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Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying the mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in the growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we studied histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks and compared them with data on their tissue of origin. We found that, besides the expected changes in short-term culture, the organoids showed profound changes in their epigenomes also during the long-term culture. The most prominent were epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We showed that a long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process was disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER) stress and Wnt activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during a long-term culture involve DNA demethylation that ceases if the metabolic adaptation is disturbed.

Background: Transplantation of the liver entails a state of altered recipient immunologic competence. There are only scarce data concerning the impact of host immunologic factors on the outcome of liver transplant recipients in the context of hepatocellular carcinoma (HCC). Material/Methods: Our study focused on evaluating the presence of tumor necrosis and frequency levels of angiopoietins and monocytes/macrophages subtypes in the host liver prior to liver transplantation (LTX) and their association with recurrence, graft rejection, survival, and clinical prognosis after LTX. Formation of tumor necrosis and tissue densities of angiopoietins and cellular immunologic infiltrates – CD68+ and CD163+ macrophages (TAMs) and TIE2-expressing monocytes (TEMs) – were quantified in recipient HCC specimens. The densities were then matched with clinicopathologic variables and patient survival after LTX (n=88). Some patients were treated prior to LTX by neoadjuvant transarterial chemoembolization (TACE, n=55). Results: Recipient hepatic infiltration with TEMs and CD68+ TAMs was associated with decreased 1-, 3-, and 5-year survival, as well as metastatic and recurrent HCC after LTX (all p

Additional file 3: Table S1. Antibodies and reagents used for immunohistology. Table S2. Association of the presence of liver steatosis with clinicopathological characteristics of patients with hepatocellular carcinoma as determined by the chi-squared (χ2) test. The Fischer test was applied when the number of patients in the subgroups was less than five (n

ChIP-qPCR for selected genes. (DOCX 114Â kb)

Comparison of epigenetic states in intestinal tissue and isolated intestinal cells [22]. (DOCX 515Â kb)

Results of the SOM analysis of the epigenetic profiles. SOM portraits and additional information about affected gene sets. (DOCX 389Â kb)

Molecular characterization of Set1 and Set2 genes in isolated intestinal cells. Published MBD- and RNA-seq data on Set1 and Set2 genes [22]. (DOCX 73Â kb)

Set1 and Set2 genes in mouse and human intestinal tissue. Comparison of Set1 and Set2 genes in mouse and human tissue [3]. (DOCX 888Â kb)

Peak characteristics of histone methylations of mouse intestinal samples [54]. (DOCX 543Â kb)

Details on the radiation response [33]. (DOCX 196Â kb)