COMPUTATIONAL ANALYSIS AND HOT SPOTS IDENTIFICATION FOR DIAGNOSIS AND

DRUG DESIGNING AGAINST TFF1 GENE IN BREAST CANCER

Alisha Adnan, Roha Akbar, Shanzay Amjad
2nd Year MBBS, Central Park Medical College, Lahore

INTRODUCTION Trefoil Factor 1 (TFF1) is an estrogen-inducible gene

associated with breast cancer. Nonsynonymous single
Breast cancer is among the most prevalent cancers globally, predominantly affecting women, though cases are nucleotide polymorphisms (nsSNPs) in TFF1 can result in
also observed in men. It is frequently inherited, contributing significantly to the global cancer burden (Soutto, alterations to the protein structure, potentially causing
Mohammed, et al., 2021). One of the key genes involved in breast cancer is the Trefoil Factor (TFF1) gene, which deleterious changes in the amino acid sequence. This
is estrogen-inducible. Mutations in the TFF1 gene can lead to alterations in the structure and function of the study employs a computational approach to identify the
encoded protein, which may be classified as either synonymous or nonsynonymous (Wan, Long, et al., 2021). most deleterious nsSNPs and predict the resulting
These mutations have the potential to contribute to cancer development by disrupting normal protein function. structural changes, to enhance our understanding of
Recent advances in bioinformatics have greatly enhanced our ability to predict the functional impact of single TFF1's role in breast cancer development.
nucleotide polymorphisms (SNPs) within cancer-associated genes like TFF1. Even minor mutations in this gene
may act as a catalyst for breast cancer progression. Early detection of such mutations is critical, particularly for Several computational tools were utilized to evaluate the
impact of these SNPs, including SIFT, PROVEAN, and
women undergoing menopause, as this group is at heightened risk of genomic instability. A deeper
POLYPHEN.
understanding of the molecular mechanisms surrounding the TFF1 gene could significantly improve early
This analysis was followed by 3D model construction
diagnosis and inform the development of targeted therapies for breast cancer.
using AlphaFold. Given the variety of algorithms
employed to assess SNPs, a consensus approach was
adopted to prioritize
[ IMAGE CAPTION the most
] Use Images to deleterious variants. Out of
METHODOLOGY AND RESULTS showcase your data in a visual form
12 initially identified SNPs, two (F58L and TOM) were
consistently flagged as harmful across multiple tools.
ENSEMBL: These variants are considered potential hot spots that
Gene Specific Ensembl provides a genome browser that acts as a single point of access to
may contribute to breast cancer progression based on
Variants Retrival: annotated genomes for mainly vertebrate species. Information about genes,
transcripts, and further annotation can be retrieved at the genome, gene, and
their prediction reliability index and high scores from the
Ensembl (online available database)
protein levels. aforementioned programs.

Transcript Selection: SIFT:

Canonical Transcript was selected SIFT (Sorting Intolerant From Tolerant) is a program that predicts
whether an amino acid substitution affects protein function so that users can
prioritize substitutions for further study. A SIFT score is a normalized
probability of observing the new amino acid at that position and ranges from
SNP Selection:
0 to 1. A value of between 0 and 0.05 is predicted to affect protein function.
Missense type of SNPs
was under consideration POLYPHEN:
Polymorphism Phenotyping v2 (PolyPhen-2) is a bioinformatics tool that
predicts the impact of a single amino acid substitution on the structure and
Function Prediction: function of human proteins. The score can be interpreted as follows: 0.0 to
0.15 -- Variants with scores in this range are predicted to be benign. 0.15 to
1. SIFT 2. PROVEAN 3. POLYPHEN 1.0 -- Variants with scores in this range are possibly damaging. 0.85 to 1.0 -
- Variants with scores in this range are more confidently predicted to be
damaging.
Conclusion
PROVEAN:
PROVEAN is useful for filtering sequence variants to identify
nonsynonymous or indel variants that are predicted to be functionally
important.If the PROVEAN score is equal to or below a predefined
threshold (e.g. -2.5), the protein variant is predicted to have a "deleterious"
effect. If the PROVEAN score is above the threshold, the variant is
predicted to have a "neutral" effect.

CONCLUSION:
This research aims to advance the understanding of the TFF1 gene’s functional dynamics. The identified
SNPs are anticipated to serve as significant hotspot regions involved in the breast cancer pathway. By
targeting these variants, we can enhance early diagnostic capabilities for breast cancer and pave the
way for innovative therapeutic interventions against this gene.

Figure 2:
3D model of wild type TFF1 protein predicted by Alpha-Fold REFRENCES:
1. WAN, LONG, ET AL. *CIRC-TFF1 FACILITATES BREAST
CANCER DEVELOPMENT VIA REGULATION OF MIR-338-
3P/FGFR1 AXIS." BIOCHEMICAL GENETICS (2021): 1-21.
2. SOUTTO. MOHAMMED, ET AL. *NF-KB-DEPENDENT
ACTIVATION OF STAT3 BY H.
PYLORI IS SUPPRESSED BY TFF1." (2021).