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Ravagnani FG, Valerio HP, Maués JHS, de Oliveira AN, Puga RD, Griesi-Oliveira K, Picosse FR, Ferraz HB, Catharino RR, Ronsein GE, de Carvalho Aguiar P. Omics profile of iPSC-derived astrocytes from Progressive Supranuclear Palsy (PSP) patients. Parkinsonism Relat Disord 2023; 116:105847. [PMID: 37844348 DOI: 10.1016/j.parkreldis.2023.105847] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 10/18/2023]
Abstract
INTRODUCTION Progressive Supranuclear Palsy (PSP) is a neurodegenerative tauopathy and, to date, the pathophysiological mechanisms in PSP that lead to Tau hyperphosphorylation and neurodegeneration are not clear. In some brain areas, Tau pathology in glial cells appears to precede Tau aggregation in neurons. The development of a model using astrocyte cell lines derived from patients has the potential to identify molecules and pathways that contribute to early events of neurodegeneration. We developed a model of induced pluripotent stem cells (iPSC)-derived astrocytes to investigate the pathophysiology of PSP, particularly early events that might contribute to Tau hyperphosphorylation, applying omics approach to detect differentially expressed genes, metabolites, and proteins, including those from the secretome. METHODS Skin fibroblasts from PSP patients (without MAPT mutations) and controls were reprogrammed to iPSCs, further differentiated into neuroprogenitor cells (NPCs) and astrocytes. In the 5th passage, astrocytes were harvested for total RNA sequencing. Intracellular and secreted proteins were processed for proteomics experiments. Metabolomics profiling was obtained from supernatants only. RESULTS We identified hundreds of differentially expressed genes. The main networks were related to cell cycle re-activation in PSP. Several proteins were found exclusively secreted by the PSP group. The cellular processes related to the cell cycle and mitotic proteins, TriC/CCT pathway, and redox signaling were enriched in the secretome of PSP. Moreover, we found distinct sets of metabolites between PSP and controls. CONCLUSION Our iPSC-derived astrocyte model can provide distinct molecular signatures for PSP patients and it is useful to elucidate the initial stages of PSP pathogenesis.
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Affiliation(s)
| | - Hellen P Valerio
- Institute of Chemistry, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Jersey H S Maués
- Hematology and Hemotherapy Center, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arthur N de Oliveira
- Innovare Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Fabíola R Picosse
- Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Henrique B Ferraz
- Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Laboratory, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | | | - Patrícia de Carvalho Aguiar
- Hospital Israelita Albert Einstein, São Paulo, Brazil; Department of Neurology and Neurosurgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Tomaz V, Griesi-Oliveira K, Puga RD, Conti BJ, Santos FPS, Hamerschlak N, Campregher PV. Molecular Characterization of a First-in-Human Clinical Response to Nimesulide in Acute Myeloid Leukemia. Front Oncol 2022; 12:874168. [PMID: 35756679 PMCID: PMC9215211 DOI: 10.3389/fonc.2022.874168] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic malignancy associated with high morbidity and mortality. Here we describe a case of a patient with AML who presented a partial response after utilization of the non-steroidal anti-inflammatory drug nimesulide. The response was characterized by complete clearance of peripheral blood blasts and an 82% decrease of bone marrow blasts associated with myeloblast differentiation. We have then shown that nimesulide induces in vitro cell death and cell cycle arrest in all AML cell lines (HL-60, THP-1, OCI-AML2, and OCI-AML3). Weighted Correlation Network Analysis (WGCNA) of serial whole-transcriptome data of cell lines treated with nimesulide revealed that the sets of genes upregulated after treatment with nimesulide were enriched for genes associated with autophagy and apoptosis, and on the other hand, the sets of downregulated genes were associated with cell cycle and RNA splicing. Serial transcriptome of bone marrow patient sample confirmed the upregulation of genes associated with autophagy after the response to nimesulide. Lastly, we demonstrated that nimesulide potentiates the cytotoxic in vitro effect of several Food and Drug Administration (FDA)-approved chemotherapy drugs used in AML, including cytarabine.
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Affiliation(s)
- Victória Tomaz
- Experimental Research Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Renato D Puga
- Medicina Personalizada, Grupo Pardini, São Paulo, Brazil
| | - Bruno J Conti
- Experimental Research Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Fabio P S Santos
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Nelson Hamerschlak
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Paulo V Campregher
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
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Santana DA, Bedrat A, Puga RD, Turecki G, Mechawar N, Faria TC, Gigek CO, Payão SL, Smith MA, Lemos B, Chen ES. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer's disease patients. Epigenomics 2022; 14:651-670. [PMID: 35588246 DOI: 10.2217/epi-2022-0096] [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] [Indexed: 11/21/2022] Open
Abstract
Aims: To evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and elderly controls, and to identify AD region-specific abnormalities. Methods: Brain samples of auditory cortex, hippocampus and cerebellum from AD patients and controls underwent chromatin immunoprecipitation sequencing, RNA sequencing and network analyses. Results: We found a hyperacetylation of AD cerebellum and a slight hypoacetylation of AD hippocampus. The transcriptome revealed differentially expressed genes in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. Conclusions: These findings suggest that some crucial mechanisms, such as Rho GTPase activity and cytoskeletal organization, are differentially dysregulated in brain regions of AD patients at the epigenetic and transcriptomic levels, and might contribute toward future research on AD pathogenesis.
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Affiliation(s)
- Daliléia A Santana
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Amina Bedrat
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Renato D Puga
- Hermes Pardini Institute, São Paulo, SP, 04038-030, Brazil
| | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Tathyane C Faria
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Carolina O Gigek
- Department of Pathology, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, 04023-062, Brazil
| | - Spencer Lm Payão
- Department of Genetics, Blood Center, Faculdade de Medicina de Marília (FAMEMA), Marília, SP, 17519-050, Brazil
| | - Marília Ac Smith
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Bernardo Lemos
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Elizabeth S Chen
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil.,Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
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Correia RP, Puga RD, Muto NH, Lee MLDM, Torres DC, Hassan R, Bacal NS, Hamerschlak N, Campregher PV. High-throughput sequencing of immunoglobulin heavy chain for minimal residual disease detection in B-lymphoblastic leukemia. Int J Lab Hematol 2021; 43:724-731. [PMID: 33393719 DOI: 10.1111/ijlh.13453] [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: 08/04/2020] [Revised: 11/24/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Minimal residual disease (MRD) is a cornerstone for stratification of upfront B-lymphoblastic leukemia (B-ALL) treatment protocols to decrease relapse risk. Although its detection by flow cytometry (FC) and real-time quantitative polymerase has clinical usefulness, evidence suggests that methods with increased sensitivity could lead to improved outcomes. The aim of this study was to develop an amplicon-based assay followed by high-throughput sequencing of the immunoglobulin heavy chain variable region for MRD detection in B-ALL. METHODS We analyzed 84 samples, 27 from diagnosis, 5 from relapse, 40 from post-treatment samples, and 12 from healthy controls. RESULTS Our assay was able to identify more neoplastic clones at diagnosis than Sanger sequencing including incomplete DJ rearrangements. From the 40 MRD samples evaluated 21 were positive by our new approach on high-throughput sequencing assay, but only 15 of these were positive by FC. The remaining 19 were negative by the two techniques. CONCLUSION We have developed a novel approach on high-sensitive assay for MRD detection in B-ALL, which could add clinical value in the management of patients, especially in cases negative for MRD by FC.
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Affiliation(s)
- Rodolfo P Correia
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Renato D Puga
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Nair H Muto
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Davi C Torres
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Rocio Hassan
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Nydia S Bacal
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil.,Centro de Hematologia de São Paulo, São Paulo, Brazil
| | - Nelson Hamerschlak
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Paulo V Campregher
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
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Santos FPS, Getta B, Masarova L, Famulare C, Schulman J, Datoguia TS, Puga RD, Alves Paiva RDM, Arcila ME, Hamerschlak N, Kantarjian HM, Levine RL, Campregher PV, Rampal RK, Verstovsek S. Prognostic impact of RAS-pathway mutations in patients with myelofibrosis. Leukemia 2020; 34:799-810. [PMID: 31628430 PMCID: PMC7158221 DOI: 10.1038/s41375-019-0603-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/30/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
RAS-pathway mutations are recurrent events in myeloid malignancies. However, there is limited data on the significance of RAS-pathway mutations in patients with myelofibrosis (MF). We analyzed next-generation sequencing data of 16 genes, including RAS-pathway genes, from 723 patients with primary and secondary MF across three international centers and evaluated their significance. N/KRAS variants were present in 6% of patients and were typically sub-clonal (median VAF = 20%) relative to other genes variants. RAS variants were associated with advanced MF features including leukocytosis (p = 0.02), high somatic mutation burden (p < 0.01) and the presence of established "molecular high-risk" (MHR) mutations. MF patients with N/KRAS mutations had shorter 3-year overall survival (OS) (34% vs 58%, p < 0.001) and higher incidence of acute myeloid leukemia at 3 years (18% vs 11%, p = 0.03). In a multivariate Cox model, RAS mutations were associated with decreased OS (HR 1.93, p < 0.001). We created a novel score to predict OS incorporating RAS mutations, and it predicted OS across training and validation cohorts. Patients with intermediate risk/high-risk DIPSS with RAS mutations who received ruxolitinib had a nonsignificant longer 2-year OS relative to those who did not receive ruxolitinib. These data demonstrate the importance of identifying RAS mutations in MF patients.
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Affiliation(s)
- Fabio P S Santos
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil.
| | - Bartlomiej Getta
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucia Masarova
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Schulman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tarcila S Datoguia
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Renato D Puga
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Raquel de Melo Alves Paiva
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nelson Hamerschlak
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paulo Vidal Campregher
- Centro de Hematologia e Oncologia Familia Dayan-Daycoval, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Raajit K Rampal
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Srdan Verstovsek
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Fontoura JC, Viezzer C, Dos Santos FG, Ligabue RA, Weinlich R, Puga RD, Antonow D, Severino P, Bonorino C. Comparison of 2D and 3D cell culture models for cell growth, gene expression and drug resistance. Mater Sci Eng C Mater Biol Appl 2019; 107:110264. [PMID: 31761183 DOI: 10.1016/j.msec.2019.110264] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 09/12/2019] [Accepted: 09/28/2019] [Indexed: 12/24/2022]
Abstract
In vitro drug screening is widely used in the development of new drugs, because they constitute a cost-effective approach to select compounds with more potential for therapy. They are also an attractive alternative to in vivo testing. However, most of these assays are done in two-dimensional culture models, where cells are grown on a polystyrene or glass flat surface. In order to develop in vitro models that would more closely resemble physiological conditions, three-dimensional models have been developed. Here, we introduce two novel fully synthetic scaffolds produced using the polymer polyhydroxybutyrate (PHB): a Solvent-Casting Particle-Leaching (SCPL) membrane; and an electrospun membrane, to be used for 3D cultures of B16 F10 murine melanoma cells and 4T1 murine breast cancer cells. A 2D cell culture system in regular tissue culture plates and a classical 3D model where cells are grown on a commercially available gel derived from Engelbreth-Holm Swarm (EHS) tumor were used for comparison with the synthetic scaffolds. Cells were also collected from in vivo tumors grown as grafts in syngeneic mice. Morphology, cell viability, response to chemotherapy and gene expression analysis were used to compare all systems. In the electrospun membrane model, cells were grown on nanometer-scale fibers and in the SCPL membrane, which provides a foam-like structure for cell growth, pore sizes varied. Cells grown on all 3D models were able to form aggregates and spheroids, allowing for increased cell-cell contact when compared with the 2D system. Cell morphology was also more similar between 3D systems and cells collected from the in vivo tumors. Cells grown in 3D models showed an increase in resistance to dacarbazine, and cisplatin. Gene expression analysis also revealed similarities among all 3D platforms. The similarities between the two synthetic systems to the classic EHS gel model highlight their potential application as cost effective substitutes in drug screening, in which fully synthetic models could represent a step towards higher reproducibility. We conclude PHB synthetic membranes offer a valuable alternative for 3D cultures.
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Affiliation(s)
- Julia C Fontoura
- Laboratório de Imunologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil; Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde, Porto Alegre, RS, Brazil
| | - Christian Viezzer
- Laboratório de Imunologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | | | - Rosane A Ligabue
- Laboratório de Caracterização de Materiais, PUCRS, Porto Alegre, RS, Brazil
| | | | - Renato D Puga
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Dyeison Antonow
- Institute of Petroleum and Natural Resources (IPR), Tecnopuc, PUCRS, Porto Alegre, RS, Brazil
| | | | - Cristina Bonorino
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde, Porto Alegre, RS, Brazil; Department of Surgery, School of Medicine, University of California at San Diego, United States.
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Coutinho-Camillo CM, Puga RD, Nagano CP, Sato-Kuwabara Y, Costa FD, Lopes Pinto CA, Kowalski LP, Soares FA, Lourenço SV. Abstract 4005: microRNA profiles in metastatic versus non-metastatic salivary mucoepidermoid carcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mucoepidermoid carcinoma (MEC) is the most common malignant tumor of the salivary glands, especially affecting the parotids. MEC derives from the main duct segment and is composed of mucous, intermediate, and epidermoid cells in varying combinations. Histological grading (low, intermediate, and high) is of recognized prognostic importance. This is based on the architectural formation, cytological features, perineural invasion, and the presence of necrosis. Metastatic spread occurs in up to 80% of high-grade tumors and it is a strong predictor of poor outcome, however, the mechanisms underlying this process are largely unknown. Large-scale microRNA expression profiling studies of human cancers have demonstrated that dysregulation of miRNA is frequently associated with many cancer types. MicroRNAs (miRNAs) are approximately 22 nucleotide non-coding RNA molecules that regulate gene expression post-transcriptionally and are involved in various biological processes. The aim of this study was to investigate the microRNA profile in metastatic versus non-metastatic MECs. Using Real Time RT-PCR we have analyzed the expression of 762 miRNAs and controls using the TaqMan Array Human MicroRNA A+B Cards in FFPE samples from 2 metastatic MEC, 2 non-metastatic MEC and 2 non-neoplastic human salivary gland. For the identification of differentially expressed microRNAs between tumor samples versus normal samples and between metastatic versus non-metastatic samples, bioinformatics analysis was performed using hierarchical cluster analysis and the t test with Bonferroni correction was applied. Among the 762 microRNAs and controls contained in the array panel, 353 showed an expression level below the detection limit (Ct >38) and were excluded from downstream analyses. The microRNA profile was able to discriminate between normal and tumor samples and between metastatic and non-metastatic tumors. Considering tumor and normal samples, 29 microRNAs were differentially expressed. The metastatic versus non-metastatic analysis demonstrated that 62 microRNAs were differentially expressed. Among the differentially expressed microRNAs, some have already been described as associated with the metastatic process (hsa-miR-9, hsa-miR-125, hsa-miR-145, hsa-miR-494, hsa-miR-140, hsa-miR-212, hsa-miR-146, hsa-miR-183, hsa-miR-21, hsa-miR-200, hsa-miR-638, and hsa-miR-141). Our results suggest that microRNA profiles could discriminate the metastatic potential of salivary MECs and might be helpful in diagnostic and prognostic evaluation of patients. Financial Support: FAPESP 11/02051-6
Citation Format: Cláudia M. Coutinho-Camillo, Renato D. Puga, Cibele P. Nagano, Yukie Sato-Kuwabara, Felipe D'Almeida Costa, Clóvis A. Lopes Pinto, Luiz P. Kowalski, Fernando A. Soares, Silvia V. Lourenço. microRNA profiles in metastatic versus non-metastatic salivary mucoepidermoid carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4005. doi:10.1158/1538-7445.AM2015-4005
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de Oliveira GP, Maximino JR, Maschietto M, Zanoteli E, Puga RD, Lima L, Carraro DM, Chadi G. Early gene expression changes in skeletal muscle from SOD1(G93A) amyotrophic lateral sclerosis animal model. Cell Mol Neurobiol 2014; 34:451-62. [PMID: 24442855 DOI: 10.1007/s10571-014-0029-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/07/2014] [Indexed: 02/07/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by loss of motor neurons. Familial ALS is strongly associated to dominant mutations in the gene for Cu/Zn superoxide dismutase (SOD1). Recent evidences point to skeletal muscle as a primary target in the ALS mouse model. Wnt/PI3 K signaling pathways and epithelial-mesenchymal transition (EMT) have important roles in maintenance and repair of skeletal muscle. Wnt/PI3 K pathways and EMT gene expression profile were investigated in gastrocnemius muscle from SOD1(G93A) mouse model and age-paired wild-type control in the presymptomatic ages of 40 and 80 days aiming the early neuromuscular abnormalities that precede motor neuron death in ALS. A customized cDNA microarray platform containing 326 genes of Wnt/PI3 K and EMT was used and results revealed eight up-regulated (Loxl2, Pik4ca, Fzd9, Cul1, Ctnnd1, Snf1lk, Prkx, Dner) and nine down-regulated (Pik3c2a, Ripk4, Id2, C1qdc1, Eif2ak2, Rac3, Cds1, Inppl1, Tbl1x) genes at 40 days, and also one up-regulated (Pik3ca) and five down-regulated (Cd44, Eef2 k, Fzd2, Crebbp, Piki3r1) genes at 80 days. Also, protein-protein interaction networks grown from the differentially expressed genes of 40 and 80 days old mice have identified Grb2 and Src genes in both presymptomatic ages, thus playing a potential central role in the disease mechanisms. mRNA and protein levels for Grb2 and Src were found to be increased in 80 days old ALS mice. Gene expression changes in the skeletal muscle of transgenic ALS mice at presymptomatic periods of disease gave further evidence of early neuromuscular abnormalities that precede motor neuron death. The results were discussed in terms of initial triggering for neuronal degeneration and muscle adaptation to keep function before the onset of symptoms.
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Affiliation(s)
- Gabriela P de Oliveira
- Neuroregeneration Center, Department of Neurology, University of São Paulo School of Medicine, Av. Dr. Arnaldo, 455, 2nd Floor, Room 2119, São Paulo, 01246-903, Brazil
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Maschietto M, Silva AR, Puga RD, Lima L, Pereira CB, Nakano EY, Mello B, Gama CS, Belmonte-de-Abreu P, Carraro DM, Palha JA, Brentani H. Gene expression of peripheral blood lymphocytes may discriminate patients with schizophrenia from controls. Psychiatry Res 2012; 200:1018-21. [PMID: 22633013 DOI: 10.1016/j.psychres.2012.04.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 04/04/2012] [Accepted: 04/23/2012] [Indexed: 12/22/2022]
Abstract
To identify a classifier in schizophrenia, blood gene expression profiling was applied to patients with schizophrenia under different treatments and to controls. Expression of six genes discriminated patients with sensitivity of 89.3% and specificity of 90%, supporting the use of peripheral blood as biological material for diagnosis in schizophrenia.
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Affiliation(s)
- Mariana Maschietto
- Institute of Psychiatry - University of Sao Paulo, Medical School (FMUSP), São Paulo (SP), Brazil; CIPE - AC Camargo Hospital, São Paulo (SP), Brazil
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Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LEC, Cruz LO, Degaki TL, Faria M, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CVB, Marie SKN, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MIMC, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva IDCG, da Silva NP, de Souza SJ, Tajara EH, Silva WA, Simpson AJG, Sogayar MC, Camargo AA, Carraro DM. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences. Genet Mol Res 2004; 3:493-511. [PMID: 15688316] [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: 05/01/2023]
Abstract
The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.
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Affiliation(s)
- Elisa N Ferreira
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, SP, Brazil
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Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJG, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MAV, De Souza SJ, Faria M, Giuliatti S, Kopp L, de Oliveira PSL, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LEC, Baia GS, Briones MRS, Cavaleiro-Luna AMS, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MAHZ, Furchi JRF, Giannella-Neto D, Goldman GH, Goldman MHS, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SKN, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BMC, Pandolfi JRC, Pardini MIMC, Passos Bueno MR, Passos GAS, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA, Silva IDCG, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res 2004; 14:1413-23. [PMID: 15197164 PMCID: PMC442158 DOI: 10.1101/gr.2111304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/12/2004] [Indexed: 11/24/2022]
Abstract
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.
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