Application of Artificial Neural Networks to Link Genetic and Environmental Factors to DNA Methylation in Colorectal Cancer

Abstract

Aims: We applied artificial neural networks (ANNs) to understand the connections among polymorphisms of genes involved in folate metabolism, clinico-pathological features and promoter methylation levels of MLH1, APC, CDKN2A^INK4A, MGMT and RASSF1A in 83 sporadic colorectal cancer (CRC) tissues, and to link dietary and lifestyle factors with gene promoter methylation. Materials & Methods: Promoter methylation was assessed by means of methylation-sensitive high-resolution melting and genotyping by PCR-RFLP technique. Data were analyzed with the Auto Contractive Map, a special kind of ANN able to define the strength of the association of each variable with all the others and to visually show the map of the main connections. Results: We observed a strong connection between the low methylation levels of the five CRC genes and the MTR 2756AA genotype. Several other connections were revealed, including those between dietary and lifestyle factors and the methylation levels of CRC genes. Conclusion: ANNs revealed the complexity of the interconnections among factors linked to DNA methylation in CRC.

Keywords::

• APC
• artificial neural networks
• CDKN2A
• colorectal cancer
• DNA methylation
• folate
• MGMT
• MLH1
• polymorphisms
• RASSF1A

Acknowledgements

The authors acknowledge the medical doctors and the staff of the Department of Surgery, Medical, Molecular and Critical Area Pathology of the University of Pisa for their assistance with the patients. The authors acknowledge the graphical technical support of M Lopomo.

Disclaimer

The funding organisation (Istituto Toscano Tumori) had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Financial & competing interest disclosure

This work has received funding from Istituto Toscano Tumori (ITT) ‘Correlation among epigenetic, environmental and genetic factors in colorectal carcinoma’ (Prot. AOOGRT/325424/Q.80.110 16/12/2009). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work has received funding from Istituto Toscano Tumori (ITT) ‘Correlation among epigenetic, environmental and genetic factors in colorectal carcinoma’ (Prot. AOOGRT/325424/Q.80.110 16/12/2009). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.