The heparan sulfate proteoglycan syndecan-1 regulates colon cancer stem cell function via a focal adhesion kinase—Wnt signaling axis

In colon cancer, downregulation of the transmembrane heparan sulfate proteoglycan syndecan‐1 (Sdc‐1) is associated with increased invasiveness, metastasis, and dedifferentiation. As Sdc‐1 modulates signaling pathways relevant to stem cell function, we tested the hypothesis that it may regulate a tumor‐initiating cell phenotype. Sdc‐1 small‐interfering RNA knockdown in the human colon cancer cell lines Caco2 and HT‐29 resulted in an increased side population (SP), enhanced aldehyde dehydrogenase 1 activity, and higher expression of CD133, LGR5, EPCAM, NANOG, SRY (sex‐determining region Y)‐box 2, KLF2, and TCF4/TCF7L2. Sdc‐1 knockdown enhanced sphere formation, cell viability, Matrigel invasiveness, and epithelial‐to‐mesenchymal transition‐related gene expression. Sdc‐1‐depleted HT‐29 xenograft growth was increased compared to controls. Decreased Sdc‐1 expression was associated with an increased activation of β1‐integrins, focal adhesion kinase (FAK), and wingless‐type (Wnt) signaling. Pharmacological FAK and Wnt inhibition blocked the enhanced stem cell phenotype and invasive growth. Sequential flow cytometric SP enrichment substantially enhanced the stem cell phenotype of Sdc‐1‐depleted cells, which showed increased resistance to doxorubicin chemotherapy and irradiation. In conclusion, Sdc‐1 depletion cooperatively enhances activation of integrins and FAK, which then generates signals for increased invasiveness and cancer stem cell properties. Our findings may provide a novel concept to target a stemness‐associated signaling axis as a therapeutic strategy to reduce metastatic spread and cancer recurrence.DatabasesThe GEO accession number of the Affymetrix transcriptomic screening is GSE58751

Wear Improvements Induced by Thermally Grown Oxide Layers and by Nitrogen Ion Implantation

Mild steels which have been either thermally oxidized near 300°C or implanted with nitrogen ions have been wear tested using a modified Falex Lubricant Testing machine. Both these treatments cause similar, much reduced wear rates which are about an order of magnitude better than in untreated samples. Specimens worn after treatments by both methods have been examined in detail using scanning electron microscopy and Auger spectroscopy. It is concluded that the wear induced by oxidation is the same as the wear induced by nitrogen ion implantation. Both of these treatments acted to initiate favorable sustained oxide wear and confirm the Initiator/Sustainer model. Additional studies have been done on oxidized samples using a variety of sample processing techniques and sequences including oxide layer stripping, wear recycling, and annealing. These studies clearly show that favorable wear results were caused by the grown oxide layer and not by the heat treatment. Also, it has been found that the favorable oxide wear can be stopped and started numerous times since it is able to reinitiate and sustain itself. However, if a worn oxide layer is stripped from a sample just prior to the wear run, favorable wear does not occur unless the sample was oxidized or favorably worn in the last few weeks. This occurs because wear favorable chemistry at the oxide/metal interface anneals at room temperature. Other discussions of the wear initiating and sustaining processes are presented

Nitrogen Implantation of Steels: A Treatment Which Can Initiate Sustained Oxidative Wear

Falex wear tests on mild (SAE 3135) steel samples treated by either nitrogen implantation (2.5 × 1017 N2+ cm-2 at 180 ke V) or low temperature (about 315 °C) oxidation are reported. The results show that both treatments lead to about an order-of-magnitude reduction in the long-term wear rate of the steel. In addition to the wear rate measurements, the wear member asymmetry behavior, scanning electron microscopy studies, Auger spectra and sputter profiles all indicate that the wear modes induced by both treatments are the same and are oxidative wear. These results confirm the previously proposed initiator-sustainer wear model in which implanted nitrogen simply acts as an initiator of favorable oxidative wear but is not directly involved in maintaining the sustained wear resistance. Possible mechanisms for both the initiation process and the sustained wear process are reviewed and discussed. © 1987

Ion Implantation and Thermal Oxidation as Treatments to Initiate Sustained Oxide Wear in Steels

Both nitrogen implantation (2.5×1017 N +2 /cm2 at 180 keV) and low-temperature (≊315°C) oxidation are shown to produce an order of magnitude reduction in the wear rate of an SAE 3135 steel. Measurements of the wear rates, wear member asymmetry behavior, and both scanning electron microscopy and Auger studies indicate that the same mechanism leads to the much improved wear rates. Both treatments substantiate the initiator/sustainer wear model, in which the initiation treatment reduces the wear to a low value that is sustained throughout the wear test. The sustained stage is a form of mild wear, which involves oxygen and appears to be oxidative wear

Identification of functionally related genes using data mining and data integration: a breast cancer case study

Abstract Background The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involved in regulating a cell, it is important to identify the set of genes to which it interacts with to determine cell function. In this context, the mining and the integration of a large amount of publicly available data, regarding the transcriptome and the proteome states of a cell, are a useful resource to complement biological research. Results We describe an approach for the identification of genes that interact with each other to regulate cell function. The strategy relies on the analysis of gene expression profile similarity, considering large datasets of expression data. During the similarity evaluation, the methodology determines the most significant subset of samples in which the evaluated genes are highly correlated. Hence, the strategy enables the exclusion of samples that are not relevant for each gene pair analysed. This feature is important when considering a large set of samples characterised by heterogeneous experimental conditions where different pools of biological processes can be active across the samples. The putative partners of the studied gene are then further characterised, analysing the distribution of the Gene Ontology terms and integrating the protein-protein interaction (PPI) data. The strategy was applied for the analysis of the functional relationships of a gene of known function, Pyruvate Kinase, and for the prediction of functional partners of the human transcription factor TBX3. In both cases the analysis was done on a dataset composed by breast primary tumour expression data derived from the literature. Integration and analysis of PPI data confirmed the prediction of the methodology, since the genes identified to be functionally related were associated to proteins close in the PPI network. Two genes among the predicted putative partners of TBX3 (GLI3 and GATA3) were confirmed by in vivo binding assays (crosslinking immunoprecipitation, X-ChIP) in which the putative DNA enhancer sequence sites of GATA3 and GLI3 were found to be bound by the Tbx3 protein. Conclusion The presented strategy is demonstrated to be an effective approach to identify genes that establish functional relationships. The methodology identifies and characterises genes with a similar expression profile, through data mining and integrating data from publicly available resources, to contribute to a better understanding of gene regulation and cell function. The prediction of the TBX3 target genes GLI3 and GATA3 was experimentally confirmed.</p

Occurrence of L1M Elements in Chromosomal Rearrangements Associated to Chronic Myeloid Leukemia (CML): Insights from Patient-Specific Breakpoints Characterization

Chronic myeloid leukemia (CML) is a rare myeloproliferative disorder caused by the reciprocal translocation t(9;22)(q34;q11) in hematopoietic stem cells (HSCs). This chromosomal translocation results in the formation of an extra-short chromosome 22, called a Philadelphia chromosome (Ph), containing the BCR-ABL1 fusion gene responsible for the expression of a constitutively active tyrosine kinase that causes uncontrolled growth and replication of leukemic cells. Mechanisms behind the formation of this chromosomal rearrangement are not well known, even if, as observed in tumors, repetitive DNA may be involved as core elements in chromosomal rearrangements. We have participated in the explorative investigations of the PhilosoPhi34 study to evaluate residual Ph+ cells in patients with negative FISH analysis on CD34+/lin- cells with gDNA qPCR. Using targeted next-generation deep sequencing strategies, we analyzed the genomic region around the t(9;22) translocations of 82 CML patients and one CML cell line and assessed the relevance of interspersed repeat elements at breakpoints (BP). We found a statistically higher presence of LINE elements, in particular belonging to the subfamily L1M, in BP cluster regions of both chromosome 22 and 9 compared to the whole human genome. These data suggest that L1M elements could be potential drivers of t(9;22) translocation leading to the generation of the BCR-ABL1 chimeric gene and the expression of the active BCR-ABL1-controlled tyrosine kinase chimeric protein responsible for CML

RNA-Generated and Gene-Edited Induced Pluripotent Stem Cells for Disease Modeling and Therapy

Cellular reprogramming by epigenomic remodeling of chromatin holds great promise in the field of human regenerative medicine. As an example, human-induced Pluripotent Stem Cells (iPSCs) obtained by reprograming of patient somatic cells are sufficiently similar to embryonic stem cells (ESCs) and can generate all cell types of the human body. Clinical use of iPSCs is dependent on methods that do not utilize genome altering transgenic technologies that are potentially unsafe and ethically unacceptable. Transient delivery of exogenous RNA into cells provides a safer reprogramming system to transgenic approaches that rely on exogenous DNA or viral vectors. RNA reprogramming may prove to be more suitable for clinical applications and provide stable starting cell lines for gene-editing, isolation, and characterization of patient iPSC lines. The introduction and rapid evolution of CRISPR/Cas9 gene-editing systems has provided a readily accessible research tool to perform functional human genetic experiments. Similar to RNA reprogramming, transient delivery of mRNA encoding Cas9 in combination with guide RNA sequences to target specific points in the genome eliminates the risk of potential integration of Cas9 plasmid constructs. We present optimized RNA-based laboratory procedure for making and editing iPSCs. In the near-term these two powerful technologies are being harnessed to dissect mechanisms of human development and disease in vitro, supporting both basic, and translational research. J. Cell. Physiol. 232: 1262–1269, 2017. © 2016 Wiley Periodicals, Inc