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Pedrão PG, de Carvalho AC, Possati-Resende JC, de Paula Cury F, Campanella NC, de Oliveira CM, Tavares Guerreiro Fregnani JH. DNA Recovery Using Ethanol-Based Liquid Medium from FTA Card-Stored Samples for HPV Detection. Acta Cytol 2021; 65:264-271. [PMID: 33951624 DOI: 10.1159/000515913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/09/2021] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Alternative methods of dry storage and transportation may be a viable alternative to the use of liquid storage medium for cervical samples, especially for screening programs in places with few resources. OBJECTIVE The objective of this study is to verify the viability and efficacy of human papillomavirus DNA (HPV-DNA) detection in cervical cell samples collected and stored on a Flinders Technology Associates (FTA) card (Whatman Indicating FTA® Elute Micro Card) and subsequently recovered in ethanol-based liquid medium and to compare the results to those obtained using samples stored directly in ethanol-based liquid medium. STUDY DESIGN Thirty-four women submitted to ETZ (excision of the transformation zone of the cervix) were included in this study. Before ETZ, 2 samples of exfoliated cervical cells were collected from each woman by a doctor and stored in ethanol-based liquid medium and on an FTA card. DNA recovery from FTA samples was performed using ethanol-based liquid medium. Detection of HPV-DNA in the samples was performed using the Cobas® 4800 HPV Test Platform. RESULTS AND CONCLUSIONS The HPV-DNA detection positivity rates were 70.6% for the samples collected directly in liquid medium and 64.7% for the samples stored on the FTA card, with high detection accuracy in the DNA samples recovered from the FTA card (area under the curve = 0.958; 95% confidence interval = 0.890-1.000). The concordance between the results obtained using the 2 storage media was 94.1% (Kappa = 0.866). These preliminary results suggest that collection of cervical material on an FTA card may be an alternative to storage in liquid medium since the liquid medium has some limitations. In addition, DNA recovery from the card using ethanol-based liquid medium streamlines the workflow in the laboratory and reduces the cost associated with reagents, thereby facilitating access to the HPV test in places with few resources and potentially improving cervical cancer screening.
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Affiliation(s)
- Priscila Grecca Pedrão
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | - Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristina Mendes de Oliveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- DASA Laboratories, São Paulo, Brazil
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Campanella NC, Silva EC, Dix G, de Lima Vazquez F, Escremim de Paula F, Berardinelli GN, Balancin M, Chammas R, Mendoza Lopez RV, Silveira HCS, Capelozzi VL, Reis RM. Mutational Profiling of Driver Tumor Suppressor and Oncogenic Genes in Brazilian Malignant Pleural Mesotheliomas. Pathobiology 2020; 87:208-216. [PMID: 32369821 DOI: 10.1159/000507373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 12/17/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is a highly lethal disease comprising a heterogeneous group of tumors with challenging to predict biological behavior. The diagnosis is complex, and the histologic classification includes 2 major subtypes of MPM: epithelioid (∼60% of cases) and sarcomatous (∼20%). Its identification depends upon pathological investigation supported by clinical and radiological evidence and more recently ancillary molecular testing. Treatment options are currently limited, with no known targeted therapies available. OBJECTIVES To elucidate the mutation profile of driver tumor suppressor and oncogenic genes in a cohort of Brazilian patients. METHODS We sequenced 16 driver genes in a series of 43 Brazilian malignant mesothelioma (MM) patients from 3 distinct Brazilian centers. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor tissue blocks, and the TERT promoter region was amplified by PCR followed by direct capillary sequencing. The Illumina TruSight Tumor 15 was used to evaluate 250 amplicons from 15 genes associated with solid tumors (AKT1, GNA11, NRAS, BRAF, GNAQ, PDGFRA, EGFR, KIT, PIK3CA, ERBB2, KRAS, RET, FOXL2, MET,and TP53). Library preparation with the TruSight Tumor 15 was performed before sequencing at the MiSeq platform. Data analysis was performed using Sophia DDM software. RESULTS Out of 43 MPM patients, 38 (88.4%) were epithelioid subtype and 5 (11.6%) were sarcomatoid histotype. Asbestos exposure was present in 15 (39.5%) patients with epithelioid MPM and 3 (60%) patients with sarcomatoid MPM. We found a TERT promoter mutation in 11.6% of MM, and the c.-146C>T mutation was the most common event. The next-generation sequencing was successful in 33 cases. A total of 18 samples showed at least 1 pathogenic, with a median of 1.8 variants, ranging from 1 to 6. The most mutated genes were TP53 and ERBB2 with 7 variants each, followed by NRAS BRAF, PI3KCA, EGFR and PDGFRA with 2 variants each. KIT, AKT1, and FOXL2 genes exhibited 1 variant each. Interestingly, 2 variants observed in the PDGFRA gene are classic imatinib-sensitive therapy. CONCLUSIONS We concluded that Brazilian MPM harbor mutation in classic tumor suppressor and oncogenic genes, which might help in the guidance of personalized treatment of MPM.
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Affiliation(s)
| | | | - Gustavo Dix
- Department of Surgery, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Marcelo Balancin
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | - Roger Chammas
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | - Rossana V Mendoza Lopez
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | | | - Vera Luiza Capelozzi
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil, .,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal, .,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal,
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Campanella NC, Melendez M, Leal LF, Evangelista AF, Faça VM, Reis RM. Abstract 3998: Integrative molecular analysis uncovers key molecules and signaling pathways regulated by RKIP in gastrointestinal stromal tumors (GISTs). Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3998] [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
Introduction: Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumor on the gastrointestinal tract, and are characterized by hotspot mutations in KIT and PDGFRA genes, which are predictive of imatinib-based therapy response. We showed previously that RKIP, a metastasis suppressor gene, is lost in about 17% of GIST, and it was associated with an adverse outcome. RKIP is plays a pivotal role in several signaling pathways, namely MAPK, NF-κβ, and GSK3β however a multidimensional integrative analysis to uncover its biological impact was never done in cancer and in particular in GIST.
Experimental procedures: We established a RKIP knockout GIST cell line (GIST-T1 KO) by CRISPR/Cas9 system. The differential gene and microRNA expression profile between GIST-T1 RKIP-KO and GIST-T1 negative control cells were assessed using the NanoString nCounter® technology and the nCounter® PanCancer Pathways and nCounter® miRNA Expression assays (NanoString Technologies). All procedures including sample preparation (100 ng of RNA), hybridization, detection and scanning were performed according to manufacture's instructions (NanoString Technologies). In a second step, we performed a global proteomic analysis using the Acquity UPLC M-Class chromatography system (Waters Co) linked to the mass spectrometer Synapt G2-Si (Waters Co). The protein
identification and quantification were performed in Progenesis QI for Proteomics (Waters Co) software.
Results: The nCounter gene expression analysis showed 56 genes differentially expressed: 18 downregulated and 38 upregulated genes in RKIP KO cells. The altered genes are especially involved in PI3k-AKT, MAPK and Ras signaling pathways. The global proteomic characterization showed 50 proteins differentially expressed: 5 were downregulated and 44 upregulated proteins in RKIP KO cells. In microRNA expression profile analysis we found 133 downregulated microRNAs in RKIP KO cells. Taking together, these findings uncover new molecules that are going to screen in a cohort of GIST patients.
Conclusion: For the first time, using a multidimensional integrative analysis we identified driver candidates and pathways, which will contribute the uncovered the biological role of RKIP in cancer.
Citation Format: Nathália C. Campanella, Matias Melendez, Leticia Ferro Leal, Adriane Feijo Evangelista, Vitor Marcel Faça, Rui Manuel Reis. Integrative molecular analysis uncovers key molecules and signaling pathways regulated by RKIP in gastrointestinal stromal tumors (GISTs) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3998.
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Campanella NC, Lacerda CF, Berardinelli GN, Abrahão-Machado LF, Cruvinel-Carloni A, De Oliveira ATT, Scapulatempo-Neto C, Crema E, Adad SJ, Rodrigues MAM, Henry MACA, Guimarães DP, Reis RM. Presence of microsatellite instability in esophageal squamous cell carcinoma associated with chagasic megaesophagus. Biomark Med 2018; 12:573-582. [PMID: 29873509 DOI: 10.2217/bmm-2017-0329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 12/23/2022] Open
Abstract
AIM The molecular pathogenesis of esophageal squamous cell carcinoma (ESCC) has been increasingly studied, but there is no report on the role of MSI in ESCC development associated with chagasic megaesophagus (CM).Results/methodology: In four ESCC/CM (4/19) we found microsatellite instability (MSI) alterations (21.1%), being three MSI-L (15.8%) and one MSI-H (5.3%). Four out of 35 ESCC cases showed MSI-L (11.4%) and only one out of 26 CM cases presented MSI-L (3.9%). The MSI-H was observed in an ESCC/CM patient that presents lack of MSH6 immunostaining corroborating deficiency in MMR pathway. Interestingly, the MSI-H ESCC/CM case also presented a deletion the HSP110 poly(T)17 gene. DISCUSSION/CONCLUSION Taking together, we concluded that MSI is a rare event in esophageal squamous cell carcinoma, but can be associated with CM.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Croider Franco Lacerda
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Digestive Surgery, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Pathology & Molecular Diagnostics, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Eduardo Crema
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sheila Jorge Adad
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | | | | | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life & Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Campanella NC, Scapulatempo-Neto C, Abrahão-Machado LF, Torres De Oliveira AT, Berardinelli GN, Guimarães DP, Reis RM. Lack of microsatellite instability in gastrointestinal stromal tumors. Oncol Lett 2017; 14:5221-5228. [PMID: 29113157 PMCID: PMC5662911 DOI: 10.3892/ol.2017.6884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 02/10/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022] Open
Abstract
The microsatellite instability (MSI) phenotype may constitute an important biomarker for patient response to immunotherapy, particularly to anti-programmed death-1 inhibitors. MSI is a type of genomic instability caused by a defect in DNA mismatch repair (MMR) proteins, which is present mainly in colorectal cancer and its hereditary form, hereditary nonpolyposis colorectal cancer. Gastrointestinal stromal tumor (GIST) development is associated with activating mutations of KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor α (PDGFRA), which are oncogenes that predict the response to imatinib mesylate. In addition to KIT/PDGFRA mutations, other molecular alterations are important in GIST development. In GISTs, the characterization of the MSI phenotype is scarce and the results are not consensual. The present study aimed to assess MSI in a series of 79 GISTs. The evaluation of MSI was performed by pentaplex polymerase chain reaction comprising five markers, followed by capillary electrophoresis. The expression of MMR proteins was evaluated by immunohistochemistry. Regarding the KIT/PDGFRA/B-Raf proto-oncogene, serine/threonine kinase molecular profile of the 79 GISTs, 83.6% of the tumors possessed KIT mutations, 10.1% had PDGFRA mutations and 6.3% were triple wild-type. The mutated-PDGFRA cases were associated with gastric location and a lower mitotic index compared with KIT-mutated and wild-types, and these patients were more likely to be alive and without cancer. MSI analysis identified 4 cases with instability in one marker, however, additional evaluation of normal tissue and immunohistochemical staining of MMR proteins confirmed their microsatellite-stable nature. The results of the present study indicated that MSI is not involved in GIST tumorigenesis and, therefore, cannot serve as a biomarker to immunotherapy response in GIST.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | | | | | - Gustavo N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Life and Health Sciences Research Institute, Health Sciences School, University of Minho, Guimarães, Braga 4704-553, Portugal.,Life and Health Sciences Research Institute/3B's-PT Government Associate Laboratory, University of Minho, Guimarães, Braga 4704-553, Portugal
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Campanella NC, Celestino R, Pestana A, Scapulatempo-Neto C, de Oliveira AT, Brito MJ, Gouveia A, Lopes JM, Guimarães DP, Soares P, Reis RM. Low frequency of TERT promoter mutations in gastrointestinal stromal tumors (GISTs). Eur J Hum Genet 2014; 23:877-9. [PMID: 25248398 DOI: 10.1038/ejhg.2014.195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/11/2014] [Accepted: 08/20/2014] [Indexed: 12/12/2022] Open
Abstract
Somatic mutations in the promoter region of telomerase reverse transcriptase (TERT) gene, mainly at positions c.-124 and c.-146 bp, are frequent in several human cancers; yet its presence in gastrointestinal stromal tumor (GIST) has not been reported to date. Herein, we searched for the presence and clinicopathological association of TERT promoter mutations in genomic DNA from 130 bona fide GISTs. We found TERT promoter mutations in 3.8% (5/130) of GISTs. The c.-124C>T mutation was the most common event, present in 2.3% (3/130), and the c.-146C>T mutation in 1.5% (2/130) of GISTs. No significant association was observed between TERT promoter mutation and patient's clinicopathological features. The present study establishes the low frequency (4%) of TERT promoter mutations in GISTs. Further studies are required to confirm our findings and to elucidate the hypothetical biological and clinical impact of TERT promoter mutation in GIST pathogenesis.
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Affiliation(s)
| | - Ricardo Celestino
- 1] Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal [2] School of Allied Health Sciences ESTSP, Polytechnic of Porto, Porto, Portugal
| | - Ana Pestana
- 1] Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal [2] Institute of Biomedical Sciences of University of Porto, Porto, Portugal
| | - Cristovam Scapulatempo-Neto
- 1] Molecular Oncology Research Center, Barretos Cancer Hospital, Sao Paulo, Brazil [2] Department of Pathology, Barretos Cancer Hospital, Sao Paulo, Brazil
| | | | - Maria José Brito
- Department of Pathology, Hospital Garcia de Orta, Almada, Portugal
| | | | - José Manuel Lopes
- 1] Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal [2] Department of Pathology, Centro Hospitalar de São João, Porto, Portugal [3] Department of Pathology and Oncology, Medical Faculty, University of Porto, Porto, Portugal
| | - Denise Peixoto Guimarães
- 1] Molecular Oncology Research Center, Barretos Cancer Hospital, Sao Paulo, Brazil [2] Department of Endoscopy, Barretos Cancer Hospital, Sao Paulo, Brazil
| | - Paula Soares
- 1] Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal [2] Department of Pathology and Oncology, Medical Faculty, University of Porto, Porto, Portugal
| | - Rui M Reis
- 1] Molecular Oncology Research Center, Barretos Cancer Hospital, Sao Paulo, Brazil [2] Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal [3] ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Campanella NC, Berardinelli GN, Scapulatempo-Neto C, Viana D, Palmero EI, Pereira R, Reis RM. Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers. Eur J Hum Genet 2013; 22:875-80. [PMID: 24193342 DOI: 10.1038/ejhg.2013.256] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/19/2013] [Accepted: 09/27/2013] [Indexed: 12/27/2022] Open
Abstract
Microsatellite instability (MSI) testing has been advocated for all newly diagnosed colorectal cancer patients. One of the most common tests is composed by a pentaplex panel of mononucleotides markers (NR-27, NR-21, NR-24, BAT-25, and BAT-26), which allows the analysis of MSI in tumors without the need of reference DNA. For that, it is fundamental to establish a quasi-monomorphic variation range (QMVR) for each marker. Herein, we aimed to establish the QMVR in a Brazilian healthy population, to evaluate the feasibility of MSI determination of tumors, without the matching normal DNA. Furthermore, we intend to assess their ancestry using specific ancestry-informative markers (AIMs) and correlate with QMVR. The QMVR was assessed in 214 individuals, through a pentaplex PCR followed by fragment analysis. The ancestry analysis was done by 46 AIMs in a single multiplex PCR followed by capillary electrophoresis. Following QMVR establishment, we observed 23 individuals with alleles outside the QMVR. Importantly, none of them exhibited more than one marker outside the range. Therefore, individuals with instability at ≥2 markers would be accurately classified as MSI. The European ancestry proportion was the most frequent (67.5%), followed by the African (19.6%). The comparison of the individuals with alleles within (n=191) and outside (n=23) the QMVR showed statistical difference in the proportions of European and African alleles, confirming the higher polymorphic nature of African ancestry. In conclusion, the present study reports an accurate methodology to assess MSI status without matched-normal DNA and independently of the ethnicity, even in the highly admixed population of Brazil.
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Affiliation(s)
| | | | | | - Danilo Viana
- Oncogenetic Department, Barretos Cancer Hospital, São Paulo, Brazil
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | - Rui Pereira
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Rui M Reis
- 1] Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil [2] Life and Health Sciences Research Institute, University of Minho, and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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