data. Pycallingcards offers a fully integrated environment for data visualization, motif finding, and comparative analysis with RNA-seq and ChIP-seq datasets. To illustrate its practical application, we have reanalyzed previously published mouse cortex and glioblastoma datasets. This analysis revealed novel cell-type-specific binding sites and potential sex-linked TF regulators, furthering our understanding of TF binding and gene expression relationships. Thus, Pycallingcards, with its user-friendly design and seamless interface with the Python data science ecosystem, stands as a critical tool for advancing the analysis of TF functions via CC data.

AVAILABILITY AND IMPLEMENTATION

Pycallingcards can be accessed on the GitHub repository: https://github.com/The-Mitra-Lab/pycallingcards.

Identifying Function Determining Residues in Neuroimmune Semaphorin 4A

Semaphorin 4A (Sema4A) exerts a stabilizing effect on human Treg cells in PBMC and CD4+ T cell cultures by engaging Plexin B1. Sema4A deficient mice display enhanced allergic airway inflammation accompanied by fewer Treg cells, while Sema4D deficient mice displayed reduced inflammation and increased Treg cell numbers even though both Sema4 subfamily members engage Plexin B1. The main objectives of this study were: 1. To compare the in vitro effects of Sema4A and Sema4D proteins on human Treg cells; and 2. To identify function-determining residues in Sema4A critical for binding to Plexin B1 based on Sema4D homology modeling. We report here that Sema4A and Sema4D display opposite effects on human Treg cells in in vitro PBMC cultures; Sema4D inhibited the CD4+CD25+Foxp3+ cell numbers and CD25/Foxp3 expression. Sema4A and Sema4D competitively bind to Plexin B1 in vitro and hence may be doing so in vivo as well. Bayesian Partitioning with Pattern Selection (BPPS) partitioned 4505 Sema domains from diverse organisms into subgroups based on distinguishing sequence patterns that are likely responsible for functional differences. BPPS groups Sema3 and Sema4 into one family and further separates Sema4A and Sema4D into distinct subfamilies. Residues distinctive of the Sema3,4 family and of Sema4A (and by homology of Sema4D) tend to cluster around the Plexin B1 binding site. This suggests that the residues both common to and distinctive of Sema4A and Sema4D may mediate binding to Plexin B1, with subfamily residues mediating functional specificity. We mutated the Sema4A-specific residues M198 and F223 to alanine; notably, F223 in Sema4A corresponds to alanine in Sema4D. Mutant proteins were assayed for Plexin B1-binding and Treg stimulation activities. The F223A mutant was unable to stimulate Treg stability in in vitro PBMC cultures despite binding Plexin B1 with an affinity similar to the WT protein. This research is a first step in generating potent mutant Sema4A molecules with stimulatory function for Treg cells with a view to designing immunotherapeutics for asthma.

Expression of Semaphorin 3A in Malignant and Normal Bladder Tissue: Immunohistochemistry Staining and Morphometric Evaluation

Simple Summary

Semaphorin 3A (Sema3A) was shown to play a significant role in different neoplasms. In a previous study by our team, we showed that Sema3A is overexpressed in patients with urothelial carcinoma (UC). In this study, we analyzed 43 specimens from patients with the entire spectrum of UC and compared them with samples from 14 normal urothelium using immunostaining and computerized morphometry. The results showed that patients with UC had intense Sema3A staining in the apical layer of the mucosa compared to patients without UC. Moreover, patients with higher grade UC showed intense Sema3A staining across all mucosal layers.

Abstract

Introduction: Our previous studies showed elevated levels of Semaphorin3a (Sema3A) in the urine of patients with urothelial cancer compared to healthy patients. The aim of this study was to analyze the extent of Sema3A expression in normal and malignant urothelial tissue using immune-staining microscopic and morphometric analysis. Materials and Methods: Fifty-seven paraffin-embedded bladder samples were retrieved from our pathology archive and analyzed: 14 samples of normal urothelium, 21 samples containing low-grade urothelial carcinoma, 13 samples of patients with high-grade urothelial carcinoma, 7 samples containing muscle invasive urothelial carcinoma, and 2 samples with pure urothelial carcinoma in situ. All samples were immunostained with anti Sema3A antibodies. The area of tissue stained with Sema3A and its intensity were analyzed using computerized morphometry and compared between the samples’ groups. Results: In normal bladder tissue, very light Sema3A staining was demonstrated on the mucosal basal layer and completely disappeared on the apical layer. In low-grade tumor samples, cells in the basal layer of the mucosa were also lightly stained with Sema3A, but Seama3A expression intensified upon moving apically, reaching its highest level on apical cells exfoliating to the urine. In high grade urothelial tumors, Seama3A staining was intense in the entire thickness of the mucosa. In samples containing carcinoma in situ, staining intensity was high and homogenous in all the neoplastic cells. Conclusions: Sema3A may be serve as a potential non-invasive marker of urothelial cancer.

Semaphorins as emerging clinical biomarkers and therapeutic targets in cancer

Semaphorins are a large family of developmental regulatory signals, characterized by aberrant expression in human cancers. These molecules crucially control cell-cell communication, cell migration, invasion and metastasis, tumor angiogenesis, inflammatory and anti-cancer immune responses. Semaphorins comprise secreted and cell surface-exposed molecules and their receptors are mainly found in the Plexin and Neuropilin families, which are further implicated in a signaling network controlling the tumor microenvironment. Accumulating evidence indicates that semaphorins may be considered as novel clinical biomarkers for cancer, especially for the prediction of patient survival and responsiveness to therapy. Moreover, preclinical experimental studies have demonstrated that targeting semaphorin signaling can interfere with tumor growth and/or metastatic dissemination, suggesting their relevance as novel therapeutic targets in cancer; this has also prompted the development of semaphorin-interfering molecules for application in the clinic. Here we will survey, in diverse human cancers, the current knowledge about the relevance of semaphorin family members, and conceptualize potential lines of future research development in this field.

Semaphorin-4C is upregulated in epithelial ovarian cancer

The present retrospective study aimed to investigate the expression of semaphorin-4C (Sema4C) in epithelial ovarian cancer (EOC), and to determine the association between Sema4C expression and patient clinicopathological characteristics. Sema4C mRNA expression was detected by reverse transcription-quantitative polymerase chain reaction in the tissues of 74 cases of EOC, 20 cases of ovarian epithelial benign tumor, 20 cases of ovarian borderline epithelial tumor and 15 cases of normal ovarian tissue. Immunohistochemistry was used to detect the expression and localization of Sema4C. The association between Sema4C expression level and patients clinicopathological characteristics was determined by χ² test. The results demonstrated that Sema4C expression level in ovarian epithelial carcinoma tissues was significantly higher compared with that in benign tumors, borderline epithelial tumors and normal ovarian tissues (P<0.05). In addition, Sema4C expression in ovarian cancer tissues was significantly associated with the clinical and pathological stages of tumors (P<0.05). In conclusion, the present study demonstrated that Sema4C expression was upregulated in EOC.

SEMA3A Exon 9 Expression Is a Potential Prognostic Marker of Unfavorable Recurrence-Free Survival in Patients with Tongue Squamous Cell Carcinoma

This study tried to assess the prognostic value of semaphorin (SEMA) family genes in patients with tongue squamous cell carcinoma (TSCC) and the potential epigenetic alterations of the genes. The part of third-level TSCC data in The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma (TCGA-HNSC) was extracted using the UCSC Xena browser for analysis. Among 20 SEMA genes examined, 7 were markedly upregulated, while 8 were substantially decreased in TSCC tissues compared with adjacent normal tissues. SEMA3A was the only gene with independent prognostic value in terms of recurrence-free survival (RFS) in multivariate analysis (hazard ratio [HR]: 1.697, 95% CI: 1.228-2.345, p = 0.001). Among the individual exons of SEMA3A, the exon 9 had a better prognostic value in terms of recurrence than total SEMA3A expression and its expression also independently predicted shorter RFS (HR: 2.193, 95% CI: 1.463-3.290, p < 0.001). The methylation levels of two CpG sites (cg06144675 and cg13988052) were moderately correlated with SEMA3A expression. Interestingly, cg06144675, which locates at the promoter region, showed a negative correlation with SEMA3A expression, whereas cg13988052, which is in the intron of SEMA3A gene body showed a positive correlation with SEMA3A expression. In conclusion, SEMA3A expression is aberrantly upregulated in TSCC tissues. Its exon 9 expression is a potentially valuable prognostic marker of unfavorable RFS in TSCC patients. Both promoter hypomethylation and gene body hypermethylation might contribute to the dysregulation.

The Prognostic Value of Serum Semaphorin3A and VEGF Levels in Patients with Metastatic Colorectal Cancer

PURPOSE

Despite new treatment options in metastatic colorectal cancer (mCRC), new prognostic markers are still needed to determine optimal chemoregimen especially for anti-angiogenesis drugs. In this study, we evaluated the serum semaphorin and VEGF-A levels as prognostic factors in patients with mCRC.

METHODS

Patients with diagnosed mCRC who were treated with first-line bevacizumab plus chemotherapy were included in the study. Venous blood samples of 37 patients with metastatic colon cancer were taken, and serum semaphorin 3A and VEGF-A levels were studied in pre-treatment and the 1st and third months after the treatment was initiated.

RESULTS

Totally, 37 patients were enrolled in the study. The patients' mean age was 62 years. Twenty-eight (49%) of the patients were male, and 19 (51%) were female. Serum semaphorin3A (sema3A) levels of the patients were 5.4 ± 7.4 ng/ml before the treatment, 3.5 ± 3.3 ng/ml at the first month, and 3.5 ± 3.7 ng/ml at the third month. Serum VEGF-A levels were 27.7 ± 32.9 ng/l before the treatment, 23.1 ± 28.1 ng/l at the first month, and 28.9 ± 30.2 ng/l at the third month. There was no significant correlation between the survival and pre-treatment VEGF-A level (p = 0.064). Overall survival (OS) was statistically significantly higher in patients with pre-treatment semaphorin 3A levels below 5.4 ng/ml than higher than 5.4 ng/ml (10.5 months vs 4.5 months, respectively, HR 0.23, 95% CI 19.635-11,391, p = 0.012).

CONCLUSION

Pre-treatment semaphorin 3A level can be a prognostic marker for the mCRC patients who were treated with bevacizumab in patients with metastatic colorectal cancer.