Biological Sciences and Statistics

Question: Discuss about the Biological Sciences and Statistics. Answer: Introduction According to GLOBOCON statistics, colon cancer is one of the most cancers accounting for 1.36 million of cases worldwide during the year 2012 (cancer.org, 2016). It is third common cancer in affecting men worldwide according to World Health Organization 2015 statistics (Siegel, Miller and Jemal, 2016). The colon cancer develops in the colon region in the large intestine (cancer.gov, 2016). The adenomatous polyps are generally benign being the pre-cancerous condition but can metastasize and could develop into cancer spreading outside the colon region (cancer.org 2016). The Familial Polyposis coli is one of the genetically predisposing condition causing colon cancer and characterized by thousands of polyp development in the colon (cancer.org, 2016). An individual has a lifetime risk of developing colon cancer to 100 % by the time they reaches the age of 40 (globocan.iarc.fr, 2016). The Familial Adenomatous Polyposis is an autosomal dominant disorder in which there is development of hun dreds of adenomatous polyps in the early stages of life throughout the colon (wcrf.org, 2016). If this condition persists and left untreated, the colon cancer is likely to develop by the age of 40. In the given case study of 40 year old Caucasian man (patient X) has a family history of Familial Adenomatous Polyposis (FAP) and at the age of 18 he was screened for Adenomatous Polyposis Coli gene 1 (APC 1). The Adenomatous Polyposis Coli 1 gene was sequenced and his colon cells were harvested and frozen. When he reached the age of 40 years, he showed symptoms like the abdominal pain, change in bowel habits and unexplained weight loss. Patient X underwent a biopsy of the colon tissue showed that there were hundreds of colorectal adenomatous polyps indicating Familial Polyposis Coli and the comparative study was done for cyclin D1 in the cells with his previous colon cells harvested at the age of 18. Quantitative polymerase chain reaction was done to analyze the results by cloning, sequencing and the following results were reported and interpreted for the patient X. Patient Codon Allele 1 Allele 2 Patient X 280 TCA TGA Father 280 TCA TCA Mother 280 TCA TGA The table 1 shows the sequence of Adenomatous Polyposis Coli 1 gene of patient X blood sample at the age of 18 including his mother and father. The adenomatous Polyposis coli 1 gene is a tumor suppressor gene that plays an important role in the development of colon cancer. The germ line mutation in the APC 1 gene located on 5q21-q22 band leads to Familial Adenomatous Polyposis that is hereditary colon cancer. The autosomal dominant pattern occurred in which one single altered copy of the gene is enough to cause the disorder. The genetic change meant that the codon 280 present on the exon 8 of adenomatous polyposis coli 1 gene underwent a codon change from TCA to TGA that is base pair mutation (Chromium.lovd.nl, 2016) It is a non-sense mutation in which TCA that codes for serine gets mutated to TGA that codes for stop codon. This APC gene mutated allele sequence shows that the mother has an altered copy of allele inherited from either of her parents. The patient X also inherited that altered copy of the allele from his mother and therefore showed predisposing condition of familial adenomatous polyposis at the age of 18. The other normal allele that is allele 1 coding for serine TCA has become inactivated either by deletion or mutation. The tumor suppressing function of the APC gene is lost and develops in the form of adenomatous polyps. It could be interpreted that at the age of 18, patient X underwent a mutation predisposing for the familial adenomatous polyps and was exposed to develop colon cancer in the later stage if left untreated. This figure 1A shows a biopsy of the normal colon of the patient X at the age of 18 years by performing colonoscopy. It was done to diagnose the patient X for any symptom that showed the symptoms for the predisposing familial adenomatous polyposis condition. As the patient X confirmed the germ line mutation inherited from his mother from the adenomatous polyposis coli 1 gene sequencing. The assessment of the normal biopsy is done on low and high parameters. The size, orientation, muscularis mucosa presence or absence, sub mucosa and mucosa cellularity are observed in the biopsy of colon tissue. The data could be interpreted for the normal histology of the colonic mucosa. The layers are arranged as mucosa, sub mucosa, muscularis propria called externa, sub serosa and serosa containing the loose connective tissue and mesothelial lining (Cerilli, L.A. and Greenson, J.K., 2012). The mucosa consists of tubular crypts that are aligned perpendicularly to the muscularis mucosa. There is a co nstant distance between the crypts and their inner diameter. The normal biopsy might show a little variation or branching in the intercryptal spacing, crypt architecture or occasional branching of the crypts that is considered normal. It is important to study the cellularity in the lamina propria layer surrounding the crypts. It generally consists of cells like eosinophils, plasma cells, lymphocytes and histiocytes. There is presence of normal epithelium and no depletion in the number of goblet cells. The figure 1B shows the biopsy of colon of patient X at the age of 40. The patient X experienced change in bowel habits, abdominal pain and unexplained weight loss. The biopsy showed abnormal growth formations. These conditions satisfied the symptoms of colon cancer in the patient X. When he was screened for the adenomatous polyposis coli 1 gene mutation, he was found to be positive. In his later life, he was left untreated. However, when he reached the age of forty years, he started developing the symptoms of colon cancer as he had a family history of colon cancer showing the genetic predisposing condition of familial adenomatous polyposis. When he was 18 years old, he started developing adenomatous polyps which were benign. Gradually, the pre-cancerous polyps started developing into carcinomas polyps. By the time he attended the age of 40, he developed abnormal outgrowths in the mucosa layer and developed colon cancer. The figure 1B showed tubular adenoma that are small adenomatous polyps on the small stalk that are viewed under the microscope showing disorganized, crowded mucosa of the colon. The goblet cells are less in number and showed hyper chromatic nuclei in the cells lining the polyp glands. This histology shows the benign conditions that are circumscribed, well-differentiated and there is not much invasion of the stalk. The differentiation of the neoplasm is defined by the small adenomatous polyps that are benign in the colon (Jass and Sobin 2012). The staining is done differentially in the epithelial cells present at the top of the adenoma and glandular epithelium that are normal present at the below of the mucosa in the colon. The well differentiated condition showed that the polyps are benign and not yet metastasized (Arqus et al. 2014). Differentiation is one of the variables that act as potential parameter in studying the biologic behaviour in the neoplasm. The figure 2 shows the indirect immunofluorescence and fluorescence microscopy of the stained colon cells of the patient to see the cells for the catenin. The catenin is an important protein associated with the adenomatous polyposis coli 1 gene. The catenin plays an important role in promoting the proliferation of cells and acts to control the activity and expression of the various genes. catenin also helps in the differentiation of the cells. The vital role that catenin plays is that it helps to attach the cells to one another and also in tissue formation. The catenin association with the adenomatous polyposis coli gene gives a signal to the catenin to break down and therefore it is no longer functional (Holland et al. 2013). The adenomatous polyposis coli gene acts as a negative regulator for catenin and also controls its concentration. Cadherin interacts with catenin and is involved in the cell adhesion mechanism. When the expression of catenin is seen in the immune fluo rescence microscopy by the antibody treatment to the precipitated adenomatous polyposis coli gene with the identification and sequencing of the beta-catenin is done (Clevers and Nusse 2012). This figure 2 showed the beta catenin expression and adenomatous polyposis coli is involved in the cell adhesion process. The Wnt signaling is activated during mutation that initiates the colon cancer. The beta catenin concentration in nucleus is a measure to show the stage of the colon cancer. The figure 3 shows the expression of the cyclin D1 levels at the mRNA level. The cyclin D1 levels are an indication of neoplasm in the colon. The quantitative polymerase chain reaction is an accurate tool to measure the levels of cyclin D1 expression at the mRNA level. Cyclin D1 plays an important role in the proliferation and continuity of cell cycle. The high expression of the cyclin D1 levels is an indication of the progression of cancer. It is basically a proto-oncogene and regulates the progression of the cell cycle from G1 to S phase. The cyclin D1 is a prognostic marker and helpful in assessing as it is the cell cycle checkpoints (Colussi et al. 2013). Cyclin D1 is activated when adenomatous polyposis coli gene is mutated and Wnt or beta catenin signaling is activated. This quantitative polymerase chain reaction of the cyclin D1 levels showed that the initiation of the neoplasm in the colon. The comparative study by quantitative polymerase chain reaction of patient X at the ag e of 18 and 40 years showed that the cyclin D1 levels increased at the RNA level at the age of 40 and the cyclin D1 levels decreased at the age of 40 when compared to the levels at 18 years. The table 2 shows the polymerase chain reaction results done to amplify both the copies of the patient X alleles of the adenomatous polyposis gene. The codon at the position 1338 shows a substitution and base pair mutation. It is a nonsense mutation as the allele 1 of the codon 1338 contains a stop codon that is an altered form of the two alleles of the adenomatous polyposis coli gene. The CAG codes for glutamine however, there is loss of function of the allele 2 and allele 1 has gain in function. There is loss of function of the adenomatous polyposis gene as a tumor suppressor and therefore, the mutation results in predisposing condition for progression of colon cancer. A new mutation occurred at the age of 40 in patient X and it is the actual time when he started showing the symptoms for the disease. The underlying molecular and genetic reason for patient X condition is the family history of colon cancers. The genetic predisposing condition familial adenomatous polyposis runs in the family with germ line mutation. The adenomatous polyposis coli 1 gene undergoes nonsense mutations at the codon 280 and 1338. The patient X inherited the defective allele from his mother undergoing a base pair mutation coding for stop codon. The codon 1338 also codes for stop codon from glutamine. The prognosis for patient X is that his family has a history of colon cancers. The patient X has a predisposing genetic condition that is the familial adenomatous polyposis. He inherited the defective allele from his mother and a new mutation at the age of 40 when he actually showed the symptoms for neoplasm colon cancer. The surgery would not be helpful for the patient s the polyps would continue to grow. However, removal of the polyps by colonoscopy would help to stop them from being cancerous. The non-steroidal anti-inflammatory diseases and the combination of celecoxib and cyclooxygenase 2 inhibitors would help to reduce the size of the polyps. References: Arqus, O., Chicote, I., Tenbaum, S., Puig, I. and Palmer, H.G., 2014. Quantitative procedure to analyze nuclear -catenin using immunofluorescence tissue staining. Protoc exch. cancer.gov, (2016). Genetics of Colorectal Cancer. [online] National Cancer Institute. Available at: https://www.cancer.gov/types/colorectal/hp/colorectal-genetics-pdq [Accessed 8 Dec. 2016]. cancer.org , (2016). [online] Available at: https://www.cancer.org/acs/groups/content/documents/document/acspc-042280.pdf [Accessed 8 Dec. 2016]. cancer.org, (2016). [online] Available at: https://www.cancer.org/acs/groups/content/documents/document/acspc-042280.pdf [Accessed 8 Dec. 2016]. cancer.org, (2016). Colon/Rectum Cancer | American Cancer Society. [online] Cancer.org. Available at: https://www.cancer.org/cancer/colonandrectumcancer/ [Accessed 8 Dec. 2016]. Cerilli, L.A. and Greenson, J.K., 2012. The differential diagnosis of colitis in endoscopic biopsy specimens: a review article. Archives of pathology laboratory medicine, 136(8), pp.854-864. Chromium.lovd.nl. (2016). Search unique variants - Colon cancer gene variant databases - Leiden Open Variation Database. [online] Available at: https://chromium.lovd.nl/LOVD2/colon_cancer/variants.php?select_db=APCaction=search_uniqueorder=Variant/DNA_reported,DESChide_col=show_col=all [Accessed 8 Dec. 2016]. Clevers, H. and Nusse, R., 2012. Wnt/-catenin signaling and disease.Cell,149(6), pp.1192-1205. Colussi, D., Brandi, G., Bazzoli, F. and Ricciardiello, L., 2013. Molecular pathways involved in colorectal cancer: implications for disease behavior and prevention.International journal of molecular sciences,14(8), pp.16365-16385. globocan.iarc.fr, (2016). Fact Sheets by Cancer. [online] Globocan.iarc.fr. Available at: https://globocan.iarc.fr/Pages/fact_sheets_cancer.aspx?cancer=colorectal https://onlinelibrary.wiley.com/doi/10.1002/ijc.29210/abstract [Accessed 8 Dec. 2016]. Holland, J.D., Klaus, A., Garratt, A.N. and Birchmeier, W., 2013. Wnt signaling in stem and cancer stem cells.Current opinion in cell biology,25(2), pp.254-264. Jass, J.R. and SOBIN, L., 2012.Histological typing of intestinal tumours. Springer Science Business Media. Siegel, R., Miller, K. and Jemal, A. (2016). Cancer statistics, 2016. wcrf.org, (2016). Colorectal cancer statistics | World Cancer Research Fund International. [online] Wcrf.org. Available at: https://www.wcrf.org/int/cancer-facts-figures/data-specific-cancers/colorectal-cancer-statistics [Accessed 8 Dec. 2016].