Tuesday, April 30, 2013

Data Analysis

Rankings

Run Time Ranking: 498,687

Points Generated Ranking: 414,310

Results Returned Ranking: 426,881

Total Run Time: 4 days, 1 hour, 54 minutes, 9 seconds

Total Disc usage: 450.09 Megabites

Disc usage by BIONC projects: 433.45 Megabites
Points Generated: 14,783
 
These points were from two projects, GO Fight Against Malaria and Help Conquer Cancer


 

Friday, April 19, 2013

Breast Cancer and Evolution Questions and Answers in Relation to Previous Article Posted


These questions address the Journal of Clinical Investigation article entitled “Breast Cancer: Origins and Evolution” by Polyak (2007).  Be sure to explain your answers.

 

1.      Both your interview and your article mentioned the hereditary factors involved in breast cancer.  What is the h2 of breast cancer thought to be?  Both sources also mentioned targeted therapies, especially focusing on pathways.  How does this work?

a. When dealing with breast cancer, hereditary factors are implied because one of the strongest determinants of risk is based on family history. Studies have shown that mammographic breast density is a highly heritable factor for breast cancer with h2>0.6. It has also been found that major mutations such as BRCA1/2 and TP53 cause a small percentage of heritable breast cancers. Targeted therapies have high therapeutic efficacy with a small chance of side effects. In order for a drug to be effective, it must identify tumor cell-specific molecular pathways that change with the development of the drug. Targeting these leads to a therapeutic response and clinical benefits. The targeted therapies that focus on pathways has been shown to be a more viable therapeutic approach then targeting individual genes.

 

2.      Most genes code for proteins.  Given the information in this article and the above question, why is it important to look at protein folding and mis-folding when studying cancer?

a.         It is very important to look at proper protein folding in order to better understand the protein mis-folding that leads to cancer. If we as researchers know these proteins in and out, then we can eventually have the ability to stop the protein mis-foldings and hopefully prevent tumor growth altogether. The more time and effort applied to understanding the proteins, the closer we are to stopping the widespread disease of cancer.

b.         When protein folds do not occur correctly it mainly affects a protein called p53. This protein is located in the body’s cancer resistance network. It is normally “switched off” but is activated inside of the cell if the cell becomes stressed or damaged. Cell damage can lead to genetic mutations in DNA that can cause uncontrolled division and proliferation of cells that leads to tumor formation. The p53 works by heading to the cell nucleus and begins the production of other proteins that stop the tumor formation or can trigger programmed cell death. A slight mutation in one of the nucleotides in the gene can lead to p53 proteins mis-folding. This leads to the p53 not carrying out its job and eventually tumor cell growth. This mutation of p53 occurs in fifty percent of all cancer cases and ninety-five percent of all lung cancer cases specifically.

 

3.      In an evolutionary sense, why is it informative to study cancer and its implications in flies or, especially, in mice?

a.       Studies using mice or flies have the ability to perform experiments that may be difficult, dangerous, or otherwise unethical to perform on humans. Evolutionarily, humans, mice, and flies are made of the same DNA and proteins that may be expressed in minor differences between them. In this study specifically, human breast tissue and mouse breast tissue found to have progenitor and stem cells, both of which are required for normal mammary gland development. Studying mice pathways and the evolution of tumor development can therefore give insight on human breast cancer tumor progression and hopefully means of better treatment and prevention.

4.      Apply Darwin’s postulates to the microenvironmental influences on breast cancer cells.

a.       Variation among individuals of the same species

i.        Not all tumor cells are comprised of exactly the same amount of epithelial cells, leukocytes, fibroblasts, etc. in the microenvironment. There are also differences in tumor cells as they progress and develop including in situ, invasive, and metastatic carcinomas, which are contributed by the changing cell microenvironment.

b.      At least some of these variations are hereditary

i.        Epigenetic changes (methylation, chromatin) were found in each cell type during tumor progression. Tumor-associated stromal cells maintain their altered phenotype in cells in subsequent generations, suggesting changes in microenvironment to be permanent and heritable.

c.       Every generation has more offspring than can survive

i.        We see that in breast tumor progression, while the number of fibroblasts, myofibroblasts, lymphocytes, and endothelial cells increases, the myoepithelial cells are altered and decrease in number.

d.      Natural selection operates on populations

i.        It’s possible that cancerous stem cell changes and evolution during tumor progression drives selection and other genetic/epigenetic factors allowing the survival and proliferation of the tumor cell.

5.      The author asserts that tumor heterogeneity may be the result of competition among cancer cells with different phenotypes.  Why, then, might it be important for an Oncologist to understand evolution?

a.       The genotype of the cells that cause the tumors can be heterozygous due to two models. The first being that the cells started out separately as separate cells then combined and the second being competition among tumor cells. When cells compete, they are not as stable as they would be without competition. Oncologists must understand the heterogeneity in order to diagnose, treat, and then be able to detect the new tumor genotypes before they evolve again. These genotypes constantly evolve because they are constantly competing and undergo natural selection.

Friday, February 15, 2013

Inside a General Surgeon's thoughts on Breast Cancer

We interviewed Dr. Bennita Lowe M.D. a general surgeon at Shawnee Mission Medical Center. Here are her responses to questions regarding breast cancer, evolution, and her background.

Dr. Lowe came to choose her profession because "it found her" during her clinical rotations in medical school. At first she had no interest in surgery and was actually interested in pediatric oncology. On her first day on surgery rotation she knew that she was in the right place. Her advice to us was to "choose what you're good at." She really enjoys surgery because it is so defined; you find a problem and then you fix it.
 
Her practice does all types of general surgery including gallbladder and appendix removal, however, they have made breast cancer a special focus. She feels that as a woman, studying breast cancer is a natural match. She has had patients tell her that having a female surgeon has made them very comfortable. She said that being around breast cancer patients is "constantly inspirational." From one day to the next their lives are completely changed forever, and watching them move on and stay positive is very uplifting. Often times, she is the person that has to break this bad news to these women. In addition, all breast cancer patients are followed very closely. They are seen back every other week, then every three weeks, then every month, and finally yearly. This is comforting for the patients because they know they are being taken very good care of.
 
Dr. Lowe believes that evolution is a very interesting approach to studying breast cancer because not all breast cancers are the same. Each tumor found in a patient has its own "footprint" with differing protein abnormalities and it is very important to understand these. Within the past two years, she has noticed that RNA and DNA sequencing is now the new area of studying breast cancer. These studies can show us how to tailor treatments to each different tumor because every tumor is different. Just like evolution, the treatments for breast cancer are constantly changing. Although the main tenets of chemotherapy and surgery are not changing, the molecular levels of treatment are.
 
BRCA-1 and BRCA-1 gene abnormalities cause 10% of breast cancer's according to Dr. Lowe. And women found with this gene have a 90% chance of getting breast cancer, and an increased chance of ovarian cancer. Women who are "high-risk," meaning they have first degree relatives with breast cancer or triple negative cancers, can have genetic testing done to find these gene abnormalities. This testing is a preventative measure.
 
Finally, we asked Dr. Lowe about some common misconceptions about breast cancer. Approximately two years ago a task force broke through the media and claimed the screening mammograms for women in their 40's were not at all helpful in prevention. Many doctors and specialists spoke out against the task force saying that it was indeed important. Now, it is clear that women in this age group do need to be screened. However, it can be difficult when things like this make media headlines because it is often an excuse for women who do not want to get mammograms. Another misconception is the cost of mammograms. Dr. Lowe said that "a mammogram for patients who are cash pay is actually under $100, so it is affordable in this struggling economy."
 
We would like to thank Dr. Lowe for her graciousness and openness to our questions! We were grateful she was willing to meet with us on such short notice, seeing as our original interview plans fell thru twice. Her background and knowledge gave us great insight on the subject of breast cancer. We could relate to her as a woman surgeon because we are pursuing healthcare careers ourselves. Although she wasn't certain what grid computing meant, she had heard the word before and decided it seemed like a beneficial method in acquiring a multitude of data.

Thursday, January 24, 2013

Breast Cancer and Grid Computing Introduction

One in eight women will be affected by breast cancer. Every woman will be affected by the effects of breast cancer in their life. Whether it be a loved one that is affected or a woman herself. According to the American Institute for Cancer Research, over 226,000 cases will be diagnosed a year in the United States alone and 40,000 of those will die from the cancer. Breast cancer can affect any one regardless of age, gender, and/or health history. There are measures to take to try to prevent breast cancer, but overall it is unpreventable. Cancer is a mutation in the body's normal genes inside cells. Cornell University says that breast tissue is more prone to cancer because of the amount of estrogen in the tissue. Since estrogen promotes cell division, cancer can multiply and spread rapidly in the breast.
According to how stuffworks.com, “grid computing is a computer network in which each computer's resources are shared with every other computer in the system.” Grid processes can be accessed by the public to help with a particular cause, ours happens to be breast cancer research. Breast cancer was just recently added to grid computing to connect different hospitals in the health care industries with mammograms of women. We chose "Help Conquer Cancer" on www.worldcommunitygrid.org in order to help the cancer effort as a whole. Breast Cancer Awareness and Education really hits home with our group because it is also our sorority's national philanthropy. Each of us feel deeply about each and every man and woman with breast cancer and we are excited to do our part with this service learning project!
 
Representation of how grid computing is connected to the central computer, or central nodeSource: http://computer.howstuffworks.com/grid-computing.htm
 
Model of how a normal breast cell should look and how a breast cancer cell affected by cancer looks
Source: Google Images: Breast Cancer Cells
 
 
http://www.aicr.org/

http://envirocancer.cornell.edu/factsheet/general/fs5.biology.cfm