Ionizing-radiation Toxicogenomics

In class we recently read:

Genetic analysis of radiation-induced changes in human gene expressionSmirnov DA, Morley M, Shin E, Spielman RS, Cheung VG. Nature. 2009 May 28;459(7246):587-91. Epub 2009 Apr 6.

Humans are exposed to radiation through the environment and in medical settings. To deal with radiation-induced damage, cells mount complex responses that rely on changes in gene expression. These gene expression responses differ greatly between individuals and contribute to individual differences in response to radiation. Here we identify regulators that influence expression levels of radiation-responsive genes. We treated radiation-induced changes in gene expression as quantitative phenotypes, and conducted genetic linkage and association studies to map their regulators. For more than 1,200 of these phenotypes there was significant evidence of linkage to specific chromosomal regions. Nearly all of the regulators act in trans to influence the expression of their target genes; there are very few cis-acting regulators. Some of the trans-acting regulators are transcription factors, but others are genes that were not known to have a regulatory function in radiation response. These results have implications for our basic and clinical understanding of how human cells respond to radiation.

This paper described the reseachers efforts to identify classes of genes that may serve as potential markers of radiation sensitivity. To accomplish this the investigators examined gene expression patterns of radiation exposed cells.

Tox1401 Students: How did the reseachers do this? What cells did they use and why? What is the difference between cis-regulatory and trans-regulatory factors? Give an example of each from the paper and describe the function.

Tackling childhood asthma Pharmacogenetics

Child hood asthma is part of our national health care challenge. An estimated 9.6 million children (13.1 percent) under the age of 18 have been diagnosed with asthma. It is hoped that pharmacogenomics can make treatment a bit more successful for those with asthma. The question so far has been how?

In their 2010 paper Kondo et al. describe the beginnings of a clinical workflow, based on the consolidation of a number of genetic/therapeutic correlation studies. The authors suggest that a combination of clinical evaluation steps combined with a knowledge of specific allelic subtypes  carried by the patient could provide more effective therapeutic choices. The authors point out that there are ethical considerations when genetic information is recorded and detailed. But what they provide is a remarkably simple workflow chart integrating pharmacogenomic information with clinical observation.

I have asked the Tox 1401 students to describe at least one of the gene polymorphisms and mutations from this paper, so read on in the comments if you would like to learn specifics.

3rd Toxicogenomics Laboratory ASL Activity

Last year we started using our pharmacogenomics laboratory to reach out to students in the community. This year we invited 6th through 8th graders from a local schools. I have asked the pharmacogenomic students for feedback on their experiences as they served as student teachers. A repeating cycle is one of the interesting ways to think about teaching. If you are a student responding I would ask that you comment on your use (or not) of this cycle as well as addressing the following ASL reflection points:

  • How does your service learning experience relate to the objectives of this course?
  • What did you observe?
  • What did you learn?
  • What has worked? What hasn’t?
  • Is there something more you could do to contribute to the solution?
  • What have you learned about yourself?
  • What have  you learned about teaching?
  • What have you contributed to the students?
  • What values, opinions, beliefs have changed?
  • What was the most important lesson you learned
  • How have you been challenged?
  • What impact did you have on the community?

Toxicogenomics – Many many genes…

Way back when… in 2000, microarray was the new wave of technologies to address a scientific challenge that has been around for a long time. If we think  about how an organism responds to an environmental change, disease, or new stage of development there is a corresponding change at the gene expression level. This change in gene expression provides for a host of new proteins that will be needed, and the suppression of all of the proteins that will not be needed.

The challenge was how would we be able to capture hundreds, maybe thousands of these changes… at the same time. We needed a molecular “snap-shot” of all of the mRNAs in a cell before the change, followed by another after the change, and then we needed the ability to sort out the results.

Enter the microarray. The paper referenced above provides a nice overview of the challenges the were faced, and the technologies that were developed to face these challenges.

I have asked the Tox 1401 students to pull out some of the genes mentioned in the paper and take a look at the annotated information about their gene of interest from OMIM and UniProt. If you would like to see their descriptions please move on to the comments section.

Is siRNA Therapy Safe?

Often described as the next frontier in gene therapy, siRNA has moved from the realm of the quirky biological oddity to applied therapy very quickly. I have asked the Tox1401 students to describe what they see as potential toxicological problems with this approach.

We used this paper as a description of the possible delivery approaches. The paper is freely (and fully) available from pubmed central.

Read on through the comments to see what they came up with.


How Complex Is Life?

As the human genome project’s influence grows, one of the concepts that has emerged is complexity. Scientists including biologists have appreciated for some time that genetic networks drive development and biological responses. The cell’s responses to stimuli require and ever changing cast of proteins. The instructions for the protein sequences are encoded within the genome. If we could understand how this large cast of proteins is assembled into smaller pathways and responses we would be considerably further along. The parts list is long and complex, but as the genome project began to uncover the instructions for how the “parts” are made there was a feeling that science may be able to build models that describe function and disease.

The 2010 Nature article describes this aspiration:

The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved

And indeed this did (and still does) seem like a reasonable approach. Biological networks have turned out to be as complex as we could have hoped. Systems biology is still moving forward, but the sheer number of possible rules that govern how all of the cellular parts work together and interact suggest that we will be working with this complexity for some time. There is a universe of rules that describe networks; explaining how proteins, ligands, nucleic acids and more interact and result in function.

Towards the end of the article there is an interesting quote from Bert Vogelstein:

“Humans are really good at being able to take a bit of knowledge and use it to great advantage,”

And we are. With some careful science and good detective skills we can take what we do know and put it to good use, combating disease. The fact that biological systems are complex and that this complexity is not simply going to be understood the first time we draw back the curtain is a great finding.

I am asking the Tox1401 students to look into this complexity a bit further. Let’s start with a pathway database like Choose the phase II pathways and select a single protein within that pathway, perhaps the NAT1 arylamine N-acetyltransferase. Provide a description of the protein, and the pathway that it takes part in.

Proteins With Altered Conformations As Agents Of Disease

Prions have been described for some time in the literature, and certainly are known to the public as Mad Cow Disease. You can read more about prions here.

PDB generated prion image

One of the vexing questions about prions is dose, or more simply is there any threshold amount of material contaminated with prion proteins that might be safe? Prions themselves are very tough and stable proteins. Unlike more other infective material that the public is familiar with, there is no safe way to “cook” meat contaminated with prions that will make it safe for consumption.

With this in mind a research group is looking to see if there is such a threshold dose. Using concepts cribbed from toxicology a lab has looked to see if there is a dose low enough at which prion exposure would not lead to disease. You can read the original paper here, but the take home is that there is no safe dose.

When we were looking through the literature on protein folding diseases, a second paper lept into the light, a recent Tau paper, describing the spread of a misfolded tau protein along the intertwined pathways of neuronal cells. This phenomenon is called “tauopathy”; the progressive spread of misfolded tau protein along specific routes through the brain. This pathology is associated with the development of Alzheimer’s disease. One of the unique findings to this work is the decoding of the spread from one spot to another, involving the jumping of the misfolded protein from neuron to neuron.

Though not yet reproduced this finding holds much promise for future Alzheimer’s disease therapeutics as the protein’s march from cell to cell may provide a weak spot in transmission, allowing us to halt the spread of the misfolded protein, and the progression of the disease.

I am asking the Molecular Toxicogenomics students to  write up a post describing how misfolded proteins can be the agents of disease, so if you are interested in the topic, click on through to the comments to get involved in the discussion.

Watson & Crick In 1953


watson-and-crick-1953In their 1953 “Molecular Structure Of Nucleic Acids” Watson and Crick open with the decidedly unscientific “We wish to suggest…” and in only a short page or so, take us through their thoughts on what shape DNA takes in the natural world. With a tone, that is though decidedly academic, conversational in the way it winds from chemistry to other laboratories take on what structure DNA might take. The paper is notable for what is not present as well. After a careful description or at least inventory of the facts supporting their structure, they proceed to open up a new avenue of discusion; suggesting how the model might relate to the observed biology. In one of the final paragraphs they lead with “It has not escaped our notice…”. They hint that the structure they have described, suggests that there is a very simple solution to another vexing problem remained unsolved in 1953. How does DNA copy itself, and how does it do so quickly?

Here Watson and Crick speculate that they have solved an important piece of this puzzle, and interestingly do so without directly stating what their speculation is! As is to pass off the impoliteness they assure us that these speculations and more data will follow.

They write as if they are having a conversation with you, an old colleague. When in fact they seem to have carefully crafted their thoughts so the reader can follow the unfolding story as if discovering the structure themselves.

For your first assignment I want  you to compose a paragraph or two, describing your scientific response to the idea that DNA is an anti-parallel double helix. Write for a broader audience, not just scientists. Explain why this discovery is important, not from today’s perspective, but how you imagine a scientist in 1953 might respond.

So How Did It Go?

For your final post I would like you to trouble shoot this class. You have all worked very hard learning the ins and outs of a new and growing field. If you stay in the sciences you will surely hear more about this field as you continue your careers. I am proud of how hard you have worked and the commitment that you all have put in. Now you are my experts in the class and I would ask for a few minutes of thought and some feedback.

  1. How was the textbook? Would you choose another? What about “Essential Cell Biology“?
  2. What would you change about the class? Why?
  3. What would you keep? Why?
  4. Did you find the papers useful?
  5. Did you find the peer comments useful?
  6. Did you find the writing center sessions useful?
  7. What topics would you like to hear more about?
  8. What topics would you like to hear less about?