Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin
The microRNA (miRNA) expression profile by qRT-PCR depends directly on the most appropriate normalization strategy adopted; however, currently there is no universally adequate reference gene. Therefore, this study aimed to determine, considering RNA-Seq results, the most adequate endogenous normaliz...
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/13/10884 |
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| author | Nadine de Godoy Torso Julia Coelho França Quintanilha Maria Aparecida Cursino Eder de Carvalho Pincinato Carmen Silvia Passos Lima Patricia Moriel |
| author_facet | Nadine de Godoy Torso Julia Coelho França Quintanilha Maria Aparecida Cursino Eder de Carvalho Pincinato Carmen Silvia Passos Lima Patricia Moriel |
| author_sort | Nadine de Godoy Torso |
| collection | DOAJ |
| description | The microRNA (miRNA) expression profile by qRT-PCR depends directly on the most appropriate normalization strategy adopted; however, currently there is no universally adequate reference gene. Therefore, this study aimed to determine, considering RNA-Seq results, the most adequate endogenous normalizer for use in the relative quantification of urine miRNAs from head and neck cancer patients, treated with cisplatin chemoradiotherapy. The massive sequencing was performed to identify the miRNAs differentially expressed between the group with cisplatin nephrotoxicity (<i>n</i> = 6) and the one without (<i>n</i> = 6). The candidate endogen normalizer was chosen according to four criteria: (1) the miRNA must be expressed in most samples; (2) the miRNA must have a fold change value between 0.99 and 1.01; (3) the miRNA must have a <i>p</i>-value ≥ 0.98; and (4) the miRNA must not be commented on by the final GeneGlobe (Qiagen, Hilden, Germany) analysis. Four miRNAs met all the criteria (hsa-miR-363-5p, hsa-miR-875-5p, hsa-miR-4302, and hsa-miR-6749-5p) and were selected for validation by qRT-PCR in a cohort of 49 patients (including the 12 sequencing participants). Only hsa-miR-875-5p was shown to be an adequate normalizer for the experimental condition under investigation, as it exhibited invariant expression between the two groups. |
| first_indexed | 2024-03-11T01:39:35Z |
| format | Article |
| id | doaj.art-f4617ace6b2b428ca65a2236079b7dbb |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T01:39:35Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f4617ace6b2b428ca65a2236079b7dbb2023-11-18T16:44:56ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-0124131088410.3390/ijms241310884Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with CisplatinNadine de Godoy Torso0Julia Coelho França Quintanilha1Maria Aparecida Cursino2Eder de Carvalho Pincinato3Carmen Silvia Passos Lima4Patricia Moriel5School of Medical Sciences, University of Campinas, Campinas 13083894, BrazilSchool of Medical Sciences, University of Campinas, Campinas 13083894, BrazilSchool of Medical Sciences, University of Campinas, Campinas 13083894, BrazilSchool of Medical Sciences, University of Campinas, Campinas 13083894, BrazilSchool of Medical Sciences, University of Campinas, Campinas 13083894, BrazilFaculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083970, BrazilThe microRNA (miRNA) expression profile by qRT-PCR depends directly on the most appropriate normalization strategy adopted; however, currently there is no universally adequate reference gene. Therefore, this study aimed to determine, considering RNA-Seq results, the most adequate endogenous normalizer for use in the relative quantification of urine miRNAs from head and neck cancer patients, treated with cisplatin chemoradiotherapy. The massive sequencing was performed to identify the miRNAs differentially expressed between the group with cisplatin nephrotoxicity (<i>n</i> = 6) and the one without (<i>n</i> = 6). The candidate endogen normalizer was chosen according to four criteria: (1) the miRNA must be expressed in most samples; (2) the miRNA must have a fold change value between 0.99 and 1.01; (3) the miRNA must have a <i>p</i>-value ≥ 0.98; and (4) the miRNA must not be commented on by the final GeneGlobe (Qiagen, Hilden, Germany) analysis. Four miRNAs met all the criteria (hsa-miR-363-5p, hsa-miR-875-5p, hsa-miR-4302, and hsa-miR-6749-5p) and were selected for validation by qRT-PCR in a cohort of 49 patients (including the 12 sequencing participants). Only hsa-miR-875-5p was shown to be an adequate normalizer for the experimental condition under investigation, as it exhibited invariant expression between the two groups.https://www.mdpi.com/1422-0067/24/13/10884microRNAqRT-PCRendogenous normalizerreference genecisplatin |
| spellingShingle | Nadine de Godoy Torso Julia Coelho França Quintanilha Maria Aparecida Cursino Eder de Carvalho Pincinato Carmen Silvia Passos Lima Patricia Moriel Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin International Journal of Molecular Sciences microRNA qRT-PCR endogenous normalizer reference gene cisplatin |
| title | Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin |
| title_full | Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin |
| title_fullStr | Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin |
| title_full_unstemmed | Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin |
| title_short | Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin |
| title_sort | data normalization of urine mirna profiling from head and neck cancer patients treated with cisplatin |
| topic | microRNA qRT-PCR endogenous normalizer reference gene cisplatin |
| url | https://www.mdpi.com/1422-0067/24/13/10884 |
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