SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

The reconstruction of phylogenomic trees containing multiple genes is best achieved by using a supermatrix. The advent of NGS technology made it easier and cheaper to obtain multiple gene data in one sequencing run. When numerous genes and organisms are used in the phylogenomic analysis, it is difficult to organize all information and manually align the gene sequences to further concatenate them. This study describes SPLACE, a tool to automatically SPLit, Align, and ConcatenatE the genes of all species of interest to generate a supermatrix file, and consequently, a phylogenetic tree, while handling possible missing data. In our findings, SPLACE was the only tool that could automatically align gene sequences and also handle missing data; and, it required only a few minutes to produce a supermatrix FASTA file containing 83 aligned and concatenated genes from the chloroplast genomes of 270 plant species. It is an open-source tool and is publicly available at https://github.com/reinator/splace

Anti-EGFR therapy: strategies in head and neck squamous cell carcinoma.

Epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor that activates downstream signaling pathways, including the Ras-MEK-Erk and PI3K-AKT pathways, leading to cell proliferation, resistance to apoptosis, angiogenesis and the ability to metastasize. EGFR overexpression is a significant finding in cancer, particularly in head and neck cancer, where it is also associated with a poor prognosis. In recent years, several molecules have been designed to inhibit EGFR activation. Among the many available anti-EGFR drugs, only cetuximab was approved for the treatment of head and neck cancers. However, no predictive biomarkers of cetuximab response are currently known. In the present review, we provide an updated assessment of EGFR biology and its clinical impact in head and neck cancers. A special emphasis is placed on novel patents of EGFR-inhibitors that are anticipated to diversify the anti-EGFR therapies available to treat head and neck cancers. In particular, we outline a new class of irreversible multi-target inhibitors (e.g. afatinib, icotinib, CUDC-101), which may significantly contribute to new head and neck cancer therapies.The authors would like to acknowledge Dr. Laura Mussel white for critical revision of the manuscript. André L. Carvalho and Rui M. Reis have a National Counsel of Technological and Scientific Development (CNPq) scholarship. A.C.C, has a FAPESP (2013/13834-7) scholarship.info:eu-repo/semantics/publishedVersio

Prevalence of articular cartilage lesions and surgical clinical outcomes in football (soccer) players' knees: a systematic review

"Article in Press" ; "Published Online: April 16, 2016"Purpose: To systematize the available scientific literature on the prevalence of articular cartilage and/or osteo- chondral lesions in football (soccer) playersâ knees, and overview the surgical procedures and functional outcomes and return to sports. Methods: A comprehensive search using Pubmed, Cochrane Library, SPORTDiscus, and CINAHL databases was carried out until September 30, 2015. All English language studies that assessed the outcomes of a surgical technique for the treatment of articular cartilage lesions in football playersâ knees, with a minimum follow-up of 12 months, were included. The reference list of the most relevant papers was screened. The main outcomes of interest were the clinical, arthroscopy or imaging primary outcomes and the return to sports rate. The methodological and reporting qualities were assessed according to Coleman methodology score. Results: The search provided 485 titles and abstracts. Five studies were eligible for inclusion (mean Coleman score of 37.2 points), comprising a total of 183 football players with a mean age of 25.7 years. A total of 217 articular cartilage and/or osteochondral lesions were reported, where the medial and lateral femoral condyles were the most common sites of lesion. The surgical procedures investigated were mosaicplasty, microfracture, autologous chondrocyte implantation, and chondral debridement. Conclusions: No definitive conclusion could be made in respect to the best current surgical technique for articular cartilage and osteochondral lesions. Microfracture and mosaicplasty can provide a faster return to competition and faster clinical and functional results, whereas autologous chondrocyte implantation and/or matrix-induced autologous chondrocytes implantation procedures can enhance longstanding clinical and functional results. Level of Evidence: Level IV, systematic review of Level III and IV studies

In vitro screening of cytotoxic activity of euphol from Euphorbia tirucalli on a large panel of human cancer-derived cell lines

A large number of classic antineoplastic agents are derived from plants. Euphorbia tirucalli L. (Euphorbiaceae) is a subtropical and tropical plant, used in Brazilian folk medicine against many diseases, including cancer, yet little is known about its true anticancer properties. The present study evaluated the antitumor effect of the tetracyclic triterpene alcohol, euphol, the main constituent of E. tirucalli in a panel of 73 human cancer lines from 15 tumor types. The biological effect of euphol in pancreatic cells was also assessed. The combination index was further used to explore euphol interactions with standard drugs. Euphol showed a cytotoxicity effect against several cancer cell lines (IC50 range, 1.41-38.89 µM), particularly in esophageal squamous cell (11.08 µM) and pancreatic carcinoma cells (6.84 µM), followed by prostate, melanoma, and colon cancer. Cytotoxicity effects were seen in all cancer cell lines, with more than half deemed highly sensitive. Euphol inhibited proliferation, motility and colony formation in pancreatic cancer cells. Importantly, euphol exhibited synergistic interactions with gemcitabine and paclitaxel in pancreatic and esophageal cell lines, respectively. To the best of our knowledge, this study constitutes the largest in vitro screening of euphol efficacy on cancer cell lines and revealed its in vitro anti-cancer properties, particularly in pancreatic and esophageal cell lines, suggesting that euphol, either as a single agent or in combination with conventional chemotherapy, is a potential anti-cancer drug.Amazônia Fitomedicamentos Ltda. (grant no. FITO 05/2012) and Barretos Cancer Hospital, all from Brazilinfo:eu-repo/semantics/publishedVersio

AKT can modulate the in vitro response of HNSCC cells to irreversible EGFR inhibitors

Epidermal growth factor receptor (EGFR) is overexpressed in up to 90% of head and neck squamous cell carcinoma (HNSCC) tumors. Cetuximab is the first targeted (anti-EGFR) therapy approved for the treatment of HNSCC patients. However, its efficacy is limited due to primary and secondary resistance, and there is no predict biomarkers of response. New generation of EGFR inhibitors with pan HER targeting and irreversible action, such as afatinib and allitinib, represents a significant therapeutic promise. In this study, we intend to compare the potential cytotoxicity of two anti-EGFR inhibitors (afatinib and allitinib) with cetuximab and to identify potential predictive biomarkers of response in a panel of HNSCC cell lines. The mutational analysis in the eight HNSCC cell lines revealed an EGFR mutation (p.H773Y) and gene amplification in the HN13 cells. According to the growth inhibition score (GI), allitinib was the most cytotoxic drug, followed by afatinib and finally cetuximab. The higher AKT phosphorylation level was associated with resistance to anti-EGFR agents. Therefore, we further performed drug combinations with anti-AKT agent (MK2206) and AKT1 gene editing, which demonstrated afatinib and allitinib sensitivity restored. Additionally, in silico analysis of TCGA database showed that AKT1 overexpression was present in 14.7% (41/279) of HNSCC cases, and was associated with perineural invasion in advanced stage. In conclusion, allitinib presented a greater cytotoxic profile when compared to afatinib and cetuximab. AKT pathway constitutes a predictive marker of allitinib response and combination with AKT inhibitors could restore response and increase treatment success.FINEP (MCTI/FINEP/MS/SCTIE/DECIT-01/2013 - FPXII-BIOPLAT) and the Assistance Program and Incentive Research (PAIP), Barretos Cancer Hospital São Paulo, Brazil. The authors would like to acknowledge the technical support of Gabriela Lamberti in the clonogenic assays. A.L.C and R.M.R are recipients of a National Counsel of Technological and Scientific Development (CNPq) scholarship and O.C.M is recipient of a Portuguese Foundation for Science and Technology (FCT) scholarship (SFRH/BPD/108351/2015)info:eu-repo/semantics/publishedVersio

Molecular characterization of short-term primary cultures and comparison with corresponding tumor tissue of Brazilian glioblastoma patients

Background: Glioblastoma, the most frequent and malignant adult brain tumor, has been extensively studied. However, there is no effective treatment, and to overcome this challenging scenario, it is essential to improve preclinical biological models. This study aimed to molecularly characterize short-term glioblastoma primary cultures and to compare them with patient tumor profiles. Methods: Glioblastoma cell lines were established from Barretos Cancer Hospital patients diagnosed with glioblastoma. The cells were cultured with DMEM (+)10% FBS (+)1% PS and were molecularly characterized using array CGH (aCGH), next-generation and Sanger sequencing. Results: We established four short-term glioblastoma cultures and we found that the primary cells exhibited a diversity of chromosomal aberrations, with gain of chromosome 7 and loss of chromosomes 10, 13 and 17p being the most frequent alterations. Mutation profiling showed that hotspot TERT promoter mutations were present in 3/4 cases, followed by mutations in TP53 (2/4) and in the RB1, BRAF and PTEN (1/4) genes. A similar chromosomal and mutation pattern was observed in all short-term cultures and matched frozen tumors. Conclusions: Herein, short-term glioblastoma primary cultures were successfully characterized and had genetic make-ups that were similar to those of patient tumors, suggesting that short-term primary cultures are suitable in vitro models for studies of glioblastoma biology.Universal/CNPq (475358/2011-2-Reis RM), FAPESP (2012/19590-0-Reis RM) and the MCTI/CNPq No. 73/2013 (Reis RM) grants. Bidinotto LT was a recipient of the FAPESP fellowship (2011/08523-7 and 2012/08287-4)info:eu-repo/semantics/publishedVersio

Effects of proteasome inhibitor MG-132 on the parasite Schistosoma mansoni

Proteasome is a proteolytic complex responsible for intracellular protein turnover in eukaryotes, archaea and in some actinobacteria species. Previous work has demonstrated that in Schistosoma mansoni parasites, the proteasome inhibitor MG-132 affects parasite development. However, the molecular targets affected by MG-132 in S. mansoni are not entirely known. Here, we used expression microarrays to measure the genome-wide changes in gene expression of S. mansoni adult worms exposed in vitro to MG-132, followed by in silico functional analyses of the affected genes using Ingenuity Pathway Analysis (IPA). Scanning electron microscopy was used to document changes in the parasites' tegument. We identified 1,919 genes with a statistically significant (q-value <= 0.025) differential expression in parasites treated for 24 h with MG-132, when compared with control. Of these, a total of 1,130 genes were up-regulated and 790 genes were down-regulated. A functional gene interaction network comprised of MG-132 and its target genes, known from the literature to be affected by the compound in humans, was identified here as affected by MG-132. While MG-132 activated the expression of the 26S proteasome genes, it also decreased the expression of 19S chaperones assembly, 20S proteasome maturation, ubiquitin-like NEDD8 and its partner cullin-3 ubiquitin ligase genes. Interestingly, genes that encode proteins related to potassium ion binding, integral membrane component, ATPase and potassium channel activities were significantly down-regulated, whereas genes encoding proteins related to actin binding and microtubule motor activity were significantly up-regulated. MG132 caused important changes in the worm tegumentpeeling, outbreaks and swelling in the tegument tubercles could be observed, which is consistent with interference on the ionic homeostasis in S. mansoni. Finally, we showed the down-regulation of Bax pro-apoptotic gene, as well as up-regulation of two apoptosis inhibitor genes, IAP1 and BRE1, and in contrast, down-regulation of Apaf-1 apoptotic activator, thus suggesting that apoptosis is deregulated in S. mansoni exposed to MG-132. A considerable insight has been gained concerning the potential of MG-132 as a gene expression modulator, and overall the data suggest that the proteasome might be an important molecular target for the design of new drugs against schistosomiasis.Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Bioquim & Imunol, Ribeirao Preto, SP, BrazilUniv Sao Paulo, Dept Bioquim, Inst Quim, Sao Paulo, SP, BrazilAdolfo Lutz Inst, Ctr Parasitol & Micol, Nucleo Enteroparasitas, Sao Paulo, SP, BrazilUniv Franca, Nucleo Pesquisa Ciencias Exatas & Tecnol, Grp Pesquisa Prod Nat, Franca, SP, BrazilInst Butantan, Lab Expressao Genica Eucariotos, Sao Paulo, SP, BrazilUniv Fed Uberlandia, Inst Genet Bioquim, Campus Patos de Minas, Patos De Minas, MG, BrazilUniv Fed Sao Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, Discipline Parasitol, Sao Paulo, SP, BrazilUniv Fed Rio de Janeiro, Inst Biol, Ctr Ciencias & Saude, Rio De Janeiro, RJ, BrazilUniv Fed Sao Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, Discipline Parasitol, Sao Paulo, SP, BrazilWeb of Scienc

Inconsistency in shoulder arthrometers for measuring glenohumeral joint laxity: a systematic review

There is no consensus on how to measure shoulder joint laxity and results reported in the literature are not well systematized for the available shoulder arthrometer devices. This systematic review aims to summarize the results of currently available shoulder arthrometers for measuring glenohumeral laxity in individuals with healthy or injured shoulders. Searches were conducted on the PubMed, EMBASE, and Web of Science databases to identify studies that measure glenohumeral laxity with arthrometer-assisted assessment. The mean and standard deviations of the laxity measurement from each study were compared based on the type of population and arthrometer used. Data were organized according to the testing characteristics. A total of 23 studies were included and comprised 1162 shoulders. Populations were divided into 401 healthy individuals, 278 athletes with asymptomatic shoulder, and 134 individuals with symptomatic shoulder. Sensors were the most used method for measuring glenohumeral laxity and stiffness. Most arthrometers applied an external force to the humeral head or superior humerus by a manual-assisted mechanism. Glenohumeral laxity and stiffness were mostly assessed in the sagittal plane. There is substantial heterogeneity in glenohumeral laxity values that is mostly related to the arthrometer used and the testing conditions. This variability can lead to inconsistent results and influence the diagnosis and treatment decision-making.This article is a result of the project DILATO (reference 47289) supported by the Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

Expression of tyrosine kinase receptor AXL is associated with worse outcome of metastatic renal cell carcinomas treated with sunitinib

Expression of tyrosine kinase receptor AXL is associated with worse outcome of metastatic renal cell carcinomas treated with sunitinibBackground: Renal cell carcinoma (RCC) represents 2%-3% of all cancers of the Western countries. Currently, sunitinib, a receptor tyrosine kinase inhibitor, particularly of PDGF and VEGF receptors, is the first-line therapy for metastatic RCC (mRCC), with significant improvement in clinical outcome. However, there is a lack of predictive biomarkers of sunitinib response. Recently, others and our group suggested that the receptor tyrosine kinase AXL may modify the response to sunitinib. Objective: To study the expression of AXL in a series patients with of mRCC treated with sunitinib and to correlate it with patient's clinic-pathological features and therapeutic response. Material and methods: Sixty-four patients with mRCC (51 clear cell carcinomas (CCCs) and 13 non-CCCs) were evaluated for AXL expression by immunohistochemistry in the primary tumor. Results: AXL positivity was observed in 47% (30/64) of cases, namely in 43% (22/51) of CCCs and 61% (8/13) of non-CCC. Considering only the clear cell subtype, the univariate analysis showed that AXL expression was statistically associated with a poor prognosis, with a median overall survival of 13 months vs. 43 months in patients with negative AXL. In this subtype, along with the AXL positivity, other prognostic factors were absence of nephrectomy, Karnofsky performance status, more than 1 site of metastasis and liver metastasis. Moreover, AXL expression was associated with shorter progression to sunitinib. Overall, the multivariate survival analysis showed that absence of nephrectomy (HR = 4.85, P = 0.001), more than 1 site of metastasis (HR = 2.99, P = 0.002), bone metastasis (HR = 2.95, P = 0.001), together with AXL expression (HR = 2.01, P = 0.048) were independent poor prognostic factor in patients with mRCC. Conclusion: AXL expression was associated with worse clinical outcome and may be an important prognostic biomarker in sunitinibtreated patients with metastatic renal cell carcinoma.this study was supported by Barretos Cancer Hospital Internal Research Funds (PAIP) of participant authors. Rui Manuel Reis is recipient of a National Council of Technological and Scientific Development (CNPq) scholarship.info:eu-repo/semantics/publishedVersio