The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study
Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> regulation and to determine the possible role of the e...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-12-01
|
| Series: | Journal of Clinical Medicine |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2077-0383/9/12/4020 |
| _version_ | 1797544891998273536 |
|---|---|
| author | Martyna Bednarczyk Edyta Fatyga Sylwia Dzięgielewska-Gęsiak Dariusz Waniczek Beniamin Grabarek Nikola Zmarzły Grażyna Janikowska Małgorzata Muc-Wierzgoń |
| author_facet | Martyna Bednarczyk Edyta Fatyga Sylwia Dzięgielewska-Gęsiak Dariusz Waniczek Beniamin Grabarek Nikola Zmarzły Grażyna Janikowska Małgorzata Muc-Wierzgoń |
| author_sort | Martyna Bednarczyk |
| collection | DOAJ |
| description | Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (<i>BECN1</i>—49 mRNA, <i>LAMP2</i>—62 mRNA, <i>PINK1</i>—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer. |
| first_indexed | 2024-03-10T14:07:54Z |
| format | Article |
| id | doaj.art-885b14d71c8145f0898395bc25840906 |
| institution | Directory Open Access Journal |
| issn | 2077-0383 |
| language | English |
| last_indexed | 2024-03-10T14:07:54Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Clinical Medicine |
| spelling | doaj.art-885b14d71c8145f0898395bc258409062023-11-21T00:30:55ZengMDPI AGJournal of Clinical Medicine2077-03832020-12-01912402010.3390/jcm9124020The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico StudyMartyna Bednarczyk0Edyta Fatyga1Sylwia Dzięgielewska-Gęsiak2Dariusz Waniczek3Beniamin Grabarek4Nikola Zmarzły5Grażyna Janikowska6Małgorzata Muc-Wierzgoń7Department of Internal Medicine, Medical University of Silesia in Katowice, 40-055 Katowice, PolandDepartment of Internal Medicine, Medical University of Silesia in Katowice, 40-055 Katowice, PolandDepartment of Internal Medicine, Medical University of Silesia in Katowice, 40-055 Katowice, PolandDepartment of Propedeutics Surgery, Chair of General, Colorectal and Polytrauma Surgery, Medical University of Silesia in Katowice, SHS in Katowice, 40-055 Katowice, PolandDepartment of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, University of Technology in Katowice, 40-055 Katowice, PolandDepartment of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, University of Technology in Katowice, 40-055 Katowice, PolandDepartment of Analytical Chemistry, Medical University of Silesia in Katowice, 40-055 Katowice, PolandDepartment of Internal Medicine, Medical University of Silesia in Katowice, 40-055 Katowice, PolandBackground: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (<i>BECN1</i>—49 mRNA, <i>LAMP2</i>—62 mRNA, <i>PINK1</i>—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer.https://www.mdpi.com/2077-0383/9/12/4020autophagycolorectal cancerexpression genesmicroRNAs (miRNAs)CpG islands |
| spellingShingle | Martyna Bednarczyk Edyta Fatyga Sylwia Dzięgielewska-Gęsiak Dariusz Waniczek Beniamin Grabarek Nikola Zmarzły Grażyna Janikowska Małgorzata Muc-Wierzgoń The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study Journal of Clinical Medicine autophagy colorectal cancer expression genes microRNAs (miRNAs) CpG islands |
| title | The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study |
| title_full | The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study |
| title_fullStr | The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study |
| title_full_unstemmed | The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study |
| title_short | The Expression Patterns of <i>BECN1</i>, <i>LAMP2</i>, and <i>PINK1</i> Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study |
| title_sort | expression patterns of i becn1 i i lamp2 i and i pink1 i genes in colorectal cancer are potentially regulated by micrornas and cpg islands an in silico study |
| topic | autophagy colorectal cancer expression genes microRNAs (miRNAs) CpG islands |
| url | https://www.mdpi.com/2077-0383/9/12/4020 |
| work_keys_str_mv | AT martynabednarczyk theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT edytafatyga theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT sylwiadziegielewskagesiak theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT dariuszwaniczek theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT beniamingrabarek theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT nikolazmarzły theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT grazynajanikowska theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT małgorzatamucwierzgon theexpressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT martynabednarczyk expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT edytafatyga expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT sylwiadziegielewskagesiak expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT dariuszwaniczek expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT beniamingrabarek expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT nikolazmarzły expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT grazynajanikowska expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy AT małgorzatamucwierzgon expressionpatternsofibecn1iilamp2iandipink1igenesincolorectalcancerarepotentiallyregulatedbymicrornasandcpgislandsaninsilicostudy |