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The DNA methylation of SLIT2, GYPC, and NME1 affects lung adenocarcinoma development and progression

AJAS · 2022 Medicine

Uma Paul, Elizabeth Jarowey

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Overview

Lung cancer is the leading cause of cancer-related deaths worldwide, with lung adenocarcinoma being the most common subtype. This study used statistical analysis to determine the prognostic value of GYPC, NME1, and SLIT2 DNA methylation for lung adenocarcinoma patients, which could aid in survival predictions and DNA methylation treatment. Using data from The Cancer Genome Atlas and the Gene Expression Omnibus, ANOVA was used to compare GYPC, NME1, and SLIT2 DNA methylation (as beta values) between tumor (n = 66) and non-tumor tissue (n = 60) and against demographic features (age, sex, cancer stage, smoking history). Kaplan-Meier survival analyses and log-rank tests were utilized to determine CpG sites associated with patient survival and detect differences in survival across demographic groups and DNA methylation levels of the three target genes. There was hypermethylation of two SLIT2 CpG sites (p = 4.23e04 and p = 5.01e-04) and one GYPC CpG site (p = 1.24e-04) in tumor tissue. Methylation increased by cancer stage (p = 0.0228) and varied by smoking history (p = 0.0478) for two SLIT2 CpG sites. Overall survival decreased by cancer stage (p = 0.0133), and increased methylation was associated with poor overall survival for a NME1 CpG site (p = 0.0226) and a GYPC site (p = 0.0379). An additional 1426 survival-associated CpG sites were identified. This study identified two possible lung adenocarcinoma prognostic biomarkers from the three target genes and determined CpG sites that likely play a role in lung adenocarcinoma due to differential methylation in tumor tissue. Header image credit: Moore, L., Le, T. & Fan, G. DNA Methylation and Its Basic Function. Neuropsychopharmacol 38, 23–38 (2013). https://doi.org/10.1038/npp.2012.112

My Story

My interest in oncology research was spurred by watching a family member battle cancer. The enigma of human health and cancer biology fascinated me and led to the research I have presented here.

As a part of AP Psychology, I was given the opportunity to participate in CSRSEF, the Central Sound Regional Science and Engineering Fair. After reading dozens of research papers in hopes of uncovering an interesting topic, I came across a paper connecting the expression of three genes – NME1, GYPC, and SLIT2 – to lung adenocarcinoma prognosis. The aspect of the paper that piqued my curiosity described the fact that the expression of the three genes was likely controlled by DNA methylation. My own research built off that finding by determining the role of the methylation of the three genes in lung adenocarcinoma progression.

Under the guidance of my mentor, Dr. Vicente Notario, I attempted to determine this association by learning how to code in MATLAB and applying the statistical analyses of ANOVA, Kaplan-Meier survival curves, and log-rank tests to publicly available cancer datasets. My results aid in determining the role of the three genes in lung adenocarcinoma diagnosis and prognosis.

I presented my research at my regional and state science and engineering fairs and later, at ISEF as well. Then, I heard about the AJAS conference and was given the opportunity to attend this conference as a delegate. I am looking forward to sharing all of our fascinating research!

Image credits

DNA - https://stock.adobe.com/images/cute-cartoon-dna-strand/253166993

Lungs - https://pngtree.com/freepng/hand-drawn-cartoon-lung-illustration_4627506.html

Images (18)

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Awards (1)

  • AJAS Fellows Badge

Competition history

  • AJAS 2022 Medicine

Resources

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