Periodic Reporting for period 4 - Epiherigans (Writing, reading and managing stress with H3K9me)
Berichtszeitraum: 2021-01-01 bis 2022-05-31
During development and tissue differentiation in multicellular organisms, H3K9me-mediated hetero-chromatin also represses tissue-specific genes that are inappropriate for a given tissue. Understanding how heterochromatin targets and silences these genes is key for understanding tissue generation and re-generation, for countering the misregulation of tissue specific genes in cancer and aging, and for preserving the integrity of the genome. These challenges are even more threatening in an aging society and are ever more relevant to medical application as therapies becomes targeted to specific genes or gene products. To provide just one example: immune-therapy for cancer is a powerful method that requires the reprogramming of the patient’s own T-cells to recognize and attack the tumor cells. This is only is only effective if neoantigens can be detected on the tumor cells, to prime the lymphocytes. Recent studies indicate that derepressed or misexpressed endogenous retroviral elements in the human genome are an important source of novel antigens (neoantigens) for T-cell programming. Their expression in cancer cells arises from the derepression of repetitive elements that normally would be repressed as heterochromatin. Identifying the controls over neoantigen expression and controlling thus contributes to more effective immunotherapy of cancer.
The objectives of our ERC grant were to understand what targets the H3K9 Histone methyltransferases (HMTs) to repetitive elements and to genes, and to identify what happens to cell and/or tissue identity when H3K9me3 deposition is abolished after tissue differentiation While it was assumed that the correct segregation of inactive heterochromatin and active euchromatin is essential for healthy tissue or organismal development, this becomes particularly important under conditions of stress or when cells lose their differentiated identity. We have established and characterized the role of H3K9me2/3 in restricting the expression of genes to individual tissues at various developmental stages, and we have characterized controls over the H3K9 HMT MET-2 (SETDB1 in man). Progress was also made in understanding what targets the H3K9 HMTs, MET-2 and SET-25 (G9a and SUV39 in man), and how they are controlled, which also helps us understand the genomic response to stress such as heat shock, tissue de-differentiation and viral invasion.
We then studied the role of spatial organization of heterochromatin in differentiated tissues – namely gut and muscle. We have shown that a lamin mutation causes deterioration of muscle in worms, recapitulating a human disease (Harr et al., 2020) and we have shown that in intestinal cells, the disruption of a strict sequestration of a euchromatic factor, CBP/p300, away from heterochromatin, leads to an activation of repressed tissue specific genes and loss of intestine-cell identity (Cabianca et al., 2019). Intriguingly, this depends on another histone H3 methylation mark, H3K36me2 or me3, and its reader MRG-1. Finally we have discovered a new principle of silencing that depends on selective nuclear degradation of transcripts. We showed that a complex called LSM2-8 – coupled with an RNA degrading machine (XRN-2) degrades specifically messages arising from genes repressed by the so-called Polycomb pathway, a system that maintains another histone mark on conditionally silent genes, histone H3K27me3. This mRNA degradation is the first proof that select mRNA turnover in the nucleus communicates to the compaction state of chromatin on genes. This has relevance for the innate immunity genes in man.
Our most important contribution from our ERC funded program of research was to show that continued expression of the H3K9 HMT, MET-2, is necessary for the maintenance of nondividing, differentiated tissues, such as muscle. We could show that MET-2 continuously restores H3K9me2 to repress germline and genes specific to other tissues, thereby allowing muscle cells to maintain their identity as muscle. This is achieved by preventing transcription factor access. Depending on the tissue type and stage of development, the loss of MET-2 provokes the derepression of different sets of genes, reflecting the transcription factor profile of that stage/cell type. This indicates that although H3K9me marks are dispensible for development in general, they are essential for long-term tissue maintenance.
To understand and intervene effectively in age-related diseases, we must detect degeneration early and be able to reverse or slow its progress. Our studies aim at understanding the molecular events that establish and maintain cell fate. With this, we have uncovered cellular markers that allow us to identify disease precociously whenever it is linked with a loss of tissue integrity. Not only early detection, but the use of biomarkers based on the underlying molecular mechanisms of age-related predisposition to disease, will help stratify patients for clinical trials, increasing trial efficacy. Finally, the same molecular epigenetic markers will help physicians select the most appropriate treatment or combination of treatments for an individual. The thorough implementation of genetic and epigenetic markers in patients will reduce the application of inappropriate treatments. Elucidation of cell status through epigenetic marks will also identify new drug targets. The outcome of all this is to transform medical practice such that it is no longer dependent on outdated diagnostics. In brief, understanding how euchromatin and heterochromatin states are maintained and segregated helps to advance medicine through a basic understanding of cell differentiation, cell fate determination, cell maintenance and reprogramming. Our work will profoundly impact regenerative medicine and disease modelling approaches.