Single-cell Segmentation and Fluorescent Intensity Quantification Pipeline
Session Number
Project ID: CMPS 29
Advisor(s)
Yogesh Goyal, Northwestern University Feinberg School of Medicine
Discipline
Computer Science
Start Date
17-4-2024 8:15 AM
End Date
17-4-2024 8:30 AM
Abstract
Pancreatic cancer has less than a 10% survival rate after 5 years of treatment. Drug resistance, among other issues, is one of the main reasons for tumor relapse. One of the main mutations in pancreatic cancer is in the protein KRAS, which controls cell proliferation and when mutated sends signals continuously for the cell to divide. Recently, a new FDA-approved drug called Sotorasib was released to treat cancers with the mutation KRAS G12C.
The project aimed to identify whether the treated cells' KRAS signaling pathway was on or off. To do this, we want to locate and quantify the presence of the protein ERK 1/2 downstream of KRAS in the signaling pathway.
This was accomplished by creating an image sequencing pipeline, within the pipeline we created a segmentation model with an accuracy of ~97.8%. The model produced masks that we then performed quality control methods to rectify any inaccuracies in the segmentation process. The pipeline then calculated the fluorescence intensity of the cells via the mask’s region. Ultimately, the Sotorasib-treated cells consistently exhibited lowe intensity readings of ERK 1/2 compared to both gemcitabine-treated and untreated cells, suggesting resistance to Sotorasib in the context of KRAS G12C mutation.
Single-cell Segmentation and Fluorescent Intensity Quantification Pipeline
Pancreatic cancer has less than a 10% survival rate after 5 years of treatment. Drug resistance, among other issues, is one of the main reasons for tumor relapse. One of the main mutations in pancreatic cancer is in the protein KRAS, which controls cell proliferation and when mutated sends signals continuously for the cell to divide. Recently, a new FDA-approved drug called Sotorasib was released to treat cancers with the mutation KRAS G12C.
The project aimed to identify whether the treated cells' KRAS signaling pathway was on or off. To do this, we want to locate and quantify the presence of the protein ERK 1/2 downstream of KRAS in the signaling pathway.
This was accomplished by creating an image sequencing pipeline, within the pipeline we created a segmentation model with an accuracy of ~97.8%. The model produced masks that we then performed quality control methods to rectify any inaccuracies in the segmentation process. The pipeline then calculated the fluorescence intensity of the cells via the mask’s region. Ultimately, the Sotorasib-treated cells consistently exhibited lowe intensity readings of ERK 1/2 compared to both gemcitabine-treated and untreated cells, suggesting resistance to Sotorasib in the context of KRAS G12C mutation.