Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Selection and Biopsy Collection
2.2. Organoid Establishment and Passaging
2.3. RNA Harvesting, Library Preparation, Sequencing and Pre-Processing of Colon Organoid RNA-Seq Data
2.4. Collection of Publicly Available Data
2.5. Statistical Analysis of RNA-Seq
2.6. Ethanol Treatment of FAP Colon Organoids
2.7. Quantitative PCR
3. Results
3.1. Defining the Transcriptomic Landscape of Colon Organoids of FAP Patients versus Those of Healthy Subjects
3.2. Relationship of DNA Methylation and Differential Expression in FAP Colon Organoids
3.3. Defining the Overlap in Tumor-Related Gene Expression between FAP and EOCRC
3.4. Overlap between DEGs Identified in FAP Colon Organoids and EOCRC Tumors
3.5. Technical Validation of FAP DEGs and Confirmation of Findings in Biopsies
3.6. Role of Lifestyle Factors in Driving Expression of FAP DEGs
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Estimate | Standard Error | Test Statistic | p |
---|---|---|---|---|
NKD1 | −6.069 | 1.012 | −6.001 | 5.42 × 10−4 |
EGR2 | −3.139 | 0.653 | −4.805 | 1.95 × 10−3 |
EYA2 | 3.820 | 1.326 | 2.880 | 0.024 |
EPDR1 | −2.054 | 0.823 | −2.496 | 0.047 |
IGFL1 | −2.697 | 1.116 | −2.417 | 0.052 |
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Devall, M.A.; Eaton, S.; Ali, M.W.; Powell, S.M.; Li, L.; Casey, G. Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers 2022, 14, 4138. https://doi.org/10.3390/cancers14174138
Devall MA, Eaton S, Ali MW, Powell SM, Li L, Casey G. Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers. 2022; 14(17):4138. https://doi.org/10.3390/cancers14174138
Chicago/Turabian StyleDevall, Matthew A., Stephen Eaton, Mourad W. Ali, Steven M. Powell, Li Li, and Graham Casey. 2022. "Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients" Cancers 14, no. 17: 4138. https://doi.org/10.3390/cancers14174138
APA StyleDevall, M. A., Eaton, S., Ali, M. W., Powell, S. M., Li, L., & Casey, G. (2022). Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers, 14(17), 4138. https://doi.org/10.3390/cancers14174138