B7-H6 and PD-L1 belong to the B7 family co-stimulatory molecules fine-tuning the immune response. The present work investigates the clinical effect of B7-H6 protein expression with PD-L1 status and ...the infiltration of natural killer cells as potential biomarkers in breast tumor inflammatory microenvironment. The expression levels of B7-H6 protein by cancer cells and immune infiltrating cells in human breast cancer tissues and evaluate their associations with PD-L1 expression, NK cell status, clinical pathological features and prognosis were explored. The immunohistochemistry labeling method was used to assess B7-H6 and PD-L1 proteins expression by cancer and immune cells. The associations between immune checkpoint, major clinical pathological variables and survival rates were analyzed. B7-H6 protein was depicted in both breast and immune cells. Results showed that Tumor B7-H6 expression is highly associated with Her-2 over expression. B7-H6 + immune cells are highly related to the Scarff-Bloom-Richardson grade and associated with PD-L1 expression and NK cells status. Survival analysis revealed a better prognosis in patients with low expression of B7-H6 by cancer cells. Conversely, B7-H6 + immune cells were significantly associated with longer survival. Findings strongly suggest an interaction between B7 molecules that contributes to a particular design of the inflammatory microenvironment. This may influence the efficiency of therapies based on antibodies blocking the PD-L1/PD1 pathway and can explain the detection of clinical benefits only in a fraction of patients treated with immune checkpoint inhibitors.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
CD155 is a ligand of the NK activating receptor DNAM-1, it has been described in a variety of human malignancies, but its expression in breast cancer remains unclear and poorly studied.
CD155 ...expression and NK cells infiltration were investigated in 158 patients with breast cancer by immunohistochemistry (IHC). Statistical analyses were performed to evaluate correlations of CD155 expression with clinical-pathological features, prognosis and tumor immunity.
Tumor cytoplasmic CD155 (cyt-CD155) was associated with lymphovascular invasion (p = 0.011), and membranous CD155 (m-CD155) was strongly correlated with the presence of Tumor Infiltrating natural killer cells (NK-TILs) (p = 0.0003). Survival analysis demonstrated that patients with high cyt-CD155 had a significantly worse overall survival (p < 0.001) and death free survival (p = 0.014) than those with low expression, while high levels of m-CD155 correlated with a better prognosis (p = 0.037). Furthermore, we found that patients with m-CD155Low/NKLow tumors had a significantly reduced overall survival (p = 0.012). Multivariate analysis showed that positive tumor m-CD155 status was a significant independent marker of good prognosis. Meanwhile, high cyt-CD155 expression was identified as an independent poor prognostic predictor, suggesting a key role in this malignancy.
Altogether, our results revealed that cyt-CD155 was associated with invasiveness and poorer prognosis, but the concomitant presence of m-CD155 and NK-TILs had an opposite prognostic relevance in breast cancer. These results raised the importance of CD155 IHC analysis to elucidate biomarker localization, leading to better understand and design therapeutic molecule targeting CD155 in breast tumors.
•cyt-CD155 expression correlated with clinical-pathological parameters of breast cancer patients.•Patients with high cyt-CD155 expression showed reduced overall survival and death free survival.•Patients with high m-CD155 expression showed longer overall survival.•NK-TILs go side by side with m-CD155 expression leading to a longer overall survival.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Intronless genes (IGs) fraction varies between 2.7 and 97.7% in eukaryotic genomes. Although many databases on exons and introns exist, there was no curated database for such genes which allowed ...their study in a concerted manner. Such a database would be useful to identify the functional features and the distribution of these genes across the genome. Here, a new database of IGs in eukaryotes based on GenBank data was described. This database, called IGD (Intronless Gene Database), is a collection of gene sequences that were annotated and curated. The current version of IGD contains 687 human intronless genes with their protein and CDS sequences. Some features of the entries are given in this paper. Data was extracted from GenBank release 183 using a Perl script. Data extraction was followed by a manual curation step. Intronless genes were then analyzed based on their RefSeq annotation and Gene Ontology functional class. IGD represents a useful resource for retrieval and
in silico study of intronless genes. IGD is available at
http://www.bioinfo-cbs.org/igd with comprehensive help and FAQ pages that illustrate the main uses of this resource.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Currently, Bayesian Networks (BNs) have become one of the most complete, self-sustained and coherent formalisms used for knowledge acquisition, representation and application through computer ...systems. However, learning of BNs structures from data has been shown to be an NP-hard problem. It has turned out to be one of the most exciting challenges in machine learning. In this context, the present work’s major objective lies in setting up a further solution conceived to be a remedy for the intricate algorithmic complexity imposed during the learning of BN-structure with a massively-huge data backlog.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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•We present the first large-scale study of the repertoire of IDPs in Triticum aestivum and Hordeum vulgare proteomes.•Results show that proteins in T. aestivum are significantly more ...disordered than those of H. vulgare.•IDPs in T. aestivum and H. vulgare are involved in regulation of cellular and biological processes up on response to stress.
There has been an increasing interest in Intrinsically Disordered Proteins (IDPs) ever since it was proven that they are ubiquitous and involved in key cellular functions. Interestingly, they have shown a large abundance in complete proteomes.
In the current study, we have investigated the first large-scale study of the repertoire of IDPs in Triticum aestivum and Hordeum vulgare proteomes, in order to get insight into the biological roles of IDPs in both species. Results show that proteins in T. aestivum are significantly more disordered than those of H. vulgare. Moreover, the data revealed that DNA/RNA binding domains, co-factors, heme, metal ions binding domains, ATP/GTP binding proteins, ligands, linker domains and repeats, other domains typical to transcription factors such as zinc finger, F-box domain, homeodomain-like, l-domain like and chaperones, are predominantly present and co-occur in disordered proteins in T.aestivum and H.vulgare. The Gene Ontology analysis revealed that IDPs in T. aestivum and H. vulgare are mainly involved in regulation of cellular and biological processes up on response to stress.
In future, this study may provide valuable information while considering IDPs in understanding the organism complexity and environmental adaptation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Olive tree is an emblematic crop of the Mediterranean region, mainly renowned for its fruit oil, although the species provides several industrial purposes. The Mediterranean basin constitutes the ...origin of olive species diversification and represents a valuable source of genetic variability of olive germplasm. Therefore, the evaluation of the diversity and the population structure of this Mediterranean germplasm is a challenge for olive species preservation, crop breeding and genetic improvement. In this context, our study aims to analyze the genetic diversity and the population structure of 79 Mediterranean olive accessions using 15 genomic SSRs and by applying computational model-based approaches. The used SSRs revealed a total number of 225 alleles with a mean of 15 alleles per locus. Observed and expected heterozygosity (Ho = 0.79, He = 0.805) with a Polymorphism Information Content value of 0.775 indicate high level of genetic diversity. All results of the Unweighted Pair Group Method with Arithmetic (UPGMA), Jaccard similarity index, Principal Coordinate Analysis (PCoA) and the Bayesian analyses supported the separation of the Mediterranean varieties in two sub-populations, one of which mainly composed by Spanish accessions.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Attempts have been made to express or to merge different Cry proteins in order to enhance toxic effects against various insects. Cry1A proteins of
Bacillus thuringiensis
form a typical bipyramidal ...parasporal crystal and their protoxins contain a highly conserved C-terminal region. A chimerical gene, called
cry(4Ba-1Ac),
formed by a fusion of the N-terminus part of
cry4Ba
and the C-terminus part of
cry1Ac
, was constructed. Its transformation to an acrystalliferous
B. thuringiensis
strain showed that it was expressed as a chimerical protein of 116 kDa, assembled in spherical to amorphous parasporal crystals. The chimerical gene
cry(4Ba-1Ac)
was introduced in a
B. thuringiensis kurstaki
strain. In the generated crystals of the recombinant strain, the presence of Cry(4Ba-1Ac) was evidenced by MALDI-TOF. The recombinant strain showed an important increase of the toxicity against
Culex pipiens
larvae (LC
50
= 0.84 mg l
−1
± 0.08) compared to the wild type strain through the synergistic activity of Cry2Aa with Cry(4Ba-1Ac). The enhancement of toxicity of
B. thuringiensis kurstaki
expressing Cry(4Ba-1Ac) compared to that expressing the native toxin Cry4Ba, might be related to its a typical crystallization properties. The developed fusion protein could serve as a potent toxin against different pests of mosquitoes and major crop plants.
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CEKLJ, DOBA, EMUNI, FZAB, GEOZS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Refined olive, corn, soybean, and sunflower oils were used as cooking oils for deep-frying at two different temperatures, 160 and 190 °C, and for pan-frying of potatoes at 180 °C for 10 successive ...sessions under the usual domestic practice. Several chemical parameters were assayed during frying operations to evaluate the status of the frying oils. Refined olive oil, as frying oil, was found to be more stable than the refined seed oils. In fact, this oil has proven the greatest resistance to oxidative deterioration, and its trans-fatty acid contents and percentages of total polar compounds were found to be lower at 160 °C during deep-frying. Finally, chemometric analysis has demonstrated that the lowest deterioration of the quality of all refined oils occurred in the refined olive oil during deep-frying at 160 °C and the highest deterioration occurred in the refined sunflower oil during pan-frying at 180 °C.
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IJS, KILJ, NUK, PNG, UL, UM, UPUK
Intrinsically disordered proteins (IDPs) are often involved in diseases and have been shown to be promising targets for drug development. Here, we focus on the human disordered charged biased ...proteins (HDCBPs). We have investigated the association of the HDCBPs with diseases by integrating various sources that cover public sources of gene–disease associations and intensive literature mining. The results indicate that 95% of HDCBPs are associated with multiple diseases, including mainly various cancers, nervous, endocrine, immune, hematological, and respiratory systems diseases. Our data show that the HDCBP–disease network constructed by integrating different levels of data together may improve our understanding of these complex diseases. Moreover, we present the top-ranked proteins that might be potential markers for diagnostic and drug targets.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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