Re: Making Cellular Memories, a Guest Post

Last month I wrote about my friend Devin Burrill's paper about synthetic memory in yeast cells. There were a lot of really interesting questions left in the comments, and I asked Devin if she would write a guest post to answer them. She agreed and here it is, answers to your questions straight from the author!

Hello Readers!

My name is Devin, and I am so incredibly grateful to Christina for allowing me to write an entry on her awesome blog. Christina and I are friends and work together in the lab of Pamela Silver at Harvard Medical School. I am writing in response to a number of excellent questions posted about Christina's entry on my recent paper, "Synthetic circuit identifies subpopulations with sustained memory of DNA damage" (Burrill, et al. Genes & Development, 2011).

One reader asked about the initiation of heritable damage responses: "Is damage restricted to random acts of nature, or can there be such a thing as self-damage....that will nevertheless be heritable?"

DNA damage can come from within an organism, as well as from external sources. External sources tend to be obvious and well-known by the informed public (e.g. UV or IR radiation, drugs, smoking). Less obvious is the fact that pools of a DNA damaging reagent known as reactive oxidative species (ROS for short) are created all the time by our own cells via mitochondrial respiration.

Mitochondria are organelles that likely evolved from bacteria billions of years ago. They function as the "powerhouse" of the cell, generating cellular energy in the form of adenosine triphosphate (ATP) via the respiratory chain (RC) located at the inner mitochondrial membrane. Electrons move along the RC, reducing molecular oxygen at the end. If single electrons leave the RC earlier, ROS are generated. Incompletely reduced oxygen (superoxide radicals: O2-) can be transformed to H2O2, then leading to free hydroxyl radicals. Hydroxyl radicals are one of the most damaging forms of ROS, mutating the DNA backbone and even the DNA bases themselves. This source of internal DNA damage is simply part of a cell's natural biochemistry. As people age, however, ROS production tends to worsen because the mitochondria also age and become less efficient at tracking electrons all the way along the RC. This source of internal damage is actually hypothesized to be a main contributor toward the human aging process --- as promiscuous ROS production increases, so to does DNA damage caused by ROS, resulting in dysfunctional biological processes. Thus, damaged mitochondria are inherited over time as people age, though the exact mechanisms are how this happens are not completely understood.

Another reader asked about the nature of the observed cellular memory: "Do the cells that retain this memory of an experience then pass on that memory to those they have been divided into?...And how many generations does this affect?" Yes, the idea is that a single cell experiences the damage and responds in a specific way which is somehow recorded, thus changing the cell's biological makeup. We were interested in changes that were subsequently passed on to daughter cells when the original cell divided. The fluorescent memory loop allowed us to track the damage response from the original cell that experienced it to the daughter cells. We tracked the response for 48 hours after DNA damage, which means that the original cell divided approximately 20 times, resulting in lots of fluorescent daughter cells. A sustained response that lasts 20 cell generations is remarkable, given the propensity of the yeast S. cerevisiae to re-set its biological clock when its divides. However, one could imagine studying the response for even longer periods of time. There's really no limit!

The same reader then went on to ask a very important question, which really gets at the meat of the project: "Can the effects of this experience ever be completely erased from the genome if the experience itself is replicated or repeated in a particular environment? And is this perhaps one of the ways that cells evolve to anticipate and deal strategically with a multitude of problems?" I believe the reader is asking whether experiencing and responding to the damage once can impact how the cell responds to the same experience if it happens again. This question brings forward the idea of biological hysteresis --- does a past event allow a cell or system to respond differently to future events because memory of the past event persists? It's possible that initial exposure could result in heritable epigenetic marks or stable cytoplasmic factors, for example, that will permit a "better" response to a second exposure of the same damaging agent. While some previous work has looked at cellular responses to multiple doses of damaging agents, these studies are flawed by the fact that they take place at the whole population level, thereby diluting out any long-term effects that occur within distinct subpopulations. Now that we have engineered a device that allows for the isolation of two distinctly-responsive subpopulations, we can more properly examine the role of hysteresis in DNA damage response. Will one subpopulation respond better to a second dose of damage? If the system were moved to mammalian cells, would one subpopulation be more resistant or susceptible to multiple rounds of chemotherapy? In our paper, we laid the groundwork for exploring these questions and are now pursuing these very lines of research.

I cannot say how exciting it is to get questions like the ones proposed by Christina's readers. They are very thoughtful and insightful. Thank you so very much for asking them, and thank you for letting me answer them!

Take care!

---- Devin