Decoding the Tissue of Origin of Cellular Damage from Cell-free DNA in Liquid Biopsies

从液体活检中的游离 DNA 解码细胞损伤的组织起源

• 批准号: 10441196
• 负责人: Megan Evelyn Barefoot
• 金额: $ 3.41万
• 依托单位: GEORGETOWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10441196
• 关键词: Acute; Adverse event; Allografting; Apoptosis; Area; Biliary; Biological; Biopsy; Blood Circulation; Blood Vessels; Blood specimen; COVID-19 pandemic; Cell Death; Cells; Cessation of life; Characteristics; Chimerism; Clinical; DNA; DNA Methylation; Data; Death Rate; Decision Making; Detection; Development; Diagnosis; Diagnostic; Disease; Disseminated Malignant Neoplasm; Endothelium; Engraftment; Enzymes; Exhibits; Frequencies; Functional disorder; Genetic; Genome; Genomics; Genotype; Goals; Hepatic; Hepatocyte; Heterogeneity; Homeostasis; Human; Human body; Immune; Immunosuppression; Immunosuppressive Agents; Infection; Injury; Intervention; Link; Liver; Liver Circulation; Liver Function Tests; Longitudinal Studies; Malignant Neoplasms; Malignant neoplasm of liver; Measures; Medicine; Methylation; Molecular; Molecular Analysis; Monitor; Morphology; Necrosis; Organ; Organ Donor; Organ Transplantation; Outcome; Pathologic; Physiologic Monitoring; Physiological; Population; Process; Proteins; Reaction; Recurrence; Reperfusion Injury; Research; Resources; Role; Sampling; Series; Serum; Solid; Surgical complication; System; Therapeutic; Therapeutic Intervention; Time; Tissue Donors; Tissues; Transplant Recipients; Transplantation; Treatment Efficacy; base; cell free DNA; cell injury; cell type; chemotherapy; cholangiocyte; clinical decision-making; clinically significant; genome sequencing; graft dysfunction; improved; innovation; insight; liquid biopsy; liver biopsy; liver injury; liver transplantation; longitudinal analysis; methylation biomarker; methylation pattern; methylome; minimally invasive; novel; prenatal testing; residence; targeted treatment; tool; transcriptome sequencing; whole genome

ABSTRACT Liquid biopsy applications are rapidly emerging as a minimally invasive approach to collect system-wide representative analytes for genomic monitoring of physiologic and disease-related changes. Dying cells release fragmented DNA into the circulation, referred to as cell-free DNA (cfDNA). Decoding the cellular origins of cfDNA over time can reveal altered cellular contributions reflective of dynamic changes to tissue damages in longitudinal studies. Here, I will focus on the changes in cellular and tissue homeostasis post liver transplant using molecular analyses of cfDNA. Cell-type specific methylation patterns will be used to trace the cellular origins of cfDNA molecules. In addition, solid organ transplant place a separate DNA set with the donor organ into the body of the host, allowing cfDNA molecules from the allograft to be identified and validated through genotyping using donor-derived SNPs. In this proposal, I aim to track the changing composition of cellular damage post- liver transplant and use this information to improve diagnosis and management of graft dysfunction (Aim 1). During transplant there is simultaneous transfer of tissue-resident immune cells along with the donor organ tissue. I will use immune cell-specific DNA methylation patterns together with the donor SNP analysis to distinguish the host and donor tissue-resident immune cell changes after transplant and during immunosuppressive treatment (Aim 2). The proposed research will evaluate an innovative approach to gain insights into the reaction of host cells, donor organ cells, plus host and donor-immune cells relative to different transplant outcomes. A series of proof- of-principle studies are outlined using liver transplantation as an ideal setup that introduces an organ with a distinct genome at a specific timepoint where there will be induced changes in cell homeostasis to a range of cells in the allografts as well as the host. Beyond the transplant outcome analysis, the cfDNA approach established under this proposal can be expanded to determine the cellular contributions to tissue damages in any setting. Cell type-specific methylation patterns are universal markers that can be used to trace the damaged cell origin of cfDNA irrespective of the cause of damage. Cellular damage in the liver can be due to targeted therapy, chemotherapy, immunosuppression or other interventions, initiation or recurrence of primary liver malignancy, cancer metastatic seeding or organ damage observed during the COVID-19 pandemic. We propose that distinct cellular cfDNA signatures will be observed from different types of injury. Also, there is an unmet need to gain insights into tissue damage during the development of new treatments and understand the cellular basis of adverse events relative to therapeutic efficacy. The global impact of this proposal will be to link cfDNAs in the circulation to their cellular origins and thus reveal drivers of pathophysiology.

抽象的 液体活检应用作为一种在系统范围内收集数据的微创方法正在迅速兴起 用于生理和疾病相关变化的基因组监测的代表性分析物。死亡细胞释放 进入循环系统的 DNA 片段，称为游离 DNA (cfDNA)。解码 cfDNA 的细胞起源 随着时间的推移，可以揭示细胞贡献的改变，反映纵向组织损伤的动态变化 研究。在这里，我将通过分子生物学重点关注肝移植后细胞和组织稳态的变化。 cfDNA 分析。细胞类型特异性甲基化模式将用于追踪 cfDNA 的细胞起源 分子。此外，实体器官移植将与供体器官分开的 DNA 组放入体内 宿主的 cfDNA 分子可以通过基因分型进行识别和验证 使用来自供体的 SNP。在这个提案中，我的目标是跟踪术后细胞损伤的变化组成。 肝移植并利用这些信息来改善移植物功能障碍的诊断和管理（目标 1）。 在移植过程中，组织驻留免疫细胞与供体器官同时转移 组织。我将使用免疫细胞特异性 DNA 甲基化模式以及供体 SNP 分析来 区分移植后和移植期间宿主和供体组织驻留免疫细胞的变化 免疫抑制治疗（目标 2）。 拟议的研究将评估一种创新方法，以深入了解宿主细胞的反应， 供体器官细胞，加上与不同移植结果相关的宿主细胞和供体免疫细胞。一系列证明—— 概述了原理性研究，使用肝移植作为一种理想的设置，引入具有 不同的基因组在特定的时间点会引起细胞稳态的一系列变化 同种异体移植物和宿主中的细胞。除了移植结果分析之外，cfDNA 方法 根据该提案建立的模型可以扩展以确定细胞对组织损伤的贡献 任何设置。细胞类型特异性甲基化模式是通用标记，可用于追踪受损细胞 cfDNA 的细胞来源，无论损伤原因如何。肝脏细胞损伤可能是由于靶向 治疗、化疗、免疫抑制或其他干预措施、原发性肝病的发生或复发 COVID-19 大流行期间观察到的恶性肿瘤、癌症转移播种或器官损伤。我们建议 从不同类型的损伤中可以观察到不同的细胞 cfDNA 特征。另外，还有一个未满足的 需要深入了解新疗法开发过程中的组织损伤并了解 与治疗效果相关的不良事件的细胞基础。该提案的全球影响将是 将循环中的 cfDNA 与其细胞起源联系起来，从而揭示病理生理学的驱动因素。

项目成果

Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA.

从循环的无细胞甲基化 DNA 中检测导致癌症的细胞类型。

• 发表时间: 2021
• 作者: Barefoot, Megan E;Loyfer, Netanel;Kiliti, Amber J;McDeed 4th, A Patrick;Kaplan, Tommy;Wellstein, Anton
• 通讯作者: Wellstein, Anton

Integrative Analysis of DNA Methylation and microRNA Expression Reveals Mechanisms of Racial Heterogeneity in Hepatocellular Carcinoma.

DNA 甲基化和 microRNA 表达的综合分析揭示了肝细胞癌中种族异质性的机制。

• 发表时间: 2021
• 作者: Varghese, Rency S;Barefoot, Megan E;Jain, Sidharth;Chen, Yifan;Zhang, Yunxi;Alley, Amber;Kroemer, Alexander H;Tadesse, Mahlet G;Kumar, Deepak;Sherif, Zaki A;Ressom, Habtom W
• 通讯作者: Ressom, Habtom W

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model.

使用分层整合模型鉴定肝细胞癌中的 miRNA-mRNA 关联。

• 发表时间: 2020
• 影响因子: 2.7
• 作者: Varghese, Rency S;Zhou, Yuan;Barefoot, Megan;Chen, Yifan;Di Poto, Cristina;Balla, Abdalla Kara;Oliver, Everett;Sherif, Zaki A;Kumar, Deepak;Kroemer, Alexander H;Tadesse, Mahlet G;Ressom, Habtom W
• 通讯作者: Ressom, Habtom W