Download Supplemental File S3. Tumorigenesis-Instructor

“Genetic Alterations During Colorectal-Tumor Development”
N. Engl. J. Med. 319, 525–532.
Abstract
The first paragraph (only) of the abstract from Vogelstein et al
(1988) is presented here.
The first paragraph contains enough information for students to
gain an understanding of the main points of the study without
learning the results of the study.
http://www.ncbi.nlm.nih.gov/pubmed/2841597
http://www.ncbi.nlm.nih.gov/pubmed/2841597
Vogelstein, B., Fearon, E.R., Hamilton, S.R., Kern, S.E., Preisinger,
A.C., Leppert, M., Nakamura, Y., White, R., Smits, A.M., and Bos, J.L.
(1988). Genetic alterations during colorectal-tumor development.
N. Engl. J. Med. 319, 525–532.
Methods
Only the first section of the methods entitled “Patients and Tumor
Selection” from Vogelstein et al (1988) is presented here.
This section contains enough information for students to gain an
understanding of how this clinical study was carried out.
After students have read over the selected sections of the
abstract and methods the instructor may ask student volunteers
to describe the study in a few simple sentences. Instructors can
introduce the term “retrospective study” after the students have
offered their explanations. The priming activity involving
experimental design should have helped the students interpret
the methods.
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1. Using the data presented in Table 1, calculate the totals and percentage of Class I, Class II, Class III and Carcinoma
specimens that are positive for Ras gene mutations and answer the following questions.
a.
What is a mutation?
Mutations are permanent changes in the DNA. They do not always lead to an altered protein or RNA
product. Mutations can occur anywhere in the genome; not just in a region defined as a “gene”. Mutations
occur at the level of DNA; a mistake in the transcription or translation process results in a mistake in one
copy of a product (mRNA and/or protein) which is not a mutation.
b. How do you interpret the “Mutation” column in Table 1?
The investigators are pointing out the location (Codon 12, Codon 13, etc…) of the ras mutations. Students
may point out that K-ras and N-ras genes are different genes within the ras family. The investigators are
also demonstrating the actual DNA change (GGT = wild-type, GAT = mutation) and how the DNA change
leads to a different amino acid in the final ras protein product (GLY to ASP).
2. According to Table 1, what class (es) of tumors has the highest frequencies of Ras mutations?
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Only 12.5% of Class I tumors have ras mutations while Classes II, III and carcinomas have 42%, 57.1% and 46.7%,
respectively. While Class III tumors have the highest true percentage, students should notice the low frequency of ras
mutations in Class I adenomas compared to the other types.
3. Analyze the data presented in Table 2. What histopathological feature of adenomas is most highly correlated
with Ras mutations?
Tumor size seems to correlate most strongly with ras gene mutations. Tumors that are greater than 2cm have a higher
frequency of ras mutations regardless of tumor class or other histopathological features.
Some students, who have taken a histology course or have other experience, may be more comfortable with the
terminology describing the morphology (tubular, villous) and level of dysplasia. Students can usually resolve their
confusion by discussion (with peers and instructor) or looking up these terms if they need to. It is not a major point that
students know exactly how “tubulovillous” specimens appear.
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4. Vogelstein et al. investigated allelic deletions in colorectal tumors at three different chromosomal locations. The
data is presented in Table 3. In 1988 the genes of significance located on 5q, 18q, and 17p had not yet been
identified.
What broad class of genes are most likely located in these regions of chromosome loss? Explain your reasoning.
Because these loci have been deleted (or “lost”) in tumor specimens, one would suspect that Tumor suppressor genes or
other growth-suppressor gene would most likely be found in these regions. Proto-oncogenes (or oncogenes), or other
pro-growth genes would not be likely candidates as their “loss” would not offer a selective advantage to rapidly dividing
tumor cells.
Instructors can also point out that the human genome was decades away from being completely sequenced at the time
of this publication (1988) and our knowledge of genome mapping was much less than it is now. Instructors may point
out that, in reality, more than one gene was probably located at the chromosomal regions described (5q, 18q, 17p).
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5. Use the data presented in Tables 1 and 3 to create a figure that shows the percentage of each type of genetic
abnormality found in each type of tumor (Class I, Class II, Class III and Carcinoma). Include an appropriate figure
description.
Figure X. ____________________________________________________________________________________
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Instructor notes
Vogelstein et al (1988) presented the data in a line graph (see Figure 2 of the original manuscript) but allow
students to decide on how to best present the data.
After all student groups have had enough time to work through the activity the instructor may invite one or
more groups to the white-board to sketch draw their figure for the class, especially if one group presents a
bar graph and one presents a line graph. Figure descriptions should be included.
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6. Based on the data presented in this paper, construct a model of colon tumorigenesis showing where the four
genetic alterations (ras mutation, 5q, 18q, and 17p) are most likely located on the pathway.
Instructor notes
The instructor should draw the above figure on the white-board without the genetic alterations appearing.
After all students have had time to work through the activity, one member from each group should be
invited to the white-board to indicate where they think the ras mutation, 5q, 18q, and 17p alterations
appear in the model.
Although this is a simple model containing only four alterations, all student groups should come up with the
same conclusions. If there are differences in the models, they can be explored in a group discussion.
Students may also recognize that human cancer is incredibly complex and there is no model of molecular
alterations that will hold true for 100% of the population.
The instructor should point out that students came to the same conclusions as the authors of this study.
A slightly more complex model was presented in the following publication from 1990:
Fearon, E.R., and Vogelstein, B. (1990). A genetic model for colorectal tumorigenesis. Cell 61, 759–767.
An updated model is presented in the following publication from 2009:
Walther, A., Johnstone, E., Swanton, C., Midgley, R., Tomlinson, I., and Kerr, D. (2009). Genetic prognostic
and predictive markers in colorectal cancer. Nat. Rev. Cancer 9, 489–499.
7. What are scientific models? Explain why scientists create and use scientific models.
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Answers will vary but students should recognize that models allow scientists to:
-communicate their ideas about a particular phenomenon
-evaluate/compare experimental data with existing models
-ask new questions and design new experiments about a particular phenomenon
-frame or anchor a variety of data/results in a logical way
Students may also recognize that the term “model” can refer to different things depending on the situation. Some
examples may include:
-physical, hand-held objects
-computer or mathematical algorithms
-schematic diagrams or drawings
-computer-generated images or animations
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