绘制 KMT2D 肿瘤抑制基因的硅学遗传网络图,以发现新的功能关联和癌细胞脆弱性。

IF 10.4 1区 生物学 Q1 GENETICS & HEREDITY
Yuka Takemon, Erin D Pleasance, Alessia Gagliardi, Christopher S Hughes, Veronika Csizmok, Kathleen Wee, Diane L Trinh, Ryan D Huff, Andrew J Mungall, Richard A Moore, Eric Chuah, Karen L Mungall, Eleanor Lewis, Jessica Nelson, Howard J Lim, Daniel J Renouf, Steven Jm Jones, Janessa Laskin, Marco A Marra
{"title":"绘制 KMT2D 肿瘤抑制基因的硅学遗传网络图,以发现新的功能关联和癌细胞脆弱性。","authors":"Yuka Takemon, Erin D Pleasance, Alessia Gagliardi, Christopher S Hughes, Veronika Csizmok, Kathleen Wee, Diane L Trinh, Ryan D Huff, Andrew J Mungall, Richard A Moore, Eric Chuah, Karen L Mungall, Eleanor Lewis, Jessica Nelson, Howard J Lim, Daniel J Renouf, Steven Jm Jones, Janessa Laskin, Marco A Marra","doi":"10.1186/s13073-024-01401-9","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required.</p><p><strong>Methods: </strong>Here, we computationally map genetic networks of KMT2D, a tumour suppressor gene frequently mutated in several cancer types. Using KMT2D loss-of-function (KMT2D<sup>LOF</sup>) mutations as a model, we illustrate the utility of in silico genetic networks in uncovering novel functional associations and vulnerabilities in cancer cells with LOF alterations affecting tumour suppressor genes.</p><p><strong>Results: </strong>We revealed genetic interactors with functions in histone modification, metabolism, and immune response and synthetic lethal (SL) candidates, including some encoding existing therapeutic targets. Notably, we predicted WRN as a novel SL interactor and, using recently available WRN inhibitor (HRO761 and VVD-133214) treatment response data, we observed that KMT2D mutational status significantly distinguishes treatment-sensitive MSI cell lines from treatment-insensitive MSI cell lines.</p><p><strong>Conclusions: </strong>Our study thus illustrates how tumour suppressor gene LOF alterations can be exploited to reveal potentially targetable cancer cell vulnerabilities.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":"16 1","pages":"136"},"PeriodicalIF":10.4000,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583415/pdf/","citationCount":"0","resultStr":"{\"title\":\"Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities.\",\"authors\":\"Yuka Takemon, Erin D Pleasance, Alessia Gagliardi, Christopher S Hughes, Veronika Csizmok, Kathleen Wee, Diane L Trinh, Ryan D Huff, Andrew J Mungall, Richard A Moore, Eric Chuah, Karen L Mungall, Eleanor Lewis, Jessica Nelson, Howard J Lim, Daniel J Renouf, Steven Jm Jones, Janessa Laskin, Marco A Marra\",\"doi\":\"10.1186/s13073-024-01401-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required.</p><p><strong>Methods: </strong>Here, we computationally map genetic networks of KMT2D, a tumour suppressor gene frequently mutated in several cancer types. Using KMT2D loss-of-function (KMT2D<sup>LOF</sup>) mutations as a model, we illustrate the utility of in silico genetic networks in uncovering novel functional associations and vulnerabilities in cancer cells with LOF alterations affecting tumour suppressor genes.</p><p><strong>Results: </strong>We revealed genetic interactors with functions in histone modification, metabolism, and immune response and synthetic lethal (SL) candidates, including some encoding existing therapeutic targets. Notably, we predicted WRN as a novel SL interactor and, using recently available WRN inhibitor (HRO761 and VVD-133214) treatment response data, we observed that KMT2D mutational status significantly distinguishes treatment-sensitive MSI cell lines from treatment-insensitive MSI cell lines.</p><p><strong>Conclusions: </strong>Our study thus illustrates how tumour suppressor gene LOF alterations can be exploited to reveal potentially targetable cancer cell vulnerabilities.</p>\",\"PeriodicalId\":12645,\"journal\":{\"name\":\"Genome Medicine\",\"volume\":\"16 1\",\"pages\":\"136\"},\"PeriodicalIF\":10.4000,\"publicationDate\":\"2024-11-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583415/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Medicine\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13073-024-01401-9\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Medicine","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13073-024-01401-9","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

背景:肿瘤抑制基因的功能缺失(LOF)改变无法直接靶向。方法:在此,我们通过计算绘制了 KMT2D 的遗传网络图,KMT2D 是一种在多种癌症类型中经常发生突变的肿瘤抑制基因。我们以 KMT2D 功能缺失(KMT2DLOF)突变为模型,说明了硅学遗传网络在发现新的功能关联和影响肿瘤抑制基因的 LOF 改变的癌细胞中的脆弱性方面的实用性:结果:我们发现了在组蛋白修饰、新陈代谢、免疫反应和合成致死(SL)候选基因中具有功能的基因相互作用者,包括一些编码现有治疗靶点的基因。值得注意的是,我们预测WRN是一种新型的SL相互作用因子,而且利用最近上市的WRN抑制剂(HRO761和VVD-133214)的治疗反应数据,我们观察到KMT2D突变状态可显著区分对治疗敏感的MSI细胞系和对治疗不敏感的MSI细胞系:因此,我们的研究说明了如何利用肿瘤抑制基因 LOF 改变来揭示潜在的靶向癌细胞弱点。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities.

Background: Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required.

Methods: Here, we computationally map genetic networks of KMT2D, a tumour suppressor gene frequently mutated in several cancer types. Using KMT2D loss-of-function (KMT2DLOF) mutations as a model, we illustrate the utility of in silico genetic networks in uncovering novel functional associations and vulnerabilities in cancer cells with LOF alterations affecting tumour suppressor genes.

Results: We revealed genetic interactors with functions in histone modification, metabolism, and immune response and synthetic lethal (SL) candidates, including some encoding existing therapeutic targets. Notably, we predicted WRN as a novel SL interactor and, using recently available WRN inhibitor (HRO761 and VVD-133214) treatment response data, we observed that KMT2D mutational status significantly distinguishes treatment-sensitive MSI cell lines from treatment-insensitive MSI cell lines.

Conclusions: Our study thus illustrates how tumour suppressor gene LOF alterations can be exploited to reveal potentially targetable cancer cell vulnerabilities.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Genome Medicine
Genome Medicine GENETICS & HEREDITY-
CiteScore
20.80
自引率
0.80%
发文量
128
审稿时长
6-12 weeks
期刊介绍: Genome Medicine is an open access journal that publishes outstanding research applying genetics, genomics, and multi-omics to understand, diagnose, and treat disease. Bridging basic science and clinical research, it covers areas such as cancer genomics, immuno-oncology, immunogenomics, infectious disease, microbiome, neurogenomics, systems medicine, clinical genomics, gene therapies, precision medicine, and clinical trials. The journal publishes original research, methods, software, and reviews to serve authors and promote broad interest and importance in the field.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信