Identification of novel biomarkers of prostate cancer through integrated analysis

ASPORIN: A root of the matter in tumors and their host environment

Asporin (ASPN) has been identified as one of the members of the class I small leucine-rich proteoglycans (SLRPs) family in the extracellular matrix (ECM). It is involved in classic ensigns of cancers such as self-dependent growth, resistance to growth inhibitors, restricting apoptosis, cancer metastasis, and bone-related disorders. ASPN is different from other members of SLRPs, such as decorin (DCN) and biglycan (BGN), in a way that it contains a distinctive length of aspartate (D) residues in the amino (N) -terminal region. These D-repeats residues possess germline polymorphisms and are identified to be linked with cancer progression and osteoarthritis (OA). The polyaspartate stretch in the N-terminal region of the protein and its resemblance to DCN are the reasons it is called asporin. In this review, we comprehensively summarized and updated the dual role of ASPN in various malignancies, its structure in mice and humans, variants, mutations, cancer-associated signalings and functions, the relationship between ASPN and cancer-epithelial, stromal fibroblast crosstalk, immune cells and immunosuppression in cancer and other diseases. In cancer and other bone-related diseases, ASPN is identified to be regulating various signaling pathways such as TGFβ, Wnt/β-catenin, notch, hedgehog, EGFR, HER2, and CD44-mediated Rac1. These pathways promote cancer cell invasion, proliferation, and migration by mediating the epithelial-to-mesenchymal transition (EMT) process. Finally, we discussed mouse models mimicking ASPN in vivo function in cancers and the probability of therapeutic targeting of ASPN in cancer cells, fibrosis, and other bone-related diseases.

The Potential of Extracellular Matrix- and Integrin Adhesion Complex-Related Molecules for Prostate Cancer Biomarker Discovery

Prostate cancer is among the top five cancer types according to incidence and mortality. One of the main obstacles in prostate cancer management is the inability to foresee its course, which ranges from slow growth throughout years that requires minimum or no intervention to highly aggressive disease that spreads quickly and resists treatment. Therefore, it is not surprising that numerous studies have attempted to find biomarkers of prostate cancer occurrence, risk stratification, therapy response, and patient outcome. However, only a few prostate cancer biomarkers are used in clinics, which shows how difficult it is to find a novel biomarker. Cell adhesion to the extracellular matrix (ECM) through integrins is among the essential processes that govern its fate. Upon activation and ligation, integrins form multi-protein intracellular structures called integrin adhesion complexes (IACs). In this review article, the focus is put on the biomarker potential of the ECM- and IAC-related molecules stemming from both body fluids and prostate cancer tissue. The processes that they are involved in, such as tumor stiffening, bone turnover, and communication via exosomes, and their biomarker potential are also reviewed.

Single-cell sequencing analysis reveals the relationship between tumor microenvironment cells and oxidative stress in breast cancer bone metastases

Bone metastasis (BM) is one of the main manifestations of advanced breast cancer (BC), causing complications such as pathological fractures, which seriously affects the quality of life of patients and even leads to death. In our study, a global single-cell landscape of the tumor microenvironment was constructed using single cell RNA sequencing data from BM. BC cells were found to be reduced in the BM, while mesenchymal stem cells (MSCs), Fibroblasts and other cells were significantly more abundant in the BM. The subpopulations of these cells were further identified, and the pathways, developmental trajectories and transcriptional regulation of different subpopulations were discussed. The results suggest that with the development of BM, BC cells were vulnerable to oxidative damage, showing a high level of oxidative stress, which played a key role in cell apoptosis. Fibroblasts were obviously involved in the biological processes (BPs) related to ossification and bone remodeling, and play an important role in tumor cell inoculation to bone marrow and growth. MSC subpopulations were significantly enriched in a number of BPs associated with bone growth and development and oxidative stress and may serve as key components of BC cells homing and adhesion to the ecological niche of BM. In conclusion, our research results describe the appearance of tumor microenvironment cell subpopulations in breast cancer patients, reveal the important role of some cells in the balance of BM bone remodeling and the imbalance of BM development, and provide potential therapeutic targets for BM.

Gleason Score-related MT1L as biomarker for prognosis in prostate adenocarcinoma and contribute to tumor progression in vitro

BACKGROUND

The Gleason Score is well correlated with biological behavior and prognosis in prostate adenocarcinoma (PRAD). This study was derived to determine the clinical significance and function of Gleason-Score-related genes in PRAD.

METHODS

RNA-sequencing profiles and clinical data were extracted from the The Cancer Genome Atlas PRAD database. The Gleason-Score-related genes were screened out by the Jonckheere-Terpstra rank-based test. The "limma" R package was performed for differentially expressed genes. Next, a Kaplan-Meier survival analysis was performed. Correlation MT1L expression levels with tumor stage, non-tumor tissue stage, radiation therapy, and residual tumor were analyzed. Further, MT1L expression was detected in PRAD cell lines by reverse transcription-quantitative polymerase chain reaction assay. Overexpression of MT1L was constructed and used for cell count kit-8, flow cytometric assay, transwell assay, and wound-healing assay.

RESULTS

Survival analysis showed 15 Gleason-Score-related genes as prognostic biomarkers in PRAD. The high-frequency deletion of MT1L was verified in PRAD. Furthermore, MT1L expression was decreased in PRAD cell lines than RWPE-1 cells, and overexpression of MT1L repressed cell proliferation and migration, and induced apoptosis in PC-3 cells.

CONCLUSION

Gleason-Score-related MT1L may serve as a biomarker of poor prognostic biomarker in PRAD. In addition, MT1L plays a tumor suppressor in PRAD progression, which is beneficial for PRAD diagnosis and treatment research.

Joint analysis identified FAP as a prognostic and diagnostic biomarker correlated immune infiltration in gastric cancer

Gastric cancer is one of the most malignant types of cancer in the digestive system because of its high incidence and mortality. There is a notable association between gastric cancer progression and the level and sort of immune cells infiltrating the tumor microenvironment. First, 41 up-regulated differentially expressed genes (DEGs) and 91 down-regulated DEGs were identified from the Gene Expression Omnibus (GEO) database. Among the 21 core genes, prognosis biomarkers FAP, ASPN and CTHRC1 were identified for further study via Kaplan-Meier Plotter, with FAP having the highest prognostic value among them. In addition, the ROC curves of FAP (AUC=0.992), ASPN (AUC=0.955) and CTHRC1 (AUC=0.983) also showed high diagnostic value. Then the expression and mutation levels of the biomarkers were verified by GEPIA and cBioPortal. Their high expression levels were closely correlated to the clinical stages and metastasis status of gastric cancer. Furthermore, their expression was strongly relevant to immune infiltration and macrophage marker levels. In drug response analysis, gastric cancer cell lines with overexpression of FAP and ASPN were more sensitive to PI3K and MET inhibitors, respectively. Importantly, the meta-analysis showed that FAP had an overall positive rate of 68 % (63-73 %, 95 % CI; n = 382) and the patients with high expression of FAP showed a poor prognosis in terms of OS (HR=1.82, 1.33-2.48, 95 % CI) in gastric cancer. In short, FAP, ASPN and CTHRC1 were identified as potential prognostic and diagnostic biomarkers related with immunity and might be effective therapeutic targets of gastric cancer, and the significance of FAP for the prognosis was further assessed by meta-analysis.

Comprehensive analysis of immune-related genes associated with the microenvironment of patients with unexplained infertility

Background

Disturbances in immunological responses and modulation lead to implantation and pregnancy failure and might be involved in the pathogenesis of infertility. This project aimed to screen and identify immune-related genes as potential biomarkers for treatment.

Methods

Gene expression profiles were obtained from Gene Expression Omnibus (GEO) databases. Differentially expressed genes (DEGs) were screened using GEO 2R to explore potential biomarkers. Protein-protein interaction (PPI) network analysis and functional enrichment analysis were applied to explore possible mechanisms. The deconvolution algorithm [referred to as Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT)] was employed to assess tissue-infiltrating immune cells. Western blot analysis and immunohistochemistry (IHC) were conducted for determination of protein levels.

Results

In this research, we identified 24 candidate immune-related DEGs via combined DEGs and functional analysis. We also found that the ratio of M0 macrophages and resting mast cells was higher in infertile group (P<0.05), whereas the amounts of activated natural killer (NK) cells was significantly lower compared with the control group (P<0.05). Furthermore, we evaluated the relationship between immune cells and candidate genes and found that 17 genes were related to M0 macrophages, resting mast cells, or activated NK cells. The genes CD40, PRF1, and EDN3 were chosen based on validation from independent datasets. Finally, our clinical samples confirmed the expression of the 3 genes.

Conclusions

The study recognized 3 genes that are signatures and could be potential biomarkers for unexplained infertility. These genes might guide the immunotherapy of these patients and become new treatment targets.

m6A/ m1A /m5C/m7G-related methylation modification patterns and immune characterization in prostate cancer

Methylation has a close relationship with immune reactions, metastasis, and cancer cell growth. Additionally, RNA methylation-related proteins have emerged as potential cancer therapeutic targets. The connection between the tumor microenvironment (TME) and methylation-related genes (MRGs) remains unclear. We explored the expression patterns of the MRGs in the genome and transcriptional fields of 796 prostate cancer (PCa) samples using two separate data sets. We identified a relationship between patient clinicopathological characteristics, prognosis, TME cell infiltrating qualities, and different MRG changes, as well as the identification of two distinct molecular groupings. Then, we formed an MRGs model to predict overall survival (OS), and we tested the accuracy of the model in patients with PCa. In addition, we developed a very accurate nomogram to improve the MRG model’s clinical applicability. The low-risk group had fewer tumor mutational burden (TMB), greater tumor immune dysfunction and exclusion (TIDE) ratings, fewer mutant genes, and better OS prospects. We discuss how MGRs may affect the prognosis, clinically important traits, TME, and immunotherapy responsiveness in PCa. In order to get a better understanding of MRGs in PCa, we could further explore the prognosis and create more effective immunotherapy regimens to open new avenues.

Emerging Applications of Electrochemical Impedance Spectroscopy in Tear Film Analysis

Human tear film, with a flow rate of 1-3 µL/min, is a rich bodily fluid that transmits a variety of metabolites and hormones containing proteins, lipids and electrolytes that provide clues about ocular and systemic diseases. Analysis of disease biomarkers such as proteins, mRNA, enzymes and cytokines in the tear film, collected by noninvasive methods, can provide significant results for sustaining a predictive, preventive and personalized medicine regarding various diseases such as glaucoma, diabetic retinopathy, keratoconus, dry eye, cancer, Alzheimer's disease, Parkinson's disease and COVID-19. Electrochemical impedance spectroscopy (EIS) offers a powerful technique for analyzing these biomarkers. EIS detects electrical equivalent circuit parameters related to biorecognition of receptor-analyte interactions on the electrode surface. This method is advantageous as it performs a label-free detection and allows the detection of non-electroactive compounds that cannot be detected by direct electron transfer, such as hormones and some proteins. Here, we review the opportunities regarding the integration of EIS into tear fluid sampling approaches.

Identification of candidate hub genes correlated with the pathogenesis, diagnosis, and prognosis of prostate cancer by integrated bioinformatics analysis

Background

Prostate cancer (PCa) has the second highest morbidity and mortality rates in men. Concurrently, novel diagnostic and prognostic biomarkers of PCa remain crucial.

Methods

This study utilized integrated bioinformatics method to identify and validate the potential hub genes with high diagnostic and prognostic value for PCa.

Results

Four Gene Expression Omnibus (GEO) datasets including 123 PCa samples and 76 normal samples were screened and a total of 368 differentially expressed genes (DEGs), including 120 up-regulated DEGs and 248 down-regulated DEGs, were identified. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were majorly enriched in focal adhesion, chemical carcinogenesis, drug metabolism, and cytochrome P450 pathways. Then, 11 hub genes were identified from the protein-protein interaction (PPI) network of the DEGs; 7 of the 11 genes showed the ability of distinguishing PCa from normal prostate based on receiver operating characteristic (ROC) curve analysis. And 5 of the 11 genes were correlated with clinical attributes. Lower CAV1, KRT5, SNAI2 and MYLK expression level were associated with higer Gleason score, advanced pathological T stage and N stage. Lower KRT5 and MYLK expression level were significantly correlated with poor disease-free survival, and lower KRT5 and PTGS2 expression level were significantly related to biochemical recurrence (BCR) status of PCa patients.

Conclusions

In conclusion, CAV1, KRT5, SNAI2, and MYLK show potential clinical diagnostic and prognostic value and could be used as novel candidate biomarkers and therapeutic targets for PCa.