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利用人工智能算法检测子宫内膜癌中的驱动基因突变和基因组特征。

Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms.

机构信息

Biology Program, The Ohio State University, Marion, Ohio, United States of America.

Biology Department, Xavier University, Cincinnati, Ohio, United States of America.

出版信息

PLoS One. 2024 Feb 26;19(2):e0299114. doi: 10.1371/journal.pone.0299114. eCollection 2024.


DOI:10.1371/journal.pone.0299114
PMID:38408048
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10896512/
Abstract

Analyzed endometrial cancer (EC) genomes have allowed for the identification of molecular signatures, which enable the classification, and sometimes prognostication, of these cancers. Artificial intelligence algorithms have facilitated the partitioning of mutations into driver and passenger based on a variety of parameters, including gene function and frequency of mutation. Here, we undertook an evaluation of EC cancer genomes deposited on the Catalogue of Somatic Mutations in Cancers (COSMIC), with the goal to classify all mutations as either driver or passenger. Our analysis showed that approximately 2.5% of all mutations are driver and cause cellular transformation and immortalization. We also characterized nucleotide level mutation signatures, gross chromosomal re-arrangements, and gene expression profiles. We observed that endometrial cancers show distinct nucleotide substitution and chromosomal re-arrangement signatures compared to other cancers. We also identified high expression levels of the CLDN18 claudin gene, which is involved in growth, survival, metastasis and proliferation. We then used in silico protein structure analysis to examine the effect of certain previously uncharacterized driver mutations on protein structure. We found that certain mutations in CTNNB1 and TP53 increase protein stability, which may contribute to cellular transformation. While our analysis retrieved previously classified mutations and genomic alterations, which is to be expected, this study also identified new signatures. Additionally, we show that artificial intelligence algorithms can be effectively leveraged to accurately predict key drivers of cancer. This analysis will expand our understanding of ECs and improve the molecular toolbox for classification, diagnosis, or potential treatment of these cancers.

摘要

分析子宫内膜癌 (EC) 基因组可识别分子特征,这些特征能够对这些癌症进行分类,有时还能进行预后判断。人工智能算法根据基因功能和突变频率等多种参数,将突变分为驱动突变和乘客突变。在这里,我们对目录中的 EC 癌症基因组进行了评估体细胞突变在癌症 (COSMIC),目的是将所有突变分类为驱动突变或乘客突变。我们的分析表明,大约 2.5%的突变是驱动突变,导致细胞转化和永生化。我们还对核苷酸水平的突变特征、大染色体重排和基因表达谱进行了特征描述。我们观察到子宫内膜癌与其他癌症相比,具有明显的核苷酸取代和染色体重排特征。我们还发现 CLDN18 紧密连接蛋白基因的高表达水平,该基因参与生长、存活、转移和增殖。然后,我们使用计算机蛋白质结构分析来检查某些以前未表征的驱动突变对蛋白质结构的影响。我们发现 CTNNB1 和 TP53 中的某些突变增加了蛋白质的稳定性,这可能有助于细胞转化。虽然我们的分析检索到了先前分类的突变和基因组改变,这是意料之中的,但这项研究还确定了新的特征。此外,我们还表明,人工智能算法可以有效地用于准确预测癌症的关键驱动因素。这项分析将扩展我们对 EC 的理解,并改善分类、诊断或这些癌症潜在治疗的分子工具包。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/a4f5c423fe0f/pone.0299114.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/b71d3ed6dabd/pone.0299114.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/adb44d064942/pone.0299114.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/2edcfb6fb270/pone.0299114.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/4b29e60f119c/pone.0299114.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/a4f5c423fe0f/pone.0299114.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/b71d3ed6dabd/pone.0299114.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/adb44d064942/pone.0299114.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/2edcfb6fb270/pone.0299114.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/4b29e60f119c/pone.0299114.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/70d6/10896512/a4f5c423fe0f/pone.0299114.g005.jpg

相似文献

[1]
Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms.

PLoS One. 2024

[2]
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[3]
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[4]
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引用本文的文献

[1]
Epigenetics of Endometrial Cancer: The Role of Chromatin Modifications and Medicolegal Implications.

Int J Mol Sci. 2025-7-29

[2]
An Overview of Artificial Intelligence in Gynaecological Pathology Diagnostics.

Cancers (Basel). 2025-4-16

[3]
From Genes to Clinical Practice: Exploring the Genomic Underpinnings of Endometrial Cancer.

Cancers (Basel). 2025-1-20

[4]
CD73 restrains mutant β-catenin oncogenic activity in endometrial carcinomas.

bioRxiv. 2024-11-18

[5]
In silico analysis of several frequent SLX4 mutations appearing in human cancers.

MicroPubl Biol. 2024-5-17

本文引用的文献

[1]
New developments and standard of care in the management of advanced gastric cancer.

Clin Res Hepatol Gastroenterol. 2024-1

[2]
Anti-Claudin Treatments in Gastroesophageal Adenocarcinoma: Mainstream and Upcoming Strategies.

J Clin Med. 2023-4-19

[3]
Landscape of chromatin remodeling gene alterations in endometrial carcinoma.

Gynecol Oncol. 2023-5

[4]
Estrogen receptors as potential therapeutic target in endometrial cancer.

J Recept Signal Transduct Res. 2023-2

[5]
Update in the molecular classification of endometrial carcinoma.

Int J Gynecol Cancer. 2023-3-6

[6]
Molecular Profiling of Endometrial Cancer From TCGA to Clinical Practice.

J Natl Compr Canc Netw. 2023-2

[7]
Mechanisms of mutant β-catenin in endometrial cancer progression.

Front Oncol. 2022-9-29

[8]
Cleft Palate in Apert Syndrome.

J Dev Biol. 2022-8-11

[9]
Membranous and nuclear staining of CLDN18 in HPV-independent and HPV-associated endocervical adenocarcinomas.

Cancer Med. 2023-1

[10]
High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials.

Chembiochem. 2022-9-5

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