Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level

Abstract Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from...

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Main Authors: Ruta Inciuraite, Ruta Steponaitiene, Odeta Raudze, Ugne Kulokiene, Vytautas Kiudelis, Rokas Lukosevicius, Rasa Ugenskiene, Kestutis Adamonis, Gediminas Kiudelis, Laimas Virginijus Jonaitis, Juozas Kupcinskas, Jurgita Skieceviciene
Format: Article
Language:English
Published: Nature Portfolio 2024-02-01
Series:Scientific Reports
Online Access:https://doi.org/10.1038/s41598-024-55076-8
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author Ruta Inciuraite
Ruta Steponaitiene
Odeta Raudze
Ugne Kulokiene
Vytautas Kiudelis
Rokas Lukosevicius
Rasa Ugenskiene
Kestutis Adamonis
Gediminas Kiudelis
Laimas Virginijus Jonaitis
Juozas Kupcinskas
Jurgita Skieceviciene
author_facet Ruta Inciuraite
Ruta Steponaitiene
Odeta Raudze
Ugne Kulokiene
Vytautas Kiudelis
Rokas Lukosevicius
Rasa Ugenskiene
Kestutis Adamonis
Gediminas Kiudelis
Laimas Virginijus Jonaitis
Juozas Kupcinskas
Jurgita Skieceviciene
author_sort Ruta Inciuraite
collection DOAJ
description Abstract Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
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spelling doaj.art-819509ae07bd4624808e09e732f50e092024-03-05T19:08:22ZengNature PortfolioScientific Reports2045-23222024-02-0114111010.1038/s41598-024-55076-8Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation levelRuta Inciuraite0Ruta Steponaitiene1Odeta Raudze2Ugne Kulokiene3Vytautas Kiudelis4Rokas Lukosevicius5Rasa Ugenskiene6Kestutis Adamonis7Gediminas Kiudelis8Laimas Virginijus Jonaitis9Juozas Kupcinskas10Jurgita Skieceviciene11Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesDepartment of Gastroenterology, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesDepartment of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health SciencesDepartment of Gastroenterology, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesInstitute for Digestive Research, Academy of Medicine, Lithuanian University of Health SciencesAbstract Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.https://doi.org/10.1038/s41598-024-55076-8
spellingShingle Ruta Inciuraite
Ruta Steponaitiene
Odeta Raudze
Ugne Kulokiene
Vytautas Kiudelis
Rokas Lukosevicius
Rasa Ugenskiene
Kestutis Adamonis
Gediminas Kiudelis
Laimas Virginijus Jonaitis
Juozas Kupcinskas
Jurgita Skieceviciene
Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
Scientific Reports
title Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
title_full Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
title_fullStr Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
title_full_unstemmed Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
title_short Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
title_sort prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of line 1 methylation level
url https://doi.org/10.1038/s41598-024-55076-8
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