Cell adhesion system and human cancer morphogenesis

Matrix Remodeling Associated Genes (MXRAs): structural diversity, functional significance, and therapeutic potential in tumor microenvironments

The Matrix Remodeling Associated Genes (MXRAs) family, comprising eight distinct members (MXRA1-8), plays a crucial role in the development and maintenance of higher vertebrate cells. These proteins are primarily involved in the regulation of intercellular adhesion and the remodeling of the extracellular matrix (ECM). Recent investigations have highlighted the significant roles of MXRAs in the modulation of tumor growth and progression, establishing them as vital components in the oncogenic landscape. Notably, each MXRA member exhibits unique structural characteristics and functional properties, contributing to a diverse array of regulatory effects within the tumor context. This review seeks to provide a comprehensive analysis of the structural attributes, functional contributions, and activities of MXRAs within the tumor microenvironment. By elucidating the underlying mechanisms of action, this paper aims to offer novel insights and strategic approaches for the identification of early diagnostic biomarkers, as well as potential therapeutic targets that may facilitate molecular interventions aimed at inhibiting tumor development.

Plasma cell-free DNA methylation profile before afatinib treatment is associated with progression-free and overall survival of patients with epidermal growth factor receptor gene mutation-positive non-small cell lung cancer

BACKGROUND

The present study aimed to clarify the clinical significance of the cell-free DNA (cfDNA) methylation profile of patients with non-small cell lung cancer (NSCLC) showing the epidermal growth factor receptor (EGFR) gene mutation.

METHODS

In 103 patients, genome-wide DNA methylation analysis using Infinium Methylation EPIC array was performed using samples of pre-tyrosine kinase inhibitor afatinib-treatment plasma cfDNA (n = 101) and post-afatinib cfDNA (n = 84).

RESULTS

Principal component analysis indicated that the cfDNA methylation profile was altered after afatinib treatment. Hierarchical clustering using the pre-afatinib cfDNA methylation profile revealed that cases with a fatal outcome were accumulated in specific clusters. Moreover, Kaplan-Meier analysis showed that the pre-afatinib cfDNA methylation profile was significantly associated with both progression-free survival (PFS) and overall survival (OS), whereas the post-afatinib profile was not. The genes for which pre-afatinib cfDNA methylation levels were associated with PFS were accumulated in the cadherin, Wnt, and EGFR signaling pathways. Activation of EGFR-related signaling due to DNA methylation alterations might overturn the effect of afatinib. Pre-afatinib levels of CEP170 and CHCHD6 cfDNA methylation were associated with both PFS and OS. Both pre- and post-afatinib cfDNA methylation levels of SLC9A3R2 and INTS1 were associated with bone metastasis. Using the cfDNA methylation levels at two CpG sites, cg12721600 and cg05905155, patients showing an overall response were predicted with a sensitivity of 96% or more.

CONCLUSIONS

The non-invasively measurable cfDNA methylation profile may reflect the corresponding profile in cancer cells, and that pre-treatment measurement may provide clinically useful information on EGFR mutation-positive NSCLC.

Characteristics of cell adhesion molecules expression and environmental adaptation in yak lung tissue

Cell Adhesion Molecules (CAMs) play a crucial role in regulating immune responses and repairing damage caused by hypoxia. However, the relationship between the expression characteristics of CAMs in yak lung tissues and their adaptation to the plateau environment remains unclear. To address this question, we compared lung tissues from yaks and cattle at the same altitude. After digesting the lung tissues with trypsin or Type I collagenase for varying durations, we observed that fewer cells were isolated from yak tissues compared to cattle. RNA sequencing (RNA-seq) analysis revealed that the Differentially Expressed Genes (DEGs) in lung tissues of yaks and cattle were significantly enriched in cell adhesion-related pathways. Quantitative real-time PCR (qRT-PCR) further identified changes in the expression levels of five distinct types of CAMs. Among these, the cadherin family (CDH1, CDH2, CDH11, PCDH12, CD34) exhibited significantly higher expression in yaks than in cattle. These cadherins play a critical role in regulating lung inflammation and maintaining the alveolar-capillary barrier, thereby ensuring the structural stability of the lungs. Immunohistochemical staining demonstrated that the expression patterns of cell adhesion-related proteins (CDH1, CDH11, ITGB6, SELP, CD44) were largely consistent with the qRT-PCR results. In conclusion, compared to cattle, the enhanced cell adhesion capacity of yak lung tissues contributes to their superior adaptation to the harsh plateau environment.

Probing Single-Cell Adhesion Kinetics and Nanomechanical Force with Surface Plasmon Resonance Imaging

Single cell adhesion plays a significant role in numerous physiological and pathological processes. Real-time imaging and quantification of single cell adhesion kinetics and corresponding cell-substrate mechanical interaction forces are crucial for elucidating the cellular mechanisms involved in tissue formation, immune responses, and cancer metastasis. Here, we present the development of a plasmonic-based nanomechanical sensing and imaging system (PNMSi) for the real-time measurement of single cell adhesion kinetics and associated nanomechanical forces with plasmonic tracking and monitoring of cell-substrate interactions and the accompanying nanoscale fluctuations. Both the slow binding and dynamic nanomechanical interaction processes were tracked and analyzed with a thermodynamic model to determine the adhesion kinetic parameters and quantity the mechanical forces. To demonstrate the capabilities of the PNMSi platform, we examined single cell binding interactions across four different surface modifications, and obvious alterations in binding kinetics and corresponding nanomechanical forces were observed, influenced by surface charges and interfacial hydrophilicity. Additionally, we investigated changes in mechanical interaction forces of single cells during cytoskeleton modification, revealing the cross-linking-induced cell adhesion changes. Furthermore, to demonstrate the application capability of the system, the adhesion profiling of primary tumor and metastatic tumor cells was explored, and obvious alterations were observed in the kinetic forces of single cell-substrate interaction. The PNMSi platform facilitates high-throughput single cell adhesion imaging and the quantification of adhesion interaction kinetics and nanomechanical forces with high sensitivity and serves as a promising platform for identifying biomarkers for tumor metastasis and for screening potential therapeutic agents.

Identified VCAM1 as prognostic gene in gastric cancer by co-expression network analysis

The diffuse gastric cancer (DGC) is a malignant tumor distinct from intestinal gastric cancer (IGC). This study aims to identify genetic variances and potential diagnostic and therapeutic approaches for diverse types of gastric cancer utilizing an extensive dataset. Data from RNA sequencing and clinical pathological details were acquired from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) dataset. Co-expression gene modules were constructed via Weighted Gene Co-Expression Network Analysis (WGCNA), followed by deciphering gene functions and protein-protein interaction networks within significantly associated modules. In total, analysis was conducted on 56,753 genes from 247 individuals with gastric cancer. Particularly, 621 genes from the green module exhibited strong associations with the Lauren type of gastric cancer. The prominent genes in the green module showed enrichment in processes such as signal transduction, immune response, and the positive regulation of GTPase activity. Noteworthy among these, VCAM1 was identified as the central gene linked to patients' prognosis. Moreover, 72 gastric cancer specimens were collected from The First Affiliated Hospital of University of Science and Technology of China. Immunohistochemical analysis demonstrated a significantly higher expression of VCAM1 in DGC compared to IGC (p = 0.019). Furthermore, it was confirmed that VCAM1 expression serves as a prognostic indicator for patients with DGC (p = 0.002), a correlation not observed in IGC (p = 0.760). In conclusion, this study identifies VCAM1 as a promising diagnostic and prognostic factor, suggesting novel avenues for diagnostic and therapeutic approaches in gastric cancer.

Wnt Signaling Pathway in Tumor Biology

Relapse and metastasis are the major challenges that stand in the way of cancer healing and survival, mainly attributed to cancer stem cells (CSCs). Their capabilities of self-renewal and tumorigenic potential leads to treatment resistance development. CSCs function through signaling pathways such as the Wnt/β-catenin cascade. While commonly involved in embryogenesis and adult tissues homeostasis, the dysregulation of the Wnt pathway has direct correlations with tumorigenesis, metastasis, and drug resistance. The development of therapies that target CSCs and bulk tumors is both crucial and urgent. However, the extensive crosstalk present between Wnt and other signaling networks (Hedgehog and Notch) complicates the development of efficient long-term therapies with minimal side-effects on normal tissues. Despite the obstacles, the emergence of Wnt inhibitors and subsequent modulation of the signaling pathways would provide dynamic therapeutic approaches to impairing CSCs and reversing resistance mechanisms.

Exploring Water-Soluble South African Tulbaghia violacea Harv Extract as a Therapeutic Approach for Triple-Negative Breast Cancer Metastasis

Triple-negative breast cancer (TNBC) accounts for approximately 20% of all breast cancer cases and is characterized by a lack of estrogen, progesterone, and human epidermal growth factor 2 receptors. Current targeted medicines have been unsuccessful due to this absence of hormone receptors. This study explored the efficacy of Tulbaghia violacea, a South African medicinal plant, for the treatment of TNBC metastasis. Extracts from T. violacea leaves were prepared using water and methanol. However, only the water-soluble extract showed anti-cancer activity and the effects of this water-soluble extract on cell adhesion, invasion, and migration, and its antioxidant activity were assessed using MCF-10A and MDA-MB-231 cells. The T. violacea extract that was soluble in water effectively decreased the movement and penetration of MDA-MB-231 cells through the basement membrane in scratch and invasion tests, while enhancing their attachment to a substance resembling an extracellular matrix. The sample showed mild-to-low antioxidant activity in the antioxidant assy. Nuclear magnetic resonance spectroscopy revealed 61 chemical components in the water-soluble extract, including DDMP, 1,2,4-triazine-3,5(2H,4H)-dione, vanillin, schisandrin, taurolidine, and α-pinene, which are known to have anti-cancer properties. An in-depth examination of the transcriptome showed alterations in genes linked to angiogenesis, metastasis, and proliferation post-treatment, with reduced activity in growth receptor signaling, angiogenesis, and cancer-related pathways, such as the Wnt, Notch, and PI3K pathways. These results indicate that T. violacea may be a beneficial source of lead chemicals for the development of potential therapeutic medicines that target TNBC metastasis. Additional studies are required to identify the precise bioactive chemical components responsible for the observed anti-cancer effects.

Micro tensile tester measurement of biomechanical properties and adhesion force of microtubule-polymerization-inhibited cancer cells

Both mechanical and adhesion properties of cancer cells are complex and reciprocally related to migration, invasion, and metastasis with large cell deformation. Therefore, we evaluated these properties for human cervical cancer cells (HeLa) simultaneously using our previously developed micro tensile tester system. For efficient evaluation, we developed image analysis software to modify the system. The software can analyze the tensile force in real time. The modified system can evaluate the tensile stiffness of cells to which a large deformation is applied, also evaluate the adhesion strength of cancer cells that adhered to a culture substrate and were cultured for several days with their adhesion maturation. We used the modified system to simultaneously evaluate the stiffness of the cancer cells to which a large deformation was applied and their adhesion strength. The obtained results revealed that the middle phase of tensile stiffness and adhesion force of the microtubule-depolymerized group treated with colchicine (an anti-cancer drug) (stiffness, 13.4 ± 7.5 nN/%; adhesion force, 460.6 ± 258.2 nN) were over two times larger than those of the control group (stiffness, 5.0 ± 3.5 nN/%; adhesion force, 168.2 ± 98.0 nN). Additionally, the same trend was confirmed with the detailed evaluation of cell surface stiffness using an atomic force microscope. Confocal fluorescence microscope observations showed that the stress fibers (SFs) of colchicine-treated cells were aligned in the same direction, and focal adhesions (FAs) of the cells developed around both ends of the SFs and aligned parallel to the developed direction of the SFs. There was a possibility that the microtubule depolymerization by the colchicine treatment induced the development of SFs and FAs and subsequently caused an increment of cell stiffness and adhesion force. From the above results, we concluded the modified system would be applicable to cancer detection and anti-cancer drug efficacy tests.

Aberrant cell adhesiveness due to DNA hypermethylation of KLF11 in papillary urothelial carcinomas

PURPOSE

The aim of this study was to clarify DNA methylation profiles determining the clinicopathological diversity of urothelial carcinomas.

METHODS

Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation450 BeadChip in 46 paired samples of non-cancerous urothelium (N) and corresponding cancerous tissue (T), and 26 samples of normal control urothelium obtained from patients without urothelial carcinomas (C). For genes of interest, correlation between DNA methylation and mRNA expression was examined using the Cancer Genome Atlas database. In addition, the role of a selected target for cancer-relevant endpoints was further examined in urothelial carcinoma cell lines.

RESULTS

The genes showing significant differences in DNA methylation levels between papillary carcinomas and more aggressive non-papillary (nodular) carcinomas were accumulated in signaling pathways participating in cell adhesion and cytoskeletal remodeling. Five hundred ninety-six methylation sites showed differences in DNA methylation levels between papillary and nodular carcinomas. Of those sites, that were located in CpG-islands around transcription start site, 5'-untranslated region or 1st exon, 16 genes exhibited inverse correlations between DNA methylation and mRNA expression levels. Among the latter, only the KLF11 gene showed papillary T sample-specific DNA hypermethylation in comparison to C and N samples. The DNA methylation levels of KLF11 were not significantly different between T samples and N samples or T samples and C samples for patients with papillo-nodular or nodular carcinomas. Knockdown experiments using the urothelial carcinoma cell lines HT1376 and 5637, which are considered models for papillary carcinoma, revealed that KLF11 participates in altering the adhesiveness of cells to laminin-coated dishes, although cell growth was not affected.

CONCLUSION

These data indicate that DNA hypermethylation of KLF11 may participate in the generation of papillary urothelial carcinomas through induction of aberrant cancer cell adhesion to the basement membrane.

Morphological basis of the lung adenocarcinoma subtypes

Lung adenocarcinoma (LUAD), which accounts for a large proportion of lung cancers, is divided into five major subtypes based on histologic characteristics. The clinical characteristics, prognosis, and responses to treatments vary among subtypes. Here, we demonstrate that the variations of cell-cell contact energy result in the LUAD subtype-specific morphogenesis. We reproduced the morphologies of the papillary LUAD subtypes with the cellular Potts Model (CPM). Simulations and experimental validations revealed modifications of cell-cell contact energy changed the morphology from a papillary-like structure to micropapillary or solid subtype-like structures. Remarkably, differential gene expression analysis revealed subtype-specific expressions of genes relating to cell adhesion. Knockdown experiments of the micropapillary upregulated ITGA11 gene resulted in the morphological changes of the spheroids produced from an LUAD cell line PC9. This work shows the consequences of gene mutations and gene expressions on patient prognosis through differences in tissue composing physical forces among LUAD subtypes.

Molecular pathological approach to cancer epigenomics and its clinical application

Careful microscopic observation of histopathological specimens, accumulation of large numbers of high-quality tissue specimens, and analysis of molecular pathology in relation to morphological features are considered to yield realistic data on the nature of multistage carcinogenesis. Since the morphological hallmark of cancer is disruption of the normal histological structure maintained through cell-cell adhesiveness and cellular polarity, attempts have been made to investigate abnormalities of the cadherin-catenin cell adhesion system in human cancer cells. It has been shown that the CDH1 tumor suppressor gene encoding E-cadherin is silenced by DNA methylation, suggesting that a "double hit" involving DNA methylation and loss of heterozygosity leads to carcinogenesis. Therefore, in the 1990s, we focused on epigenomic mechanisms, which until then had not received much attention. In chronic hepatitis and liver cirrhosis associated with hepatitis virus infection, DNA methylation abnormalities were found to occur frequently, being one of the earliest indications that such abnormalities are present even in precancerous tissue. Aberrant expression and splicing of DNA methyltransferases, such as DNMT1 and DNMT3B, was found to underlie the mechanism of DNA methylation alterations in various organs. The CpG island methylator phenotype in renal cell carcinoma was identified for the first time, and its therapeutic targets were identified by multilayer omics analysis. Furthermore, the DNA methylation profile of nonalcoholic steatohepatitis (NASH)-related hepatocellular carcinoma was clarified in groundbreaking studies. Since then, we have developed diagnostic markers for carcinogenesis risk in NASH patients and noninvasive diagnostic markers for upper urinary tract cancer, as well as developing a new high-performance liquid chromatography-based diagnostic system for DNA methylation diagnosis. Research on the cancer epigenome has revealed that DNA methylation alterations occur from the precancerous stage as a result of exposure to carcinogenic factors such as inflammation, smoking, and viral infections, and continuously contribute to multistage carcinogenesis through aberrant expression of cancer-related genes and genomic instability. DNA methylation alterations at the precancerous stages are inherited by or strengthened in cancers themselves and determine the clinicopathological aggressiveness of cancers as well as patient outcome. DNA methylation alterations have applications as biomarkers, and are expected to contribute to diagnosis, as well as preventive and preemptive medicine.

Clinical significance of low expression of CADM3 in breast cancer and preliminary exploration of related mechanisms

BACKGROUND

Cell adhesion molecule 3 (CADM3), a transmembrane glycoprotein on cell membranes, plays a role in the way of ligand and receptor interaction. However, there are few studies on CADM3 in tumors, and how it works in breast cancer (BC) remains unclear.

METHODS

The Cancer Genome Atlas (TCGA) database and clinical samples were used to analyze CADM3 expression and its correlation with clinicopathological factors and prognosis. Its correlation with immune infiltration was analyzed by TCGA. The effects of CADM3 on proliferation and migration were investigated by cell clonal formation, CCK-8, cell scratch and transwell assay. Protein interaction network was prepared and the function prediction of related genes was conducted. The correlation between CADM3 and MAPK pathway was further explored by western blot experiment.

RESULTS

The expression of CADM3 in BC tissues were significantly lower than that in adjacent normal tissues. High level of CADM3 was related to better prognosis of BC patients. CADM3 was an independent prognostic factor for BC. Expression of CADM3 was significantly associated with the status of ER and PR, age and PAM50 subtypes. CADM3 positively related to many immune infiltrating cells. Overexpression of CADM3 can notably reduce cell proliferation and migration. CADM3 was related to MAPK pathway and the phosphorylation of ERK1/2 and JNK1 was inhibited in BC cells with high CADM3.

CONCLUSIONS

Our research reveals the clinical significance of CADM3 in BC and indicates the critical roles of CADM3 in immune infiltration and MAPK pathway.

The potential of graphene coatings as neural interfaces

Recent advances in nanotechnology design and fabrication have shaped the landscape for the development of ideal cell interfaces based on biomaterials. A holistic evaluation of the requirements for a cell interface is a highly complex task. Biocompatibility is a crucial requirement which is affected by the interface's properties, including elemental composition, morphology, and surface chemistry. This review explores the current state-of-the-art on graphene coatings produced by chemical vapor deposition (CVD) and applied as neural interfaces, detailing the key properties required to design an interface capable of physiologically interacting with neural cells. The interfaces are classified into substrates and scaffolds to differentiate the planar and three-dimensional environments where the cells can adhere and proliferate. The role of specific features such as mechanical properties, porosity and wettability are investigated. We further report on the specific brain-interface applications where CVD graphene paved the way to revolutionary advances in biomedicine. Future studies on the long-term effects of graphene-based materials in vivo will unlock even more potentially disruptive neuro-applications.

The role of PKP1 in tumor progression in melanoma: Analysis of a cell adhesion-related model

The incidence rate of melanoma varies across regions, with Europe, the United States, and Australia having 10-25, 20-30, and 50-60 cases per 1 00 000 people. In China, patients with melanoma exhibit different clinical manifestations, pathogenesis, and outcomes. Current treatments include surgery, adjuvant therapy, and immune checkpoint inhibitors. Nonetheless, complications may arise during treatment. Melanoma development is heavily reliant on cell adhesion molecules (CAMs), and studying these molecules could provide new research directions for metastasis and progression. CAMs include the integrin, immunoglobulin, selectin, and cadherin families, and they affect multiple processes, such as maintenance, morphogenesis, and migration of adherens junction. In this study, a cell adhesion-related risk prognostic signature was constructed using bioinformatics methods, and survival analysis was performed. Plakophilin 1 (PKP1) was observed to be crucial to the immune microenvironment and has significant effects on melanoma cell proliferation, migration, invasion, and the cell cycle. This signature demonstrates high reliability and has potential for clinical applications.

Improving Cancer Survival Prediction via Graph Convolutional Neural Network Learning on Protein-Protein Interaction Networks

Cancer is one of the most challenging health problems worldwide. Accurate cancer survival prediction is vital for clinical decision making. Many deep learning methods have been proposed to understand the association between patients' genomic features and survival time. In most cases, the gene expression matrix is fed directly to the deep learning model. However, this approach completely ignores the interactions between biomolecules, and the resulting models can only learn the expression levels of genes to predict patient survival. In essence, the interaction between biomolecules is the key to determining the direction and function of biological processes. Proteins are the building blocks and principal undertakings of life activities, and as such, their complex interaction network is potentially informative for deep learning methods. Therefore, a more reliable approach is to have the neural network learn both gene expression data and protein interaction networks. We propose a new computational approach, termed CRESCENT, which is a protein-protein interaction (PPI) prior knowledge graph-based convolutional neural network (GCN) to improve cancer survival prediction. CRESCENT relies on the gene expression networks rather than gene expression levels to predict patient survival. The performance of CRESCENT is evaluated on a large-scale pan-cancer dataset consisting of 5991 patients from 16 different types of cancers. Extensive benchmarking experiments demonstrate that our proposed method is competitive in terms of the evaluation metric of the time-dependent concordance index( Ctd) when compared with several existing state-of-the-art approaches. Experiments also show that incorporating the network structure between genomic features effectively improves cancer survival prediction.

A review of electrochemical impedance as a tool for examining cell biology and subcellular mechanisms: merits, limits, and future prospects

Herein the development of cellular impedance biosensors, electrochemical impedance spectroscopy, and the general principles and terms associated with the cell-electrode interface is reviewed. This family of techniques provides quantitative and sensitive information into cell responses to stimuli in real-time with high temporal resolution. The applications of cell-based impedance biosensors as a readout in cell biology is illustrated with a diverse range of examples. The current state of the field, its limitations, the possible available solutions, and the potential benefits of developing biosensors are discussed.

microRNA silencing in a whole worm cestode model provides insight into miR-71 function

Parasites belonging to the class Cestoda include zoonotic species such as Echinococcus spp. and Taenia spp. that cause morbidity and mortality in endemic areas, mainly affecting pastoral and rural communities in low income countries but also upper middle income countries. Cestodes show remarkable developmental plasticity, implying tight regulation of gene expression throughout their complex life cycles. Despite the recent availability of genomic data for cestodes, little progress was made on postgenomic functional studies. MicroRNAs (miRNAs) are key components of gene regulatory systems that guide diverse developmental processes in multicellular organisms. miR-71 is a highly expressed miRNA in cestodes, which is absent in vertebrates and targets essential parasite genes, representing a potential key player in understanding the role of miRNAs in cestodes biology. Here we used transfection with antisense oligonucleotides to perform whole worm miRNA knockdown in tetrathyridia of Mesocestoides vogae (syn. Mesocestoides corti), a laboratory model of cestodes. We believe this is the first report of miRNA knockdown at the organism level in these parasites. Our results showed that M. vogae miR-71 is involved in the control of strobilation in vitro and in the establishment of murine infection. In addition, we identified miR-71 targets in M. vogae, several of them being de-repressed upon miR-71 knockdown. This study provides new knowledge on gene expression regulation in cestodes and suggests that miRNAs could be evaluated as new selective therapeutic targets for treating Neglected Tropical Diseases prioritised by the World Health Organization.

Centrosome amplification promotes cell invasion via cell-cell contact disruption and Rap-1 activation

Centrosome amplification (CA) is a prominent feature of human cancers linked to tumorigenesis in vivo. Here, we report mechanistic contributions of CA induction alone to tumour architecture and extracellular matrix (ECM) remodelling. CA induction in non-tumorigenic breast cells MCF10A causes cell migration and invasion, with underlying disruption of epithelial cell-cell junction integrity and dysregulation of expression and subcellular localisation of cell junction proteins. CA also elevates expression of integrin β-3, its binding partner fibronectin-1 and matrix metalloproteinase enzymes, promoting cell-ECM attachment, ECM degradation, and a migratory and invasive cell phenotype. Using a chicken embryo xenograft model for in vivo validation, we show that CA-induced (+CA) MCF10A cells invade into the chick mesodermal layer, with inflammatory cell infiltration and marked focal reactions between chorioallantoic membrane and cell graft. We also demonstrate a key role of small GTPase Rap-1 signalling through inhibition using GGTI-298, which blocked various CA-induced effects. These insights reveal that in normal cells, CA induction alone (without additional oncogenic alterations) is sufficient to confer early pro-tumorigenic changes within days, acting through Rap-1-dependent signalling to alter cell-cell contacts and ECM disruption.

Differential Protein Expression Patterns of HOXA13 and HOXB13 Are Associated with Bladder Cancer Progression

Bladder cancer is a common urological cancer and has the highest recurrence rate of any cancer. The aim of our study was to profile and characterize the protein expression of homeobox A13 (HOXA13) and homeobox B13 (HOXB13) genes in Malaysian bladder cancer patients. The protein expression of HOXA13 and HOXB13 in formalin-fixed paraffin-embedded (FFPE) bladder cancer tissues was determined by immunohistochemistry (IHC) analysis. The association between HOXA13/HOXB13 protein expression and demographic/clinicopathological characteristics of the bladder cancer patients was determined by chi-square analysis. Approximately 63.6% of the bladder cancer tissues harbored high HOXA13 expression. High HOXA13 expression was significantly associated with non-muscle invasive bladder cancer, lower tumor grade, higher number of lymph node metastases, and recurrence risk. In contrast, low HOXB13 expression (including those with negative expression) was observed in 71.6% of the bladder cancer tissues analyzed. Low HOXB13 expression was significantly associated with muscle-invasive bladder cancer, higher tumor stage, tumor grade, and metastatic risk. Both HOXA13 and HOXB13 protein expression were found to be associated with bladder tumorigenesis. The putative oncogenic and tumor suppressive roles of HOXA13 and HOXB13, respectively, suggest their potential utility as biomarkers in bladder cancer.

Differentiating brain metastasis from glioblastoma by time-dependent diffusion MRI

BACKGROUND

This study was designed to investigate the use of time-dependent diffusion magnetic resonance imaging (MRI) parameters in distinguishing between glioblastomas and brain metastases.

METHODS

A retrospective study was conducted involving 65 patients with glioblastomas and 27 patients with metastases using a diffusion-weighted imaging sequence with oscillating gradient spin-echo (OGSE, 50 Hz) and a conventional pulsed gradient spin-echo (PGSE, 0 Hz) sequence. In addition to apparent diffusion coefficient (ADC) maps from two sequences (ADC50Hz and ADC0Hz), we generated maps of the ADC change (cADC): ADC50Hz - ADC0Hz and the relative ADC change (rcADC): (ADC50Hz - ADC0Hz)/ ADC0Hz × 100 (%).

RESULTS

The mean and the fifth and 95th percentile values of each parameter in enhancing and peritumoral regions were compared between glioblastomas and metastases. The area under the receiver operating characteristic curve (AUC) values of the best discriminating indices were compared. In enhancing regions, none of the indices of ADC0Hz and ADC50Hz showed significant differences between metastases and glioblastomas. The mean cADC and rcADC values of metastases were significantly higher than those of glioblastomas (0.24 ± 0.12 × 10-3mm2/s vs. 0.14 ± 0.03 × 10-3mm2/s and 23.3 ± 9.4% vs. 14.0 ± 4.7%; all p < 0.01). In peritumoral regions, no significant difference in all ADC indices was observed between metastases and glioblastomas. The AUC values for the mean cADC (0.877) and rcADC (0.819) values in enhancing regions were significantly higher than those for ADC0Hz5th (0.595; all p < 0.001).

CONCLUSIONS

The time-dependent diffusion MRI parameters may be useful for differentiating brain metastases from glioblastomas.

Circular RNA mediated gene regulation in human breast cancer: A bioinformatics analysis

Circular RNAs (circRNAs) are a new acknowledged class of RNAs that has been shown to play a major role in several biological functions both in physiological and pathological conditions, operating as critical part of regulatory processes, like competing endogenous RNA (ceRNA) networks. The ceRNA hypothesis is a recently discovered molecular mechanism that adds a new key layer of post-transcriptional regulation, whereby various types of RNAs can reciprocally influence each other's expression competing for binding the same pool of microRNAs, even affecting disease development. In this study, we build a network of circRNA-miRNA-mRNA interactions in human breast cancer, called CERNOMA, that is a bipartite graph with one class of nodes corresponding to differentially expressed miRNAs (DEMs) and the other one corresponding to differentially expressed circRNAs (DEC) and mRNAs (DEGs). A link between a DEC (or DEG) and DEM is placed if it is predicted to be a target of the DEM and shows an opposite expression level trend with respect to the DEM. Within the CERNOMA, we highlighted an interesting deregulated circRNA-miRNA-mRNA triplet, including the up-regulated hsa_circRNA_102908 (BRCA1 associated RING domain 1), the down-regulated miR-410-3p, and the up-regulated ESM1, whose overexpression has been already shown to promote tumor dissemination and metastasis in breast cancer.

Communication between bone marrow mesenchymal stem cells and multiple myeloma cells: Impact on disease progression

Multiple myeloma (MM) is a hematological malignancy characterized by the accumulation of immunoglobulin-secreting clonal plasma cells at the bone marrow (BM). The interaction between MM cells and the BM microenvironment, and specifically BM mesenchymal stem cells (BM-MSCs), has a key role in the pathophysiology of this disease. Multiple data support the idea that BM-MSCs not only enhance the proliferation and survival of MM cells but are also involved in the resistance of MM cells to certain drugs, aiding the progression of this hematological tumor. The relation of MM cells with the resident BM-MSCs is a two-way interaction. MM modulate the behavior of BM-MSCs altering their expression profile, proliferation rate, osteogenic potential, and expression of senescence markers. In turn, modified BM-MSCs can produce a set of cytokines that would modulate the BM microenvironment to favor disease progression. The interaction between MM cells and BM-MSCs can be mediated by the secretion of a variety of soluble factors and extracellular vesicles carrying microRNAs, long non-coding RNAs or other molecules. However, the communication between these two types of cells could also involve a direct physical interaction through adhesion molecules or tunneling nanotubes. Thus, understanding the way this communication works and developing strategies to interfere in the process, would preclude the expansion of the MM cells and might offer alternative treatments for this incurable disease.

Single-Cell Quantification of the Mechanical Stability of Cell-Cell Adherens Junction Using Glass Micropipettes

Micropipette-based methods have been widely used for the manipulation of cells and characterization of the mechanical properties at the cell or tissue level. Here, we introduce the glass micropipette-based mechanical assays for the stability of cell-cell adhesion. A probing microbead coated with specific adhesion ligands, captured by a glass micropipette, is manipulated to form the adhesion complexes with the corresponding receptors on a single cell. Once the cell is moving away from the micropipette, forces are generated from 20 pN to 100 nN to the adhesion complexes, which are quantified in real-time based on the bending of the glass micropipette. We specifically emphasize the principle and method to probe the rupturing forces of the adhesion complexes at controlled force loading rates, the ligand coating on the probe microbeads, the force calibration of the glass micropipette, and the applications of the method to probe the E-cadherin-based cell-cell adhesions. The principles can be broadly applied to other cell adhesions such as cell-matrix adhesions, neuronal synapses, and bacterial-cell adhesions.

The anticancer effects of curcumin and clinical research progress on its effects on esophageal cancer

Esophageal cancer (EC) is a common tumor of the gastrointestinal system and a major threat to human health. The etiology and incidence of EC vary depending on the type of pathology. Owing to the unique physiological structure of the esophagus and the poor biological behavior of EC, the treatment modalities available are limited, and the prognosis of patients is relatively poor. Curcumin is a type of natural phytochemical belonging to the class of phenolic compounds. It exerts favorable anticancer effects on various cancers. A growing body of evidence indicates that curcumin suppresses tumor development and progression by inhibiting tumor cell proliferation, invasion, and migration, thus inducing apoptosis, regulating microRNA expression, reversing multidrug resistance, and inducing sensitivity to the therapeutic effect of chemoradiotherapy. Multiple cellular molecules, growth factors, and genes encoding proteins participating in different signaling pathways interact with each other to contribute to the complex and orderly anticancer effect. The efficacy and safety of curcumin have been established in preclinical studies for EC and clinical trials for other cancers. However, the low bioavailability of curcumin limits its clinical application. Therefore, the modification of curcumin analogs, the combination of curcumin with other drugs or therapies, and the use of novel nanocarriers have been widely investigated to improve the clinical effects of curcumin in EC.

Leucine zipper protein 2 serves as a prognostic biomarker for prostate cancer correlating with immune infiltration and epigenetic regulation

Background

We sought to determine whether leucine zipper protein 2 (LUZP2) could benefit men with prostate cancer (PCa) undergoing radical radiotherapy (RT) or prostatectomy (RP).

Methods

Analysis was done on differentiating expression, clinical prognosis, co-expressed genes, immune infiltration, and epigenetic changes. All of our analyses were done using the R software (version 3.6.3) and the appropriate packages.

Results

In terms of PCa, tumor samples expressed LUZP2 more than normal samples did. In the TCGA database and GSE116918, we found that LUZP2 was the only independent risk factor for PCa. The shared enriched pathways for patients undergoing RP or RT were cell-cell adhesion, regulation of filopodium assembly, and extracellular matrix containing collagen. With the exception of TNFRSF14, we discovered that LUZP2 was negatively correlated with 21 immune checkpoints in PCa patients receiving RT. We found a significant inverse relationship between LUZP2 expression and the tumor immune environment, which included B cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, stromal score, immune score, and estimate score, in patients receiving RP or RT. Additionally, tumor purity was positively correlated with LUZP2. We found that the drug bortezomib may be susceptible to the LUZP2. DNA methylation was significantly associated with the mRNA expression of LUZP2 in PCa patients from the TCGA database, and LUZP2 methylation was positively correlated with immune cells. The proliferative activity of various PCa cells, which correlated to different stages of this disease, was also found to be significantly reduced by LUZP2 reduction, according to the results of our experimental work.

Conclusions

We proposed a relatively comprehensive understanding of the roles of LUZP2 on PCa from the fresh perspective of senescence.

Adhesion strength and anti-tumor agents regulate vinculin of breast cancer cells

The onset and progression of cancer are strongly associated with the dissipation of adhesion forces between cancer cells, thus facilitating their incessant attachment and detachment from the extracellular matrix (ECM) to move toward metastasis. During this process, cancer cells undergo mechanical stresses and respond to these stresses with membrane deformation while inducing protrusions to invade the surrounding tissues. Cellular response to mechanical forces is inherently related to the reorganization of the cytoskeleton, the dissipation of cell–cell junctions, and the adhesion to the surrounding ECM. Moreover, the role of focal adhesion proteins, and particularly the role of vinculin in cell attachment and detachment during migration, is critical, indicating the tight cell–ECM junctions, which favor or inhibit the metastatic cascade. The biomechanical analysis of these sequences of events may elucidate the tumor progression and the potential of cancer cells for migration and metastasis. In this work, we focused on the evaluation of the spreading rate and the estimation of the adhesion strength between breast cancer cells and ECM prior to and post-treatment with anti-tumor agents. Specifically, different tamoxifen concentrations were used for ER⁺ breast cancer cells, while even concentrations of trastuzumab and pertuzumab were used for HER2⁺ cells. Analysis of cell stiffness indicated an increased elastic Young’s modulus post-treatment in both MCF-7 and SKBR-3 cells. The results showed that the post-treatment spreading rate was significantly decreased in both types of breast cancer, suggesting a lower metastatic potential. Additionally, treated cells required greater adhesion forces to detach from the ECM, thus preventing detachment events of cancer cells from the ECM, and therefore, the probability of cell motility, migration, and metastasis was confined. Furthermore, post-detachment and post-treatment vinculin levels were increased, indicating tighter cell–ECM junctions, hence limiting the probability of cell detachment and, therefore, cell motility and migration.

A van der Waals force-based adhesion study of stem cells exposed to cold atmospheric plasma jets

Cold atmospheric plasma has established its effect on cell adhesion. Given the importance of cell adhesion in stem cells, the current study investigates the effect of plasma treatment on Human Bone Marrow Mesenchymal Stem Cells (HBMMSCs) adhesion by which the differentiation and fate of cells are determined. In this paper, adhesion modification is considered not only for cell- ECM (Extra cellular Matrix), but also between suspended cells, and enhanced adhesions were found in both circumstances. Regarding the previous works, the increase of the cell–ECM adhesion during the plasma therapy was mostly attributed to the enhancement of the production and activity of integrin proteins. Nevertheless, considering the importance of van der Waals forces at the cellular level, the effect of cold plasma on VDWFs and so its effect on adhesion is investigated in this work for the first time, to the best of our knowledge. For this purpose, employing the semi-empirical methods, the role of the plasma therapy on the VDWF between the cells has been studied at three levels; (a) plasma-induced dipole formation, (b) Hammaker coefficient modification of culture medium, and c) cell roughness modification. For suspended cell condition, we conclude and support that van der Waals forces (VDWFs) enhancement has a key role in cell adhesion processes. We believe that, the present work gives a new physical insight in studying the plasma therapy method at the cellular level.

Adhesion molecules in multiple myeloma oncogenesis and targeted therapy

Every day we march closer to finding the cure for multiple myeloma. The myeloma cells inflict their damage through specialized cellular meshwork and cytokines system. Implicit in these interactions are cellular adhesion molecules and their regulators which include but are not limited to integrins and syndecan-1/CD138, immunoglobulin superfamily cell adhesion molecules, such as CD44, cadherins such as N-cadherin, and selectins, such as E-selectin. Several adhesion molecules are respectively involved in myelomagenesis such as in the transition from the precursor disorder monoclonal gammopathy of undetermined significance to indolent asymptomatic multiple myeloma (smoldering myeloma) then to active multiple myeloma or primary plasma cell leukemia, and in the pathological manifestations of multiple myeloma.

Down-Regulated CLDN10 Predicts Favorable Prognosis and Correlates With Immune Infiltration in Gastric Cancer

Background: CLDN10, an important component of the tight junctions of epithelial cells, plays a crucial role in a variety of tumors. The effect of CLDN10 expression in gastric cancer, however, has yet to be elucidated.

Methods: Differential expression of CLDN10 at the mRNA and protein levels was evaluated using Oncomine, ULCAN, HPA and TIMER2.0 databases. Real-time polymerase chain reaction (RT-PCR) was utilized to further verify the expression of CLDN10 in vitro. Correlations between CLDN10 expression and clinical outcomes of gastric cancer were explored by Kaplan-Meier Plotter. Gene set enrichment analysis (GSEA) and protein-protein interaction (PPI) were performed via LinkedOmics and GeneMANIA. The correlations between CLDN10 expression and immune cell infiltration and somatic copy number alternations (SCNA) in gastric cancer were explored by TIMER2.0 and GEPIA2.0.

Results: CLDN10 expression was lower in gastric cancer compared to adjacent normal tissues, and associated with better prognosis. CLDN10 also showed significant differences at different T stages, Lauren classification, treatments and HER2 status. PPI and GSEA analysis showed that CLDN10 might be involved in signal transmission, transmembrane transport and metabolism. In some major immune cells, low expression of CLDN10 was associated with increased levels of immune cell infiltration. In addition, it was found that different SCNA status in CLDN10 might affect the level of immune cell infiltration. Furthermore, the expression of CLDN10 was significantly associated with the expression of several immune cell markers, especially B cell markers, follicular helper T cell (Tfh) markers and T cell exhaustion markers.

Conclusion: Down-regulated CLDN10 was associated with better overall survival (OS) in gastric cancer. And CLDN10 may serve as a potential prognostic biomarker and correlate to immune infiltration levels in gastric cancer.

Predicting drug sensitivity of cancer cells based on DNA methylation levels

Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular features may help to optimize drug-development pipelines and explain mechanisms behind treatment responses. In this study, we focus on DNA methylation profiles as one type of molecular feature that is known to drive tumorigenesis and modulate treatment responses. Using genome-wide, DNA methylation profiles from 987 cell lines in the Genomics of Drug Sensitivity in Cancer database, we used machine-learning algorithms to evaluate the potential to predict cytotoxic responses for eight anti-cancer drugs. We compared the performance of five classification algorithms and four regression algorithms representing diverse methodologies, including tree-, probability-, kernel-, ensemble-, and distance-based approaches. We artificially subsampled the data to varying degrees, aiming to understand whether training based on relatively extreme outcomes would yield improved performance. When using classification or regression algorithms to predict discrete or continuous responses, respectively, we consistently observed excellent predictive performance when the training and test sets consisted of cell-line data. Classification algorithms performed best when we trained the models using cell lines with relatively extreme drug-response values, attaining area-under-the-receiver-operating-characteristic-curve values as high as 0.97. The regression algorithms performed best when we trained the models using the full range of drug-response values, although this depended on the performance metrics we used. Finally, we used patient data from The Cancer Genome Atlas to evaluate the feasibility of classifying clinical responses for human tumors based on models derived from cell lines. Generally, the algorithms were unable to identify patterns that predicted patient responses reliably; however, predictions by the Random Forests algorithm were significantly correlated with Temozolomide responses for low-grade gliomas.

Immunohistochemical Expression of the Epithelial to Mesenchymal Transition Proteins E-cadherin and ß-catenin in Grades of Oral Squamous Cell Carcinoma

Background

E-Cadherin/β-Catenin protein complexes play a major role in epithelial to mesenchymal transition (EMT) and vice versa. Such types of EMT are implicated physiologically during embryonic development and pathologically in tissue fibrosis and tumorigenesis.

Aims

The aim was the evaluation of E-Cadherin and β-Catenin immunoreactivity in various grades of oral squamous cell carcinoma (OSCC) and to correlate their pattern of expression.

Materials and Methods

Immunohistochemical expression of E-Cadherin/β-Catenin was evaluated in a total n = 30 tissue samples comprising of n = 10 well-differentiated squamous cell carcinoma (WDSCC), n = 10 moderately differentiated squamous cell carcinoma (MDSCC), and n = 10 poorly differentiated squamous cell carcinoma (PDSCC). Based on the intensity of staining, an immunoreactivity scoring was calculated.

Statistical Analysis

The scorings obtained were subjected to independent t-test, paired t-test, Chi-square test, and ANOVA test using SPSS version 20.0 statistical analysis software. P < 0.05 was considered statistically significant.

Results

A significant difference was observed in the expression of β-Catenin between normal mucosa and WDSCC; normal mucosa and MDSCC. A gradual decrease in the immunoreactivity score of E-Cadherin is seen in WDSCC, MDSCC, and PDSCC.

Conclusion

Therefore, dysregulation of these proteins can lead to tumor progression, invasion, and metastasis. Further studies are warranted to specify the role of these EMT proteins as prognostic/therapeutic markers in patients suffering from OSCC.

Immunohistochemical Localization of Phosphorylated and Unphosphorylated Form of β-catenin With Regard to Shadow Cell and Squamous Differentiation in Cutaneous Pilomatricoma

Pilomatricoma usually contains a mutation in CTNNB1 that encodes β-catenin (BC). It also shows nuclear accumulation of BC protein, which plays an important role in tumorigenesis of pilomatricoma. In vitro studies have indicated that mutant BC protein is unphosphorylated and shows nuclear accumulation, but this theory has not been confirmed in various tumors with CTNNB1 mutation. We examined immunohistochemical localization of phosphorylated BC (pBC) and unphosphorylated BC (npBC) with regard to the modes of cell death or differentiation in 25 cases of pilomatricoma. As for the component showing shadow cell differentiation, BC was detected in cytoplasm/nucleus and along cell membrane in basaloid cells, whereas only in the latter in transitional cells in all cases. Meanwhile, npBC was localized along cell membrane of transitional cells, but not in basaloid cells, nor in nucleus of any components. The components with squamous differentiation also revealed the staining patterns similar to those seen in shadow cell differentiation in some cases. pBC was found in some cell fragments in the amorphous debris containing apoptotic bodies among shadow cell nests. These results suggested that npBC plays an important role in cell adhesion during differentiation and that pBC expression is associated with apoptosis of basaloid cells in pilomatricoma. BC accumulated in the nucleus was not immunoreactive for npBC possibly due to post-translational modification or conformational changes that resulted in loss of or masked antigenicity when BC is assumed to be unphosphorylated.

Functional and Clinical Characteristics of Cell Adhesion Molecule CADM1 in Cancer

The cell adhesion molecule CADM1, which participates in cell adhesion and signal transduction, has a regulatory effect on the development of tumors. CADM1 is often involved in malignant tumors of multiple organ systems, such as the respiratory and digestive systems. Upregulated CADM1 promotes tumor cell apoptosis and inhibits malignant proliferation. Along with cell cycle-related proteins, it participates in regulating signaling pathways, such as EMT, STAT3, and AKT, and plays an important role in inhibiting invasion and migration. Considering clinical characteristics, low CADM1 expression is associated with aggressive tumors and poor prognosis. In addition, some long non-coding RNAs (lncRNAs) or miRNAs directly or indirectly act on CADM1 to regulate tumor growth and motility. Interestingly, CADM1 function differs in adult T-cell leukemia/lymphoma (ATLL), and NF-κB is thought to be involved in this process. Taken together, CADM1 could be a potential biomarker for early diagnosis and a target for cancer treatment in future clinical practices.

Cooperative participation of epigenomic and genomic alterations in the clinicopathological diversity of gastric adenocarcinomas: significance of cell adhesion and epithelial-mesenchymal transition-related signaling pathways

The present study was conducted to clarify the cooperative significance of epigenomic and genomic abnormalities during gastric carcinogenesis. Using 21 samples of normal control gastric mucosa (C), 109 samples of non-cancerous gastric mucosa (N) and 105 samples of cancerous tissue (T) from 109 patients with primary gastric adenocarcinomas, genome-wide DNA methylation analysis was performed using Infinium assay. Among these samples, 66 paired N and corresponding T samples were subjected to whole-exome and single nucleotide polymorphism array analyses. As had been shown in our previous study, 109 patients were clustered clinicopathologically into least aggressive Cluster A (n = 20), most aggressive Cluster B1 (n = 20) and Cluster B2 (n = 69). Most DNA methylation alterations in each cluster had already occurred even in N samples compared with C samples, and DNA methylation alterations at the precancerous N stage were inherited by the established cancers themselves. Recurrent single nucleotide variants and insertions/deletions resulting in functional disruption of the proteins encoded by the ABCA10, BNC2, CDH1, CTNNB1, SMAD4 and VAV2 genes were specific to Cluster B1, whereas those of the APC, EGFR, ERBB2, ERBB3, MLH1 and MUC6 genes were specific to Cluster A. MetaCore pathway analysis revealed that the epigenomically affected TWIST1 gene and genomically affected CDH1, CTNNB1, MMP9, TLN2, ROCK1 and SMAD4 genes were accumulated in signaling pathways related to cell adhesion, cytoskeleton remodeling and epithelial–mesenchymal transition in Cluster B1. These data indicate that epigenomic alterations at the precancerous stage are important in gastric carcinogenesis and that epigenomic and genomic alterations cooperatively underlie the aggressiveness of gastric adenocarcinomas.

Ubiquitin-specific peptidase 53 inhibits the occurrence and development of clear cell renal cell carcinoma through NF-κB pathway inactivation

Background

Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignant diseases in the urinary system with more than 140,000 related deaths annually. Ubiquitination–deubiquitination homeostasis is an important factor in ccRCC progression; ubiquitin‐specific peptidase 53 (USP53) belongs to the family of deubiquitinating enzymes, but its functions are rarely reported.

Methods

Databases obtained from GEO and TCGA were analyzed to reveal the role of USP53 in ccRCC. CCK‐8/BrdU and EDU assays were used to detect the proliferation of ccRCC after USP53 overexpression or knockdown. A tumor xenograft experiment was used to verify the effect of the proliferation of ccRCC after USP53 knockdown. Transwell assays were used to detect the metastasis of ccRCC after USP53 overexpression or knockdown. RNA sequencing and western blot analysis were employed to detect the change in genes after USP53 overexpression and knockdown. Then we tested the effect of USP53 on IκBα protein stability through western blot analysis. Detect the effect of USP53 on IκBα ubiquitination in vitro by immunoprecipitation method.

Results

USP53 expression was downregulated in ccRCC tissues and USP53 expression was significantly negatively correlated with the tumor progression and clinical prognosis. The ability of growth and metastasis of ccRCC was inhibited after USP53 overexpression. In addition, USP53 knockdown promoted ccRCC growth and metastasis. Moreover, USP53 knockdown promoted the ability of clone formation of ccRCC in vivo. NF‐κB signaling pathway significantly enriched and downregulated in USP53 overexpressed cells, and genes in the NF‐κB pathway (such as IL1B, CXCL1‐3, RELA, RELB, etc.) were obviously downregulated in USP53 overexpressed cells. USP53 overexpression decreased the phosphorylation of IKKβ and P65 in both Caki‐1 and 786‐O cells, and the expression of IκBα was increased. Phosphorylation of IKKβ and P65 was increased in both Caki‐1 and 786‐O cells after USP53 knockdown. As the expression of USP53 increases, the protein expression of IκBα was also gradually increased and USP53 reduced the ubiquitination of IκBα.

Conclusion

In summary, our data indicate that USP53 inhibits the inactivation of the NF‐κB pathway by reducing the ubiquitination of IκBα to further inhibit ccRCC proliferation and metastasis. These findings may help understand the pathogenesis of ccRCC and introduce new potential therapeutic targets for kidney cancer patients.

GATA3 is downregulated in HCC and accelerates HCC aggressiveness by transcriptionally inhibiting slug expression

Previous studies have reported that GATA3 is downregulated in multiple types of tumours, including gastric cancer and osteosarcoma. The aim of this study was to explore whether GATA3 serves as a tumour suppressor to inhibit hepatocellular carcinoma (HCC) development. Tumour tissue specimens and adjacent normal tissue specimens were obtained from 162 patients diagnosed with HCC in the Affiliated Hospital of Shaoxing University from July 2000 to May 2018. The result of the present study demonstrated that GATA3 was downregulated in HCC tumour tissues compared with that of adjacent normal tissues. The expression of GATA3 was also negatively associated with tumour size, TNM stage and lymph node metastasis. Additionally, analysis of the follow-up data revealed that low GATA3 expression was closely correlated with poor survival. Gain and loss of function analyses revealed that overexpression of GATA3 decreased the ability of proliferation, migration and invasion in HCC cell lines, whereas inhibition of GATA3 promoted the ability of proliferation, migration and invasion. In addition, GATA3 suppressed EMT through the regulation of slug expression. Additionally, slug overexpression attenuated the inhibitory effects of GATA3 overexpression on cancer cell proliferation, migration and invasion. Thus, GATA3 is downregulated in HCC, and suppresses cell proliferation, migration and invasion. Moreover, GATA3 transcriptionally inhibits slug expression, thereby suppressing EMT in HCC.

CLDN10 associated with immune infiltration is a novel prognostic biomarker for clear cell renal cell carcinoma

Aims: To identify the clinical roles of CLDN10 in clear cell renal cell carcinoma (ccRCC). Materials & methods: Using data from TCGA-KIRC, GEO DataSets and laboratory experiments to determine the prognostic and clinicopathological characteristics of CLDN10. Results: CLDN10 expression was remarkably reduced in ccRCC. Downregulated CLDN10 was related to metastasis and poor prognosis. Multivariate Cox analysis determined that elevated CLDN10 expression was independently correlated with longer OS and DFS. Moreover, CLDN10 expression was negatively associated with the methylation levels of cg10305311 and cg16275739. CLDN10 expression was also associated with naive CD4 and memory T-cell and dendritic cell infiltration. Conclusions: Immune-related CLDN10 is an independent prognostic biomarker of ccRCC. DNA hypermethylation plays an important role in decreased CLDN10 expression.

Extracellular Matrix-Mediated Breast Cancer Cells Morphological Alterations, Invasiveness, and Microvesicles/Exosomes Release

Breast cancer is a leading disease in women. Several studies are focused to evaluate the critical role of extracellular matrix (ECM) in various biochemical and molecular aspects but also in terms of its effect on cancer cell morphology and therefore on cancer cell invasion and metastatic potential. ECM fibrillar components, such as collagen and fibronectin, affect cell behavior and properties of mammary cancer cells. The aim of this study was to investigate using the scanning electron microscopy (SEM) how the highly invasive MDA-MB-231 breast cancer cells, interplaying with ECM substrates during cell migration/invasion, modify their morphological characteristics and cytoplasmic processes in relation to their invasive potential. In particular we reproduced and analyzed how natural structural barriers to cancer cell invasion, such as the basement membrane (Matrigel) and fibrillar components of dermis (fibronectin as well as the different concentrations/array of type I collagen), could induce morphological changes in 3D cultures. Interestingly, we demonstrate that, even with different effects, all collagen concentrations/arrays lead to morphological alterations of breast cancer cells. Intriguingly, the elongated mesenchymal shaped cells were more prominent in 3D cultures with a dense and thick substrate (thick Matrigel, high concentrated collagen network, and densely packed collagen fibers), even though cells with different shape produced and released microvesicles and exosomes as well. It is therefore evident that the peri-tumoral collagen network may act not only as a barrier but also as a dynamic scaffold which stimulates the morphological changes of cancer cells, and modulates tumor development and metastatic potential in breast cancer.

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer

Long non-coding RNA (lncRNA)-mediated competitive endogenous RNA (ceRNA) networks act as essential mechanisms in tumor initiation and progression, but their diagnostic and prognostic significance in prostate cancer (PCa) remains poorly understood. Presently, using the RNA expression data derived from multiple independent PCa-related studies, we constructed a high confidence and PCa-specific core ceRNA network by employing three lncRNA-gene inference approaches and key node filter strategies and then established a logistic model and risk score formula to evaluate its diagnostic and prognostic values, respectively. The core ceRNA network consists of 10 nodes, all of which are significantly associated with clinical outcomes. Combination of expression of the 10 ceRNAs with a logistic model achieved AUC of ROC and PR curve up to ∼96 and 99% in excluding normal prostate samples, respectively. Additionally, a risk score formula constructed with the ceRNAs exhibited significant association with disease-free survival. More importantly, utilizing the expression of RNAs in the core ceRNA network as a molecular signature, the TCGA-PRAD cohort was divided into four novel clinically relevant subgroups with distinct expression patterns, highlighting a feasible way for improving patient stratification in the future. Overall, we constructed a PCa-specific core ceRNA network, which provides diagnostic and prognostic value.

Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma

Objective: This study was aimed to identify prognostic factors in glioma by analysis of the gene expression and DNA methylation data. Methods: The RNAseq and DNA methylation data associated with glioma were downloaded from GEO and TCGA databases to analyze the differentially expressed genes (DEGs) and methylated genes between tumor and normal tissues. Function and pathway analyses, co-expression network and survival analysis were performed based on these DEGs. The intersection genes of DEGs and differentially methylated genes were obtained followed by function analysis. Results: Total 2190 DEGs were identified between tumor and normal tissues, which were significantly enriched in neuron differentiation associated functions, as well as ribosome pathway. There were 6186 methylation sites (2834 up-regulated and 3352 down-regulated) with significant differences in tumor vs. normal. In the constructed co-expression network, DPP6, MAPK10 and RPL3 were hub genes. Survival analysis of 20 DEGs obtained 18 prognostic genes, among which 9 were differentially methylated, such as LHFPL tetraspan subfamily member 3 (LHFPL3), cadherin 20 (CDH20), complexin 2 (CPLX2), and tenascin R (TNR). The intersection of DEGs and differentially methylated genes (632 genes) were significantly enriched in functions of neuron differentiation. Conclusion: DPP6, MAPK10 and RPL3 may play important roles in tumorigenesis of glioma. Additionally, methylation of LHFPL3, CDH20, CPLX2, and TNR may serve as prognostic factors of glioma.

Recent advances in porphyrin-based nanocomposites for effective targeted imaging and therapy

Porphyrins are organic compounds that continue to attract much theoretical interest, and have been called the "pigments of life". They have a wide role in photodynamic and sonodynamic therapy, along with uses in magnetic resonance, fluorescence and photoacoustic imaging. There is a vast range of porphyrins that have been isolated or designed, but few of them have real clinical applications. Due to the hydrophobic properties of porphyrins, and their tendency to aggregate by stacking of the planar molecules they are difficult to work with in aqueous media. Therefore encapsulating them in nanoparticles (NPs) or attachment to various delivery vehicles have been used to improve delivery characteristics. Porphyrins can be used in a composite designed material with properties that allow specific targeting, immune tolerance, extended tissue lifetime and improved hydrophilicity. Drug delivery, healing and repairing of damaged organs, and cancer theranostics are some of the medical uses of porphyrin-based nanocomposites covered in this review.

Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton

Choroid plexus papilloma (CPP) is a rare benign tumor of the central nervous system that is usually confined to the cerebral ventricles. According to the World Health Organization, CPP corresponds to a grade I atypical CPP (a-CPP); however, it can become more aggressive and reach grade II, which can rarely undergo malignant transformation into a choroid plexus carcinoma (grade III). To the best of our knowledge, identification of these tumors mutations by next generation DNA sequencing (NGS) has not been yet reported. In the present study, NGS analysis of an a-CPP case was performed. Data were analyzed using Advaita Bioinformatics i-VariantGuide and Ion Reporter 5.6 programs. The results from NGS identified 12 novel missense mutations in the following genes: NOTCH1, ATM, STK36, MAGI1, DST, RECQL4, NUMA1, THBS1, MYH11, MALT1, SMARCA4 and CDH20. The PolyPhen score of six variants viz., DST, RECQL4, NUMA1, THBS1, MYHI1 and SMARCA4 were high, which suggested these variants represents pathogenic variants. Two novel insertions that caused frameshift were also found. Furthermore, two novel nonsense mutations and 14 novel intronic variants were identified in this tumor. The novel missense mutation detected in ATM gene was situated in c.5808A>T; p. (Leu1936Phe) in exon 39, and a known ATM mutation was in c.5948A>G; p. (Asn1983Ser). These novel mutations had not been reported in previous database. Subsequently, the quality statistics of these variants, including allele coverage, allele ratio, P-value, Phred quality score, sequencing coverage, PolyPhen score and alleles frequency was performed. For all variants, P-value was highly significant and the Phred quality score was high. In addition, the results from sequencing coverage demonstrated that 97.02% reads were on target and that 97.88% amplicons had at least 500 reads. These findings may serve at determining new strategies to distinguish the types of choroid plexus tumor, and at developing novel targeted therapies. Development of NGS technologies in the Kingdom of Saudi Arabia may be used in molecular pathology laboratories.

Efficient protocols and methods for high-throughput utilization of the Collaborative Cross mouse model for dissecting the genetic basis of complex traits

The Collaborative Cross (CC) mouse model is a next-generation mouse genetic reference population (GRP) designated for a high-resolution quantitative trait loci (QTL) mapping of complex traits during health and disease. The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild-derived strains. Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions. In this article, we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases, including type 2 diabetes and metabolic diseases, body composition, immune response, colorectal cancer, susceptibility to Aspergillus fumigatus, Klebsiella pneumoniae, Pseudomonas aeruginosa, sepsis, and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum, which were conducted at our laboratory using the CC mouse population. These traits are observed at multiple levels of the body systems, including metabolism, body weight, immune profile, susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present full protocols and step-by-step methods, implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines, mapping the gene underlying the host response to these infections and chronic diseases. The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits, including chronic and infectious diseases.

Nanomechanical sub-surface mapping of living biological cells by force microscopy

Atomic force microscopy allows for the nanomechanical surface characterization of a multitude of types of materials with highest spatial precision in various relevant environments. In recent years, researchers have refined this methodology to analyze living biological materials in vitro. The atomic force microscope thus has become an essential instrument for the (in many cases) non-destructive, high-resolution imaging of cells and visualization of their dynamic mechanical processes. Mapping force versus distance curves and the local evaluation of soft samples allow the operator to "see" beneath the sample surface and to capture the local mechanical properties. In this work, we combine atomic force microscopy with fluorescence microscopy to investigate cancerous epithelial breast cells in culture medium. With unprecedented spatial resolution, we provide tomographic images for the local elasticity of confluent layers of cells. For these particular samples, a layer of higher elastic modulus located directly beneath the cell membrane in comparison with the average elastic properties was observed. Strikingly, this layer appears to be perforated at unique locations of the sample surface of weakest mechanical properties where distinct features were visible permitting the tip to indent farthest into the cell's volume. We interpret this layer as the cell membrane mechanically supported by the components of the cytoskeleton that is populated with sites of integral membrane proteins. These proteins act as breaking points for the indenter thus explaining the mechanical weakness at these locations. In contrast, the highest mechanical strength of the cell was found at locations of the cell cores as cross-checked by fluorescence microscopy images of staining experiments, in particular at nucleoli sites as the cumulative elastic modulus there comprises cytoskeletal features and the tight packing ribosomal DNA of the cell.

Nerves and Pancreatic Cancer: New Insights into a Dangerous Relationship

Perineural invasion (PNI) is defined as the presence of neoplastic cells along nerves and/or within the different layers of nervous fibers: epineural, perineural and endoneural spaces. In pancreatic cancer-particularly in pancreatic ductal adenocarcinoma (PDAC)-PNI has a prevalence between 70 and 100%, surpassing any other solid tumor. PNI has been detected in the early stages of pancreatic cancer and has been associated with pain, increased tumor recurrence and diminished overall survival. Such an early, invasive and recurrent phenomenon is probably crucial for tumor growth and metastasis. PNI is a still not a uniformly characterized event; usually it is described only dichotomously ("present" or "absent"). Recently, a more detailed scoring system for PNI has been proposed, though not specific for pancreatic cancer. Previous studies have implicated several molecules and pathways in PNI, among which are secreted neurotrophins, chemokines and inflammatory cells. However, the mechanisms underlying PNI are poorly understood and several aspects are actively being investigated. In this review, we will discuss the main molecules and signaling pathways implicated in PNI and their roles in the PDAC.

Alternative splicing-derived intersectin1-L and intersectin1-S exert opposite function in glioma progression

Intersectin1 (ITSN1) contains two isoforms: ITSN1-S and ITSN1-L, which is highly regulated by alternative splicing. However, the alteration of alternative splicing and its importance in cancer is still unknown. In this study, our transcriptome analysis by using a large glioma cohort indicated the two isoforms exerted opposite function in glioma progression. Our previous results had shown ITSN1-S could promote glioma development; however, the function of ITSN1-L remained unknown. In this study, we first confirmed that ITSN1-L exerted an inhibitory role in glioma progression both in vivo and in vitro, which was contrary to the function of ITSN1-S. In additional, we also elucidated the mechanisms of ITSN1-L in inhibiting tumor progression. First, we revealed ITSN1-L could interact with α-tubulin to promote HDAC6-dependent deacetylation of ac-tubulin leading to decreased cell motility. Second, ITSN1-L could attenuate cell-substrate adhesion through FAK/integrin β3 pathway. Third, ITSN1-L was able to strengthen cell-cell adhesion by upregulating N-cadherin expression and its re-localization to membrane by ANXA2 and TUBB3/TUBB4. In conclusion, we found for the first time that two isoforms produced by alternative splicing exerted opposite functions in glioma development. Therefore, upregulation of ITSN1-L expression as well as downregulation of ITSN1-S expression probably was a better strategy in glioma treatment. Our present study laid a foundation for the importance of alternative splicing in glioma progression and raised the possibility of controlling glioma development completely at an alternative splicing level to be a more effective strategy.

Mammalian Cell Behavior on Hydrophobic Substrates: Influence of Surface Properties

The influence of different surface properties holding to a modification of the substrate towards hydrophobic or superhydrophobic behavior was reviewed in this paper. Cell adhesion, their communication, and proliferation can be strongly manipulated, acting on interfacial relationship involving stiffness, surface charge, surface chemistry, roughness, or wettability. All these features can play mutual roles in determining the final properties of biomedical applications ranging from fabrics to cell biology devices. The focus of this work is the mammalian cell viability in contact with moderate to highly water repellent coatings or materials and also in combination with hydrophilic areas for more specific application. Few case studies illustrate a range of examples in which these surface properties and design can be fruitfully matched to the specific aim.

Disruption of oncogenic liver-intestine cadherin (CDH17) drives apoptotic pancreatic cancer death

Liver-intestine cadherin (CDH17) has been known to function as a tumor stimulator and diagnostic marker for almost two decades. However, its function in highly malignant pancreatic cancer (PC) has yet to be elucidated. Using different strategies including siRNA, shRNA, and CRISPR technology, we successfully induced knockdown and knockout of CDH17 in Panc02-H7 cells and established the corresponding stable cell lines. With these cells, we demonstrated that loss of CDH17 function not only suppressed Panc02-H7 cell growth in vitro but also significantly slowed orthotopic tumor growth in vivo, resulting in the significant life extension. In vitro studies demonstrated that impairing CDH17 inhibited cell proliferation, colony formation, and motility by mechanistically modulating pro- and anti-apoptosis events in PC cells, as CDH17 suppression obviously increased expression of Bad, cytochrome C, cleaved caspase 3, and cleaved PARP, and reduced expression of Bcl-2, Survivin, and pAkt. In vivo studies showed CDH17 knockout resulted in apoptotic PC tumor death through activating caspase-3 activity. Taken together, CDH17 functions as an oncogenic molecule critical to PC growth by regulating tumor apoptosis signaling pathways and CDH17 could be targeted to develop an anti-PC therapeutic approach.

Glycan-decorated protocells: novel features for rebuilding cellular processes

In synthetic biology approaches, lipid vesicles are widely used as protocell models. While many compounds have been encapsulated in vesicles (e.g. DNA, cytoskeleton and enzymes), the incorporation of glycocalyx components in the lipid bilayer has attracted much less attention so far. In recent years, glycoconjugates have been integrated in the membrane of giant unilamellar vesicles (GUVs). These minimal membrane systems have largely contributed to shed light on the molecular mechanisms of cellular processes. In this review, we first introduce several preparation and biophysical characterization methods of GUVs. Then, we highlight specific applications of protocells investigating glycolipid-mediated endocytosis of toxins, viruses and bacteria. In addition, we delineate how prototissues have been assembled from glycan-decorated protocells by using lectin-mediated cross-linking of opposed glycoreceptors (e.g. glycolipids and glycopeptides). In future applications, glycan-decorated protocells might be useful for investigating cell-cell interactions (e.g. adhesion and communication). We also speculate about the implication of lectin-glycoreceptor interactions in membrane fusion processes.