GROUP 2:        

INDEPENDENT BERRIOTIC CHEESECAKES

Also Known As : Kelly Hoberg Liz  Sehi  Ebony Harmon Theresa Hoang 'S

"Using Bioinformatics to study the FHIT gene and its relationship to lung cancer."

    As a team, we chose the topic of lung cancer because we each know people who smoke.  For example, Liz has a grandfather and an uncle who smoked, but they quit after twenty years.  However, neither of them developed lung cancer.  Theresa  has relatives who smoked and quit as well after many years of smoking.  Kelly's  grandmother smoked and lost a battle to lung cancer.  She fears that many smokers she knows may eventually develop lung cancer.  Ebony's grandmother was a smoker and died of lung cancer.  Therefore, we were curious to know if lung cancer was hereditary and if there was a genetic mutation that causes cancer.  

        After research, our team discovered that lung cancer is rarely inherited.  We found that many scientists believe that there are mutations, caused by environmental factors,  in the FRA3B region of the FHIT gene that may cause lung cancer.  Believing that this would be a good focus for our investigation, we chose to do our investigation on the FHIT gene and its relationship to lung cancer.   Our research has provided us with a better understanding of lung cancer and the involvement of the FHIT gene in causing the disease.  If further investigations are pursued by scientists on this gene's relationship to lung cancer, it could lead to the discovery of the exact mutation that plays a role in causing lung cancer.  This mutation then could bring researchers closer to finding new treatments in which a good copy of the gene would be injected into the infected person. The good gene could create a correct protein that will successfully suppress other tumors from forming.  

  
??? Questions ??? 

    After much discussion on the topic of lung cancer, we wanted to answer the following questions:

      Where in the FRA3B portion of the FHIT gene are the highest frequencies of mutation

Terms to Know:

    Another cause of lung cancer is radon, which is considered the second leading cause of this disease. Radon is an odorless, invisible radioactive gas that is naturally found in rock and soil. It is formed by the natural breakdown of radium, the product of decaying uranium. This gas has been identified in every state in the United States. To tell if a person is being exposed to radon, the place of possible exposure would be tested for radon. Most levels of radon are not at a high level, but your home should be tested. To have your home tested for radon, call your State Radon Contact or go to: http://www.epa.gov/iaq/radon/proficiency.html.

    A new treatment for lung cancer is PDT, or Photodynamic therapy. PDT is a kind of laser therapy that uses certain chemicals and a laser light to kill cancer cells. The chemicals are injected into the bloodstream. The chemicals are absorbed by all the cells in the body, but leave the normal cells quickly and stay in the cancer cells for a long time. Next, a laser light is pointed at the cancer regions which activates the chemical inside the cancer cells. This chemical will then kill the cancer cells. This therapy can be used to either reduce symptoms or to treat very small tumors in patients who do not qualify for other treatments.

American Lung Association
http://www.lungusa.org/diseases/lungcanc.html

American Cancer Society
http://www3.cancer.org/cancerinfo/load_cont.asp?st=pr&ct=26&language=english

Virginia Mason; "Is Lung Cancer Hereditary?"
http://www.vmmc.org/dbLungCancer/sec61387.htm

CNN, "Genetic Breakdown Leaked to Lung Cancer"
http://www.cnn.com/HEALTH/9604/05/nfm/lung_cancer_gene

The lung cancer pictures have been taken from the following website:  http://medicolegal.tripod.com/preventlungcancer.htm.

Currently, the Medical College of Ohio is investigating the inheritance of lung cancer. For information on this ground breaking research, go to: http://www.mco.edu/depts/peds/lungstudy.html.

    1.  Google Search Engine

    Our primary research tool was the National Center for Biotechnology Information (NCBI) web site. Using NCBI’s GenBank database, we searched for organisms that had genes with sequences similar to that of the human’s FHIT gene. We found that yeast, mice, rats, fruit flies, and C. elegan worms had genes which had similar sequences to the human FHIT gene. Additionally, we used this tool to find various sequences of a FHIT gene that had been mutated.

    Using CLUSTALW, we individually aligned each mutant form of the human FHIT gene with the correct one to determine the regions where the most frequent mutations appeared in the gene. Additionally, we used CLUSTALW to align the sequence of the human FHIT gene with the sequences of the genes from the chosen organisms. An unrooted tree of the alignment was created in order to indicate what organism(s) had a nucleotide sequence most similar to the human’s FHIT gene sequence.  On the tree, short branches between organisms tell us that their sequences are similar.  If the branches are long, then there are more differences between the organisms' nucleotide sequences.

    Where in the FRA3B portion of the FHIT gene are the highest frequencies of mutations located?

      We found seven mutated sequences of the FHIT gene in humans, each with many mutations,  from the NCBI Database.  We divided the sequences into regions of fifty nucleotides and counted the number of mutations in each region.  For each region, we took the average of the mutations in the seven sequences and created a bar graph.

    What organism would be the best "model organism" for study of the FHIT gene in lung cancer?

    ClustalW Unrooted Tree
Nucleotide Sequence Relationships Between Human and Five Organisms

    Using the NCBI Database, only five organisms were found to have the FHIT gene or a related gene.  We compared the worm and fruit fly's NITFHIT gene, the yeast's HNT2 gene,  and the mouse and rat's FHIT gene to the human's FHIT gene.  This unrooted tree shows the similarities and differences between the six organisms' genes.  Short branches between organisms express close similarities in the gene sequences where as long branches indicate more differences in the sequences.  Clusters such as the one between the human, mouse, and rat genes show a reasonable similarity in the nucleotide sequence.  The yeast, located on a long branch, has a greater difference in its sequence as compared to the cluster mentioned.

Clustal Distance Matrix
Distance Comparisons to the Human FHIT Gene

    This matrix shows the information of the tree in percentage values.  The closer the organisms' number is to zero, the more similar its gene sequence is to the human FHIT gene.

Conclusions

Where are the highest frequencies?
    After analyzing the graph, we determined that there is no set region where the mutations occur the most. The graph has high mutation rates in each region as seen in the graph above.  Some regions contain a higher mutation rate than others but not by a large number.  All regions except region 451-500 had twenty to thirty mutations.  Region 451 to 500 had only ten mutations because a few of the mutated sequences did not extend past 450 nucleotides.  Therefore, many mutations in this gene may be associated with lung cancer.

What organism would be the best model organism?
    We infer from the unrooted tree that either the rat or the mouse would be the best model organisms for the study of the FHIT gene and its relationship to lung cancer. The branches of the mouse and the rat are very short and are located close to the human branch, indicating similarity.  The three organisms are also together in a cluster, illustrating the similarity of the nucleotides.  The worm, yeast, and fruit fly branches were farther from the human branch than the mouse and rat branches, therefore expressing dissimilarity.  
    In looking at the Clustal Distance Matrix, the mouse and rat difference values are very close to zero.  This shows that their genes are similar to the human gene.  The mouse gene has a 12.6% difference from the human gene, and the rat has a 15.1% difference from the human gene.  These organisms are the closest as compared to the yeast (51.0% difference), the fruit fly (50.1% difference), and the worm (46.2% difference).

Possible sources of error:
   One possible source of error in this investigation is the possibility of incorrect alignment. It is possible that the mutated sequences were not edited correctly by our group and therefore did not line up with the actual FHIT gene precisely. It is also possible that we have miscounted the number of mutations in each region slightly.

      Should scientists use model organisms, such as mice and rats, to study lung cancer? Are
there any other alternatives to using model organisms?

       While looking for possible model organisms, we found only six organisms. If the gene is located in the round worm and in the fruit fly, it is most likely located in many other organisms. Where is the FHIT gene located in the DNA of other organisms?

      Is the purpose of the FHIT gene really a tumor suppressor gene for lung cancer?

      Which mutation region of the FHIT gene is really important in causing lung cancer? Which regions do not affect the development of lung cancer?

      If the purpose of the FHIT gene is a tumor suppressor, does it cause any other type of cancer?

      Is your chance of lung cancer higher if you have more mutations in the FHIT gene?