Functional Genomics of LINE-1 Retrotransposition
LINE-1 逆转录转座的功能基因组学
基本信息
- 批准号:10337555
- 负责人:
- 金额:$ 64.39万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2022
- 资助国家:美国
- 起止时间:2022-04-21 至 2027-01-31
- 项目状态:未结题
- 来源:
- 关键词:Aromatic Polycyclic HydrocarbonsAutomobile DrivingBenzo(a)pyreneBindingBiologicalBiological AssayBiological MarkersCRISPR screenCancer cell lineCancerousCarcinogensCell LineCell RespirationCellsChromatin StructureCitiesClustered Regularly Interspaced Short Palindromic RepeatsComplexDNADNA AdductsDNA DamageDNA MethylationDNA sequencingDevelopmentDiseaseElementsEnvironmental CarcinogensEnvironmental PollutionEpigenetic ProcessEpithelial CellsEventExposure toFamilyFemaleGenesGeneticGenetic PolymorphismGenetic Predisposition to DiseaseGenetic RecombinationGenetic studyGenomeGenomic InstabilityHeterogeneityHumanHuman GenomeHydrocarbonsIn VitroInstructionInvestigationKRAS2 geneKnowledgeLaboratoriesLengthLightLinkLiverLocationLong Interspersed ElementsLungMalignant - descriptorMalignant neoplasm of lungMediatingMediator of activation proteinMusMutateNon-Small-Cell Lung CarcinomaOncogenicOutcomeParentsPathogenicityPopulationPredispositionProcessProtocols documentationRespiratory DiseaseRetroelementsRetrotranspositionRetrotransposonRoleSignal TransductionTP53 geneTechnologyTestingTimeToxic effectValidationVariantbasecancer typecarcinogenicitycombatdesignexposed human populationfunctional genomicsgene environment interactiongenetic manipulationgenome-widein silicoin vivoinducible gene expressioninsertion/deletion mutationinsightmalemembermouse modelnovel therapeuticspromoterrenal epitheliumrespiratory healthresponsesingle-cell RNA sequencingtranscriptomicstumor
项目摘要
Abstract
Functional genomics studies have unraveled many of the instructions encoded in the human genome. Taking
advantage of significant advances in parallel sequencing and a wide diversity of other protocols, studies are
proposed in this application to resolve gene-environment interactions that determine variations in the
susceptibility to lung cancer. These studies are timely in light of the worsening levels of environmental pollution
in many US cities that contribute to the development of respiratory disease and to disparities across populations.
Of concern is the persistence of polycyclic aromatic hydrocarbon (PAH) contaminants, such as benzo(a)pyrene
(BaP), and their ability to damage the DNA of lung epithelial cells. While the mutagenicity of BaP has been
extensively characterized, questions remain about the degree to which DNA damage intersects with epigenetic
disruption in driving the overwhelming carcinogenic response of BaP. Genome-wide assessments of BaP toxicity
in the Ramos Laboratory revealed that the parent hydrocarbon and its metabolites activate LINE-1
retrotransposons in lung epithelial cells via epigenetic mechanisms. LINE-1 (Long Interspersed Element-1)
activation is associated with oncogenic signaling, changes in chromatin structure, disruption of epigenetic
control, and malignant transformation. LINE-1 is a family of mobile elements with the ability to copy their own
DNA and use these complementary sequences to randomly insert at other locations within the genome. This
process can be highly mutagenic and associated with genomic instability. We posit that alterations in the lifecycle
of LINE-1 retroelements is a key missing link in our understanding of the complex genetic and epigenetic deficits
associated with BaP carcinogenicity. Of ~100 full-length LINE-1 elements that remain competent for
retrotransposition, nine are recognized as “hot” LINE-1s responsible for the vast majority of pathogenic events.
These hot elements are polymorphic in humans and may therefore contribute to heterogeneity in genetic
susceptibility to environmental PAH toxicity. In response to RFA-ES-20-018, we propose to use in vitro functional
genomics for discovery and validation to test the hypothesis that polymorphic LINE-1 elements differentially
regulate oncogenic signaling in lung epithelial cells and account for differences in susceptibility to BaP. In Aim
1, we will examine hot LINE-1 elements and their constitutive and inducible expression in normal lung and
cancerous epithelial cells by targeted DNA sequencing and single cell RNA sequencing (scRNA-seq). In Aim 2,
we will use CRISPR/dCas9m to edit the LINE-1 promoter to either enhance or silence retrotransposition and its
impact on chromatin structure and transcriptomic landscapes. In Aim 3, we will use computational approaches
to study genetic relationships across variable networks defined by polymorphic LINE-1 variants, with a focus on
TP53, AHR, and RB. These studies will reveal important mechanistic insights into the activation of LINE-1 by
PAH carcinogens and illuminate our understanding of the human variability in carcinogen susceptibility. This
knowledge will lead to better biomarker designs and novel therapies to combat environmental toxicities.
摘要
功能基因组学研究已经解开了人类基因组中编码的许多指令。拿走
利用并行测序的重大进展和广泛多样的其他方案,研究包括
在本应用程序中提出,以解决基因-环境交互作用,这些交互作用决定了
易患肺癌。鉴于环境污染的恶化程度,这些研究是适时的。
在美国许多城市,这导致了呼吸道疾病的发展和人口之间的差异。
令人关切的是多环芳烃(PAH)污染物的持久性,如苯并(A)芘
(BaP),以及它们损伤肺上皮细胞DNA的能力。虽然BaP的致突变性已经被
被广泛描述的问题仍然是DNA损伤与表观遗传的交叉程度
破坏了BaP的压倒性致癌反应。全基因组对苯并苯毒性的评估
拉莫斯实验室发现,母体碳氢化合物及其代谢产物激活了LINE-1
肺上皮细胞中的反转录转座子通过表观遗传机制。LINE-1(长散布元素-1)
激活与致癌信号、染色质结构的变化、表观遗传学的中断有关
控制和恶变。Line-1是一系列移动元素,能够复制自己的元素
并使用这些互补序列在基因组中的其他位置随机插入。这
这一过程可能是高度诱变的,并与基因组的不稳定性有关。我们假设生命周期中的变化
LINE-1逆转录元件是我们理解复杂的遗传和表观遗传缺陷的关键缺失的一环
与BaP的致癌性有关。-1\f25~100个全长-1\f25 LINE-1\f6元件
逆转录转座,其中9条被认为是导致绝大多数致病事件的“热线”。
这些热点元素在人类中是多态的,因此可能导致基因的异质性
对环境多环芳烃毒性的敏感性。为了响应RFA-ES-20-018,我们建议使用体外功能
发现和验证基因组学以检验多态LINE-1元件存在差异的假设
调节肺上皮细胞的致癌信号,并解释对BaP易感性的差异。在AIM
1,我们将检测热线-1元件及其在正常肺和正常肺中的结构性和诱导性表达
靶向DNA测序和单细胞RNA测序(scRNA-seq)。在目标2中,
我们将使用CRISPR/dCas9m编辑LINE-1启动子,以增强或抑制逆转录转座及其
对染色质结构和转录景观的影响。在目标3中,我们将使用计算方法
研究由多态LINE-1变异体定义的不同网络间的遗传关系,重点是
TP53、AHR和RB。这些研究将揭示对LINE-1激活的重要机制见解
多环芳烃是致癌物,并阐明了我们对人类致癌物易感性的变异性的理解。这
知识将导致更好的生物标记物设计和抗击环境毒性的新疗法。
项目成果
期刊论文数量(0)
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科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Kenneth S. Ramos其他文献
Health equity innovation in precision medicine: data stewardship and agency to expand representation in clinicogenomics
- DOI:
10.1186/s12961-024-01258-9 - 发表时间:
2024-12-19 - 期刊:
- 影响因子:3.200
- 作者:
Patrick J. Silva;Vasiliki Rahimzadeh;Reid Powell;Junaid Husain;Scott Grossman;Adam Hansen;Jennifer Hinkel;Rafael Rosengarten;Marcia G. Ory;Kenneth S. Ramos - 通讯作者:
Kenneth S. Ramos
Transcriptional Profiling and Functional Genomics Reveal a Role for AHR Transcription Factor in Nephrogenesis
转录谱和功能基因组学揭示 AHR 转录因子在肾发生中的作用
- DOI:
10.1196/annals.1371.045 - 发表时间:
2006 - 期刊:
- 影响因子:5.2
- 作者:
Kenneth S. Ramos - 通讯作者:
Kenneth S. Ramos
Rabbit aortic smooth muscle cell culture. A model for the pharmacological study of diabetes-induced alterations in cell proliferation.
兔主动脉平滑肌细胞培养。
- DOI:
10.1016/0160-5402(91)90045-7 - 发表时间:
1991 - 期刊:
- 影响因子:0
- 作者:
C. Alipui;T. Tenner;Kenneth S. Ramos - 通讯作者:
Kenneth S. Ramos
Osteopontin mRNA Expression in a Chemically‐Induced Model of Atherogenesis
化学诱导动脉粥样硬化模型中骨桥蛋白 mRNA 的表达
- DOI:
- 发表时间:
1995 - 期刊:
- 影响因子:5.2
- 作者:
A. Parrish;Kenneth S. Ramos - 通讯作者:
Kenneth S. Ramos
Allylamine enhances c-Ha-ras protooncogene expression in rat aortic smooth muscle cells.
烯丙胺增强大鼠主动脉平滑肌细胞中 c-Ha-ras 原癌基因的表达。
- DOI:
10.1016/0378-4274(93)90007-k - 发表时间:
1993 - 期刊:
- 影响因子:3.5
- 作者:
R. C. Bowes;Kenneth S. Ramos - 通讯作者:
Kenneth S. Ramos
Kenneth S. Ramos的其他文献
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{{ truncateString('Kenneth S. Ramos', 18)}}的其他基金
Functional Genomics of LINE-1 Retrotransposition
LINE-1 逆转录转座的功能基因组学
- 批准号:
10612492 - 财政年份:2022
- 资助金额:
$ 64.39万 - 项目类别:
Role of Retroelements in Environmental Atherogenesis
逆转录因子在环境动脉粥样硬化形成中的作用
- 批准号:
7740689 - 财政年份:2009
- 资助金额:
$ 64.39万 - 项目类别:
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