Subtypes of Lung Carcinoids
By: Smriti Sankaran
Biomarkers are substances whose presence is indicative of a phenomenon such as a disease. Recently biomarkers are being used to predict and identify different diseases such as cancer in humans. Different combinations of biomarkers are present in different strains of cancer. These different biomarker substances are created as a result of variations in genes. I created a network that maps gene mutations that are present in patients with three different subtypes of lung cancer. The networks show which mutations are common to all three subtypes and which gene mutations are more present in only one subtype, or a few rare cases.
The data used in the model is from a study conducted by the Rutgers Cancer Institute of New Jersey. The data shows the variations of genes present in the tumors of thirty lung cancer patients. The thirty patients come from various age groups and backgrounds and suffer from 3 different strains of lung cancer. Since thirty patients is a small sample size, this acts as a limiting factor for the accuracy of the study.
Cytoscape was chosen for this model since it is a great tool for visualizing gene networks. The Cytoscape model visualizes which gene mutations are most commonly associated with which strain of the three strains of lung cancer based on the thirty patients’ data. While a lot of the gene variations were common across patients with any of the three subtypes of lung cancer, some gene variations were more commonly associated with certain subtypes.
This is a picture of the whole network. The outer nodes are the 30 patients whose data I used. The inner nodes are the different gene mutations. This image shows that almost all the lung cancer patients, regardless of subtype, have multiple mutations in their DNA, that make their DNA from people who do not suffer from lung cancer.
While most of the gene mutations are common to all the subtypes of lung cancer, these four, shown in the image, are only present in a few cases out of the 30 patients. These four mutations occur in the S100G gene, S100A7A gene, ASCL4 gene, and S100A7 gene.
The four mutated genes that were specified genes are all protein coding genes. Based on the data, the S100G and S100A7A gene mutations are almost exclusively found in woman with subtype 1 lung cancer. The ASCL4 gene mutation is found in woman, regardless of lung cancer subtype, and the S100A7 gene, is exclusively found in Subtype 1 patients. This research can be used to help doctors diagnose lung cancer.
Laddha SV. GEO Accession viewer. National Center for Biotechnology Information. 2019 [accessed 2020]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118131
Laddha SV; da Silva EM; Robzyk K; Untch BR; Ke H; Rekhtman N; Poirier JT; Travis WD; Tang LH; Chan CS; Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids. Cancer research. 2019 [accessed 2020]. https://pubmed.ncbi.nlm.nih.gov/31300474/
National Center for Biotechnology Information. [accessed 2020]. https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484631
Studies : Browse : Sequence Read Archive : NCBI/NLM/NIH. National Center for Biotechnology Information. 2019 [accessed 2020]. https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP156394