ABSTRACT
The human-robot collaboration (HRC) solutions presented so far have the disadvantage that the interaction between humans and robots is based on the human's state or on specific gestures purposely performed by the human, thus increasing the time required to perform a task and slowing down the pace of human labor, making such solutions uninteresting. In this study, a different concept of the HRC system is introduced, consisting of an HRC framework for managing assembly processes that are executed simultaneously or individually by humans and robots. This HRC framework based on deep learning models uses only one type of data, RGB camera data, to make predictions about the collaborative workspace and human action, and consequently manage the assembly process. To validate the HRC framework, an industrial HRC demonstrator was built to assemble a mechanical component. Four different HRC frameworks were created based on the convolutional neural network (CNN) model structures: Faster R-CNN ResNet-50 and ResNet-101, YOLOv2 and YOLOv3. The HRC framework with YOLOv3 structure showed the best performance, showing a mean average performance of 72.26% and allowed the HRC industrial demonstrator to successfully complete all assembly tasks within a desired time window. The HRC framework has proven effective for industrial assembly applications.
Subject(s)
Deep Learning , Robotics , Humans , Neural Networks, Computer , GesturesABSTRACT
As ageing structures and infrastructures become a global concern, structural health monitoring (SHM) is seen as a crucial tool for their cost-effective maintenance. Promising results obtained for modern and conventional constructions suggested the application of SHM to historical masonry buildings as well. However, this presents peculiar shortcomings and open challenges. One of the most relevant aspects that deserve more research is the optimisation of the sensor placement to tackle well-known issues in ambient vibration testing for such buildings. The present paper focuses on the application of optimal sensor placement (OSP) strategies for dynamic identification in historical masonry buildings. While OSP techniques have been extensively studied in various structural contexts, their application in historical masonry buildings remains relatively limited. This paper discusses the challenges and opportunities of OSP in this specific context, analysing and discussing real-world examples, as well as a numerical benchmark application to illustrate its complexities. This article aims to shed light on the progress and issues associated with OSP in masonry historical buildings, providing a detailed problem formulation, identifying ongoing challenges and presenting promising solutions for future improvements.
ABSTRACT
Intestinal stem cells (ISCs) fuel the lifelong self-renewal of the intestinal tract and are paramount for epithelial repair. In this context, the Wnt pathway component LGR5 is the most consensual ISC marker to date. Still, the effort to better understand ISC identity and regulation remains a challenge. We have generated a Mex3a knockout mouse model and show that this RNA-binding protein is crucial for the maintenance of the Lgr5+ ISC pool, as its absence disrupts epithelial turnover during postnatal development and stereotypical organoid maturation ex vivo. Transcriptomic profiling of intestinal crypts reveals that Mex3a deletion induces the peroxisome proliferator-activated receptor (PPAR) pathway, along with a decrease in Wnt signalling and loss of the Lgr5+ stem cell signature. Furthermore, we identify PPARγ activity as a molecular intermediate of MEX3A-mediated regulation. We also show that high PPARγ signalling impairs Lgr5+ ISC function, thus uncovering a new layer of post-transcriptional regulation that critically contributes to intestinal homeostasis.
Subject(s)
Intestinal Mucosa , Stem Cells , Animals , Intestines , Mice , Organoids , Receptors, G-Protein-Coupled/genetics , Wnt Signaling PathwayABSTRACT
Group A Streptococcus (GAS) is one of the most important agents of oropharyngeal infection. To avoid unnecessary antibiotic prescription, it is recommended the confirmation of GAS infection in pharyngeal swabs using culture or rapid antigen detection test (RADT). This study aimed to retrospectively analyse the incidence of GAS oropharyngeal infection, detected by RADT, in a paediatric population in the Centre of Portugal. Data was collected from the database of the Paediatric Hospital Emergency Department (ED) regarding patients admitted with symptoms suggesting acute pharyngitis, from January 2013 to December 2018, in a total of 18,304 cases. Among these, 130 clinical files were searched for symptoms, complications and additional visits to the ED. The results showed an average GAS infection prevalence of 33%, with seasonal variation. In preschool children, especially in patients less than 3 years old, where the guidelines do not routinely encourage RADT, GAS tonsillitis assumed an unexpected importance, with 731 positive tests in a total of 3128 cases. Scarlatiniform rash and oral cavity petechiae had significant correlation with streptococcal aetiology (p < 0.05). The statistical analysis also showed that different signs and symptoms assume different weights depending on the age group of the patient. The main conclusion is that the incidence of GAS infection in the studied population is higher than generally described in preschool children, suggesting the need for a more cautious approach to children under 3 years presenting acute pharyngitis, and that RADT in this age group would contribute to a decrease in the number of unnoticed cases.
Subject(s)
Antigens, Bacterial/analysis , Immunologic Tests/methods , Pharyngitis/diagnosis , Streptococcal Infections/diagnosis , Streptococcus pyogenes/immunology , Adolescent , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Pharyngitis/epidemiology , Pharyngitis/microbiology , Portugal/epidemiology , Retrospective Studies , Sensitivity and Specificity , Streptococcal Infections/epidemiology , Streptococcal Infections/microbiology , Streptococcus pyogenes/isolation & purificationABSTRACT
Mucosal T lymphocytes from patients with ulcerative colitis (UC) were previously shown to display a deficiency in branched N-glycosylation associated with disease severity. However, whether this glycosylation pathway shapes the course of the T cell response constituting a targeted-specific mechanism in UC remains largely unknown. In this study, we demonstrated that metabolic supplementation of ex vivo mucosal T cells from patients with active UC with N-acetylglucosamine (GlcNAc) resulted in enhancement of branched N-glycosylation in the T cell receptor (TCR), leading to suppression of T cell growth, inhibition of the T helper 1 (Th1)/Th17 immune response, and controlled T cell activity. We further demonstrated that mouse models displaying a deficiency in the branched N-glycosylation pathway (MGAT5-/-, MGAT5+/-) exhibited increased susceptibility to severe forms of colitis and early-onset disease. Importantly, the treatment of these mice with GlcNAc reduced disease severity and suppressed disease progression due to a controlled T cell-mediated immune response at the intestinal mucosa. In conclusion, our human ex vivo and preclinical results demonstrate the targeted-specific immunomodulatory properties of this simple glycan, proposing a therapeutic approach for patients with UC.
Subject(s)
Acetylglucosamine/pharmacology , CD4-Positive T-Lymphocytes/immunology , Colitis, Ulcerative/immunology , N-Acetylglucosaminyltransferases/physiology , Polysaccharides/metabolism , Adaptive Immunity , Animals , CD4-Positive T-Lymphocytes/drug effects , CD4-Positive T-Lymphocytes/metabolism , Case-Control Studies , Colitis, Ulcerative/chemically induced , Colitis, Ulcerative/drug therapy , Colitis, Ulcerative/metabolism , Cytokines/metabolism , Glycosylation , Humans , Lymphocyte Activation , Mice , Mice, Inbred C57BL , Mice, Knockout , Receptors, Antigen, T-Cell/metabolismABSTRACT
Automobile laser brazing remains a complex process whose results are affected by several process variables that may result in nonacceptable welds. A multisensory customized inspection system is proposed, with two distinct non-destructive techniques: the potential drop method and eddy current testing. New probes were designed, simulated, produced, and experimentally validated in automobile's laser-brazed weld beads with artificially introduced defects. The numerical simulations allowed the development of a new four-point probe configuration in a non-conventional orthogonal shape demonstrating a superior performance in both simulation and experimental validation. The dedicated inspection system allowed the detection of porosities, cracks, and lack of bonding defects, demonstrating the redundancy and complementarity these two techniques provide.
ABSTRACT
BACKGROUND: Basal-like breast cancer (BLBC) is a poor prognosis subgroup of triple-negative carcinomas that still lack specific target therapies and accurate biomarkers for treatment selection. P-cadherin is frequently overexpressed in these tumors, promoting cell invasion, stem cell activity and tumorigenesis by the activation of Src-Family kinase (SRC) signaling. Therefore, our aim was to evaluate if the treatment of BLBC cells with dasatinib, the FDA approved SRC inhibitor, would impact on P-cadherin induced tumor aggressive behavior. METHODS: P-cadherin and SRC expression was evaluated in a series of invasive Breast Cancer and contingency tables and chi-square tests were performed. Cell-cell adhesion measurements were performed by Atomic Force Microscopy, where frequency histograms and Gaussian curves were applied. 2D and 3D cell migration and invasion, proteases secretion and self-renew potential were evaluated in vitro. Student's t-tests were used to determine statistically significant differences. The cadherin/catenin complex interactions were evaluated by in situ proximity-ligation assay, and statistically significant results were determined by using Mann-Whitney test with a Bonferroni correction. In vivo xenograft mouse models were used to evaluate the impact of dasatinib on tumor growth and survival. ANOVA test was used to evaluate the differences in tumor size, considering a confidence interval of 95%. Survival curves were estimated by the Kaplan-Meier's method, using the log-rank test to assess significant differences for mice overall survival. RESULTS: Our data demonstrated that P-cadherin overexpression is significantly associated with SRC activation in breast cancer cells, which was also validated in a large series of primary tumor samples. SRC activity suppression with dasatinib significantly prevented the in vitro functional effects of P-cadherin overexpressing cells, as well as their in vivo tumorigenic and metastatic ability, by increasing mice overall survival. Mechanistically, SRC inhibition affects P-cadherin downstream signaling, rescues the E-cadherin/p120-catenin complex to the cell membrane, recovering cell-cell adhesion function. CONCLUSIONS: In conclusion our findings show that targeting P-cadherin/SRC signaling and functional activity may open novel therapeutic opportunities for highly aggressive and poor prognostic basal-like breast cancer.
Subject(s)
Breast Neoplasms/pathology , Cadherins/metabolism , Protein Kinase Inhibitors/pharmacology , Signal Transduction/drug effects , src-Family Kinases/antagonists & inhibitors , Animals , Carcinogenesis/drug effects , Catenins/metabolism , Cell Adhesion/drug effects , Cell Line, Tumor , Cell Membrane/drug effects , Cell Membrane/metabolism , Dasatinib/pharmacology , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Mice , Neoplasm Metastasis , Delta CateninABSTRACT
Deregulation of tRNAs, aminoacyl-tRNA synthetases and tRNA modifying enzymes are common in cancer, raising the hypothesis that protein synthesis efficiency and accuracy (mistranslation) are compromised in tumors. We show here that human colon tumors and xenograft tumors produced in mice by two epithelial cancer cell lines mistranslate 2- to 4-fold more frequently than normal tissue. To clarify if protein mistranslation plays a role in tumor biology, we expressed mutant Ser-tRNAs that misincorporate Ser-at-Ala (frequent error) and Ser-at-Leu (infrequent error) in NIH3T3 cells and investigated how they responded to the proteome instability generated by the amino acid misincorporations. There was high tolerance to both misreading tRNAs, but the Ser-to-Ala misreading tRNA was a more potent inducer of cell transformation, stimulated angiogenesis and produced faster growing tumors in mice than the Ser-to-Leu misincorporating tRNA. Upregulation of the Akt pathway and the UPR were also observed. Most surprisingly, the relative expression of both misreading tRNAs increased during tumor growth, suggesting that protein mistranslation is advantageous in cancer contexts. These data highlight new features of protein synthesis deregulation in tumor biology.
Subject(s)
Carcinoma , Codon , Colonic Neoplasms , Neoplasm Proteins , Proteome , RNA, Neoplasm , RNA, Transfer , Animals , Carcinoma/genetics , Carcinoma/metabolism , Carcinoma/pathology , Cell Line, Tumor , Chick Embryo , Colonic Neoplasms/genetics , Colonic Neoplasms/metabolism , Colonic Neoplasms/pathology , Humans , Mice , NIH 3T3 Cells , Neoplasm Proteins/biosynthesis , Neoplasm Proteins/genetics , Proteome/biosynthesis , Proteome/genetics , RNA, Neoplasm/genetics , RNA, Neoplasm/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolismABSTRACT
Optimal research results rely on the selection of cellular models capable of recapitulating the characteristics of primary tumours from which they originate. The expression of mucins (MUC16 and MUC1) and truncated O-glycans (Tn, STn and T) represents a characteristic footprint of serous ovarian carcinomas (SOCs). Therefore, selecting ovarian cancer (OVCA) cell lines that reflect this phenotype is crucial to explore the putative biological role of these biomarkers in the SOC setting. Here, we investigated a panel of OVCA cell lines commonly used as SOC models, and tested whether, when cultured in 2D and 3D conditions, these recapitulate the mucin and O-glycan expression profiles of SOCs. We further explored the role of truncating the O-glycosylation capacity in OVCAR3 cells through knockout of the COSMC chaperone, using in vitro and in vivo assays. We found that the majority of OVCA cell lines of serous origin do not share the mucin and truncated O-glycan footprint of SOCs, although 3D cultures showed a higher resemblance. We also found that genetic truncation of the O-glycosylation capacity of OVCAR3 cells did not enhance oncogenic features either in vitro or in vivo. This study underscores the importance of well-characterized cellular models to study specific features of ovarian cancer.
Subject(s)
CA-125 Antigen/metabolism , Cystadenocarcinoma, Serous/metabolism , Membrane Proteins/metabolism , Mucin-1/metabolism , Ovarian Neoplasms/metabolism , Polysaccharides/metabolism , Animals , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , CA-125 Antigen/genetics , Cell Line, Tumor , Cystadenocarcinoma, Serous/genetics , Cystadenocarcinoma, Serous/pathology , Female , Gene Expression Profiling , Glycosylation , Humans , Membrane Proteins/genetics , Mice, Nude , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Mucin-1/genetics , Ovarian Neoplasms/genetics , Ovarian Neoplasms/pathology , Phenotype , Transplantation, HeterologousABSTRACT
The search for novel anticancer small molecules and strategies remains a challenge. Our previous studies have identified TXA1 (1-{[2-(diethylamino)ethyl]amino}-4-propoxy-9H- thioxanthen-9-one) as a hit compound, with in vitro antitumor potential by modulating autophagy and apoptosis in human tumor cell lines. In the present study, the mechanism of action and antitumor potential of the soluble salt of this molecule (TXA1.HCl) was further investigated using in vitro and mouse xenograft tumor models of NSCLC. Our results showed that TXA1.HCl affected steroid biosynthesis, increased RagD expression, and caused abnormal cellular cholesterol localization. In addition, TXA1.HCl treatment presented no toxicity to nude mice and significantly reduced the growth of human NSCLC cells xenografts in mice. Overall, this work provides new insights into the mechanism of action of TXA1, which may be relevant for the development of anticancer therapeutic strategies, which target cholesterol transport.
Subject(s)
Antineoplastic Agents/pharmacology , Carcinoma, Non-Small-Cell Lung , Cholesterol/metabolism , Lung Neoplasms , Xanthones/pharmacology , Animals , Antineoplastic Agents/chemistry , Apoptosis/drug effects , Autophagy/drug effects , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/metabolism , Cell Line, Tumor , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/metabolism , Mice , Mice, Nude , Thioxanthenes/chemistry , Thioxanthenes/pharmacology , Xanthones/chemistryABSTRACT
Gastric cancer (GC) is the 3rd deadliest cancer worldwide, due to limited treatment options and late diagnosis. Human epidermal growth factor receptor-2 (HER2) is overexpressed in â¼20% of GC cases and anti-HER2 antibody trastuzumab in combination with conventional chemotherapy, is recognized as standard therapy for HER2-positive metastatic GC. This strategy improves GC patients' survival by 2-3 months, however its optimal results in breast cancer indicate that GC survival may be improved. A new photoimmunoconjugate was developed by conjugating a porphyrin with trastuzumab (Trast:Porph) for targeted photodynamic therapy in HER2-positive GC. Using mass spectrometry analysis, the lysine residues in the trastuzumab structure most prone for porphyrin conjugation were mapped. The in vitro data demonstrates that Trast:Porph specifically binds to HER2-positive cells, accumulates intracellularly, co-localizes with lysosomal marker LAMP1, and induces massive HER2-positive cell death upon cellular irradiation. The high selectivity and cytotoxicity of Trast:Porph based photoimmunotherapy is confirmed in vivo in comparison with trastuzumab alone, using nude mice xenografted with a HER2-positive GC cell line. In the setting of human disease, these data suggest that repetitive cycles of Trast:Porph photoimmunotherapy may be used as an improved treatment strategy in HER2-positive GC patients.
Subject(s)
Antineoplastic Agents/therapeutic use , Cell Death , Immunotherapy/methods , Photochemotherapy/methods , Porphyrins/therapeutic use , Receptor, ErbB-2 , Stomach Neoplasms/drug therapy , Trastuzumab/therapeutic use , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacokinetics , Cell Line, Tumor , Cell Survival/drug effects , Humans , Lysine/chemistry , Lysosomal Membrane Proteins/pharmacokinetics , Male , Mass Spectrometry , Mice, Nude , Porphyrins/chemistry , Porphyrins/pharmacokinetics , Random Allocation , Stomach Neoplasms/metabolism , Trastuzumab/chemistry , Trastuzumab/pharmacokinetics , Xenograft Model Antitumor AssaysABSTRACT
The role of E-cadherin in tumorigenesis has been attributed to its ability to suppress invasion and metastization. However, E-cadherin impairment may have a wider impact on tumour development. We have previously shown that overexpression of mutant human E-cadherin in Drosophila produces a phenotype characteristic of downregulated Notch. Hence, we hypothesized that Notch signalling may be influenced by E-cadherin and may mediate tumour development associated with E-cadherin deficiency. De novo expression of wild-type E-cadherin in two cellular models led to a significant decrease in the activity of the Notch pathway. In contrast, the ability to inhibit Notch-1 signalling was lost in cells transfected with mutant forms of E-cadherin. Increased Notch-1 activity in E-cadherin-deficient cells correlated with increased expression of Bcl-2, and increased resistance to apoptotic stimuli. After Notch-1 inhibition, E-cadherin-deficient cells were re-sensitized to apoptosis in a similar degree to wild-type E-cadherin cells. We also show that Notch-inhibiting drugs are able to significantly inhibit the growth of E-cadherin-deficient cells xenografted into nude mice. This effect was comparable with the one observed in animals treated with the chemotherapeutic agent taxol, a chemical inducer of cell death. In conclusion, our results show that aberrant Notch-1 activation, Bcl-2 overexpression and increased cell survival are likely to play a crucial role in neoplastic transformation associated with E-cadherin impairment. These findings highlight the possibility of new targeted therapeutical strategies for the treatment of tumours associated with E-cadherin inactivation.
Subject(s)
Cadherins/physiology , Cell Survival/physiology , Proto-Oncogene Proteins c-bcl-2/physiology , Receptors, Notch/physiology , Up-Regulation/physiology , HumansABSTRACT
MOTIVATION: Logical (Boolean or multi-valued) modelling is widely used to study regulatory or signalling networks. Even though these discrete models constitute a coarse, yet useful, abstraction of reality, the analysis of large networks faces a classical combinatorial problem. Here, we propose to take advantage of the intrinsic modularity of inter-cellular networks to set up a compositional procedure that enables a significant reduction of the dynamics, yet preserving the reachability of stable states. To that end, we rely on process algebras, a well-established computational technique for the specification and verification of interacting systems. RESULTS: We develop a novel compositional approach to support the logical modelling of interconnected cellular networks. First, we formalize the concept of logical regulatory modules and their composition. Then, we make this framework operational by transposing the composition of logical modules into a process algebra framework. Importantly, the combination of incremental composition, abstraction and minimization using an appropriate equivalence relation (here the safety equivalence) yields huge reductions of the dynamics. We illustrate the potential of this approach with two case-studies: the Segment-Polarity and the Delta-Notch modules.
Subject(s)
Models, Biological , Signal Transduction , Algorithms , Body Patterning , Cell Communication , Computational Biology/methods , Intracellular Signaling Peptides and Proteins/metabolism , Membrane Proteins/metabolism , Receptors, Notch/metabolismABSTRACT
P-cadherin overexpression is associated with worse breast cancer survival, being a poor prognostic marker as well as a putative therapeutic target for the aggressive triple-negative and basal-like carcinomas (TNBCs). Previously, we have shown that P-cadherin promotes breast cancer invasion of cells where membrane E-cadherin was maintained; however, it suppresses invasion in models without endogenous cadherins, like melanomas. Here, we investigated if P-cadherin expression would interfere with the normal adhesion complex and which were the cellular/molecular consequences, constituting, in this way, a new mechanism by which E-cadherin invasive-suppressor function was disrupted. Using breast TNBC models, we demonstrated, for the first time, that P-cadherin co-localizes with E-cadherin, promoting cell invasion due to the disruption caused in the interaction between E-cadherin and cytoplasmic catenins. P-cadherin also induces cell migration and survival, modifying the expression profile of cells expressing wild-type E-cadherin and contributing to alter their cellular behaviour. Additionally, E- and P-cadherin co-expressing cells significantly enhanced in vivo tumour growth, compared with cells expressing only E- or only P-cadherin. Finally, we still found that co-expression of both molecules was significantly correlated with high-grade breast carcinomas, biologically aggressive, and with poor patient survival, being a strong prognostic factor in this disease. Our results show a role for E- and P-cadherin co-expression in breast cancer progression and highlight the potential benefit of targeting P-cadherin in the aggressive tumours expressing high levels of this protein.
Subject(s)
Breast Neoplasms/metabolism , Cadherins/metabolism , Animals , Antigens, CD , Breast Neoplasms/genetics , Breast Neoplasms/mortality , Breast Neoplasms/pathology , Cadherins/genetics , Cell Line, Tumor , Cell Movement , Cell Survival , Disease-Free Survival , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Mice , Mice, Nude , Neoplasm Grading , Neoplasm Invasiveness , Prognosis , RNA Interference , RNA, Messenger/metabolism , Signal Transduction , Time Factors , Transfection , Tumor BurdenABSTRACT
INTRODUCTION AND OBJECTIVES: The 2021 European Society of Cardiology guidelines on cardiovascular disease (CVD) prevention introduced the more accurate SCORE2 risk model as a replacement for the earlier SCORE, which is still used in primary care software in Portugal. Our objective is to determine whether the difference between risk assessment using SCORE and SCORE2, in the same patient population, is statistically significant. METHODS: A total of 1642 patients aged 40-65 without previous CVD, from the medical records of two Family Health Units, were included in this cross-sectional study. SCORE and SCORE2 were calculated using the variables gender, age, smoking status, lipid profile and systolic blood pressure. A statistical analysis was performed on the results. RESULTS: Using SCORE, 98% of the patients were in the low-moderate risk categories and 2% in the high or very high risk categories. When using SCORE2, the corresponding percentages were 55% and 45%, respectively. Reclassification with SCORE2 into higher categories was more often observed in younger (under 50 years of age) and male patients. With SCORE, 38.61% of patients were within the LDL-C target range; this figure fell to 20.28% with SCORE2. These differences are statistically significant (p<0.0001). CONCLUSION: Our findings show that a significant number of patients in this cohort who were classified through SCORE at lower risk levels were reclassified into higher risk categories with SCORE2. Similarly, the number of patients within the LDL-C target range for LDL-C was also lower using SCORE2.
Subject(s)
Cardiovascular Diseases , Primary Health Care , Humans , Male , Middle Aged , Portugal/epidemiology , Female , Primary Health Care/statistics & numerical data , Cross-Sectional Studies , Risk Assessment/methods , Cardiovascular Diseases/epidemiology , Aged , AdultABSTRACT
Cadherins are cell-cell adhesion proteins which have been strongly implicated in cancer invasion, dissemination and metastasis capacity; thus, they are key players in the epithelial-to-mesenchymal transition (EMT) program. However, their role in glioblastoma (GBM), a primary central nervous system aggressive tumor, remains to be clarified. N-, E- and P-cadherin expression was analyzed on a large series of GBMs, characterized with clinical, imaging and neuropathological parameters, as well as with patients' survival data. In addition, cadherins' expression was studied in match-recurrent cases. Using TCGA data, cadherin expression profiles were also evaluated according to GBM transcription subtypes. N-cadherin expression was observed in 81.5% of GBM, followed by E-cadherin in 31% and P-cadherin in 20.8%. Upon tumor recurrence, P-cadherin was the only significantly upregulated cadherin compared with the primary tumor, being positive in 65.8% of the cases. Actually, P-cadherin gain was observed in 51.4% of matched primary-recurrent cases. Cadherins' co-expression was also explored. Interestingly, E- and N-cadherin co-expression identified a GBM subgroup with frequent epithelial differentiation and a significant survival benefit. On the other hand, subgroups with P-cadherin expression carried the worse prognosis. P- and N-cadherin co-expression correlated with the presence of a mesenchymal phenotype. Expressions of isolated P-cadherin or E- and P-cadherin co-expression were associated with imaging characteristics of aggressiveness, to highly heterogeneous tumors, an d to worse patient survival. Classical cadherins co-expression subgroups present consistent clinical, imaging, neuropathological and survival differences, which probably reflect different states of an EMT-like program in GBM.
ABSTRACT
MOTIVATION: The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular miRNA-maturation machinery. A natural way to tackle this problem is to perform clustering over the candidate structures along with known miRNA precursor structures. Mixed clusters allow then the identification of candidates that are similar to known precursors. Given the large number of pre-miRNA candidates that can be identified in single-genome approaches, even after applying several filters for precursor robustness and stability, a conventional structural clustering approach is unfeasible. RESULTS: We propose a method to represent candidate structures in a feature space, which summarizes key sequence/structure characteristics of each candidate. We demonstrate that proximity in this feature space is related to sequence/structure similarity, and we select candidates that have a high similarity to known precursors. Additional filtering steps are then applied to further reduce the number of candidates to those with greater transcriptional potential. Our method is compared with another single-genome method (TripletSVM) in two datasets, showing better performance in one and comparable performance in the other, for larger training sets. Additionally, we show that our approach allows for a better interpretation of the results. AVAILABILITY AND IMPLEMENTATION: The MinDist method is implemented using Perl scripts and is freely available at http://www.cravela.org/?mindist=1. CONTACT: backofen@informatik.uni-freiburg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Algorithms , MicroRNAs/chemistry , Software , Animals , Anopheles/genetics , Base Sequence , Cluster Analysis , Computational Biology/methods , Drosophila melanogaster/genetics , Genome , MicroRNAs/genetics , Nucleic Acid Conformation , Principal Component Analysis , ROC CurveABSTRACT
Although the luminal progenitor cell of the normal mammary gland hierarchy has been proposed as the cell-of-origin for basal-like breast cancers, finding the cancer stem cell (CSC) phenotype for this malignancy has proven a difficult task, mostly due to the lack of specific markers. Recently, basal-like sporadic and familial cases of breast cancer have been linked to BRCA1 gene inactivation, which enables the upregulation of the target-repressed CDH3/P-cadherin gene, an important biomarker of basal-like breast carcinomas. Previously, we demonstrated that P-cadherin overexpression can mediate aggressive behavior in these tumors. Thus, our aim was to test whether P-cadherin mediates stem cell properties in basal-like breast carcinomas. Using a series of breast cancer cell lines and primary tumors, we showed that P-cadherin was directly associated with the expression of the breast stem markers CD44, CD49f, and aldehyde dehydrogenase 1 in the basal subtype. Moreover, cell population enriched for P-cadherin expression comprised increased in vitro mammosphere-forming efficiency and capacity to grow colonies in three-dimensional cultures as well as greater tumorigenicity. Importantly, an association was found with stem-/progenitor-like phenotypes of the breast, including the luminal progenitor population, CD49f(+) CD24(+). Additionally, P-cadherin expression conferred resistance to x-ray-induced cell death, sustaining a role for this molecule in another stem cell property. In summary, we demonstrated, for the first time, that P-cadherin mediates stem cell properties, which could be explored in order to better define the CSC phenotype of basal-like breast tumors and the cell-of-origin of this malignancy.
Subject(s)
Breast Neoplasms/metabolism , Cadherins/biosynthesis , Gene Expression Regulation, Neoplastic , Hyaluronan Receptors/biosynthesis , Integrin alpha6/biosynthesis , Neoplasm Proteins/biosynthesis , Neoplasms, Basal Cell/metabolism , Neoplastic Stem Cells/metabolism , Aldehyde Dehydrogenase 1 Family , Breast Neoplasms/pathology , Cell Death/radiation effects , Cell Line, Tumor , Female , Humans , Isoenzymes/biosynthesis , Neoplasms, Basal Cell/pathology , Neoplastic Stem Cells/pathology , Retinal Dehydrogenase/biosynthesis , X-RaysABSTRACT
Although adenotonsillectomy is the recommended treatment of obstructive sleep apnea (OSA) in children, some patients with preoperative severe OSA (Apnea-hypopnea index/AHI > 10) remain symptomatic after surgery and may need further workup. This study aims to: (1) analyse preoperative factors and its relation with surgical failure/persistent OSA (AHI > 5 after adenotonsillectomy) in severe pediatric OSA; (2) determine the levels of airway collapse during DISE (drug induced sleep endoscopy) in cases of surgical failure; (3) evaluate the efficacy of targeted surgery based on DISE findings. This retrospective study was conducted between August and September 2020. Across 9 years (from 2011 to 2020), all children diagnosed with severe OSA in our Hospital underwent adenotonsillectomy and repeated type 1 polysomnography (PSG) 3 months after surgery. Cases of surgical failure underwent DISE for planning eventual directed surgery. Chi-square test was used to assess the relationship between persistent OSA and preoperative patients' characteristics. 80 cases of severe pediatric OSA were diagnosed (68.8% males; mean age: 4.3 years-standard deviation: 2.49; mean AHI: 16.3-standard deviation 7.14) in the aforementioned period. We found a significant association between surgical failure (11.3% of cases; mean AHI: 6.9-SD 0.91) and obesity (p = 0.002; confidence level of 95%). Neither preoperative AHI nor other PSG parameters were associated with surgical failure. In cases of surgical failure, epiglottis collapse was present in every DISEs and adenoid tissue was present in 66% of children. All cases of surgical failure had directed surgery and surgical cure (AHI ≤ 5) was obtained in 100% of cases. This study suggests that obesity is the strongest predictor of surgical failure in children with severe OSA who undergo adenotonsillectomy. Epiglottis collapse and presence of adenoid tissue are the most common findings in postoperative DISEs of children with persistent OSA after primary surgery. DISE based surgery seems a safe and effective tool to manage persistent OSA after adenotonsillectomy.
ABSTRACT
Mixed lineage kinase 3 (MLK3) is a serine/threonine kinase, regulating MAPkinase signalling, in which cancer-associated mutations have never been reported. In this study, 174 primary gastrointestinal cancers (48 hereditary and 126 sporadic forms) and 7 colorectal cancer cell lines were screened for MLK3 mutations. MLK3 mutations were significantly associated with MSI phenotype in primary tumours (P = 0.0005), occurring in 21% of the MSI carcinomas. Most MLK3 somatic mutations identified were of the missense type (62.5%) and more than 80% of them affected evolutionarily conserved residues. A predictive 3D model points to the functional relevance of MLK3 missense mutations, which cluster in the kinase domain. Further, the model shows that most of the altered residues in the kinase domain probably affect MLK3 scaffold properties, instead of its kinase activity. MLK3 missense mutations showed transforming capacity in vitro and cells expressing the mutant gene were able to develop locally invasive tumours, when subcutaneously injected in nude mice. Interestingly, in primary tumours, MLK3 mutations occurred in KRAS and/or BRAF wild-type carcinomas, although not being mutually exclusive genetic events. In conclusion, we have demonstrated for the first time the presence of MLK3 mutations in cancer and its association to mismatch repair deficiency. Further, we demonstrated that MLK3 missense mutations found in MSI gastrointestinal carcinomas are functionally relevant.