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Michaelsen GL, da Silva LDRE, de Lima DS, Jaeger MDC, Brunetto AT, Dalmolin RJS, Sinigaglia M. A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma. J Mol Neurosci 2024; 74:47. [PMID: 38662144 DOI: 10.1007/s12031-024-02203-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/26/2024]
Abstract
Medulloblastoma (MB) is one of the most common pediatric brain tumors and it is estimated that one-third of patients will not achieve long-term survival. Conventional prognostic parameters have limited and unreliable correlations with MB outcome, presenting a major challenge for patients' clinical improvement. Acknowledging this issue, our aim was to build a gene signature and evaluate its potential as a new prognostic model for patients with the disease. In this study, we used six datasets totaling 1679 samples including RNA gene expression and DNA methylation data from primary MB as well as control samples from healthy cerebellum. We identified methylation-driven genes (MDGs) in MB, genes whose expression is correlated with their methylation. We employed LASSO regression, incorporating the MDGs as a parameter to develop the prognostic model. Through this approach, we derived a two-gene signature (GS-2) of candidate prognostic biomarkers for MB (CEMIP and NCBP3). Using a risk score model, we confirmed the GS-2 impact on overall survival (OS) with Kaplan-Meier analysis. We evaluated its robustness and accuracy with receiver operating characteristic curves predicting OS at 1, 3, and 5 years in multiple independent datasets. The GS-2 showed highly significant results as an independent prognostic biomarker compared to traditional MB markers. The methylation-regulated GS-2 risk score model can effectively classify patients with MB into high and low-risk, reinforcing the importance of this epigenetic modification in the disease. Such genes stand out as promising prognostic biomarkers with potential application for MB treatment.
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Affiliation(s)
- Gustavo Lovatto Michaelsen
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - Lívia Dos Reis Edinger da Silva
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Federal University of Health Sciences of Porto Alegre, Porto Alegre, 90050-170, RS, Brazil
| | - Douglas Silva de Lima
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, RS, Brazil
| | - Mariane da Cunha Jaeger
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - André Tesainer Brunetto
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, 59064-741, RN, Brazil
| | - Marialva Sinigaglia
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil.
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil.
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil.
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2
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Laschuk Herlinger A, Lovatto Michaelsen G, Sinigaglia M, Fratini L, Nogueira Debom G, Braganhol E, Brunetto de Farias C, Lunardi Brunetto A, Tesainer Brunetto A, da Cunha Jaeger M, Roesler R. Modulation of Viability, Proliferation, and Stemness by Rosmarinic Acid in Medulloblastoma Cells: Involvement of HDACs and EGFR. Neuromolecular Med 2023; 25:573-585. [PMID: 37740824 DOI: 10.1007/s12017-023-08758-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Medulloblastoma (MB) is a heterogeneous group of malignant pediatric brain tumors, divided into molecular groups with distinct biological features and prognoses. Currently available therapy often results in poor long-term quality of life for patients, which will be afflicted by neurological, neuropsychiatric, and emotional sequelae. Identifying novel therapeutic agents capable of targeting the tumors without jeopardizing patients' quality of life is imperative. Rosmarinic acid (RA) is a plant-derived compound whose action against a series of diseases including cancer has been investigated, with no side effects reported so far. Previous studies have not examined whether RA has effects in MB. Here, we show RA is cytotoxic against human Daoy (IC50 = 168 μM) and D283 (IC50 = 334 μM) MB cells. Exposure to RA for 48 h reduced histone deacetylase 1 (HDAC1) expression while increasing H3K9 hyperacetylation, reduced epidermal growth factor (EGFR) expression, and inhibited EGFR downstream targets extracellular-regulated kinase (ERK)1/2 and AKT in Daoy cells. These modifications were accompanied by increased expression of CDKN1A/p21, reduced expression of SOX2, and a decrease in proliferative rate. Treatment with RA also reduced cancer stem cell markers expression and neurosphere size. Taken together, our findings indicate that RA can reduce cell proliferation and stemness and induce cell cycle arrest in MB cells. Mechanisms mediating these effects may include targeting HDAC1, EGFR, and ERK signaling, and promoting p21 expression, possibly through an increase in H3K9ac and AKT deactivation. RA should be further investigated as a potential anticancer agent in experimental MB.
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Affiliation(s)
- Alice Laschuk Herlinger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil.
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil.
| | - Gustavo Lovatto Michaelsen
- Graduate Program in Bioinformatics, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, RN, 59078-400, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Marialva Sinigaglia
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil
- Graduate Program in Bioinformatics, Digital Metropolis Institute, Federal University of Rio Grande do Norte, Natal, RN, 59078-400, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Lívia Fratini
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
| | - Gabriela Nogueira Debom
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, 90050-170, Brazil
| | - Elizandra Braganhol
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, 90050-170, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Algemir Lunardi Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - André Tesainer Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Mariane da Cunha Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil.
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS, 90035-003, Brazil.
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil.
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3
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Silveira DA, Gupta S, da Cunha Jaeger M, Brunetto de Farias C, Mombach JCM, Sinigaglia M. A logical model of Ewing sarcoma cell epithelial-to-mesenchymal transition supports the existence of hybrid cellular phenotypes. FEBS Lett 2023; 597:2446-2460. [PMID: 37597508 DOI: 10.1002/1873-3468.14724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023]
Abstract
Ewing sarcoma (ES) is a highly aggressive pediatric tumor driven by the RNA-binding protein EWS (EWS)/friend leukemia integration 1 transcription factor (FLI1) chimeric transcription factor, which is involved in epithelial-mesenchymal transition (EMT). EMT stabilizes a hybrid cell state, boosting metastatic potential and drug resistance. Nevertheless, the mechanisms underlying the maintenance of this hybrid phenotype in ES remain elusive. Our study proposes a logical EMT model for ES, highlighting zinc finger E-box-binding homeobox 2 (ZEB2), miR-145, and miR-200 circuits that maintain hybrid states. The model aligns with experimental findings and reveals a previously unknown circuit supporting the mesenchymal phenotype. These insights emphasize the role of ZEB2 in the maintenance of the hybrid state in ES.
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Affiliation(s)
- Daner A Silveira
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | | | - Mariane da Cunha Jaeger
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | - Caroline Brunetto de Farias
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
| | | | - Marialva Sinigaglia
- Children's Cancer Institute, Porto Alegre, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, Brazil
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4
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Andreis TF, de Souza KIW, Vieira IA, Alemar B, Sinigaglia M, de Araújo Rocha YM, Artigalás O, Bittar C, Oliveira Netto CB, Ashton-Prolla P, Rosset C. Challenges in periodic revision of genetic testing results: Comparison of the main classification guidelines and report of a retrospective analysis involving BRCA1/BRCA2 variants of uncertain significance. Gene 2023; 862:147281. [PMID: 36775216 DOI: 10.1016/j.gene.2023.147281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
In the context of cancer predisposition syndromes, it is widely known that the correct interpretation of germline variants identified in multigene panel testing is essential for adequate genetic counseling and clinical decision making, in which variants of uncertain significance (VUS) are not considered actionable findings. Thus, their periodic re-evaluation using appropriate guidelines is notably important. In the present study, we compared the performance of the main variant classification guidelines (ACMG, Sherloc and ENIGMA) in variant reassessment, using as input a BRCA1/2 VUS case series (retrospective analysis) from Brazil, an ethnically diverse and admixed country with substantial challenges in VUS reclassification. As main findings, two of the 15 VUS analyzed were reclassified as likely pathogenic by the 3 guidelines, BRCA1 c.4987-3C > G (rs397509213) and BRCA2 c.7868A > G (rs80359012). Moreover, challenges in variant classification and reassessment are described and additional in silico data about structural impact of the variant BRCA2 c.7868A > G are provided. We hypothesize that the establishment of a framework to reassess VUS could improve this process in health centers that have not yet implemented this practice. Results of this study underscore that periodic monitoring of the functional, clinical, and bioinformatics data of a VUS by a multidisciplinary team are of utmost importance in clinical practice. When there is a specific guideline for a given gene, such as ENIGMA for BRCA1/2, it should be considered the first option for variant assessment. Finally, recruitment of VUS carriers and their relatives to participate in variant segregation studies and publication of VUS reclassification results in the international scientific literature should be encouraged.
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Affiliation(s)
- Tiago Finger Andreis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Kayana Isabel Weber de Souza
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Igor Araujo Vieira
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Escola de Saúde, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Rio Grande do Sul, Brazil
| | - Bárbara Alemar
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Yasminne Marinho de Araújo Rocha
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Osvaldo Artigalás
- Hospital Moinhos de Vento (HMV), Porto Alegre, Rio Grande do Sul, Brazil
| | - Camila Bittar
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Hospital Moinhos de Vento (HMV), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Unidade de Pesquisa Laboratorial (UPL) - Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil.
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5
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Fratini L, Dalmolin MGS, Sinigaglia M, da Silveira Perla A, de Farias CB, Brunetto AL, Brunetto AT, da Cunha Jaeger M, Roesler R. ZEB1 is a Subgroup-Specific Marker of Prognosis and Potential Drug Target in Medulloblastoma. Neuromolecular Med 2023; 25:64-74. [PMID: 35716340 DOI: 10.1007/s12017-022-08716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Medulloblastoma (MB) is a malignant brain tumor that afflicts mostly children and adolescents and presents four distinct molecular subgroups, known as WNT, SHH, Group 3, and Group 4. ZEB1 is a transcription factor that promotes the expression of mesenchymal markers while restraining expression of epithelial and polarity genes. Because of ZEB1 involvement in cerebellum development, here we investigated the role of ZEB1 in MB. We found increased expression of ZEB1 in MB tumor samples compared to normal cerebellar tissue. Expression was higher in the SHH subgroup when compared to all other MB molecular subgroups. High ZEB1 expression was associated with poor prognosis in Group 3 and Group 4, whereas in patients with WNT tumors poorer prognosis were related to lower ZEB1 expression. There was a moderate correlation between ZEB1 and MYC expression in Group 3 and Group 4 MB. Treatment with the immunomodulator and histone deacetylase (HDAC) inhibitor fingolimod (FTY720) reduced ZEB1 expression specifically in D283 cells, which are representative of Group 3 and Group 4 MB. These findings reveal novel subgroup-specific associations of ZEB1 expression with survival in patients with MB and suggest that ZEB1 expression can be reduced by pharmacological agents that target HDAC activity.
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Affiliation(s)
- Livia Fratini
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil.
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90050-170, Brazil.
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil.
| | - Matheus Gibeke Siqueira Dalmolin
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Marialva Sinigaglia
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Alexandre da Silveira Perla
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90050-170, Brazil
- Neurology Service, São José Hospital, Santa Casa de Misericórdia Porto Alegre Hospital Complex, Porto Alegre, RS, 90020-090, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Algemir L Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - André T Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Mariane da Cunha Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
- Children's Cancer Institute, Porto Alegre, RS, 90620-110, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil.
- Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90050-170, Brazil.
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil.
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6
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Silveira DA, Gupta S, Sinigaglia M, Mombach JCM. The Wnt pathway can stabilize hybrid phenotypes in the epithelial-mesenchymal transition: A logical modeling approach. Comput Biol Chem 2022; 99:107714. [PMID: 35763962 DOI: 10.1016/j.compbiolchem.2022.107714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
The Wnt pathway is important to regulate a variety of biochemical functions and can contribute to cancer development through its influence on the epithelial-mesenchymal transition (EMT). Multiple circuits have been reported to participate in the regulation of the Wnt signaling, however, the way these circuits coordinately regulate this signaling is still unclear. Moreover, the mechanisms responsible for the appearance of hybrid phenotypes (cells presenting both E and M features) are not well determined. The hybrid phenotype can present much higher metastatic potential than the mesenchymal phenotype. In this study, we propose a Boolean model of the Wnt pathway signaling contemplating recent published biochemical information on hepatocarcinoma. The model presents good coherence with experimental data for perturbed and wild-type cases. With the model, we propose two new molecular circuits involving several molecules that can stabilize hybrid states during the EMT. Moreover, we found that the two well studied circuits, AKT1/β-catenin and SNAIL1/miR-34, can cooperate with the predicted ones to favor the stabilization of the hybrid states. These findings highlight some possible unrecognized mechanisms during Wnt signaling and may provide alternative therapeutic strategies to control cancer metastatization.
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Affiliation(s)
- Daner Acunha Silveira
- Department of Physics, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil; Children's Cancer Institute, Porto Alegre, Rio Grande do Sul, Brazil
| | - Shantanu Gupta
- Department of Physics, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
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7
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Mikail N, Sinigaglia M, Kefti C, Meseguer E, Guidoux C, Cabrejo L, Chequer R, Lavallee P, Le Guludec D, Feldman LJ, Amarenco P, Hyafil F. P305Value of aortic TBR measured on FDG-PET for the prediction of atherothrombotic events in a cohort of patients with overt coronary and carotid atherosclerotic disease. Eur Heart J Cardiovasc Imaging 2019. [DOI: 10.1093/ehjci/jez148.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- N Mikail
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
| | - M Sinigaglia
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
| | - C Kefti
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
| | - E Meseguer
- Hospital Bichat-Claude Bernard, Neurology, Paris, France
| | - C Guidoux
- Hospital Bichat-Claude Bernard, Neurology, Paris, France
| | - L Cabrejo
- Hospital Bichat-Claude Bernard, Neurology, Paris, France
| | - R Chequer
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
| | - P Lavallee
- Hospital Bichat-Claude Bernard, Neurology, Paris, France
| | - D Le Guludec
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
| | - L J Feldman
- Hospital Bichat-Claude Bernard, Cardiology, Paris, France
| | - P Amarenco
- Hospital Bichat-Claude Bernard, Neurology, Paris, France
| | - F Hyafil
- AP-HP Hopital Bichat-Claude Bernard, Department of Nuclear Medicine, Paris, France
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8
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Horbach L, Sinigaglia M, Da Silva CA, Olguins DB, Gregianin LJ, Brunetto AL, Brunetto AT, Roesler R, De Farias CB. Gene expression changes associated with chemotherapy resistance in Ewing sarcoma cells. Mol Clin Oncol 2018; 8:719-724. [PMID: 29844902 PMCID: PMC5958871 DOI: 10.3892/mco.2018.1608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/13/2018] [Indexed: 12/17/2022] Open
Abstract
Ewing Sarcoma (ES) is a highly aggressive bone and soft tissue childhood cancer. The development of resistance to chemotherapy is common and remains the main cause of treatment failure. We herein evaluated the expression of genes associated with chemotherapy resistance in ES cell lines. A set of genes (CCAR1, TUBA1A, POLDIP2, SMARCA4 and SMARCB1) was data-mined for resistance against doxorubicin and vincristine, which are the standard drugs used in the treatment of patients with ES. The expression of each gene in SK-ES-1 ES cells was reported before and after exposure to a drug resistance-inducing protocol. There was a significant downregulation of CCAR1 and TUBA1A in doxorubicin-resistant cells, with low expression of TUBA1A in vincristine-resistant cells. By contrast, POLDIP2 was significantly upregulated in cells resistant to either drug, and the expression of the SMARCB1 and SMARCA4 genes was upregulated in doxorubicin-resistant cells. These findings indicate that resistance to specific chemotherapeutic agents was accompanied by differential changes in gene expression in ES tumors.
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Affiliation(s)
- Leonardo Horbach
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil
| | | | - Camila Alves Da Silva
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil
| | - Danielly Brufatto Olguins
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil
| | - Lauro José Gregianin
- Pediatric Oncology Service, Clinical Hospital, Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil.,Department of Pediatrics, Faculty of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil
| | | | - André Tesainer Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil.,Children's Cancer Institute (ICI), Porto Alegre, RS 90620-110, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS 9005-170, Brazil
| | - Caroline Brunetto De Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil.,Children's Cancer Institute (ICI), Porto Alegre, RS 90620-110, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS 9005-170, Brazil
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9
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Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF. Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. Front Immunol 2017; 8:1210. [PMID: 29046675 PMCID: PMC5632759 DOI: 10.3389/fimmu.2017.01210] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Immunotherapy has become one of the most promising avenues for cancer treatment, making use of the patient’s own immune system to eliminate cancer cells. Clinical trials with T-cell-based immunotherapies have shown dramatic tumor regressions, being effective in multiple cancer types and for many different patients. Unfortunately, this progress was tempered by reports of serious (even fatal) side effects. Such therapies rely on the use of cytotoxic T-cell lymphocytes, an essential part of the adaptive immune system. Cytotoxic T-cells are regularly involved in surveillance and are capable of both eliminating diseased cells and generating protective immunological memory. The specificity of a given T-cell is determined through the structural interaction between the T-cell receptor (TCR) and a peptide-loaded major histocompatibility complex (MHC); i.e., an intracellular peptide–ligand displayed at the cell surface by an MHC molecule. However, a given TCR can recognize different peptide–MHC (pMHC) complexes, which can sometimes trigger an unwanted response that is referred to as T-cell cross-reactivity. This has become a major safety issue in TCR-based immunotherapies, following reports of melanoma-specific T-cells causing cytotoxic damage to healthy tissues (e.g., heart and nervous system). T-cell cross-reactivity has been extensively studied in the context of viral immunology and tissue transplantation. Growing evidence suggests that it is largely driven by structural similarities of seemingly unrelated pMHC complexes. Here, we review recent reports about the existence of pMHC “hot-spots” for cross-reactivity and propose the existence of a TCR interaction profile (i.e., a refinement of a more general TCR footprint in which some amino acid residues are more important than others in triggering T-cell cross-reactivity). We also make use of available structural data and pMHC models to interpret previously reported cross-reactivity patterns among virus-derived peptides. Our study provides further evidence that structural analyses of pMHC complexes can be used to assess the intrinsic likelihood of cross-reactivity among peptide-targets. Furthermore, we hypothesize that some apparent inconsistencies in reported cross-reactivities, such as a preferential directionality, might also be driven by particular structural features of the targeted pMHC complex. Finally, we explain why TCR-based immunotherapy provides a special context in which meaningful T-cell cross-reactivity predictions can be made.
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Affiliation(s)
- Dinler A Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Maurício M Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Imunologia Celular e Molecular, Instituto de Pesquisas Biomédicas (IPB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Martiela V Freitas
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcus F A Mendes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gregory Lizée
- Lizée Lab, Department of Melanoma Medical Oncology - Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - Lydia E Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Liisa K Selin
- Selin Lab, Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Markus Cornberg
- Cornberg Lab, Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), Partner-Site Hannover-Braunschweig, Hannover, Germany
| | - Gustavo F Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Porto Alegre, Brazil
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10
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Arevalo‐Villena M, Briones‐Perez A, Corbo M, Sinigaglia M, Bevilacqua A. Biotechnological application of yeasts in food science: Starter cultures, probiotics and enzyme production. J Appl Microbiol 2017; 123:1360-1372. [DOI: 10.1111/jam.13548] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/22/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022]
Affiliation(s)
- M. Arevalo‐Villena
- Ciencia Y Tecnologia de Alimentos Castilla La Mancha University Ciudad Real Spain
| | - A. Briones‐Perez
- Ciencia Y Tecnologia de Alimentos Castilla La Mancha University Ciudad Real Spain
| | - M.R. Corbo
- Department of the Science of Agriculture Food and Environment University of Foggia Foggia Italy
| | - M. Sinigaglia
- Department of the Science of Agriculture Food and Environment University of Foggia Foggia Italy
| | - A. Bevilacqua
- Department of the Science of Agriculture Food and Environment University of Foggia Foggia Italy
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11
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Vieira GC, Vieira GF, Sinigaglia M, da Silva Valente VL. Linking epigenetic function to electrostatics: The DNMT2 structural model example. PLoS One 2017; 12:e0178643. [PMID: 28575027 PMCID: PMC5456315 DOI: 10.1371/journal.pone.0178643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 11/25/2022] Open
Abstract
The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- * E-mail:
| | - Gustavo Fioravanti Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marialva Sinigaglia
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Instituto do Câncer Infantil, Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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12
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Landriscina L, D'Agnello P, Bevilacqua A, Corbo M, Sinigaglia M, Lamacchia C. Impact of gluten-friendly™ technology on wheat kernel endosperm and gluten protein structure in seeds by light and electron microscopy. Food Chem 2017; 221:1258-1268. [DOI: 10.1016/j.foodchem.2016.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/13/2016] [Accepted: 11/07/2016] [Indexed: 01/19/2023]
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13
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Hardy J, Sinigaglia M, Aziza R, Zerdoud S, Boulinguez S, Sibaud V, Paul C, Meyer N. Critères prédictifs de la réponse à l’ipilimumab : une place pour l’interféron ? Ann Dermatol Venereol 2016. [DOI: 10.1016/j.annder.2016.09.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Sinigaglia M, Benouaich Amiel A, Salabert AS, Aziz AL, Payoux P. Efficacité diagnostique et pronostique de la 18F-FET TEP/TDM dans la prise en charge des gliomes hémisphériques de l’adulte classés bas grade à l’IRM initiale. Médecine Nucléaire 2016. [DOI: 10.1016/j.mednuc.2016.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Figueiredo DF, Antunes DA, Rigo MM, Mendes MF, Silva JP, Mayer FQ, Matte U, Giugliani R, Vieira GF, Sinigaglia M. Lessons from molecular modeling human α-l-iduronidase. J Mol Graph Model 2014; 54:107-13. [DOI: 10.1016/j.jmgm.2014.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/12/2014] [Accepted: 10/08/2014] [Indexed: 01/11/2023]
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16
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Antunes DA, Rigo MM, Sinigaglia M, de Medeiros RM, Junqueira DM, Almeida SEM, Vieira GF. New insights into the in silico prediction of HIV protease resistance to nelfinavir. PLoS One 2014; 9:e87520. [PMID: 24498124 PMCID: PMC3909182 DOI: 10.1371/journal.pone.0087520] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/22/2013] [Indexed: 11/24/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 protease enzyme (HIV-1 PR) is one of the most important targets of antiretroviral therapy used in the treatment of AIDS patients. The success of protease-inhibitors (PIs), however, is often limited by the emergence of protease mutations that can confer resistance to a specific drug, or even to multiple PIs. In the present study, we used bioinformatics tools to evaluate the impact of the unusual mutations D30V and V32E over the dynamics of the PR-Nelfinavir complex, considering that codons involved in these mutations were previously related to major drug resistance to Nelfinavir. Both studied mutations presented structural features that indicate resistance to Nelfinavir, each one with a different impact over the interaction with the drug. The D30V mutation triggered a subtle change in the PR structure, which was also observed for the well-known Nelfinavir resistance mutation D30N, while the V32E exchange presented a much more dramatic impact over the PR flap dynamics. Moreover, our in silico approach was also able to describe different binding modes of the drug when bound to different proteases, identifying specific features of HIV-1 subtype B and subtype C proteases.
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Affiliation(s)
- Dinler A. Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Departamento de Genética, Universidade Federal do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Maurício M. Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Departamento de Genética, Universidade Federal do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Departamento de Genética, Universidade Federal do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Rúbia M. de Medeiros
- Technological and Scientific Development Center (CDCT), State Foundation in Production and Health Research (FEPPS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Dennis M. Junqueira
- Technological and Scientific Development Center (CDCT), State Foundation in Production and Health Research (FEPPS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Sabrina E. M. Almeida
- Technological and Scientific Development Center (CDCT), State Foundation in Production and Health Research (FEPPS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gustavo F. Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Departamento de Genética, Universidade Federal do Rio Grande do Sul. Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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17
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Petruzzi L, Bevilacqua A, Baiano A, Beneduce L, Corbo MR, Sinigaglia M. In vitro removal of ochratoxin A by two strains of Saccharomyces cerevisiae and their performances under fermentative and stressing conditions. J Appl Microbiol 2013; 116:60-70. [PMID: 24112596 DOI: 10.1111/jam.12350] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this research was to study the effect of time, temperature, sugar content and addition of diammonium phosphate (DAP) on ochratoxin A (OTA) removal by two strains of Saccharomyces cerevisiae using a completely randomized design. METHODS AND RESULTS The strains were grown in a medium containing OTA (2 μg l(-1)), two sugar levels (200 and 250 g l(-1)), with or without DAP (300 mg l(-1)), and incubated at 25-30°C. The yeasts were able to decrease the toxin amount by c. 70%, with the highest removing effect observed after 3 days at 30°C in the presence of 250 g l(-1) of sugars and with DAP; after 10 days, the toxin was partially released into the medium. The strains produced high ethanol and glycerol contents, showed high tolerance to single/combined stress conditions and possessed β-d-glucosidase, pectinase and xylanase activities. CONCLUSIONS Ochratoxin A removal was affected by time, temperature, sugar and addition of DAP. Moreover, the phenomenon was reversible. SIGNIFICANCE AND IMPACT OF THE STUDY Ochratoxin A removal could be an interesting trait for the selection of promising strains; however, the strains removing efficiently the toxin could release it back; thus, the selection of the starter should take into account both the removal and the binding ability of OTA.
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Affiliation(s)
- L Petruzzi
- Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, Foggia, Italy
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18
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Rosset C, Vieira IA, Sinigaglia M, Gorziza RP, Salzano FM, Bandinelli E. Detection of new mutations and molecular pathology of mild and moderate haemophilia A patients from southern Brazil. Haemophilia 2013; 19:773-81. [DOI: 10.1111/hae.12172] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2013] [Indexed: 01/17/2023]
Affiliation(s)
- C. Rosset
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
| | - I. A. Vieira
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
| | - M. Sinigaglia
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
| | - R. P. Gorziza
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
| | - F. M. Salzano
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
| | - E. Bandinelli
- Genetics Department; Biosciences Institute; Federal University of Rio Grande do Sul; Porto Alegre; RS; Brazil
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19
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Sinigaglia M, Antunes DA, Rigo MM, Chies JAB, Vieira GF. CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes. Database (Oxford) 2013; 2013:bat002. [PMID: 23396301 PMCID: PMC3567486 DOI: 10.1093/database/bat002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The CrossTope is a highly curate repository of three-dimensional structures of peptide:major histocompatibility complex (MHC) class I complexes (pMHC-I). The complexes hosted by this databank were obtained in protein databases and by large-scale in silico construction of pMHC-I structures, using a new approach developed by our group. At this moment, the database contains 182 ‘non-redundant’ pMHC-I complexes from two human and two murine alleles. A web server provides interface for database query. The user can download (i) structure coordinate files and (ii) topological and charges distribution maps images from the T-cell receptor-interacting surface of pMHC-I complexes. The retrieved structures and maps can be used to cluster similar epitopes in cross-reactivity approaches, to analyse viral escape mutations in a structural level or even to improve the immunogenicity of tumour antigens. Database URL: http://www.crosstope.com.br
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Affiliation(s)
- Marialva Sinigaglia
- NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Universidade Federal do Rio Grande do Sul, 9500 Bento Gonçalves Avenue, Bldg 43323, Rm 225, 91501-970 Porto Alegre, RS, Brazil
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20
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Rigo MM, Antunes DA, Cibulski SP, Sinigaglia M, Chies JAB, Vieira GF. Immunogenic epitopes of Hantaviruses' N protein are restricted to conserved regions. Front Biosci (Landmark Ed) 2012; 17:1582-8. [PMID: 22201821 DOI: 10.2741/4004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Bunyaviridae virus family is composed by five genera, of which the Hantavirus genus is one of the most important representatives. Occasionally, these viruses can be transmitted to humans, giving rise to severe diseases that present high mortality rates. We analyzed the amino acid sequences of the nucleocapsid (N) proteins of 34 different hantaviruses to investigate the potential mechanisms involved in immunogenicity against hantaviruses. Immunogenic epitopes described in the literature through experimental analyses for Sin Nombre (SNV), Puumala (PUUV), and Hantaan (HTNV) viruses' species were retrieved. We identified and characterized the regions believed to be responsible for the induction of immune response in hosts. We found that N protein epitopes described in the literature for PUUV, SNV and HTNV viruses are all located in highly conserved regions of the protein. The high conservation of these regions suggests that a cross-reactive immune response among different hantaviruses can be induced.
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Affiliation(s)
- Mauricio Menegatti Rigo
- Nucleo de Bioinformatica do Laboratorio de Imunogenetica, Departamento de Genetica, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves, 9500 - Predio 43323, Porto Alegre, RS, Brasil
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21
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Simão ÉM, Sinigaglia M, Bugs CA, Castro MAA, Librelotto GR, Alves R, Mombach JCM. Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development. Mol BioSyst 2012; 8:3003-9. [DOI: 10.1039/c2mb25242b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF. Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele. Mol Immunol 2011; 48:1461-7. [DOI: 10.1016/j.molimm.2011.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/15/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
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23
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Antunes DA, Vieira GF, Rigo MM, Cibulski SP, Sinigaglia M, Chies JAB. Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment. PLoS One 2010; 5:e10353. [PMID: 20442757 PMCID: PMC2860844 DOI: 10.1371/journal.pone.0010353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 03/28/2010] [Indexed: 11/19/2022] Open
Abstract
The immune system is engaged in a constant antigenic surveillance through the Major Histocompatibility Complex (MHC) class I antigen presentation pathway. This is an efficient mechanism for detection of intracellular infections, especially viral ones. In this work we describe conformational patterns shared by epitopes presented by a given MHC allele and use these features to develop a docking approach that simulates the peptide loading into the MHC cleft. Our strategy, to construct in silico MHC:peptide complexes, was successfully tested by reproducing four different crystal structures of MHC-I molecules available at the Protein Data Bank (PDB). An in silico study of cross-reactivity potential was also performed between the wild-type complex HLA-A2-NS31073 and nine MHC:peptide complexes presenting alanine exchange peptides. This indicates that structural similarities among the complexes can give us important clues about cross reactivity. The approach used in this work allows the selection of epitopes with potential to induce cross-reactive immune responses, providing useful tools for studies in autoimmunity and to the development of more comprehensive vaccines.
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Affiliation(s)
- Dinler A. Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - Gustavo F. Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - Maurício M. Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - Samuel P. Cibulski
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - José A. B. Chies
- Núcleo de Bioinformática do Laboratório de Imunogenética, Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
- * E-mail:
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Speranza B, Bevilacqua A, Mastromatteo M, Sinigaglia M, Corbo M. Modelling the interactions between
Pseudomonas putida
and
Escherichia coli
O157:H7 in fish‐burgers: use of the lag‐exponential model and of a combined interaction index. J Appl Microbiol 2010; 109:667-678. [DOI: 10.1111/j.1365-2672.2010.04692.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. Speranza
- Department of Food Science, Faculty of Agricultural Science, University of Foggia, via Napoli 25, 71100, Foggia, Italy
| | - A. Bevilacqua
- Department of Food Science, Faculty of Agricultural Science, University of Foggia, via Napoli 25, 71100, Foggia, Italy
- Istituto per la Ricerca e le Applicazioni Biotecnologiche per la Sicurezza e la Valorizzazione dei Prodotti Tipici e di Qualità (BIOAGROMED), University of Foggia, via Napoli 25, 71100, Foggia, Italy
| | - M. Mastromatteo
- Department of Food Science, Faculty of Agricultural Science, University of Foggia, via Napoli 25, 71100, Foggia, Italy
| | - M. Sinigaglia
- Department of Food Science, Faculty of Agricultural Science, University of Foggia, via Napoli 25, 71100, Foggia, Italy
- Istituto per la Ricerca e le Applicazioni Biotecnologiche per la Sicurezza e la Valorizzazione dei Prodotti Tipici e di Qualità (BIOAGROMED), University of Foggia, via Napoli 25, 71100, Foggia, Italy
| | - M.R. Corbo
- Department of Food Science, Faculty of Agricultural Science, University of Foggia, via Napoli 25, 71100, Foggia, Italy
- Istituto per la Ricerca e le Applicazioni Biotecnologiche per la Sicurezza e la Valorizzazione dei Prodotti Tipici e di Qualità (BIOAGROMED), University of Foggia, via Napoli 25, 71100, Foggia, Italy
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Speranza B, Corbo M, Conte A, Sinigaglia M, Del Nobile M. Microbiological and Sensorial Quality Assessment of Ready-to-Cook Seafood Products Packaged under Modified Atmosphere. J Food Sci 2009; 74:M473-8. [DOI: 10.1111/j.1750-3841.2009.01369.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Del Nobile M, Di Benedetto N, Suriano N, Conte A, Corbo M, Sinigaglia M. Combined effects of chitosan and MAP to improve the microbial quality of amaranth homemade fresh pasta. Food Microbiol 2009; 26:587-91. [DOI: 10.1016/j.fm.2009.03.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 03/27/2009] [Accepted: 03/28/2009] [Indexed: 10/20/2022]
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27
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Castro MAA, Filho JLR, Dalmolin RJS, Sinigaglia M, Moreira JCF, Mombach JCM, de Almeida RMC. ViaComplex: software for landscape analysis of gene expression networks in genomic context. ACTA ACUST UNITED AC 2009; 25:1468-9. [PMID: 19369498 DOI: 10.1093/bioinformatics/btp246] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm. AVAILABILITY (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex).
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Affiliation(s)
- Mauro A A Castro
- Unidade de Bioinformática, Departamento de Bioquímica, Instituto de Física, Núcleo de Bioinformática, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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28
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Del Nobile M, Di Benedetto N, Suriano N, Conte A, Lamacchia C, Corbo M, Sinigaglia M. Use of natural compounds to improve the microbial stability of Amaranth-based homemade fresh pasta. Food Microbiol 2009; 26:151-6. [DOI: 10.1016/j.fm.2008.10.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 09/26/2008] [Accepted: 10/09/2008] [Indexed: 11/24/2022]
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29
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Bevilacqua A, Costa C, Corbo M, Sinigaglia M. Effects of the high pressure of homogenization on some spoiling micro-organisms, representative of fruit juice microflora, inoculated in saline solution. Lett Appl Microbiol 2009; 48:261-7. [DOI: 10.1111/j.1472-765x.2008.02527.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Cechin AL, Sinigaglia M, Mombach JC, Echeverrigaray S, Lemke N, Cabrera OG, Pereira GA, Javier Medrano F. Can Nep1-like proteins form oligomers? Plant Signal Behav 2008; 3:906-7. [PMID: 19704537 PMCID: PMC2634412 DOI: 10.4161/psb.3.10.6643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 07/21/2008] [Indexed: 05/11/2023]
Abstract
Nep1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis that induce a hypersensitive-like response in dicot plants. The spatial structure and role of these proteins are yet unknown. In a paper published in BMC Plant Biology (2008; 8:50) we have proposed that the core region of Nep1-like proteins (NLPs) belong to the Cupin superfamily. Based on what is known about the Cupin superfamily, in this addendum to the paper we discuss how NLPs could form oligomers.
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Affiliation(s)
- Adelmo L Cechin
- Programa de Pós-Graduação em Computação Aplicada; Unisinos, São Leopoldo Brasil
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31
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Corbo M, Speranza B, Filippone A, Granatiero S, Conte A, Sinigaglia M, Del Nobile M. Study on the synergic effect of natural compounds on the microbial quality decay of packed fish hamburger. Int J Food Microbiol 2008; 127:261-7. [DOI: 10.1016/j.ijfoodmicro.2008.07.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/08/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
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32
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Cibelli F, Ciccarone C, Altieri C, Bevilacqua A, Sinigaglia M. Proteolytic activity of molds and their metabiotic association with Salmonella in a model system. J Food Prot 2008; 71:2129-32. [PMID: 18939766 DOI: 10.4315/0362-028x-71.10.2129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this study was to investigate the proteolytic ability of some strains of aspergilli, fusaria, and penicillia and the metabiotic effect of Fusarium oxysporum and Penicillium expansum on Salmonella. The proteolytic activity of the target molds was determined on tomato juice agar and tomato juice, whereas the metabiotic effect of F. oxysporum and P. expansum on Salmonella was assessed in a model system consisting of tryptone soy broth with different amounts of tomato juice added. Fusaria, some aspergilli, and one strain of penicillium showed a proteolytic activity on tomato juice agar. In addition, Salmonella survival was enhanced in tryptone soy broth plus 20 or 50% tomato juice in the model system previously inoculated with F. oxysporum.
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Affiliation(s)
- F Cibelli
- Department of Agro-Environmental Sciences, Chemistry and Crop Protection, Faculty of Agricultural Science, Foggia University, Italy
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33
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Cechin AL, Sinigaglia M, Lemke N, Echeverrigaray S, Cabrera OG, Pereira GAG, Mombach JCM. Cupin: a candidate molecular structure for the Nep1-like protein family. BMC Plant Biol 2008; 8:50. [PMID: 18447914 PMCID: PMC2396628 DOI: 10.1186/1471-2229-8-50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 04/30/2008] [Indexed: 05/10/2023]
Abstract
BACKGROUND NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known. RESULTS We predict a 3d-structure for the beta-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position. CONCLUSION We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the 3d-structure, we are proposing some possible functions for the NLPs.
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Affiliation(s)
- Adelmo L Cechin
- Programa de Pós-Graduação em Computação Aplicada, Unisinos, Av. Unisinos – 950, São Leopoldo, Brasil
| | - Marialva Sinigaglia
- Programa de Pós-Graduação em Computação Aplicada, Unisinos, Av. Unisinos – 950, São Leopoldo, Brasil
| | - Ney Lemke
- Departamento de Física e Biofísica, UNESP, Dist. Rubião Jr. sn, Botucatu, Brasil
| | - Sérgio Echeverrigaray
- Instituto de Biotecnologia, UCS, R. Francisco Getúlio Vargas 1130, Caxias do Sul, Brasil
| | - Odalys G Cabrera
- Departamento de Genética e Evolução, IB/UNICAMP, Campinas, Brasil
| | | | - José CM Mombach
- Centro de Ciências Rurais, UFPampa/UFSM, São Gabriel, Brasil
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36
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Bevilacqua A, Corbo MR, Mastromatteo M, Sinigaglia M. Combined effects of pH, yeast extract, carbohydrates and di-ammonium hydrogen citrate on the biomass production and acidifying ability of a probiotic Lactobacillus plantarum strain, isolated from table olives, in a batch system. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9666-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Conte A, Buonocore GG, Sinigaglia M, Lopez LC, Favia P, d'Agostino R, Del Nobile MA. Antimicrobial activity of immobilized lysozyme on plasma-treated polyethylene films. J Food Prot 2008; 71:119-25. [PMID: 18236671 DOI: 10.4315/0362-028x-71.1.119] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study we tested the antimicrobial activity of polyethylene films modified by means of plasma processes that were followed by the chemical immobilization of lysozyme, an antimicrobial enzyme. To chemically immobilize the enzyme in its active form at the surface of polyethylene, substrates that had been plasma treated under different experimental conditions were soaked in lysozyme solutions at different concentrations. The immobilization of the enzyme was checked, and the antimicrobial activity of the films was investigated by observing the death rate of Micrococcus lysodeikticus cells suspended in phosphate buffer in contact with the films. The results clearly indicate that plasma-treated films loaded with lysozyme are active against the selected microorganism. A modified version of the Gompertz equation was used to quantitatively valuate the dependence of the antimicrobial activity of the films under both plasma treatment conditions and lysozyme concentrations.
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Affiliation(s)
- A Conte
- Department of Food Science, University of Foggia, Via Napoli, 25-71100 Foggia, Italy
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38
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Quinto M, Spadaccino G, Rotunno T, Sinigaglia M, Ciccarone C, Fox P. Effects of different surface treatments on ripening of Canestrato Pugliese cheese. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2007.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Bevilacqua A, Cibelli F, Corbo MR, Sinigaglia M. Effects of high-pressure homogenization on the survival of Alicyclobacillus acidoterrestris in a laboratory medium. Lett Appl Microbiol 2007; 45:382-6. [PMID: 17897380 DOI: 10.1111/j.1472-765x.2007.02219.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS This study was aimed to investigate the effectiveness of high-pressure homogenization (HPH) against Alicyclobacillus acidoterrestris. METHODS AND RESULTS The susceptibility of three different strains of A. acidoterrestris (DSMZ 2498, Gamma4 and c8) to HPH (500-1700 bar) was studied. The experiments were performed in a laboratory medium (malt extract broth) on cells and spores. HPH caused a significant reduction of the initial cell number (1-2 log CFU ml(-1) at the highest pressures) in Gamma4 and DSMZ 2498 strains, whereas the effect on the spores was less significant. CONCLUSIONS This study showed that the susceptibility of A. acidoterrestris to HPH was strain-dependent: DSMZ 2498 seemed the most susceptible strain, whereas c8 was the most resistant one. SIGNIFICANCE AND IMPACT OF THE STUDY The results of our study will provide useful information on the sensitivity of an emerging spoilage micro-organism, such as A. acidoterrrestris, to HPH.
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Affiliation(s)
- A Bevilacqua
- Department of Food Science, Faculty of Agricultural Science, Foggia University, Foggia, Italy
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40
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Abstract
A quantitative investigation was conducted on the antimicrobial effect of lemon extract against some food spoilage microorganisms: yeasts, Bacillus species, and lactic acid bacteria. Growth kinetics and dose-response profiles were determined from experimental data obtained with a suitable macrodilution methodology based on a turbidimetric technique. Growth and no-growth status of microbial suspensions were expressed in terms of noninhibitory concentration (NIC) and MIC. Lemon extract was effective in inhibiting the growth of the investigated vegetative cells and spores of microorganisms; effects were similar for bacteria and yeasts. The NICs for all microorganisms were very small, at around 10 ppm. Based on MICs, among the Bacillus species, the more resistant was Bacillus licheniformis. For yeasts, Saccharomyces cerevisiae was the least resistant, and similar results were obtained for Pichia subpelliculosa. Candida lusitaniae had an MIC of more than 100 ppm. Both Lactobacillus species were more resistant to lemon extract; concentrations necessary to provoke complete inhibition were approximately 150 ppm.
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Affiliation(s)
- A Conte
- Department of Food Science, University of Foggia, Via Napoli, 25-71100 Foggia, Italy
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Abstract
In this work the effectiveness of different antimicrobial packaging systems on the microbial quality decay kinetics during storage of Mozzarella cheese was evaluated. Lemon extract, at 3 different concentrations, was used as active agent, in combination with brine and with a gel solution made of sodium alginate. Shelf life tests were run at 15 degrees C to simulate thermal abuse. The cell load of spoilage and dairy functional microorganisms were monitored at regular time intervals during storage. By fitting the experimental data through a modified version of the Gompertz equation, the shelf life of dairy products packaged in the different systems was calculated. Results show an increase in the shelf life of all active packaged Mozzarella cheeses, confirming that the investigated substance may exert an inhibitory effect on the microorganisms responsible for spoilage phenomena without affecting the functional microbiota of the product.
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Affiliation(s)
- A Conte
- Department of Food Science, University of Foggia, Via Napoli, 25-71100 Foggia, Italy
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43
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Furlanetto MP, Sinigaglia M, Amaral VSD, Dihl RR, de Andrade HHR. Effect of vanillin on toxicant-induced lethality in the Drosophila melanogaster DNA repair test. Environ Mol Mutagen 2007; 48:67-70. [PMID: 17177210 DOI: 10.1002/em.20275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Vanillin (VA) modulates the genotoxicity of chemical and physical agents in a complex manner. Previous studies indicate that VA inhibits the mutagenicity but increases the mitotic homologous recombination caused by at least some genotoxic agents. In the present study, we have evaluated the effects of VA on the repair of lethal damage produced by three genotoxins, N-ethyl-N-nitrosourea (ENU), ethyl methanesulfonate (EMS), and mitomycin C (MMC), using the DNA repair test (DRT) in Drosophila melanogaster. VA, 0.25% and 0.5% (w/v), increased the toxicity of MMC and EMS in repair-deficient flies, as measured by a decrease in the proportion of male to female progeny in the DRT; sex ratios decreased from 18-48% for MMC and 21-97% for EMS. These effects may be caused by the inhibition of nonhomologous DNA end joining caused by VA. In contrast to the results with MMC and EMS, VA protected against the lethality of ENU in repair-defective flies, as measured by a 43-207% increase in the survival of male flies in the DRT. It was inferred that the protective effect was due to VA modulating stages prior to the induction of ENU lesions in DNA, including modulating the antioxidant properties of VA and/or to its interference with the metabolic activation and/or detoxification of specific genotoxins. The results from this study indicate that the characterization of VA as a promising agent for preventing damage to genes and chromosomes should be tempered by observations that VA can increase the toxicity of chemical agents.
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Affiliation(s)
- Magda Patrícia Furlanetto
- Laboratório de Diagnóstico da Toxicidade Genética-TOXIGEN, Universidade Luterana, do Brasil-ULBRA, Canoas, Rio Grande do Sul, Brazil
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Abstract
The potential use of lemon extract as a natural preservative to inhibit the growth of Oenococcus oeni and Lactobacillus plantarum, microorganisms involved in the malotactic fermentation of wine, was studied. Growth tests were run at 30 degrees C using laboratory media. Carbon dioxide concentration in the vial headspace was used as metabolic activity index of the investigated microorganisms. The MIC and the noninhibiting concentration (NIC) were calculated for each microorganism. Results suggest that lemon extract was active on each phase of the growth cycle for the tested microorganisms. It was also shown that lemon extract exhibits a nonlinear dose-related inhibitory effect on microbial growth. In particular, the active compound could be added at concentrations slightly higher than the NIC levels in order to appreciably slow down the microbial growth rate as well as to reduce the maximum microbial growth level.
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Affiliation(s)
- A Conte
- Department of Food Science, University of Foggia, Via Napoli, 25-71100 Foggia, Italy
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45
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Sinigaglia M, Lehmann M, Baumgardt P, do Amaral VS, Dihl RR, Reguly ML, de Andrade HHR. Vanillin as a modulator agent in SMART test: Inhibition in the steps that precede N-methyl-N-nitrosourea-, N-ethyl-N-nitrosourea-, ethylmethanesulphonate- and bleomycin-genotoxicity. Mutation Research/Genetic Toxicology and Environmental Mutagenesis 2006; 607:225-30. [PMID: 16777474 DOI: 10.1016/j.mrgentox.2006.04.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 04/20/2006] [Accepted: 04/26/2006] [Indexed: 11/20/2022]
Abstract
Vanillin (VA), the world's major flavoring compound used in food industry and confectionery products - that has antimutagenic and anticarcinogenic activity against a variety of mutagenic/carcinogenic agents - was tested for the interval between the formation of premutational lesion and it is finalization as a DNA lesion. The overall findings using co-treatment protocols in SMART test suggest that VA can lead to a significant protection against the general genotoxicity of ethylmethanesulphonate (EMS), N-ethyl-N-nitrosourea (ENU), N-methyl-N-nitrosourea (MNU) and bleomycin sulphate (BLEO). Considering MNU, ENU and EMS the desmutagenic activity observed could result from VA-stimulation of detoxification, via induction of glutathione S-transferase. However, the protector effect related to BLEO could be attributed to its powerful scavenger ability, which has the potential to prevent oxidative damage induced by BLEO.
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Affiliation(s)
- Marialva Sinigaglia
- Laboratório de Mutagênese, Departamento de Genética, Universidade Federal do Rio Grande do Sul, CP 15053, 91501-970 Porto Alegre, RS, Brazil
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46
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Nobile M, Cannarsi M, Altieri C, Sinigaglia M, Favia P, Iacoviello G, D'Agostino R. Effect of Ag-containing Nano-composite Active Packaging System on Survival of Alicyclobacillus acidoterrestris. J Food Sci 2006. [DOI: 10.1111/j.1365-2621.2004.tb09899.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Conte A, Buonocore GG, Bevilacqua A, Sinigaglia M, Del Nobile MA. Immobilization of lysozyme on polyvinylalcohol films for active packaging applications. J Food Prot 2006; 69:866-70. [PMID: 16629031 DOI: 10.4315/0362-028x-69.4.866] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A new technique for the immobilization of lysozyme onto the surface of polyvinylalcohol films is presented. The active compound was sprayed along with a suitable bonding agent onto the surface of the cross-linked polymeric matrix. Active compound release tests determined the amount of lysozyme immobilized on the film surface. With the use of Micrococcus lysodeikticus, the antimicrobial activity of the films was determined and the results correlated with the amount of immobilized lysozyme. This new technique was effective for immobilizing the enzyme, and the developed films were active against the test microorganism. Results were compared with those obtained with a different immobilizing technique, in which the active compound was bound into the bulk of the polymeric film. As expected, the surface-immobilized lysozyme films have a higher antimicrobial activity than bulk-bound films.
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Affiliation(s)
- A Conte
- Department of Food Science, University of Foggia, Italy
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48
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Silva JPMD, Lemke N, Mombach JC, Souza JGCD, Sinigaglia M, Vieira R. Exploring molecular networks using MONET ontology. Genet Mol Res 2006; 5:182-92. [PMID: 16755509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The description of the complex molecular network responsible for cell behavior requires new tools to integrate large quantities of experimental data in the design of biological information systems. These tools could be used in the characterization of these networks and in the formulation of relevant biological hypotheses. The building of an ontology is a crucial step because it integrates in a coherent framework the concepts necessary to accomplish such a task. We present MONET (molecular network), an extensible ontology and an architecture designed to facilitate the integration of data originating from different public databases in a single- and well-documented relational database, that is compatible with MONET formal definition. We also present an example of an application that can easily be implemented using these tools.
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Affiliation(s)
- João Paulo Müller da Silva
- Laboratório de Bioinformática e Biologia Computacional, Universidade do Vale do Rio dos Sinos, Unisinos, 93022-000 São Leopoldo, RS, Brazil
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do Amaral VS, Sinigaglia M, Reguly ML, de Andrade HHR. Genetic toxicity in surface water from Guaíba Hydrographic Region under the influence of industrial, urban and agricultural sewage in the Drosophila wing-spot test. Environ Pollut 2006; 139:469-76. [PMID: 16112782 DOI: 10.1016/j.envpol.2005.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 06/03/2005] [Indexed: 05/04/2023]
Abstract
Mutagenic and recombinagenic activity of surface waters in the Guaíba Hydrographic Region (RS, Brazil) was investigated using the SMART in Drosophila melanogaster. Two positive results in Caí River (September 2000 and August 2001) and in Taquari River (August 2001 and February 2002)--linked to direct recombinagenic toxicants were observed. In Jacuí samples, an indirect mutagenic and recombinagenic action was detected in a September 2000 collection and a direct recombinational activity was observed in February 2002. Also in February 2002--samples from Dilúvio Brook and Guaíba Lake (GPC) were able to induce wing spots by mitotic recombinagenesis. The former sampling site showed toxicants to have a direct action, and the latter an increment in mitotic recombination that depended on metabolic action. The SMART wing test shows that all positive responses were mainly related to homologous mitotic recombination.
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Affiliation(s)
- Viviane Souza do Amaral
- Laboratório de Mutagênese, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Altieri C, Speranza B, Del Nobile MA, Sinigaglia M. Suitability of bifidobacteria and thymol as biopreservatives in extending the shelf life of fresh packed plaice fillets. J Appl Microbiol 2005; 99:1294-302. [PMID: 16313401 DOI: 10.1111/j.1365-2672.2005.02740.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The present study was aimed to evaluate the microbiological and sensory characteristics of biopreserved packed fresh plaice (Pleuronectes platessa), during storage. METHODS AND RESULTS Fish samples were treated with a Bifidobacterium bifidum strain and thymol as preservatives, stored at different temperatures (4 and 12 degrees C) and package atmospheres (in air, under vacuum, modified atmosphere). Data about the total viable count (TVC) were used to predict the shelf life of the fish fillets as affected by the preservatives used and the storage conditions. Data obtained revealed that B. bifidum could perform an efficient synergy with thymol, in controlling the hygiene biological markers. Besides, the tested bifidobacterial species, combined with low storage temperature and anoxia/hypoxia, showed a great efficacy against the main fresh packaged fish spoilage species (Pseudomonas spp., Photobacterium phosphoreum). CONCLUSIONS The studied technique could be considered effective in fresh fish spoilage control. SIGNIFICANCE AND IMPACT OF THE STUDY Great interest is developing on food biopreservation, because of the ever increasing needs to protect consumers' and environment's health, and to revalorize some important food characteristics, such as naturalness and authenticity, without leaving the safety aside.
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Affiliation(s)
- C Altieri
- Department of Food Science, Faculty of Agricultural, Foggia University, Foggia, Italy.
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