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Oliveira D, Morales-Vicente DA, Amaral MS, Luz L, Sertié AL, Leite FS, Navarro C, Kaid C, Esposito J, Goulart E, Caires L, Alves LM, Melo US, Figueiredo T, Mitne-Neto M, Okamoto OK, Verjovski-Almeida S, Zatz M. Different gene expression profiles in iPSC-derived motor neurons from ALS8 patients with variable clinical courses suggest mitigating pathways for neurodegeneration. Hum Mol Genet 2021; 29:1465-1475. [PMID: 32280986 DOI: 10.1093/hmg/ddaa069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis type 8 (ALS8) is an autosomal dominant form of ALS, which is caused by pathogenic variants in the VAPB gene. Here we investigated five ALS8 patients, classified as 'severe' and 'mild' from a gigantic Brazilian kindred, carrying the same VAPB mutation but displaying different clinical courses. Copy number variation and whole exome sequencing analyses in such individuals ruled out previously described genetic modifiers of pathogenicity. After deriving induced pluripotent stem cells (iPSCs) for each patient (N = 5) and controls (N = 3), motor neurons were differentiated, and high-throughput RNA-Seq gene expression measurements were performed. Functional cell death and oxidative metabolism assays were also carried out in patients' iPSC-derived motor neurons. The degree of cell death and mitochondrial oxidative metabolism were similar in iPSC-derived motor neurons from mild patients and controls and were distinct from those of severe patients. Similar findings were obtained when RNA-Seq from such cells was performed. Overall, 43 genes were upregulated and 66 downregulated in the two mild ALS8 patients when compared with severe ALS8 individuals and controls. Interestingly, significantly enriched pathways found among differentially expressed genes, such as protein translation and protein targeting to the endoplasmic reticulum (ER), are known to be associated with neurodegenerative processes. Taken together, the mitigating mechanisms here presented appear to maintain motor neuron survival by keeping translational activity and protein targeting to the ER in such cells. As ALS8 physiopathology has been associated with proteostasis mechanisms in ER-mitochondria contact sites, such differentially expressed genes appear to relate to the bypass of VAPB deficiency.
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Affiliation(s)
- Danyllo Oliveira
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - David A Morales-Vicente
- Laboratory of Gene Expression in Eukaryotes, Instituto Butantan, São Paulo 05503-900, Brazil.,Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Murilo S Amaral
- Laboratory of Gene Expression in Eukaryotes, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Livia Luz
- Laboratory of DNA Repair, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | | | - Felipe S Leite
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Claudia Navarro
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil
| | - Carolini Kaid
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Joyce Esposito
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Ernesto Goulart
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Luiz Caires
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Luciana M Alves
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Uirá S Melo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Thalita Figueiredo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil.,Faculty of Medicine, Federal University of Alagoas, Maceió 57972-900, Brazil
| | - Miguel Mitne-Neto
- Fleury Group, Research and Development. São Paulo, São Paulo 04344-070, Brazil
| | - Oswaldo K Okamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Sergio Verjovski-Almeida
- Laboratory of Gene Expression in Eukaryotes, Instituto Butantan, São Paulo 05503-900, Brazil.,Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Mayana Zatz
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
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Rivas M, Costa CD, Toledo S, Cypriano M, Caires L, Goulart E, Carraro D, Werneck I, Rosenberg C, Zatz M, Krepischi A. Abstract A10: Epigenetic mechanisms in liver tumors: Gene expression analysis of epigenetic machinery in hepatoblastomas. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a10] [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
Liver tumors in children are rare and account for only 1-4% of all pediatric solid tumors. While hepatocellular carcinoma is predominant in adults, the most common liver cancer in children is hepatoblastoma, an embryonal tumor. The prognosis of patients with advanced tumor stages remains poor as well as surviving children often face severe effects following aggressive chemotherapy.
Hepatoblastomas carry a low mutational burden, and the impairment of epigenetic mechanisms, which are the core of embryogenesis and development, stands out as an alternative route for tumorigenesis.
The main objective of this study was to explore the role of genes associated with methylation and hydroxymethylation in hepatoblastomas. The expression of seven genes of the epigenetic machinery (DNMT1, DNMT3A, DNMT3L, UHRF1, TET1, TET2, and TET3) was analyzed by qPCR (Taqman). The cohort of tumors consisted of 21 hepatoblastomas and a control group of 8 non-tumor differentiated liver tissues. Additionally, a 5hmC quantification assay (Quest 5-hmC DNA ELISA Kit) was applied to assess the level of 5hmC in tumors.
TET1 and TET2 genes, whose proteins are responsible for the active demethylation of 5-methylcytosine (5mC), and consequent production of 5-hydroxymethylcytosine (5hmC), were found to be upregulated. A significant increase in the 5hmC levels was also evident in tumor samples when compared to nontumoral tissues.
We have shown in hepatoblastomas an upregulated profile of TET1 and TET2 enzymes with a resulting elevation of 5hmC level in tumors. Our data suggest that hepatoblastomas could present a pluripotency pattern of gene expression when compared to differentiated livers; to address this issue, the expression levels of three genes associated with pluripotency (POU5F1, SOX2 and NANOG) were evaluated, with no significant alteration.
Therefore, although hepatoblastomas have a more undifferentiated molecular profile than mature hepatocytes, our results indicate that tumor cells are already commited with the differentiation process. Altogether, these data suggest that the development of hepatoblastomas is associated with a blockage in the stages of hepatoblasts.
Citation Format: Maria Rivas, Cecília da Costa, Silvia Toledo, Monica Cypriano, Luiz Caires, Ernesto Goulart, Dirce Carraro, Isabela Werneck, Carla Rosenberg, Mayana Zatz, Ana Krepischi. Epigenetic mechanisms in liver tumors: Gene expression analysis of epigenetic machinery in hepatoblastomas [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A10.
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Affiliation(s)
- Maria Rivas
- 1University of São Paulo, São Paulo, SP, Brazil,
| | | | - Silvia Toledo
- 3Grupo de Apoio ao Adolescente e Criança com Câncer - GRAACC, São Paulo, SP, Brazil
| | - Monica Cypriano
- 3Grupo de Apoio ao Adolescente e Criança com Câncer - GRAACC, São Paulo, SP, Brazil
| | - Luiz Caires
- 1University of São Paulo, São Paulo, SP, Brazil,
| | | | | | | | | | - Mayana Zatz
- 1University of São Paulo, São Paulo, SP, Brazil,
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