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High serum levels of osteoprotegerin (OPG) are found in patients with obesity, type 2 diabetes, sepsis, or septic shock and are associated with a high mortality rate in stroke. The primary known function of OPG is to bind to the receptor activator of NF-κB ligand (RANKL), and by doing so, it inhibits the binding between RANKL and its receptor (RANK). TLR4 signaling in macrophages involves TRAF6 recruitment and contributes to low-grade chronic inflammation in adipose tissue. LPS is a classical activator of the TLR4 pathway and induces the expression of inflammatory cytokines in macrophages. We have previously observed that in the presence of RANKL, there is no LPS-induced activation of TLR4 in macrophages. In this study, we investigated the crosstalk between RANK and TLR4 pathways in macrophages stimulated with both RANKL and LPS to unveil the role of OPG in inflammatory processes. We found that RANKL inhibits TLR4 activation by binding to RANK, promoting the binding between TRAF6 and RANK, lowering TLR4 activation and the expression of proinflammatory mediators. Furthermore, high OPG levels aggravate inflammation by inhibiting RANKL. Our findings elect RANKL as a candidate for drug development as a way to mitigate the impact of obesity-induced inflammation in patients.

O sequenciamento de RNA de célula única (scRNA-seq) é uma técnica revolucionária que permite caracterizar os transcriptomas de muitas células individuais em uma amostra. A aplicação desta abordagem é imprescindível para conhecer os mecanismos moleculares que regulam a progressão tumoral, na busca de novos alvos elegíveis para o desenvolvimento de novos biomarcadores e aprimoramento de terapias já existentes. Neste trabalho, exploramos dados públicos de melanoma e dados gerados in house de Câncer de Pulmão de Pequenas Células (CPPC) para buscar um melhor entendimento destas doenças. Utilizamos ferramentas para avaliar as subpopulações de células, tipos celulares, vias enriquecidas, trajetórias e comunicação célula-célula. Em melanoma, identificamos um lncRNA chamado TRHDE-AS1 que parece atuar na via transição epitélio-mesenquima (EMT) em parceria com o HOTAIR. Com isso foi possível propor um circuito gênico regulado por feedback negativo, onde o HOTAIR regula positivamente o TRHDE-AS1, e o TRHDE-AS1, ao atingir um certo nível de expressão, passa a regular negativamente o HOTAIR. A partir da análise de inferência de trajetória entre os tipos celulares foi possível identificar um ponto de diferenciação onde há a ativação da via de EMT a partir da presença de células endoteliais e fibroblastos associados ao câncer (CAF). Para CPPC avaliou-se o perfil transcricional das células únicas e concluiu-se que os dados estão de acordo com a classificação atual de subtipos moleculares, expressando NEUROD1, POU2F3 e ASCL1. Não foram identificadas amostras YAP1 nesse estudo. Por fim, a via de sinalização NOTCH é demonstrada como um papel importante para a plasticidade transcricional em CPPC além das vias de sinalização MK, JAM, PTN, CD99, NMU, CADM e NCAM, identificadas a partir da comunicação célula-célula, que possuem um papel importante para o desenvolvimento de terapias e biomarcadores. Este estudo fornece abordagens para a identificação de novos biomarcadores e desenvolvimento de terapias a partir de dados de sequenciamento de RNA de células únicas. Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology that allows the characterization of the transcriptomes of many individual cells in one sample. The application of this approach is indispensable to know the molecular mechanisms regulating tumor progression in the search for eligible new targets for the development of new biomarkers and enhancement of existing therapies. In this work, we exploit public melanoma data and in-house generated Small Cell Lung Cancer (SCLC) data to seek a better understanding of these diseases. We use tools to assess cell subpopulations, cell types, enriched pathways, trajectories, and cell-cell communication. In melanoma, we identified a lncRNA called TRHDE-AS1 that appears to act in the epithelium-mesenchymal transition (EMT) pathway in partnership with HOTAIR. With this, it was possible to propose a negative feedback regulated gene circuit, where HOTAIR positively regulates TRHDE-AS1, and TRHDE-AS1, upon reaching a certain expression level, negatively regulates HOTAIR. From the pathway inference analysis between cell types, it was possible to identify a point of differentiation where there is the activation of the EMT pathway from the presence of endothelial cells and cancer-associated fibroblasts (CAF). For SCLC, we evaluated the transcriptional profile of single cells and concluded that the data agree with the current classification of molecular subtypes, expressing NEUROD1, POU2F3, and ASCL1. No YAP1 samples were identified in this study. Finally, the NOTCH signaling pathway is shown to play an essential role for transcriptional plasticity in SCLC in addition to the MK, JAM, PTN, CD99, NMU, CADM, and NCAM signaling pathways identified from cell-cell communication, which have an essential role in the development of therapies and biomarkers. This study provides approaches for identifying novel biomarkers and developing therapies from single-cell RNA sequencing data.

Aberrant expression of long non-coding RNAs (lncRNAs) has been detected in several types of cancer, including acute lymphoblastic leukemia (ALL), but lncRNA mapped on transcribed ultraconserved regions (T-UCRs) are little explored. The T-UCRs uc.112, uc.122, uc.160 and uc.262 were evaluated by quantitative real-time PCR in bone marrow samples from children with T-ALL (n = 32) and common-ALL/pre-B ALL (n = 30). In pediatric ALL, higher expression levels of uc.112 were found in patients with T-ALL, compared to patients with B-ALL. T-cells did not differ significantly from B-cells regarding uc.112 expression in non-tumor precursors from public data. Additionally, among B-ALL patients, uc.112 was also found to be increased in patients with hyperdiploidy, compared to other karyotype results. The uc.122, uc.160, and uc.262 were not associated with biological or clinical features. These findings suggest a potential role of uc.112 in pediatric ALL and emphasize the need for further investigation of T-UCR in pediatric ALL.

Our previous work using a melanoma progression model composed of melanocytic cells (melanocytes, primary and metastatic melanoma samples) demonstrated various deregulated genes, including a few known lncRNAs. Further analysis was conducted to discover novel lncRNAs associated with melanoma, and candidates were prioritized for their potential association with invasiveness or other metastasis-related processes. In this sense, we found the intergenic lncRNA U73166 (ENSG00000230454) and decided to explore its effects in melanoma. For that, we silenced the lncRNA U73166 expression using shRNAs in a melanoma cell line. Next, we experimentally investigated its functions and found that migration and invasion had significantly decreased in knockdown cells, indicating an essential association of lncRNA U73166 for cancer processes. Additionally, using naïve and vemurafenib-resistant cell lines and data from a patient before and after resistance, we found that vemurafenib-resistant samples had a higher expression of lncRNA U73166. Also, we retrieved data from the literature that indicates lncRNA U73166 may act as a mediator of RNA processing and cell invasion, probably inducing a more aggressive phenotype. Therefore, our results suggest a relevant role of lncRNA U73166 in metastasis development. We also pointed herein the lncRNA U73166 as a new possible biomarker or target to help overcome clinical vemurafenib resistance.

Melanoma is the deadliest form of skin cancer, and little is known about the impact of deregulated expression of long noncoding RNAs (lncRNAs) in the progression of this cancer. In this study, we explored RNA-Seq data to search for lncRNAs associated with melanoma progression. We found distinct lncRNA gene expression patterns across melanocytes, primary and metastatic melanoma cells. Also, we observed upregulation of the lncRNA ZEB1-AS1 (ZEB1 antisense RNA 1) in melanoma cell lines. Data analysis from The Cancer Genome Atlas (TCGA) confirmed higher ZEB1-AS1 expression in metastatic melanoma and its association with hotspot mutations in BRAF (B-Raf proto-oncogene, serine/threonine kinase) gene and RAS family genes. In addition, a positive correlation between ZEB1-AS1 and ZEB1 (zinc finger E-box binding homeobox 1) gene expression was verified in primary and metastatic melanomas. Using gene expression signatures indicative of invasive or proliferative phenotypes, we found an association between ZEB1-AS1 upregulation and a transcriptional profile for invasiveness. Enrichment analysis of correlated genes demonstrated cancer genes and pathways associated with ZEB1-AS1. We suggest that the lncRNA ZEB1-AS1 could function by activating ZEB1 gene expression, thereby influencing invasiveness and phenotype switching in melanoma, an epithelial-to-mesenchymal transition (EMT)-like process, which the ZEB1 gene has an essential role.

Made available in DSpace on 2021-06-25T15:05:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-18 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) There is increasing evidence showing positive association between changes in oral microbiome and the occurrence of oral squamous cell carcinoma (OSCC). Alcohol- and nicotine-related products can induce microbial changes but are still unknown if these changes are related to cancerous lesion sites. In an attempt to understand how these changes can influence the OSCC development and maintenance, the aim of this study was to investigate the oral microbiome linked with OSCC as well as to identify functional signatures and associate them with healthy or precancerous and cancerous sites. Our group used data of oral microbiomes available in public repositories. The analysis included data of oral microbiomes from electronic cigarette users, alcohol consumers, and precancerous and OSCC samples. An R-based pipeline was used for taxonomic and functional prediction analysis. The Streptococcus spp. genus was the main class identified in the healthy group. Haemophilus spp. predominated in precancerous lesions. OSCC samples revealed a higher relative abundance compared with the other groups, represented by an increased proportion of Fusobacterium spp., Prevotella spp., Haemophilus spp., and Campylobacter spp. Venn diagram analysis showed 52 genera exclusive of OSCC samples. Both precancerous and OSCC samples seemed to present a specific associated functional pattern. They were menaquinone-dependent protoporphyrinogen oxidase pattern enhanced in the former and both 3 ',5 '-cyclic-nucleotide phosphodiesterase (purine metabolism) and iron(III) transport system ATP-binding protein enhanced in the latter. We conclude that although precancerous and OSCC samples present some differences on microbial profile, both microbiomes act as iron chelators-like potentially contributing to tumor growth. Univ Fed Rio Grande do Sul, Fac Dent, Prevent & Community Dent Dept, BR-90035003 Porto Alegre, RS, Brazil Univ Sao Paulo, Fac Med Ribeirao Preto, Postgrad Program Clin Oncol Stem Cells & Cell The, BR-14049900 Ribeirao Preto, SP, Brazil Reg Blood Ctr Ribeirao Preto, Natl Inst Sci & Technol Stem Cell & Cell Therapy, Ctr Cell Based Therapy CEPID FAPESP, Mol Genet & Bioinfonnat Lab MGBL, Rua Tenente Catao Roxo 2501, BR-14049900 Ribeirao Preto, SP, Brazil Univ Sao Paulo, Ribeirio Preto Med Sch, Dept Genet, BR-14049900 Ribeirao Preto, SP, Brazil Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Entomol & Acarol, BR-13418900 Piracicaba, SP, Brazil Univ Sao Paulo, Ribeirao Preto Med Sch, BR-14049900 Ribeirao Preto, SP, Brazil Univ Sao Paulo, Sch Publ Hlth, Dept Nutr, BR-01246904 Sao Paulo, SP, Brazil Univ Sao Paulo, Sao Carlos Sch Engn, Dept Hydraul & Sanitat, BR-13563120 Sao Carlos, SP, Brazil Inst Canc Res IPEC, BR-85015430 Guarapuava, PR, Brazil Univ Estadual Centro Oeste, Dept Med, BR-85015430 Guarapuava, PR, Brazil Sao Paulo State Univ, Sch Pharmaceut Sci, Dept Food & Nutr, Araraquara, SP, Brazil Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, Ribeirao Preto, SP, Brazil Univ Paulista, Inst Hlth Sci, Undergrad Biol Sci, Ribeirao Preto, SP, Brazil Univ Fed Parana, Grad Program Bioinformat Profess & Technol Educ S, Curitiba, Parana, Brazil Univ Fed Amapa, Dept Biol Sci & Hlth, Macapa, AP, Brazil Embrapa Southeast Livestock EMBRAPA, Sao Paulo, Brazil FARVET, Labs Invest & Desarrollo, Chincha Alta, Ica, Peru Univ San Martin de Porres, Ctr Invest Genet & Biol Mol CIGBM, Lima, Peru Para State Univ, Grad Program Parasit Biol Amazon, Belem, Para, Brazil Para State Univ, Inst Technol, Dept Elect & Biomed Engn, Belem, Para, Brazil Fundacao Ctr Controle Oncol Estado Amazonas, Dept Educ & Res, Manaus, Amazonas, Brazil Univ Fed Goias, Inst Pathol Trop & Publ Hlth, Goiania, Go, Brazil Univ Sao Paulo, Sch Dent Ribeirao Preto, Dept Oral Maxillofacial Surg & Periodontol, Ribeirao Preto, SP, Brazil Univ Sao Paulo, Sch Arts Sci & Humanities, Sao Paulo, Brazil Blood Ctr Ribeirao Preto, Ctr Cell Based Therapy CEPID FAPESP, Mol Genet & Bioinformat Lab MGBL, Rua Tenente Catao Roxo 2501, BR-14051140 Ribeirao Preto, SP, Brazil Sao Paulo State Univ, Sch Pharmaceut Sci, Dept Food & Nutr, Araraquara, SP, Brazil CNPq: 465539/2014-9 FAPESP: 2013/08135-2 FAPESP: 17/23205-8 FAPESP: 19/08528-0

Background Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. Results Here, we developed the R package “CeTF” that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems — for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle. Conclusion This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor (http://bioconductor.org/packages/CeTF) and GitHub (http://github.com/cbiagii/CeTF).

Made available in DSpace on 2022-05-01T10:18:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-01 Bundesministerium für Bildung und Forschung American Historical Association Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Deutsche Forschungsgemeinschaft National Institutes of Health Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Adipose tissue has been classified based on its morphology and function as white, brown, or beige/brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, going beyond simply defined morphology but also by their cellular origin, adaptation to metabolic stress, and plasticity. Here, we performed an in-depth analysis of publicly available single-nuclei RNAseq from adipose tissue and utilized a workflow template to characterize adipocyte plasticity, heterogeneity, and secretome profiles. The reanalyzed dataset led to the identification of different subtypes of adipocytes including three subpopulations of thermogenic adipocytes, and provided a characterization of distinct transcriptional profiles along the adipocyte trajectory under thermogenic challenges. This study provides a useful resource for further investigations regarding mechanisms related to adipocyte plasticity and trans-differentiation. Department of Genetics Ribeirão Preto Medical School University of São Paulo Center for Cell-Based Therapy (CEPID/FAPESP) National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq) Regional Blood Center of Ribeirão Preto Institute for Cancer Research IPEC Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP) Department of Translational Genomics Medical Faculty University of Cologne Department of Biochemistry School of Medicine Boston University Department of Integrated Biotechnology University of Mogi das Cruzes Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP) Bundesministerium für Bildung und Forschung: 01ZX1901A American Historical Association: 17POST33660875 CNPq: 311319/2018-1 CNPq: 311530/2019-2 Deutsche Forschungsgemeinschaft: 413326622 CNPq: 870415/1997-2 National Institutes of Health: DK117161 National Institutes of Health: DK117163 National Institutes of Health: P30-DK-046200 Deutsche Forschungsgemeinschaft: SFB1399

Made available in DSpace on 2020-12-12T02:25:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) COVID-19 can result in severe lung injury. It remained to be determined why diabetic individuals with uncontrolled glucose levels are more prone to develop the severe form of COVID-19. The molecular mechanism underlying SARS-CoV-2 infection and what determines the onset of the cytokine storm found in severe COVID-19 patients are unknown. Monocytes and macrophages are the most enriched immune cell types in the lungs of COVID-19 patients and appear to have a central role in the pathogenicity of the disease. These cells adapt their metabolism upon infection and become highly glycolytic, which facilitates SARS-CoV-2 replication. The infection triggers mitochondrial ROS production, which induces stabilization of hypoxia-inducible factor-1α (HIF-1α) and consequently promotes glycolysis. HIF-1α-induced changes in monocyte metabolism by SARS-CoV-2 infection directly inhibit T cell response and reduce epithelial cell survival. Targeting HIF-1ɑ may have great therapeutic potential for the development of novel drugs to treat COVID-19. Diabetic people with uncontrolled blood glucose levels have a greater risk to develop severe COVID-19 disease. Codo et al. show that elevated glucose levels and glycolysis promote SARS-CoV-2 (CoV-2) replication and cytokine production in monocytes through a mitochondrial ROS/hypoxia-inducible factor-1α dependent pathway, resulting in T cell dysfunction and epithelial cell death. Laboratory of Immunometabolism Department of Genetics Evolution Microbiology and Immunology Institute of Biology University of Campinas Department of Genetics Evolution Microbiology and Immunology Institute of Biology University of Campinas Department of Biochemistry and Tissue Biology Institute of Biology University of Campinas Department of Genetics at Ribeirao Preto Medical School University of Sao Paulo, Ribeirao Preto Department of Clinical and Toxicological analyses School of Pharmaceutical Sciences University of São Paulo Brazilian Biosciences National Laboratory (LNBio), Campinas Department of Animal Biology Institute of Biology University of Campinas, Campinas Department of Internal Medicine School of Medical Sciences University of Campinas, Campinas Department of Clinical Medicine School of Medical Sciences University of Campinas, Campinas Hematology and Hemotherapy Center University of Campinas, Campinas Obesity and Comorbidities Research Center (OCRC) University of Campinas Experimental Medicine Research Cluster (EMRC) University of Campinas Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), Botucatu D'Or Institute for Research and Education (IDOR) Instituto Nacional de Biomarcadores em Neuropsiquiatria Conselho Nacional de Desenvolvimento Científico e Tecnológico Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), Botucatu FAPESP: 20/04579-7 FAPESP: 2015/15626-8 FAPESP: 2016/18031-8 FAPESP: 2016/23328-0 FAPESP: 2017/01184-9 FAPESP: 2018/22505-0 FAPESP: 2019/00098-7 FAPESP: 2019/06372-3 FAPESP: 2020/04522-5 FAPESP: 2020/04558-0 FAPESP: 2020/04583-4 FAPESP: 2020/04746-0 FAPESP: 2020/04919-2 Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas: 2274/20

Filamentous fungus Purpureocillium lilacinum is an emerging pathogen that infects immunocompromised and immunocompetent individuals and is resistant to several azole molecules. Although azole resistance mechanisms are well studied in Aspergillus sp. and Candida sp., there are no studies to date reporting P. lilacinum molecular response to these molecules. The aim of this study was to describe P. lilacinum molecular mechanisms involved in antifungal response against fluconazole and itraconazole. Transcriptomic analyses showed that gene expression modulation takes place when P. lilacinum is challenged for 12 h with fluconazole (64 μg/mL) or itraconazole (16 μg/mL). The antifungals acted on the ergosterol biosynthesis pathway, and two homologous genes coding for cytochrome P450 51 enzymes were upregulated. Genes coding for efflux pumps, such as the major facilitator superfamily transporter, also displayed increased expression in the treated samples. We propose that P. lilacinum develops antifungal responses by raising the expression levels of cytochrome P450 enzymes and efflux pumps. Such modulation could confer P. lilacinum high levels of target enzymes and could lead to the constant withdrawal of antifungals, which would force an increase in the administration of antifungal medications to achieve fungal morbidity or mortality. The findings in this work could aid in the decision-making for treatment strategies in cases of P. lilacinum infection.

Macrophages are classified upon activation as classical activated M1 and M2 anti-inflammatory regulatory populations. This macrophage polarization is well characterized in humans and mice, but M1/M2 profile in cattle has been far less explored.Bos primigeniustaurus (taurine) andBos primigenius indicus(indicine) cattle display contrasting levels of resistance to infection and parasitic diseases such as C57BL/6J and Balb/c murine experimental models of parasite infection outcomes based on genetic background. Thus, we investigated the differential gene expression profile of unstimulated and LPS stimulated monocyte-derived macrophages (MDMs) from Holstein (taurine) and Gir (indicine) breeds using RNA sequencing methodology. For unstimulated MDMs, the contrast between Holstein and Gir breeds identified 163 Differentially Expressed Genes (DEGs) highlighting the higher expression of C-C chemokine receptor type five(CCR5) andBOLA-DQgenes in Gir animals. LPS-stimulated MDMs from Gir and Holstein animals displayed 1,257 DEGs enriched for cell adhesion and inflammatory responses. Gir MDMs cells displayed a higher expression of M1 related genes likeNitric Oxide Synthase 2(NOS2),Toll like receptor 4(TLR4),Nuclear factor NF-kappa-B 2(NFKB2) in addition to higher levels of transcripts for proinflammatory cytokines, chemokines, complement factors and the acute phase protein Serum Amyloid A (SAA). We also showed that gene expression of inflammatory M1 population markers, complement and SAA genes was higher in Gir in buffy coat peripheral cells in addition to nitric oxide concentration in MDMs supernatant and animal serum. Co-expression analyses revealed that Holstein and Gir animals showed different transcriptional signatures in the MDMs response to LPS that impact on cell cycle regulation, leukocyte migration and extracellular matrix organization biological processes. Overall, the results suggest that Gir animals show a natural propensity to generate a more pronounced M1 inflammatory response than Holstein, which might account for a faster immune response favouring resistance to many infection diseases.

SummaryFinding meaningful gene-gene associations and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. CeTF is an R package that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems — for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis.AvailabilityCeTF is available as R package in Bioconductor (https://bioconductor.org/packages/CeTF), GitHub (https://github.com/cbiagii/CeTF) and as docker image (https://hub.docker.com/r/biagii/cetf). More information on how to use the package can be found in the Supplemental File 1.

Made available in DSpace on 2020-12-12T02:22:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Two in silico methodologies were implemented to reveal the molecular signatures of inorganic hydroxyapatite and β-TCP materials from a transcriptome database to compare biomaterials. To test this new methodology, we choose the array E-MTAB-7219, which contains the transcription profile of osteoblastic cell line seeded onto 15 different biomaterials up to 48 hr. The expansive potential of the methodology was tested from the construction of customized signatures. We present, for the first time, a methodology to compare the performance of different biomaterials using the transcriptome profile of the cell through the Gene set variation analysis (GSVA) score. To test this methodology, we implemented two methods based on MSigDB collections, using all the collections and sub-collections except the Hallmark collection, which was used in the second method. The result of this analysis provided an initial understanding of biomaterial grouping based on the cell transcriptional landscape. The comparison using GSVA score combined efforts and expand the potential to compare biomaterials using transcriptome profile. Altogether, our results provide a better understanding of the comparison of different biomaterials and suggest a possibility of the new methodology be applied to the prospection of new biomaterials. Laboratory of Bioassays and Cellular Dynamics Department of Chemistry and Biochemistry Institute of Biosciences São Paulo State University UNESP Genomic Medicine Center Department of Genetics of the Ribeirao Preto Medical School University of Sao Paulo Laboratory of Bioassays and Cellular Dynamics Department of Chemistry and Biochemistry Institute of Biosciences São Paulo State University UNESP

COVID-19 can result in severe lung injury. It remained to be determined why diabetic individuals with uncontrolled glucose levels are more prone to develop the severe form of COVID-19. The molecular mechanism underlying SARS-CoV-2 infection and what determines the onset of the cytokine storm found in severe COVID-19 patients are unknown. Monocytes/macrophages are the most enriched immune cell types in the lungs of COVID-19 patients and appear to have a central role in the pathogenicity of the disease. These cells adapt their metabolism upon infection and become highly glycolytic, which facilitates SARS-CoV-2 replication. The infection triggers mitochondrial ROS production, which induces stabilization of hypoxia-inducible factor- 1α (HIF - 1α) and consequently promotes glycolysis. HIF- 1α-induced changes in monocyte metabolism by SARS-CoV-2 infection directly inhibit T cell response and reduce epithelial cell survival. Targeting HIF-1 ɑ may have great therapeutic potential for the development of novel drugs to treat COVID-19.

Simple Summary Medulloblastoma (MB) is the most common malignant brain tumor in childhood. Currently, MB is assigned in four molecular subgroups (SHH, WNT, Group 3, and Group 4) and subtyped in 12 variants. The alpha subtype of the SHH subgroup bears TP53 mutation and is considered very high risk by the World Health Organization (WHO). In the current study, we have investigated the role of YAP1 expression in SHH MBs. Herein, we show: (1) SHH MB patients genotypically profiled as resistant to SMOi and the aggressive alpha subtype overexpress YAP1; (2) SHH-like cell lines bearing TP53 mutation show improved responsiveness to SMOi upon YAP1 depletion; (3) Sonidegib (smoothened inhibitor) and Verteporfin (YAP1 inhibitor) synergize at specific doses; (4) distinct cell populations in the single-cell RNA-seq patient setting express YAP1 and SMO. Abstract Advances in genomics have led to the identification of twelve relevant molecular subtypes within medulloblastoma (MB). The alpha subtype of Sonic hedgehog-driven MB is resistant to therapy (including smoothened inhibitors) due to activation of genes from the non-canonical SHH pathway, such as MYCN, YAP1, or TP53. Using retrospective cohort microarray data, we found that YAP1 is overexpressed in SHH alpha MB and patients profiled as resistant to SMO inhibitors compared to good responders. Here, we performed YAP1 depletion via CRISPR/Cas9 in two in vitro models of SHH-like MB cells and found that this protein is involved in responsiveness to the SMO inhibitor regarding proliferation, apoptosis, and colony formation. Further, considering the synergic combination of YAP1 depletion with SMO inhibition, we assessed single-cell RNA-seq data from five patients and found that SMO and YAP1 are enriched within cells of SHH MB. Importantly, our data suggest that YAP1 is not only a reliable biomarker for cellular response to SMOi but may indicate prospective testing of combination therapy using YAP1 and SMO inhibitors in preclinical models of SHH MB.

Next-generation sequencing platforms are routinely used for molecular assignment due to their high impact for risk stratification and prognosis in medulloblastomas. Yet, low and middle-income countries still lack an accurate cost-effective platform to perform this allocation. TaqMan Low Density array (TLDA) assay was performed using a set of 20 genes in 92 medulloblastoma samples. The same methodology was assessed in silico using microarray data for 763 medulloblastoma samples from the GSE85217 study, which performed MB classification by a robust integrative method (Transcriptional, Methylation and cytogenetic profile). Furthermore, we validated in 11 MBs samples our proposed method by Methylation Array 450 K to assess methylation profile along with 390 MB samples (GSE109381) and copy number variations. TLDA with only 20 genes accurately assigned MB samples into WNT, SHH, Group 3 and Group 4 using Pearson distance with the average-linkage algorithm and showed concordance with molecular assignment provided by Methylation Array 450 k. Similarly, we tested this simplified set of gene signatures in 763 MB samples and we were able to recapitulate molecular assignment with an accuracy of 99.1% (SHH), 94.29% (WNT), 92.36% (Group 3) and 95.40% (Group 4), against 97.31, 97.14, 88.89 and 97.24% (respectively) with the Ward.D2 algorithm. t-SNE analysis revealed a high level of concordance (k = 4) with minor overlapping features between Group 3 and Group 4. Finally, we condensed the number of genes to 6 without significantly losing accuracy in classifying samples into SHH, WNT and non-SHH/non-WNT subgroups. Additionally, we found a relatively high frequency of WNT subgroup in our cohort, which requires further epidemiological studies. TLDA is a rapid, simple and cost-effective assay for classifying MB in low/middle income countries. A simplified method using six genes and restricting the final stratification into SHH, WNT and non-SHH/non-WNT appears to be a very interesting approach for rapid clinical decision-making. Electronic supplementary material The online version of this article (10.1186/s40478-019-0681-y) contains supplementary material, which is available to authorized users.

Mitochondria are central key players in cell metabolism, and mitochondrial DNA (mtDNA) instability has been linked to metabolic changes that contribute to tumorigenesis and to increased expression of pro-tumorigenic genes. Here, we use melanoma cell lines and metastatic melanoma tumors to evaluate the effect of mtDNA alterations and the expression of the mtDNA packaging factor, TFAM, on energetic metabolism and pro-tumorigenic nuclear gene expression changes. We report a positive correlation between mtDNA copy number, glucose consumption, and ATP production in melanoma cell lines. Gene expression analysis reveals a down-regulation of glycolytic enzymes in cell lines and an up-regulation of amino acid metabolism enzymes in melanoma tumors, suggesting that TFAM may shift melanoma fuel utilization from glycolysis towards amino acid metabolism, especially glutamine. Indeed, proliferation assays reveal that TFAM-down melanoma cell lines display a growth arrest in glutamine-free media, emphasizing that these cells rely more on glutamine metabolism than glycolysis. Finally, our data indicate that TFAM correlates to VEGF expression and may contribute to tumorigenesis by triggering a more invasive gene expression signature. Our findings contribute to the understanding of how TFAM affects melanoma cell metabolism, and they provide new insight into the mechanisms by which TFAM and mtDNA copy number influence melanoma tumorigenesis.