Microbiome R Analysis: Fusobacterium nucleatum in Breast Cancer

GitHub URL: https://github.com/drbenedictpaul/microbiome_R

This repository contains R scripts and associated files for the study: "Association of Fusobacterium nucleatum with Breast Cancer Progression and Virulence Factor Profiling in South Indian Patients."

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About the Study

Title: Association of Fusobacterium nucleatum with Breast Cancer Progression and Virulence Factor Profiling in South Indian Patients

Authors: Kiruthika Vijayakumar*, Sudandira Doss C, Manickavasagam M, Sudha Warrier, Benedict Paul C#

Affiliation: Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, (Deemed to be University), Porur, Chennai - 600116, Tamil Nadu State, India.

*Presenting Author #Corresponding Author: Benedict Paul C ([email protected])

Presented at: The Rencontres de Quy Nhon VII: International Biology Conference 2024 (Oral Presentation)

Background

Breast cancer is a complex disease, and recent research suggests a link between the oral bacterium Fusobacterium nucleatum and cancer development, progression, and chemotherapeutic resistance. F. nucleatum can colonize tumors, modulate the tumor microenvironment, and protect tumor cells from immune detection. Its virulence factors, notably fadA (promotes cancer-related gene expression) and fipA (inhibits T cell immune responses), are of particular interest. Understanding this association is crucial for improving breast cancer management.

Study Aim

This study investigated the incidence of F. nucleatum and its virulence factors, fadA and fipA, in oral samples from South Indian breast cancer patients (n=30) at Sri Ramachandra Medical Center.

Methods

• Ethical clearance was obtained, and patients with all breast cancer stages were included.
• Oral wash samples were collected.
• PCR amplification using 16S rRNA primers was used to identify F. nucleatum positive samples.
• The presence of fadA and fipA was determined using sequence-specific oligonucleotide primers.
• Data analysis was conducted using R programming.

Key Findings

• 73.3% (n=22) of samples were positive for F. nucleatum.
• Among F. nucleatum positive samples:
  • 45.45% (n=10) were positive for fadA.
  • 54.54% (n=12) were positive for fipA.
• A higher frequency of F. nucleatum was observed in later stages of breast cancer.
• fadA and fipA did not show a significant influence on disease progression in this cohort.
• F. nucleatum incidence was higher in hormone-sensitive breast cancer, with no significant presence in triple-negative cases.

Conclusion

This study provides preliminary evidence linking F. nucleatum to breast cancer progression in a South Indian cohort. While a larger sample size is needed for more definitive conclusions, the data suggest that other virulence factors might also be involved in disease progression. Comprehensive profiling of virulence factors is warranted to better understand pathogenic mechanisms and potentially improve therapeutic strategies.

Keywords: Fusobacterium nucleatum, Breast Cancer, Virulence Factors, Tumor Microenvironment, Chemotherapeutic Resistance.

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Purpose of this Repository

This repository contains the R scripts used for the statistical analysis and visualization of the data presented in the study. It includes:

• Anonymized datasets (if ethically permissible and prepared for sharing).
• R markdown files for reproducible reports.
• Figures generated from the analysis.

The aim is to promote transparency and reproducibility in our research.

Repository Contents

(This section describes the general structure. Please adapt if your specific structure differs.)

• /data/: Contains or will contain anonymized dataset(s) used for the analysis (e.g., patient_data.csv).
• /scripts/: Contains the R scripts for:
  • Data cleaning and preparation.
  • Statistical analysis (e.g., frequency calculations, chi-squared tests, logistic regression).
  • Data visualization (e.g., bar plots, association plots).
• /results/ or /figures/: Contains or will contain output figures and tables generated by the scripts.
• README.md: This file.

Usage

(Please update this section with specific instructions for your scripts and any dependencies.)

To use the scripts in this repository:

1. Clone the repository:

   git clone https://github.com/drbenedictpaul/microbiome_R.git

2. Navigate to the project directory:

   cd microbiome_R

3. Open the R scripts (e.g., located in the /scripts/ folder) in RStudio or your preferred R environment.
4. Install necessary R packages: Ensure you have the required R packages installed. Common packages for data analysis and visualization include dplyr, ggplot2, tidyr, etc. You may need to specify others based on your scripts.

   # Example: install.packages(c("dplyr", "ggplot2", "tidyr", "specific_package_for_your_analysis"))

5. Run the scripts as per their intended order or individual purpose. Ensure data files are correctly pathed if they are read by the scripts.

Citation

If you use any code or data from this repository or refer to the findings of this study, please cite the original presentation/publication:

Vijayakumar, K., Doss, S. C., Manickavasagam, M., Warrier, S., & Paul, B. C. (2024). Association of Fusobacterium nucleatum with Breast Cancer Progression and Virulence Factor Profiling in South Indian Patients. Oral Presentation at The Rencontres de Quy Nhon VII: International Biology Conference 2024.

Contact

For any questions regarding the study or the contents of this repository, please contact: Dr. Benedict Christopher Paul Email: [email protected]

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Note: This study presents preliminary findings. Further research with a larger sample size is ongoing.