Solved by a verified expert:Colon Cancer: A Case of Genetic Bad Luck?Anne M. CasperDepartment of Molecular Genetics and MicrobiologyDuke UniversityPart I— Just Bad Luck?Brrrring! Brrrring! Jane checked the caller ID on her phone. “Sam! Great!” she thought. It was always nice to geta call from her older brother. But a little twinge of worry tugged at her. It was just a couple of weeks ago that hehad mentioned making an appointment with his doctor about some abdominal pain he had been having.“Hi Sam! It’s great to hear from you,” Jane answered.“Hi Jane. Well I appreciate that you still pick up, anyway. You know I call just to give you a hard time aboutsomething, little sis.”“Very funny. So, how are you planning to pick on me today?”“Honestly, I wish this call was for fun,” Sam said. “But it’s only serious stu? this time. Remember I said that Ihad made an appointment with my doctor? Well, the news isn’t good. My doctor says I have colon cancer.”“Oh, no, Sam! I remember when Dad died from colon cancer when we were kids.” The words tumbled outall in a rush. Jane felt a lump gathering in her throat.“Hold on,” Sam said. “This isn’t an early death sentence yet. The doctor says that although they found lotsof tumors in my colon, it’s still at an early stage, so treatment is possible. Drastic, though. My doctor issuggesting that the best thing to do is to surgically remove my colon altogether. And Sis, the doctor saidthat since both Dad and I have the same type of cancer, it would be a good idea for you to have your colonchecked, too.”After the phone conversation with her brother, Jane was worried there could be more than just “bad luck”running in her family’s medical history. Their father’s too-early death from colon cancer was still a painfulmemory. She knew that her grandfather on her father’s side had died of some type of cancer even beforeshe was born, although that was so long ago the family didn’t talk about it much. Had her grandfather diedof colon cancer too, Jane wondered. Would it be her turn next? And what was the risk to her young twins,Mark and Caroline?Questions. Draw this family’s pedigree, focusing on the family relationships and shading the individuals a?ectedwith cancer.. Do you think Jane has good reason to be worried? Why or why not?“Colon Cancer” by Anne M. CasperPagePart II—A Visit to the Doctor“Good afternoon, Jane,” Dr. Peters said as she entered the examination room. “I understand that you’re hereto talk about some concerns related to cancer in your family.”Jane explained the history of cancer in her family, including her father’s early death from colon cancer andher brother’s recent diagnosis of the same disease, ending with the recommendation from her brother’sdoctor to have her own colon checked.“What does that mean, to have my colon ‘checked’?” As she asked the question, Jane was already feeling alittle uncomfortable about it.“I know that the idea of having a procedure done to look at your colon is a little o?-putting,” Dr. Petersbegan, “but it really can be one of the most important tests if your family has a history of colon cancer.”She continued to explain: “The procedure that allows the interior of the colon to be examined is called acolonoscopy. The purpose of such a screening is to look for sites of increased cell growth in the colon, calledpolyps or adenomas. These adenomas are small benign tumors that form in the intestinal lining. Peoplewho inherit a predisposition to colon cancer are at higher risk to form these adenomas, and at an early age.Although the adenomas are benign, the cells within them are one step closer to becoming malignant. So,colonoscopy screenings don’t prevent cancer, but they do allow sites of altered cell growth to be detected,so that treatment can begin as soon as they appear. By detecting these adenomas early and removing thembefore they become malignant, we can prevent colon cancer.“So regular colonoscopy screenings, beginning at an early age, are highly recommended for people with afamilial predisposition to colon cancer,” Dr. Peters continued. “And even if a person doesn’t have a familyhistory of colon cancer, it’s still recommended to have a colonoscopy screening once a year beginning at age .”“I understand now why it would be important to have my colon checked,” Jane said, “but is there some way Ican ?nd out for sure whether I have inherited a predisposition to colon cancer?”“I was just getting to that topic,” Dr. Peters replied. “In some cases, genetic testing can reveal whether youare predisposed to colon cancer. Normally those kinds of genetic tests are done ?rst on family members whoare a?ected. Since your brother lives nearby, I’d suggest you talk with him about making an appointmenttogether with a genetic counselor for more information about testing.”Questions. What does it mean if a tumor is classi?ed as “benign”? What does it mean if a tumor is “malignant”?. Why is it easier to treat a benign tumor than a malignant tumor?. What does it mean to be predisposed to getting cancer?. If someone is predisposed to getting cancer, does that mean that he or she will definitely getcancer someday?“Colon Cancer” by Anne M. CasperPagePart III—Genetic Testing“Hello Sam and Jane, I’m Diane Meeker, and I’ll be your genetic counselor. I understand that you’re bothhere to talk about possibly having genetic testing to see whether you inherited a predisposition to coloncancer.”“Yes,” Jane replied, “I’m concerned because our dad died of colon cancer when we were kids, and now Samhas it too—and he’s only !”“Why don’t we start there, then, and review your family history. First, do you know of any other familymembers that have been diagnosed with cancer?” Ms. Meeker asked.“Well, besides Sam and our dad, I know that our grandpa on our father’s side also had cancer,” Jane replied.“But he died long before either of us was born and I don’t know what kind of cancer it was. No one else inour family has had cancer that I know of.”“Based on what you’ve told me about the medical history of your family, I’ve created a pedigree to diagramyour family relationships and which individuals have cancer. The extremely early development of coloncancer in both you, Sam, and your father, and the fact that a direct relative of your father died early fromsome type of cancer suggests that familial adenomatous polyposis (FAP) may be the cause of hereditarycolon cancer in your family,” Ms. Meeker said.“But what exactly is it that is being inherited in our family that causes us to develop colon cancer? It’ssomething about our DNA, right?” Jane asked.“You’re right,” Ms. Meeker replied, “it does have to do with your DNA. The DNA in your cells containsgenes, which are the instructions for making proteins. Proteins in the cell control how that cell grows anddevelops and divides. A mutation in the DNA sequence of a gene can alter the protein made from that gene,so that the protein no longer functions properly. So, some mutations can cause a change in protein functionthat allows a cell to grow out of control and become cancerous.”“So maybe there’s a mutation in my DNA,” Sam replied. “But if you do a genetic test, how do you knowwhat to look for in my DNA? Don’t humans have lots of DNA? What exactly would you be testing?”“Finding an inherited mutation in a person’s DNA does sound like looking for a needle in a haystack, doesn’tit?” Ms. Meeker replied. “But we do have some clues to suggest where we can look. For example, fromother families with FAP, we already know that this syndrome can be caused by an inherited mutation in theadenomatous polyposis coli (APC) gene.”“I see,” Sam replied. “So you won’t be looking at all of my DNA. You only need to look at that one gene andsee if it has a mutation, right?”“You’ve got it,” Ms. Meeker said. “So, by taking some of your blood, isolating your DNA, and thensequencing your APC gene, we can compare your sequence to the known normal APC sequence and look fordi?erences.”“That sounds so simple. So then if you ?nd a mutation in my APC gene, you could look to see whether ornot my sister inherited that mutation too, right?” Sam said.“Colon Cancer” by Anne M. CasperPage“Yes, because you have been diagnosed with colon cancer, we’ll start by looking for a mutation in yourDNA ?rst, Sam,” Ms. Meeker con?rmed. “And I wish it was as clear-cut as it sounds, but actually I haveto caution you both about this genetic test. The process of searching for mutations can be time-consumingand expensive, because often each FAP family carries a mutation at a unique site in the APC gene—and theAPC gene is large! In fact, the gene is so large that we don’t actually sequence the DNA for the gene. Instead,we sequence the mRNA, which is the part of the gene that your body uses to make the APC protein. ThemRNA is smaller because it cuts out some parts of the sequence of the gene, called introns. Here, let meshow you in a drawing,” Ms. Meeker continued as she began to pull out a piece of paper.In order to sequence the mRNA of a gene, scientists ?rst make a DNA copy of the mRNA. This DNAcopy is called a cDNA, and it is more stable and easier to work with than the original mRNA. ThecDNA is then sequenced. Let’s compare Sam’s APC cDNA sequence with the known normal APC cDNAsequence. To do this, ?rst go to the main NCBI home page ( and followthe instructions below.• In the dark blue bar across the top, choose the link to “BLAST.”• On the BLAST page, under the “Basic BLAST” category, click the link to“nucleotide blast.”• On the next page, in the “Enter Query Sequence” section, click the box next to theoption “Blast sequences.”• Find the normal sequence of APC cDNA on the NCBI website. Open a new browserwindow and go to the NCBI home page ( In the toplight blue bar, change the “All Databases” search to a search for “Nucleotide.” Then inthe search box, enter m (which is the accession number for APC) and click “go.”On the search results page, click on the blue link to m. You will need to scrolldown the page to ?nd the normal APC sequence. Copy and paste this sequence into thetop box on the BLAST page (the Query sequence box).• Ask your instructor where to ?nd Sam’s sequence. Copy and paste Sam’s APC cDNAsequence in the bottom box on the BLAST page (the Subject sequence box).• Click the “BLAST” button at the bottom of the page.• On the BLAST results page, you can scroll down to see the alignment of normal APC(the Query sequence) with Sam’s APC (the Subject sequence). Note though that thisformat makes it di?cult to see mismatches between these two sequences.• To change the results format to one that makes it easier to look for mismatches,scroll back to the top of the BLAST results page, and click the blue “FormattingOptions” link.• In the “Alignment View” box, change the view from “Pairwise” to “Pairwise with dotsfor identities.” Then click the “Reformat” button in the upper right corner. On there-formatted results page, each base of Sam’s APC (the Subject sequence) that matchesnormal APC (the Query sequence) is shown as a dot.“Colon Cancer” by Anne M. CasperPageQuestions. What did you ?nd when you compared Sam’s APC sequence to the known normal APC sequence inthe national database? Look carefully, and scroll all the way down through the comparison! Check youranswer with your instructor before moving on.. What are three possible consequences of the mutation you found in Sam’s APC sequence?Now let’s translate both the normal APC sequence and Sam’s APC sequence into a protein in order tocompare them. To do this, go again to the NCBI home page at• Choose the “Tools” link on the left side of the page (you may need to scroll down to?nd it).• On the “Tools” page, scroll down until you ?nd the link to “ORF ?nder.”• Copy and paste the normal APC sequence into the box and then click the “ORF ?nd”button.• You will see six colored bars at the top of the page. Each bar represents a possible proteintranslation of the entered sequence. You see six di?erent bars because there are sixdi?erent possible open reading frames for the sequence (three possible frames startingfrom each end). The ORF ?nder program colors in blue any codons between a startcodon and a stop codon. You will see one reading frame that is nearly completely blue;this is the normal reading frame. This is the reading frame that you should comparewith Sam’s. Keep this browser window open while you do the next step.• Open an additional browser window, go to the ORF Finder program, copy and pasteSam’s APC sequence into the box and click the “ORF ?nd” button.• Looking at both browser windows, compare the translation of the normal APC sequencewith Sam’s APC sequence.. What do you notice when you compare Sam’s APC protein translation to the normal APC protein?. Of the three possible consequences you listed in your answer to Question above, which one is theconsequence of the mutation in Sam’s APC gene?. In a small number of patients whose families appear to have all the classical characteristics of FAP, amutation cannot be found in the APC cDNA. What are two possible reasons for why mutations maynot be found in some patients whose families appear to have FAP?“Colon Cancer” by Anne M. CasperPagePart IV—The APC Protein“Sam, I’m really worried about seeing my test results today,” Jane said as they headed in for another visit withtheir genetic counselor. “After Ms. Meeker explained your results to us, I’ve been dreading hearing whetheror not I have the mutation too.”Sam nodded, saying, “I can understand how you feel. I’m glad I can be here at the appointment to supportyou. Whatever happens, you know your family is here for you.”Ms. Meeker arrived in the waiting room. “Jane and Sam, I’m glad you’re here. Please come in and let’stalk,” she said, leading them into her o?ce. “I’m sorry Jane, but your genetic testing results show that youinherited the same mutation in the APC gene that Sam has. As we discussed earlier, familial adenomatouspolyposis, or FAP, is caused by a mutation in the APC gene. You inherited one normal copy and one mutantcopy of the APC gene, and because of that, you are one step closer to cancer than a person who inheritedtwo good copies of the gene. If the remaining good copy of the APC gene in your cells is damaged, this willlead to the development of colon cancer.”Sam wrapped Jane in a bear hug. “I don’t know what to think,” Jane replied. “I guess I’m feeling numb.What is it about this APC protein that connects it to cancer? And what am I supposed to do next?”“If you like, we can talk more about what APC does, and why this protein is important for control ofcell growth,” Ms. Meeker o?ered. “And, I’d like to talk with you sometime soon about what we wouldrecommend you should do next for your health management.”“Why don’t we start with some more information about the APC protein,” Ms. Meeker continued. “APCinteracts with and binds to other proteins in the cell. The APC protein is large, and we know that there aresub-regions within this protein. Each sub-region is specialized for binding to some other di?erent protein.When APC binds to other proteins, it in?uences the function of these other proteins. I have two ?gures toshow you that I think will help make this clearer. Let me walk you through them,” she said as she handedJane and Sam a printout of two ?gures.The two ?gures that Ms. Meeker presented to Jane and Sam are shown below. Figure is a description ofthe APC protein domains, including which regions of APC are known to bind to other proteins. Figure isa diagram showing one of APC’s cellular functions. Examine these ?gures and then use the information youlearn from them to answer the questions that follow.“Colon Cancer” by Anne M. CasperPageQuestions. Would you expect Jane and Sam’s APC mutation to increase or decrease the ability of the APC proteinto bind to ?-catenin?. If the remaining normal APC gene is damaged in one of Jane’s cells, how would this a?ect ?-catenin inthat cell? How could this change a?ect the growth of that cell?. What are three categories of genes that when mutated can lead to tumor formation? Describe thecharacteristics of each category.. In which of these three categories would you classify APC? How would you classify ?-catenin?. Based on what you learned in this case study, what do you think Ms. Meeker would recommend thatJane do to manage her condition?Credits: Figure is based on a ?gure in Kinzler and Vogelstein, Cell :– (). Figure is by the author of this casestudy, Anne M. Casper.Case copyright © by the National Center for Case Study Teaching in Science. Originally published December , at Please see our usage guidelines, which outline our policy concerningpermissible reproduction of this work.“Colon Cancer” by Anne M. Casper