Epigenetics: The Interface between Nature, Nurture and Malignant Disease

 

An earlier post from February described experimental evidence of the complexity in our understanding of causative factors behind carcinogenesis. Although driven in many instances by alterations in the genetic code, mutational events alone proved insufficient to account for cancer development or lack thereof in some experiments. Research pointed instead to the importance of timing of mutational events and the context in which they were occurring. Implicated in these experiments and of considerable interest for cancer ecology was the contributing effect of environmental factors on likelihood of cancer development.

If this is true, that is that environmental factors, including both intrinsic as well as extrinsic influences contribute to oncogenesis, as seems likely from much cumulative experience from environmental studies, then it raises the question of just how is that those environmental signals, which themselves may not be mutagenic, would none-the-less come to influence chances for neoplastic development. Where is the interface between the environment and the genome, between nature and nurture? How too connected? The answer at least in part stems from an understanding of a key regulatory system governing the activation and transcription of genes into RNA, that is the expression of a gene. The system controlling this access of nuclear transcription machinery to information stored within the genome has been termed the epigenome (epi- from Latin, to be above, upon).

This control is achieved through a set of alterations to either DNA itself in the form of covalently bound methyl groups (one carbon atom surrounded by three hydrogen atoms) to the nucleotide cytosine or to alterations in chromatin, the nucleoprotein constituting our chromosomes. These changes in either the DNA molecule itself or to chromatin, sometimes referred to as marks, act to either block RNA polymerase binding to DNA causing the gene to be silent or in the case of chromatin, leading to conformational changes in the chromosomes having a similar controlling effects of gene expression. Attached below is a link to a talk by Carlos Guerrero-Bosagna, Senior Lecturer, Uppsala University, illustrating this system. 

https://youtu.be/_aAhcNjmvhc?si=Fb4xN3f8x-NNAIn9

The study of epigenetics has proven to be essential in understanding one of life’s greatest mysteries, that of ontogeny, our development. It addresses the paradox of how it could be that every cell in an organism’s body contain essentially the exact same genomic information but yet in development lead to the occurrence of multiple cell subtypes within that organism, each distinguished by a specific functional capability, what is termed a cell’s phenotype, its character. Epigenetics has allowed the description of pathways or channels, their formation acting to guide cells from an initial state possessing a broad range of potential capabilities, termed stem cells or ‘seed cells’, toward that of a narrower or differentiated state, sometimes referred to as that cell’s fate.

These channels are formed and maintained by an epigenetic information network of genes whose expression products are enzymes capable of modifying DNA and chromatin. These modifications then may have several effects on either silencing or alternatively enhancing regions the expression of genetic information allowing the expression of a more selected set of genes for read out, that is the particular genetic information needed for subsequent cell maturation to achieve that cell’s destiny. Also, recently we have learned how this regulatory capability of the epigenome is subject to reversibility permitting a return to a more stem-like state of pluripotency, the ability to give rise to multiple cell types. Importantly, this process of gene output control through DNA/chromatin modification proves to be vulnerable to random change, what is termed stochasticity. Such disruption of the ordinarily parsimonious selection of genetic information permitting differentiated cell state development has important implications for oncology as we are now beginning to understand how this process of turning on and off specific genetic information for phenotypic expression may become corrupted potentially leading to neoplasia.

Some cells however retain their ability to alter their character, reverting back to a pluripotent state, a process referred to as lineage plasticity. This retained flexibility serves as a means by which tissue regeneration may occur allowing an organ system to respond to and recover from injury. Such a response includes a reversal of a differentiated state back into an earlier state of stemness, termed stem cell fate switching, needed to repopulate a cell community. This needed phenotypic flexibility enables cells to migrate to areas of injury, expend energy, communicate with vascular and immune response elements as well as sponsoring cellular growth leading to wound repair. Reversibility of cell state then represents an important mechanism for mature organisms to surmount organ injury and recover normal organ homeostasis.

Unfortunately, it also provides an avenue for dysregulated injury response. In situations where there is a failure to resolve lineage plasticity following injury recovery that failure will have the effect of opening the door for an untoward neoplastic response in an environment of sustained dedifferentiation. Cancer has been described as a wound that cannot heal. When organ injury becomes chronic, such as prolonged exposure to toxins or chronic inflammation, a state of persistent stemness in affected tissue may result. This need for an expanded repertoire of responses to chronic injury in turn requires ongoing, broad access to genetic information, a more open ‘library’ of active genes to sustain the multiple phenotypic traits needed to address the unending insult. In such a situation, where much genetic information is being generated at a large scale, the chances for miscommunication can only grow.

Andrew Fineberg, Professor of Biomedical Engineering at Johns Hopkins University has described cancer as a disease of phenotypic plasticity. He has described this development as a consequence of accompanying disordered epigenomic regulation to account for several of cancer’s notorious characteristics including alteration in cell metabolism, tumor cell heterogeneity, an ability of malignant cells to invade surrounding tissue and then disperse through metastasis and the development of resistance to treatment (A Fineberg, NEJM 378;14, 1323-34). To understand this, he describes in a graphic listed below first the normal state of genome balance, poised between regions of condensed chromatin, termed heterochromatin, recognizable by cytologists as dark staining, clumpy material, usually aligned along the periphery of a cell’s nucleus and associated with an accompanying restrictive environment for DNA transcription. This contrasts with euchromatin, chromatin found in an ‘unwound’ configuration, often centrally located within the nucleus, allowing transcriptional access for gene expression and recognizable by microscopy as areas of ‘open’ or less condensed chromatin.

The Cellular Nature of Epigenetic Information.

The DNA double helix is modified at the nucleotide cytosine by DNA methylation (brown dots). The nucleosomes around which the DNA is coiled undergo post-translational modifications of their component histones (green dots, depicting activation marks; red dots depict silencing marks), leading to gene activation (light-blue nucleosomes, with RNA transcripts originating nearby) or silencing (dark-blue nucleosomes). Higher-order chromatin structure involves nucleosomal compaction often near the nuclear membrane (heterochromatin) or nucleosomal accessibility (euchromatin). The nuclear periphery is primarily repressive but probably also contains transcriptionally permissive subcompartments. Higher-order large blocks of heterochromatin often involve large epigenomic domains termed lamina-associated domains (LADs) and large, organized chromatin lysine (K) modifications (LOCKs). In cancer, both large and smaller heterochromatic domains become euchromatic. In addition, epigenetic modulators such as environmental exposure and aging, as well as cancer mutations in epigenetic modifier genes, affect the expression of epigenetic mediators controlling pluripotency and cellular self-renewal. All these factors lead to increased stochastic gene expression in cancer, promoting tumor-cell heterogeneity and cancer-cell survival in a changing environment (e.g., as a result of metastasis or chemotherapy).

 Imagine for a moment a situation in which the epigenetic control of this balance between open and closed reading for gene expression became less predictable, that is it became more stochastic. In such a situation, an increasing randomness of gene output would be expected, affecting what ordinarily is an energy efficient, dynamic, and highly conserved operation of that affected cell. The resulting dependability to maintain a cell’s phenotype necessary for organ homeostasis would in turn become less reliable. The resulting effect for organism health on account of this unpredictability might be consequential. Using a metaphor from human society, loss of diminished civil authority might encourage a ‘mutiny’ to break out.

This problem of impeded fidelity for reading information from a source and transmitting that information to a receiver in an accurate fashion was recognized a little less than a century ago. Pioneered initially by Claude Shannon, working in a research lab of the Bell Telephone Company, then interested in improving the quality of telecommunications. As an example of this problem, consider the static sound a listener might hear on a long distance telephone call or when trying to listen to their favorite radio station. Efforts to suppress this informational ‘noise’ might include adjusting the frequency of the receiver or just turning up the volume. The efficiency of a communication system in suppressing this noise and successfully transmitting a signal retaining its information content has been termed that system’s entropy and reflects the inevitable occurrence of randomness inherent in storing and sending information. It is analogous to the physical chemistry concept of entropy as a measure of system disorder and loss of system energy available for useful work.   

Central then to a discussion of cancer causation is an acknowledgement of the importance in understanding perturbations in the epigenome to account for this phenotypic instability characteristic of malignancy. Fineberg has proposed a classification system of epigenetic information based on the mechanism by which DNA and chromatin alterations occur. In this classification, the primary epigenetic controllers, termed epigenetic modifiers, are those genes, often subject to mutation, whose enzymes products directly methylate DNA to silence their expression or conduct post translational modification of histones of nucleosomes through enzymatic addition of one of several types of ligands, often the amino acid lysine. The effects of that ligation may lead to an alteration in chromatin’s three dimensional configuration, closing off sometimes entire regions of chromatin to have a similar effect. These marks are not necessarily permanent however and are subject to ‘erasure’ by an additional set of enzymes allowing the important mechanism of phenotype switching to support wound healing. As an aside, that some of these marks may be retained during cell division and then transmitted through heredity has enormous potential implications for understanding hereditary disease.

Fineberg describes a second class of epigenetic influence occurring upstream from the gene modifiers, the epigenetic modulators, a set of influences extrinsic to a cell including those from the environmental, from inflammation, malnutrition and aging which may have the effect of altering the intracellular environment and adjusting the regulatory supervision of the genome by the modifier genes. This modulation, which Fineberg describes as a ‘bridge’ between the environment and the genome allows to connect these external forces in understanding carcinogenesis. These modulating external forces may have the effect of destabilizing the normal epigenetic state, refocusing the transcriptional process to influence the downstream effects on target genes of the epigenetic modifiers, termed the epigenetic mediators. For cancer ecology, interested in how environmental factors affect neoplastic development and progression, this important linkage between exposure to a ‘deleterious’ neighborhood and the resulting increase in epigenetic disorder, an increase in network entropy, is worth exploring. It provides a basis for understanding a common pathway by which stochastic gene expression, occurring by way of either mutational impairment in a program of epigenetic modification and/or environment-influenced gene modulation will undermine cellular order and then lead to  subsequent cancer.  

An upcoming post will take a closer look at the relationship between lineage plasticity mediated through epigenetics and its relationship with gene expression entropy. This discussion has been brought about by advances in molecular biology including the ability to sequence the RNA of individual cells to better understand how stochasticity contributes to cancer. That discussion will include a renewed look at what had been previously an historic description of developmental pathways, the epigenetic landscape, to visualize how stochasticity leads to phenotypic plasticity, epigenetic instability, and cancer.