Differential expression of R- and N-cadherin in neural and mesodermal tissues during early chicken development

R-cadherin is a newly identified member of the cadherin family of cell adhesion receptors. The expression of R-cadherin in early chicken embryos was studied using affinity-purified antibodies to this molecule, comparing it with that of N-cadherin. Immunoblot analysis of various organs of 10.5-day embryos showed that R-cadherin is most abundantly expressed in the retina and brain. Immunostaining of the cervical and thoracic regions of embryos revealed that R- and N-cadherin are expressed in all neural tissues. In the neural tube, R-cadherin appears at around stage 21, although N-cadherin expression begins at a much earlier stage. The distribution of R-cadherin in the neural tube differs from that of N-cadherin; for example, some regions of the tube express only R-cadherin, and other regions only N-cadherin. In the peripheral ganglia, these two cadherins are also expressed in different patterns which change during development. Some mesenchymal tissues including the notochord, the myotome, myotubes and perichondria also express these cadherins, again in different patterns. Thus, R- and N-cadherin are differentially expressed in all the tissues examined, and they may contribute to the spatial segregation of heterogeneous cells in a tissue.

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Differential expression of nectin cell adhesion molecule 3 in cancers of the breast.

10.31219/osf.io/4wrce ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Cell Adhesion ◽

Differential Expression ◽

Adhesion Molecule ◽

Survival Data ◽

Cell Adhesion Molecule ◽

Normal Breast ◽

Differentially Expressed ◽

Significant Differential Expression ◽

Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding nectin cell adhesion molecule 3, NECTIN3, when comparing primary tumors of the breast to the tissue of origin, the normal breast. NECTIN3 was also differentially expressed in the brain metastases of patients with metastatic breast cancer. NECTIN3 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of NECTIN3 in primary tumors of the breast was correlated with distant metastasis-free survival in patients with luminal B subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by PAM50 molecular subtype. NECTIN3 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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Differential expression of cell adhesion molecule with homology to L1CAM, CHL1, in cancers of the breast.

10.31219/osf.io/bf2zs ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Cell Adhesion ◽

Differential Expression ◽

Adhesion Molecule ◽

Survival Data ◽

Cell Adhesion Molecule ◽

Normal Breast ◽

Differentially Expressed ◽

Significant Differential Expression ◽

Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding cell adhesion molecule with homology to L1CAM, CHL1, when comparing primary tumors of the breast to the tissue of origin, the normal breast. CHL1 was also differentially expressed in the tumor cells of patients with triple negative breast cancer. CHL1 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of CHL1 in primary tumors of the breast was correlated with overall survival in patients with basal subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by molecular subtype. CHL1 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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Patterning of cell assemblies regulated by adhesion receptors of the cadherin superfamily

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2000.0624 ◽

2000 ◽

Vol 355 (1399) ◽

pp. 885-890 ◽

Cited By ~ 51

Author(s):

Masatoshi Takeichi ◽

Shinichi Nakagawa ◽

Shinya Aono ◽

Tadao Usui ◽

Tadashi Uemura

Keyword(s):

Cell Adhesion ◽

Neural Tube ◽

Planar Cell Polarity ◽

Cell Types ◽

Carcinoma Cells ◽

Adhesion Receptors ◽

Cell Assemblies ◽

Cell Association ◽

Cadherin Superfamily ◽

Cell Cell

During morphogenesis, cell–cell association patterns are dynamically altered. We are interested in how cell adhesion molecules can regulate the patterning of cellular assemblies. Cadherins, a group of cell–cell adhesion receptors, are crucial for the organized assembly of many cell types, but they also regulate dynamic aspects of cell association. For example, during neural crest emigration from the neural tube, the cadherin subtypes expressed by crest cells are switched from one subtype to another. Artificial perturbation of this switch results in blocking of their escape from the neural tube. Intracellular modulations of cadherin activity also seem to play a role in regulation of cell adhesion. We identified p120 ctn as a regulator of cadherin function in carcinoma cells. With such regulators, cells may make a choice as to whether they should maintain stable cell contacts or disrupt their association. Finally, we found another type of cadherin–mediated cell patterning: Flamingo, a seven–pass transmembrane cadherin, regulates planar cell polarity in Drosophila imaginal discs. Thus, the cadherin superfamily receptors control the patterning of cell assemblies through a variety of mechanisms.

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Differential Expression of Platelet-Endothelial Cell Adhesion Molecule-1 (PECAM-1) in Murine Tissues

Microcirculation ◽

10.1038/sj.mn.7300012 ◽

1998 ◽

Vol 5 (2-3) ◽

pp. 179-188 ◽

Cited By ~ 6

Author(s):

MICHAEL J EPPIHIMER ◽

J A N I C E RUSELL ◽

R O B E R T LANGLEY ◽

G I N A VALLIEN ◽

DONALD C ANDERSON ◽

...

Keyword(s):

Cell Adhesion ◽

Endothelial Cell ◽

Differential Expression ◽

Adhesion Molecule ◽

Cell Adhesion Molecule ◽

Endothelial Cell Adhesion Molecule ◽

Platelet Endothelial Cell Adhesion ◽

Cell Adhesion Molecule 1 ◽

Endothelial Cell Adhesion

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Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration

Genome Biology and Evolution ◽

10.1093/gbe/evaa028 ◽

2020 ◽

Vol 12 (4) ◽

pp. 243-258 ◽

Cited By ~ 3

Author(s):

Wen-Juan Ma ◽

Fantin Carpentier ◽

Tatiana Giraud ◽

Michael E Hood

Keyword(s):

Differential Expression ◽

Differentially Expressed Genes ◽

Mating Type ◽

Sex Chromosomes ◽

Sex Chromosome ◽

Gc Content ◽

Differentially Expressed ◽

Mating Types ◽

Sexual Antagonism ◽

Recombination Suppression

Abstract Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.

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High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

Human Genomics ◽

10.1186/s40246-021-00308-5 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Weitong Cui ◽

Huaru Xue ◽

Lei Wei ◽

Jinghua Jin ◽

Xuewen Tian ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression ◽

Small Sample ◽

Differentially Expressed ◽

Cancer Type ◽

Rna Seq ◽

Sample Sizes ◽

Large Sample ◽

Expression Levels ◽

Gene Expression Levels

Abstract Background RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. Results Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. Conclusions High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

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A Practical Multifaceted Approach to Selecting Differentially Expressed Genes

Cancer Informatics ◽

10.1177/117693510700300032 ◽

2007 ◽

Vol 3 ◽

pp. 117693510700300

Author(s):

Yingye Zheng ◽

Margaret Pepe

Keyword(s):

Differential Expression ◽

Gene Selection ◽

Error Rates ◽

Cancer Prognosis ◽

Differentially Expressed ◽

Expression Array ◽

Statistical Research ◽

P Values ◽

Control Error ◽

Strength Of Evidence

Consider a gene expression array study comparing two groups of subjects where the goal is to explore a large number of genes in order to select for further investigation a subset that appear to be differently expressed. There has been much statistical research into the development of formal methods for designating genes as differentially expressed. These procedures control error rates such as the false detection rate or family wise error rate. We contend however that other statistical considerations are also relevant to the task of gene selection. These include the extent of differential expression and the strength of evidence for differential expression at a gene. Using real and simulated data we first demonstrate that a proper exploratory analysis should evaluate these aspects as well as decision rules that control error rates. We propose a new measure called the mp-value that quantifies strength of evidence for differential expression. The mp-values are calculated with a resampling based algorithm taking into account the multiplicity and dependence encountered in microarray data. In contrast to traditional p-values our mp-values do not depend on specification of a decision rule for their definition. They are simply descriptive in nature. We contrast the mp-values with multiple testing p-values in the context of data from a breast cancer prognosis study and from a simulation model.

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Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽

10.3390/genes11070823 ◽

2020 ◽

Vol 11 (7) ◽

pp. 823

Author(s):

Xiayi Liu ◽

Xiaochen Wang ◽

Jing Liu ◽

Xiangyu Wang ◽

Haigang Bao

Keyword(s):

Candidate Genes ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Gallus Gallus ◽

Differentially Expressed ◽

Tibet Plateau ◽

Embryonic Liver ◽

Selection Signature ◽

Chicken Embryos ◽

Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

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The Small GTPase Rap1b: A Bidirectional Regulator of Platelet Adhesion Receptors

Journal of Signal Transduction ◽

10.1155/2012/412089 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 20

Author(s):

Gianni Francesco Guidetti ◽

Mauro Torti

Keyword(s):

Cell Adhesion ◽

Signaling Pathways ◽

Platelet Adhesion ◽

Thrombus Formation ◽

Small Gtpases ◽

Small Gtpase ◽

Complex Pattern ◽

Adhesive Properties ◽

Adhesion Receptors ◽

Inside Out

Integrins and other families of cell adhesion receptors are responsible for platelet adhesion and aggregation, which are essential steps for physiological haemostasis, as well as for the development of thrombosis. The modulation of platelet adhesive properties is the result of a complex pattern of inside-out and outside-in signaling pathways, in which the members of the Rap family of small GTPases are bidirectionally involved. This paper focuses on the regulation of the main Rap GTPase expressed in circulating platelets, Rap1b, downstream of adhesion receptors, and summarizes the most recent achievements in the investigation of the function of this protein as regulator of platelet adhesion and thrombus formation.

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