Related Experiment Video

Updated: Jul 15, 2025

In Vivo CRISPR/Cas9 Screening to Simultaneously Evaluate Gene Function in Mouse Skin and Oral Cavity
07:52

In Vivo CRISPR/Cas9 Screening to Simultaneously Evaluate Gene Function in Mouse Skin and Oral Cavity

Published on: November 2, 2020

6.5K

An in-silico study to determine susceptibility to cancer by evaluating the coding and non-coding non-synonymous

Sadri Fatemeh1, Zarei Mahboobeh1, Ahmadi Khadijeh2

  • 1Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.

Journal of Biomolecular Structure & Dynamics
|September 27, 2023
PubMed

Insights

This study identifies damaging Single Nucleotide Variants (SNVs) in the SOCS3 gene, crucial for cancer suppression. Findings highlight specific SNVs impacting protein function and gene expression, aiding future cancer risk research.

Area of Science:

  • Genetics and Molecular Biology
  • Cancer Research
  • Bioinformatics

Background:

  • Single Nucleotide Variants (SNVs) can alter gene expression and protein function, contributing to cancer risk.
  • SOCS3 (suppressor of cytokine signaling 3) is a key tumor suppressor in the JAK/STAT pathway, often suppressed in cancers.
  • Understanding the impact of SOCS3 genetic variations is crucial for cancer research.

Purpose of the Study:

  • To screen for non-coding and potentially deleterious coding SNVs within the SOCS3 gene.
  • To evaluate the functional consequences of identified SNVs on SOCS3 protein stability, activity, and gene expression.
  • To establish a computational pipeline for assessing SNVs in tumor suppressor genes.

Main Methods:

  • Utilized multiple bioinformatics tools (PredictSNP1.0, ConSurf, ModPred, I-Mutant, MUpro, UTRSite, SNP2TFBS, miRNA SNP) for SNV analysis.
  • Performed molecular docking and molecular dynamics (MD) simulations to assess the impact of SNVs on SOCS3-JAK interactions.
  • Screened 2786 SOCS3 SNVs to identify functionally significant variants in both coding and non-coding regions.

Main Results:

  • Identified 10 coding SNVs and 49 non-coding SNPs affecting gene function.
  • Three coding SNVs (W48R, R71C, N198S) were predicted as highly damaging by multiple tools.
  • One coding SNV (R194W) showed significant deleterious effects when analyzed with molecular docking and MD simulations.

Conclusions:

  • The study successfully screened and identified functionally relevant SNVs in the SOCS3 gene.
  • Specific SNVs (W48R, R71C, N198S, R194W) are proposed as potentially critical for SOCS3's tumor-suppressive role.
  • Developed a comprehensive computational approach for future studies on SNVs impacting protein function and cancer risk.
Keywords:
SNVsSOCS3bioinformatics toolscancergenetic variationtumor suppressor

More Related Videos

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.4K
In Vivo Modeling of the Morbid Human Genome using Danio rerio12:31

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Published on: August 24, 2013

20.7K

Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
13.6K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.2K
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
7.5K
Cancers Originate from Somatic Mutations in a Single Cell02:21

Cancers Originate from Somatic Mutations in a Single Cell

Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
12.0K
Cancer Survival Analysis01:21

Cancer Survival Analysis

Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
380
In-vitro Mutagenesis01:16

In-vitro Mutagenesis

To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
14.0K