Differential DNA Methylation in Prostate Tumors from Puerto Rican Men
In 2020, approximately 191,930 new prostate cancer (PCa) cases are estimated in the United States (US). Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. This study aims to assess methylation patterns between aggressive and indolent PCa including DNA repair genes along wit...
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| Language: | English |
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MDPI AG
2021-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/2/733 |
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| author | Gilberto Ruiz-Deya Jaime Matta Jarline Encarnación-Medina Carmen Ortiz-Sanchéz Julie Dutil Ryan Putney Anders Berglund Jasreman Dhillon Youngchul Kim Jong Y. Park |
| author_facet | Gilberto Ruiz-Deya Jaime Matta Jarline Encarnación-Medina Carmen Ortiz-Sanchéz Julie Dutil Ryan Putney Anders Berglund Jasreman Dhillon Youngchul Kim Jong Y. Park |
| author_sort | Gilberto Ruiz-Deya |
| collection | DOAJ |
| description | In 2020, approximately 191,930 new prostate cancer (PCa) cases are estimated in the United States (US). Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. This study aims to assess methylation patterns between aggressive and indolent PCa including DNA repair genes along with ancestry proportions. Prostate tumors classified as aggressive (<i>n</i> = 11) and indolent (<i>n</i> = 13) on the basis of the Gleason score were collected. Tumor and adjacent normal tissue were annotated on H&E (Haemotoxylin and Eosin) slides and extracted by macro-dissection. Methylation patterns were assessed using the Illumina 850K DNA methylation platform. Raw data were processed using the Bioconductor package. Global ancestry proportions were estimated using ADMIXTURE (k = 3). One hundred eight genes including <i>AOX1</i> were differentially methylated in tumor samples. Regarding the PCa aggressiveness, six hypermethylated genes (<i>RREB1, FAM71F2, JMJD1C, COL5A3, RAE1,</i> and <i>GABRQ</i>) and 11 hypomethylated genes (<i>COL9A2, FAM179A, SLC17A2, PDE10A, PLEKHS1, TNNI2, OR51A4, RNF169, SPNS2, ADAMTSL5,</i> and <i>CYP4F12</i>) were identified. Two significant differentially methylated DNA repair genes, <i>JMJD1C</i> and <i>RNF169</i>, were found. Ancestry proportion results for African, European, and Indigenous American were 24.1%, 64.2%, and 11.7%, respectively. The identification of DNA methylation patterns related to PCa in H/L men along with specific patterns related to aggressiveness and DNA repair constitutes a pivotal effort for the understanding of PCa in this population. |
| first_indexed | 2024-03-09T04:56:51Z |
| format | Article |
| id | doaj.art-135b1b290e4844738e709927f3850c61 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T04:56:51Z |
| publishDate | 2021-01-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-135b1b290e4844738e709927f3850c612023-12-03T13:04:43ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-01-0122273310.3390/ijms22020733Differential DNA Methylation in Prostate Tumors from Puerto Rican MenGilberto Ruiz-Deya0Jaime Matta1Jarline Encarnación-Medina2Carmen Ortiz-Sanchéz3Julie Dutil4Ryan Putney5Anders Berglund6Jasreman Dhillon7Youngchul Kim8Jong Y. Park9Department of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University-School of Medicine, Ponce 00716-2347, Puerto RicoDepartment of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University-School of Medicine, Ponce 00716-2347, Puerto RicoDepartment of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University-School of Medicine, Ponce 00716-2347, Puerto RicoDepartment of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University-School of Medicine, Ponce 00716-2347, Puerto RicoDepartment of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University-School of Medicine, Ponce 00716-2347, Puerto RicoDepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USAIn 2020, approximately 191,930 new prostate cancer (PCa) cases are estimated in the United States (US). Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. This study aims to assess methylation patterns between aggressive and indolent PCa including DNA repair genes along with ancestry proportions. Prostate tumors classified as aggressive (<i>n</i> = 11) and indolent (<i>n</i> = 13) on the basis of the Gleason score were collected. Tumor and adjacent normal tissue were annotated on H&E (Haemotoxylin and Eosin) slides and extracted by macro-dissection. Methylation patterns were assessed using the Illumina 850K DNA methylation platform. Raw data were processed using the Bioconductor package. Global ancestry proportions were estimated using ADMIXTURE (k = 3). One hundred eight genes including <i>AOX1</i> were differentially methylated in tumor samples. Regarding the PCa aggressiveness, six hypermethylated genes (<i>RREB1, FAM71F2, JMJD1C, COL5A3, RAE1,</i> and <i>GABRQ</i>) and 11 hypomethylated genes (<i>COL9A2, FAM179A, SLC17A2, PDE10A, PLEKHS1, TNNI2, OR51A4, RNF169, SPNS2, ADAMTSL5,</i> and <i>CYP4F12</i>) were identified. Two significant differentially methylated DNA repair genes, <i>JMJD1C</i> and <i>RNF169</i>, were found. Ancestry proportion results for African, European, and Indigenous American were 24.1%, 64.2%, and 11.7%, respectively. The identification of DNA methylation patterns related to PCa in H/L men along with specific patterns related to aggressiveness and DNA repair constitutes a pivotal effort for the understanding of PCa in this population.https://www.mdpi.com/1422-0067/22/2/733prostate cancerDNA methylationaggressive prostate cancerindolent prostate cancerGleason scoreHispanic/Latino |
| spellingShingle | Gilberto Ruiz-Deya Jaime Matta Jarline Encarnación-Medina Carmen Ortiz-Sanchéz Julie Dutil Ryan Putney Anders Berglund Jasreman Dhillon Youngchul Kim Jong Y. Park Differential DNA Methylation in Prostate Tumors from Puerto Rican Men International Journal of Molecular Sciences prostate cancer DNA methylation aggressive prostate cancer indolent prostate cancer Gleason score Hispanic/Latino |
| title | Differential DNA Methylation in Prostate Tumors from Puerto Rican Men |
| title_full | Differential DNA Methylation in Prostate Tumors from Puerto Rican Men |
| title_fullStr | Differential DNA Methylation in Prostate Tumors from Puerto Rican Men |
| title_full_unstemmed | Differential DNA Methylation in Prostate Tumors from Puerto Rican Men |
| title_short | Differential DNA Methylation in Prostate Tumors from Puerto Rican Men |
| title_sort | differential dna methylation in prostate tumors from puerto rican men |
| topic | prostate cancer DNA methylation aggressive prostate cancer indolent prostate cancer Gleason score Hispanic/Latino |
| url | https://www.mdpi.com/1422-0067/22/2/733 |
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