Cis-clustering of cadherin-23 controls the kinetics of cell-cell adhesion

Cis and trans-interactions in cadherins are the foundations of multicellularity. While the trans-interaction mediate cell-cell adhesion, the cis-interaction is postulated as strengthening to trans by clustering. The well-accepted model in cadherin-adhesion is that the trans precedes cis via a diffusion-trap kinetic model. Here we report that cadherin-23, a non-classical cadherin with an extended extracellular region, undergoes clustering in solution via lateral interactions independent of trans and phase separate as liquid droplets. In cellulo using fluorescence-recovery after the photobleaching, we noticed a significantly slow-diffusion of cadherin-23 at the intercellular junctions, indicating the diffusion of a cluster. The cis-clustering accelerates the cell-cell adhesion and, thus, kinetically controls cell-adhesion via cis precedes trans model. Though the connection of cis-clustering with the rapid adhesion is yet to explore, M2-macrophages that predominantly express cadherin-23 undergo fast attachments to circulatory tumor cells during metastasis.

Expression of lncRNAs in children with pancreaticobiliary maljunction: functional analysis and potential biomarkers

IntroductionPancreaticobiliary maljunction (PBM) leads to higher rates of complications, including cholangitis,pancreatitis, and malignancies. The present study was to investigat the expression profile of long non-coding RNAs (lncRNAs) and their potential role as biomarkers in children with pancreaticobiliary maljunction.Material and methodsThe differential expression of lncRNAs and mRNAs from 15 pediatric patients with pancreaticobiliary maljunction and 15 control subjects were analyzed using a commercial microarray and validated with qRT-PCR. The potential biological functions of differentially expressed genes were explored based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment. The ability of potential lncRNA biomarkers to predict pancreaticobiliary maljunction was assessed based on the area under the receiver operating characteristic curve (AUC).ResultsThere were 2915 mRNAs and 173 lncRNAs upregulated, and 2121 mRNAs and 316 lncRNAs downregulated in pancreaticobiliary maljunction cases compared to controls. The enriched Gene Ontology categories associated with differentially expressed mRNAs were extracellular matrix, extracellular region, and kinetochore. The most enriched Kyoto Encyclopedia pathway was protein digestion and absorption, which has been associated with cancer and PI3K-Akt signaling. Analysis of cis- and trans-target genes predicted that a single lncRNA was able to regulate several mRNAs. The qRT-PCR results for NR_110876, NR_132344, XR_946886, and XR_002956345 were consistent with the microarray results, and the difference was statistically significant for NR_132344, XR_946886, and XR_002956345 (p < 0.05). AUC was significant only for XR_946886 (0.837, p < 0.001).ConclusionsOur results implicate lncRNAs in common bile duct pathogenesis in pancreaticobiliary maljunction, and they identify XR_946886 as a potential biomarker for the disease.

Selection of Cashmere Fineness Functional Genes by Translatomics

Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber, but its fineness is not ideal. Therefore, it is important to find genes involved in cashmere fineness that can be used in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new developments through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With these data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes. From these, 343 genes were upregulated in the fine LCG group in relation to the coarse LCG group, and 186 were downregulated in the same relationship. Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of the human papillomavirus infection pathway was seen the most. We found that the COL6A5 gene may affect cashmere fineness.

Extracellular domains of E-cadherin determine key mechanical phenotypes of an epithelium through cell- and non-cell-autonomous outside-in signaling

Cadherins control intercellular adhesion in most metazoans. In vertebrates, intercellular adhesion differs considerably between cadherins of type-I and type-II, predominantly due to their different extracellular regions. Yet, intercellular adhesion critically depends on actomyosin contractility, in which the role of the cadherin extracellular region is unclear. Here, we dissect the roles of the Extracellular Cadherin (EC) Ig-like domains by expressing chimeric E-cadherin with E-cadherin and cadherin-7 Ig-like domains in cells naturally devoid of cadherins. Using cell-cell separation, cortical tension measurement, tissue stretching and migration assays, we show that distinct EC repeats in the extracellular region of cadherins differentially modulate epithelial sheet integrity, cell-cell separation forces, and cell cortical tension with the Cdc42 pathway, which further differentially regulate epithelial tensile strength, ductility, and ultimately collective migration. Interestingly, dissipative processes rather than static adhesion energy mostly dominate cell-cell separation forces. We provide a framework for the emergence of epithelial phenotypes from cell mechanical properties dependent on EC outside-in signaling.

Detecting the Different Responses of Roots and Shoots to Gravity in Salix matsudana (Koidz)

The study of the gravity response of roots and shoots is of great significance when exploring the polarity of plants and the development of the forest industry. In our study, normal and inverted cuts of Salix matsudana (Koidz) were cultured. The total RNAs of roots and shoots were extracted. Based on the comparative transcriptome, 412 and 668 genes were differentially expressed. The plasma membrane-, cell wall-, and extracellular region-related genes were up-regulated in the shoots, while the carbon metabolism and the nitrogen metabolism were up-regulated in the roots. Combining the alternative splicing genes, we found a potential gravity response network: in the shoots, LecRLKs were highly sensitive to gravity and further affected the alternative splicing of SNARE, as well as inducing an inhomogeneous distribution of auxin and a negative geotropism curve. In the roots, AP2/ERFs and STRKs were highly sensitive to gravity and regulated the expression level of STPKs and WAKs, finally resulting in a geotropism curve. Moreover, cell division was suppressed in both the roots and the shoots under inverted conditions with different mechanisms. Cell division inhibitors (KRPs) were up-regulated in the roots, while DNA helicase MCMs were down-regulated in the shoots. These results provide an important foundation for further studies of the molecular mechanisms and genetic regulation of plant responses to gravity and the plant polarity of forest trees.

Identification of Key Genes Involved in the Progression of Renal Fibrosis and Associated with Kidney Renal Clear Cell Carcinoma

Purpose: Renal fibrosis (RF) is the necessary way for Chronic kidney disease (CKD) to develop to End Stage Renal Disease (ESRD). Patients with chronic kidney disease suffer from high morbidity and premature death due to various complications and even cancer. Therefore, this study aims to identify key genes in the pathogenesis of RF and Kidney Renal Clear Cell Carcinoma (KIRC).Method: We analyzed the gene expression characteristics of two databases (GSE6344 and GSE22459) and used geo2R tools to obtain the differentially expressed genes (DEG). Then, use Database for Annotation, Visualization and Integrated Discovery (DAVID) for Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) path analysis. Subsequently, we used the STRING database and built the protein-protein-interactions (PPI) network, the cytoHubba plug-ins of Cytoscape were used to select the hub. Then, we used The Cancer Genome Atlas(TCGA) database to verify hub genes and further screen out core genes. Then, TargetScanHuman, miRTarbase and miRWalk databases were used to reverse-predict targeted miRNA regulated by core genes and screen out core miRNA. mRNA and miRNA mutual aid network were established. At the same time, Gene Expression Profiling Interactive Analysis（GEPIA）database was used for survival analysis of screened core genes to find genes related to prognosis. Tumor Immune Estimation Resource（TIMER）database was used to evaluate the correlation between the expression of core genes and immune cell penetration. Then use the Gene Set Enrichment Analysis (GSEA) tool to analyze the LYZ gene, and finally use the Human Protein Atlas (HPA) online database to verify the expression level of the identified central gene.Result: We filtered 2755 DEGs from the GSE6344 database, including 1292 upregulated DEGs and 1463 downregulated DEGs; 2552 DEGs were filtered from the GSE22459 database, including 2022 downregulated DEGs and 530 upregulated DEGs. We did functional enrichment analysis of down-regulated and up-regulated differential genes, Functional enrichment analysis of up-regulated genes shows that DEGs involves many functions and expression pathways. such as immune response, plasma membrane, membrane, integral component of plasma membrane, signal transduction, extracellular region and extracellular space. It is demonstrated in the PPI network constructed by 67 nodes (proteins) and 546 PPI edges (interactions); Functional enrichment analysis of down-regulated genes also shows that DEGs involves many functions and expression pathways. such as integral component of plasma membrane, plasma membrane, extracellular space and extracellular region. It is demonstrated in the PPI network constructed by 141 nodes (proteins) and 624 PPI edges (interactions). Then a gene LYZ was selected step by step in three rounds of validation through TCGA data set, GTEx data set, Timer database and HPA database. LYZ expression was significantly correlated with the immune infiltration levels of CD4+ T cells, CD8+ T cells, Macrophage, Myeloid dendritic, Neutrophil and B cell. The upstream hub miRNA that regulate this gene were identified: has-miR-4649-3p and has-miR-873-3p. Based on these findings, it is proposed that LYZ may be a potential novel diagnostic and prognostic biomarker of KIRC at the mRNA and protein levels, and has-miR-4649-3p and has-miR-873-3p at the molecular level, and can help us better manage the progression of renal fibrosis.Conclusion: Our findings suggest that immune response, inflammation and other pathways play an extremely important role in RF and KIRC. LYZ, has-miR-4649-3p and has-miR-873-3p may become potential prognostic biomarkers of KIRC and contribute to the prevention and treatment of renal fibrosis, which also shows us a new therapeutic idea that provides the possibility to treat renal fibrosis from the perspective of immunity.

Hsa-mir-3163 and CCNB1 may be potential biomarkers and therapeutic targets for androgen receptor positive triple-negative breast cancer

Breast cancer (BC) is the most common malignancy in female, but the role of androgen receptor (AR) in triple-negative breast cancer (TNBC) is still unclear. This study aimed to exam the performance of innovative biomarkers for AR positive TNBC in diagnosis and therapies. Four datasets (GSE42568, GSE45827, GSE54002 and GSE76124) were analyzed by bioinformatic methods and the differential expression genes (DEGs) between the AR positive TNBC tissues and normal tissues were firstly identified by limma package and Venn diagrams. Next, Gene Ontologies (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to explore the relationship between these DEGs. Then, the Protein-protein interaction (PPI) network was constructed. CytoHubba and bioinformatic approaches including Molecular Complex Detection (MCODE), Gene Expression Profiling Interactive Analysis (GEPIA), the Kaplan–Meier (KM) plotter and The Human Pro-tein Atlas (THPA) were used to identify the hub genes. Lastly, a miRNA-hub-gene regulatory axis was constructed by use of Target Scan database and ENCORI database. As a result, a total of 390 common DEGs were identified, including 250 up-regulated and 140 down-regulated. GO and KEGG enrichment analysis showed that the up-regulated DEGs were mostly enriched in the cell division, mitotic nuclear division, nucleosome, midbody, protein heterodimerization activity, cadherin binding involved in cell−cell adhesion, systemic lupus erythematosus and alcoholism, while the down-regulated DEGs were mainly enriched in carbohydrate metabolic process, extracellular space, extracellular region, zinc ion binding and microRNAs in cancer. Then, 13 hub genes (CCNB2, FOXM1, HMMR, MAD2L1, RRM2, TPX2, TYMS, CEP55, AURKA, CCNB1, CDK1, TOP2A, PBK) were selected. The survival analysis revealed that only CCNB1 was associated with significantly poor survival (P <0.05) in TNBC patients. Finally, we found that hsa-miR-3163 took part in the regulation of CCNB1 and constructed a potential hsa-miR-3163-CCNB1 regulatory axis. The results of current study suggest that CCNB1 and hsa-miR-3163 may serve as highly potential prognostic markers and therapeutic targets for AR positive TNBC. Our findings may make contributions to the diagnosis and therapies of AR positive TNBC.

The EGF Domains of MUC4 Oncomucin Mediate HER2 Binding Affinity and Promote Pancreatic Cancer Cell Tumorigenesis

The HER2 receptor and its MUC4 mucin partner form an oncogenic complex via an extracellular region of MUC4 encompassing three EGF domains that promotes tumor progression of pancreatic cancer (PC) cells. However, the molecular mechanism of interaction remains poorly understood. Herein, we decipher at the molecular level the role and impact of the MUC4EGF domains in the mediation of the binding affinities with HER2 and the PC cell tumorigenicity. We used an integrative approach combining in vitro bioinformatic, biophysical, biochemical, and biological approaches, as well as an in vivo study on a xenograft model of PC. In this study, we specified the binding mode of MUC4EGF domains with HER2 and demonstrate their “growth factor-like” biological activities in PC cells leading to stimulation of several signaling proteins (mTOR pathway, Akt, and β-catenin) contributing to PC progression. Molecular dynamics simulations of the MUC4EGF/HER2 complexes led to 3D homology models and identification of binding hotspots mediating binding affinity with HER2 and PC cell proliferation. These results will pave the way to the design of potential MUC4/HER2 inhibitors targeting the EGF domains of MUC4. This strategy will represent a new efficient alternative to treat cancers associated with MUC4/HER2 overexpression and HER2-targeted therapy failure as a new adapted treatment to patients.

Voltage sensor movements of CaV1.1 during an action potential in skeletal muscle fibers

In excitation–contraction coupling (ECC), when the skeletal muscle action potential (AP) propagates into the transverse tubules, it modifies the conformational state of the voltage-gated calcium channels (CaV1.1). CaV1.1 serves as the voltage sensor for activation of calcium release from the sarcoplasmic reticulum (SR); however, many questions about this function persist. CaV1.1 α1 subunits contain four distinct homologous domains (I–IV). Each repeat includes six transmembranal helical segments; the voltage-sensing domain (VSD) is formed by S1–S4 segments, and the pore domain is formed by helices S5–S6. Because, in other voltage-gated channels, individual VSDs appear to be differentially involved in specific aspects of channel gating, here we thus hypothesized that not all the VSDs in CaV1.1 contribute equally to calcium-release activation. Yet, the voltage-sensor movements during an AP (the physiological stimulus for the muscle fiber) have not been previously measured in muscle. Reorientation of VSDs I–IV in CaV1.1 during an AP should generate a small but measurable electrical current. Still, neither the voltage-sensor charge movement during the AP nor the contribution of the individual VSDs to voltage-gated calcium release have been previously monitored. Here, we electrically monitor VSD movements using an AP voltage-clamp technique applied to muscle fibers. We introduce AP-fluorometry, a variant of the functional site-directed fluorescence, to track the movement of each VSD via a cysteine substitution on the extracellular region of S4 of each VSD and its labeling with a cysteine-reacting fluorescent probe, which served as an optical reporter of local rearrangements. Independent optical recordings of AP and calcium transients were performed to establish the temporal correlation between AP, AP-elicited charge movement, VSDs conformational changes, and calcium release flux. Our results support the hypothesis that not all VSDs in CaV1.1 contribute to ECC.