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Ghost in Your Genes

Classroom Activity

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Activity Summary
Students model how scientists use DNA microarrays to determine levels of gene expression in breast cancer patients, and then choose treatments based on what they learn.

Learning Objectives
Students will be able to:

  • define DNA microarray and gene expression.

  • describe how microarrays are used to determine gene expression.

  • explain how understanding gene expression can lead to improved treatments for disease.

Materials for Teacher
  • 1 white plastic ice cube tray per team, with at least 12 wells
  • 500 mL vinegar
  • 600 mL salt water (600 mL water mixed with 6 Tbsp. salt)
  • 500 mL of water
  • pipettes
  • small self-stick notes
Materials for each team
  • copy of the "Checking Up on Genes" student handout
    (PDF or HTML)
  • copy of the "How DNA Microarrays Work" student handout
    (PDF or HTML)
  • copy of the "Gene Locations on Array" student handout
    (PDF or HTML)
  • copy of the "Cancer Therapies" student handout
    (PDF or HTML)
  • 15 mL of phenolphthalein
  • pipettes

Background
Normal-functioning DNA codes for proteins through the processes of transcription and translation. During transcription, one strand of DNA in a cell's nucleus is used to synthesize a strand of mRNA. After the mRNA is produced, it moves into the cell's cytoplasm. During translation, transfer RNA (tRNA) and the cell's ribosome work together to create a protein by building a series of amino acid sequences specified by the nucleotides in the mRNA. (The tRNA transports the amino acids while the ribosome synthesizes them into proteins.) Proteins are involved in nearly every aspect of the physiology and biochemistry of living organisms.

Transcription diagram

If a DNA molecule mutates, it may produce faulty proteins. If these proteins are involved in controlling the processes of cell growth and division, the mutation could trigger a cell to become abnormal and divide uncontrollably. For many years, this was the only mechanism known to cause cancer. Treatment of this type of cancer mainly relied on trying to destroy the mutated cells.

But researchers have now discovered that cancer can be triggered by epigenetic changes—modifications to mechanisms associated with DNA that alter gene expression without mutating the original DNA. These changes are like switches turning genes on and off. Some epigenetic effects turn on, or activate, genes that stimulate tumor growth; other effects turn off, or silence, genes that would normally suppress tumor growth. Since epigenetic changes do not alter the DNA sequence itself, they hold the promise of being chemically reversed with drug (and potentially nutritional) therapies.

Cancer may be caused by several different mutations or epigenetic changes that cause genes to be expressed (turned on) and/or silenced (turned off) when they should not be. By identifying which genes in the cancer cells are working abnormally, doctors can better diagnose and treat cancer.

One way scientists try to determine which genes are working abnormally is to use a DNA microarray (see "How DNA Microarrays Work" student handout for a complete description of how these arrays function). These gene-expression "fingerprints" allow a doctor to determine both the genes involved in a patient's cancer and the possible reaction of each patient to different drug treatments. This activity models how doctors use microarrays to determine levels of gene expression in breast cancer patients and then choose treatments based on what they learn.


Key Terms

chromosome: A tightly coiled macromolecule of DNA and its associated proteins. Chromosomes contain many genes. Sexually reproducing organisms have two of each chromosome, one from each parent. Organisms vary in the number of chromosomes they have.

complementary DNA (cDNA): A single strand of DNA synthesized in the lab to complement the bases in a given strand of messenger RNA. Complementary DNA represents the parts of a gene that are expressed in a cell to produce a protein.

deoxyribonucleic acid (DNA): A double-stranded chain of nucleotides. It carries a cell's genetic information and is found in the cells of all living organisms. It is capable of self-replication and the synthesis of RNA.

DNA microarray: A collection of microscopic DNA spots attached to a solid surface, such as glass, plastic, or silicon chip, forming an array. Scientists use DNA microarrays to measure gene expression levels.

gene: The basic unit of inheritance. A gene is made up of a sequence of four different bases: A (adenine), T (thymine), G (guanine), and C (cytosine). The way that these bases are combined determines the gene's function. Genes control the production of proteins.

gene expression: The process by which the information encoded in DNA is converted into a final gene product (i.e., a protein or any of several types of RNA).

genome: An organism's basic complement of DNA.

messenger RNA (mRNA): Serves as a template for protein synthesis.

transfer RNA (tRNA): A set of RNA molecules that transfer amino acids to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA. (Each type of tRNA molecule is linked to a particular amino acid.)


Procedure
  1. Before class, prepare enough microarrays for the number of teams you will be organizing. The activity is designed for a tray with 16 wells. If needed, you can delete columns 7 and 8 for trays with fewer wells. Columns 1–6 are needed to complete the activity. The microarray models you will be creating work on the basis of an acid, base, and neutral. The solutions you prepare will be simulating the genes that are already on a microarray before a patient's cDNA is added. To prepare the trays:

    • Use a self-stick note to mark "TL" on the top left and "BR" on the bottom right of each ice cube tray.

    • Put 15 mL of the pure vinegar, salt water solution, or water in the wells (or test tubes) according to the following key for each patient.

      A = acid—vinegar (will stay clear)

      B = base—salt water (will turn light pink)

      N = neutral—water (will turn dark pink)

    • Set up an equal number of Patient 1 and Patient 2 microarrays. (The materials list specifies enough materials for up to eight arrays, four of Patient 1 and four of Patient 2.)

      Patient 1 Profile

       

      1

      2

      3

      4

      5

      6

      7

      8

      A

      A

      A

      B

      B

      N

      B

      N

      A

      B

      N

      A

      N

      A

      B

      N

      B

      N


      Patient 2 Profile

       

      1

      2

      3

      4

      5

      6

      7

      8

      A

      N

      B

      N

      B

      A

      B

      A

      N

      B

      A

      B

      A

      B

      B

      N

      B

      A

  2. Tell students they will by playing the role of oncologists specializing in breast cancer and will be conducting microarray analyses on two newly diagnosed breast cancer patients, Mrs. Jones and Mrs. Brown. Inform students that Mrs. Jones is a 46-year-old African-American woman with no family history of breast cancer and that Mrs. Brown is a 63-year-old Caucasian woman who has had breast cancer on her mother's side of the family.

  3. Organize students into teams. Assign half the students Patient 1 and the other half Patient 2. Distribute the copies of student handouts to each team. Review the activity with students.

  4. Make sure students understand the flow of DNA to mRNA to protein (see Background and Key Terms above for more information).

  5. Have students read the "Checking Up on Genes" handout that explains how they will do the activity. Then have them read the "How DNA Microarrays Work" handout. Clarify any misunderstandings about any terminology (see Key Terms above) or the technology before students work with their own microarray. (Note: For this activity, the technique has been simplified.)

  6. Distribute the trays you have prepared to each team, the phenolphthalein, and the pipettes. Have students use the phenolphthalein solution to add three drops to each of the spots on their array. After all the spots have been treated, have students interpret the results using the key on their "Gene Locations on Array" handout. Then have each team record the result for its patient under each gene name on the same handout.

  7. After teams have interpreted their results, have them use their "Cancer Therapy Options" handout to determine which therapies might be indicated for their patients. Point out that if the genes listed in the "Do not use if" category for each therapy are expressed in the manner indicated, then the patient would react badly or not respond to the treatment. Ask students to use this information to determine which treatments are safe to use for each patient. Have them record their answers on the handout.

  8. Discuss students' results and answers to the questions on the "Checking Up on Genes" student handout. If student DNA microarray results differ, ask students why that might be. (Some reasons include that the substances in the prepared microarray were not distributed evenly or that students may have added different amounts of the substance representing the cDNA.) Ask a representative from a Patient 1 team and a representative from a Patient 2 team to report the treatment choices for each patient. Are they the same? (No.) Ask students why, if both women have breast cancer, the treatments are different. (The two recommendations are different because even though both patients have breast cancer, their gene expression profiles are different, and call for different treatment regimens.)

  9. To illustrate how chemicals in the body can control gene expression, show students the portion of the program at right (2:32) that describes and animates this process.

    After students have viewed the video, ask them to describe two ways researchers know how genes can be turned on and off. (Chemical tags, such as methyl groups, can attach directly to DNA and switch genes on or off, or tags can grab onto proteins called histones around which genes are wrapped. Tightening or loosening the histones effectively hides [turns off] or exposes [turns on] the genes.)

  10. As an extension, have students choose two of the genes in the microarray profile and research what cell regulation processes the genes control. Have students report to the class what they learned. Students can find the genes in the National Center for Biotechnology Information Gene database at

    www.ncbi.nlm.nih.gov/sites/entrez?db=gene


Safety Note
If students spill any of the phenolphthalein on their skin, have them immediately rinse it off thoroughly with water. After completion of the activity, rinse the tubes and droppers with a weak acid, such as vinegar.


Activity Answer

Gene Locations on Array

Patient 1 Profile

 

1

2

3

4

5

6

7

8

A

ESR1
0

ABC-C6
0

BCL2
-

DPYD
-

TOP2A
+

GSTP1
-

CDC2
+

GATA3
0

B

DHFR
+

EGFR
0

ERB-B2
+

ABC-B2
0

MT1
-

TGFB3
+

ANXA
-

GRB7
+


Patient 2 Profile

 

1

2

3

4

5

6

7

8

A

ESR1
+

ABC-C6
-

BCL2
+

DPYD
-

TOP2A
0

GSTP1
-

CDC2
0

GATA3
+

B

DHFR
0

EGFR
-

ERB-B2
0

ABC-B2
-

MT1
-

TGFB3
+

ANXA
-

GRB7
0

Key
+ = overexpressed (dark pink)
- = underexpressed (light pink)
0 = normal (clear)


Cancer Therapy Worksheet
Cyclophosphamide: Patient 1: yes; Patient 2: yes
Doxorubicin: Patient 1: yes; Patient 2: yes
Fluorouracil (5-FU): Patient 1: yes; Patient 2: no
Methotrexate: Patient 1: no; Patient 2: no
Paclitaxel: Patient 1: no; Patient 2: no
Tamoxifen: Patient 1: no; Patient 2: yes
Trastuzumab: Patient 1: yes; Patient 2: no


Student Handout Questions

  1. Which treatment or treatments would you recommend for your patient? Patient 1: a combination of cyclophosphamide, doxorubicin, fluorouracil, and trastuzumab. Patient 2: a combination of cyclophosphamide, doxorubicin, and tamoxifen.

  2. Some genes, such as ERB-B2 and ESR1, have been found to be associated with particular diseases or conditions such as cancer. Other genes, such as the ABC-B2 gene, are not associated with a disease but are involved in resistance to certain drugs or treatments. Why would it be useful to test for the expression of genes like the ABC-B2 gene on a microarray? If the gene is strongly expressed, it would mean that a particular treatment might not work, or might even be harmful to the person taking that drug.


Links and Books

Web Sites

NOVA—Ghost in Your Genes
www.pbs.org/nova/genes/
Contains articles and multimedia features to accompany the NOVA program.

Backgrounder: Epigenetics and Imprinted Genes
www.hopkinsmedicine.org/press/2002/November/epigenetics.htm
Provides a basic introduction to epigenetics.

DNA Is Not Destiny
discovermagazine.com/2006/nov/cover
Explains some ways that epigenetic changes unfold at the biochemical level and details recent research in epigenetics.

DNA Microarray
learn.genetics.utah.edu/units/biotech/microarray
Offers a step-through interactive that explains how microarrays work.

Epigenetics: The Science of Change
www.ehponline.org/members/2006/114-3/focus.html
Provides an overview, with a diagram, of the connection between epigenetic factors and disease in humans.

What Is Epigenetics?
epigenome-noe.net/aboutus/epigenetics.php
Offers a brief yet informative overview of the field of epigenetics.


Book

The Epigenome: Molecular Hide and Seek
by Stephan Beck and Alexander Olek (editors). Wiley, 2003.
Presents nine essays that cover the historical origins of epigenetics and its role in development, gene regulation, disease, diet, and aging.


Standards

The "Checking Up on Genes" activity aligns with the following National Science Education Standards (see books.nap.edu/html/nses).

Grades 9-12
Life Science

The cell
The molecular basis of heredity

Science and Technology
Understandings about science and technology

Science in Personal and Social Perspectives
Personal and community health


Classroom Activity Author

Margy Kuntz has written and edited educational materials for 20 years. She has authored numerous educational supplements, basal text materials, and trade books on science, math, and computers.

Teacher's Guide
Ghost in Your Genes
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