Building a spatial transcriptomics infrastructure for isoform profiling in aging pre-neoplastic tissues

建立空间转录组学基础设施，用于老化肿瘤前组织的异构体分析

• 批准号: 10742047
• 负责人: OLGA ANCZUKOW-CAMARDA
• 金额: $ 25.87万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10742047
• 关键词: Address; Advanced Development; Age; Aging; Alternative Splicing; Atlases; Biology of Aging; Breast; Breast Cancer Early Detection; Breast Cancer Risk Factor; Breast Epithelial Cells; Cancer Biology; Carcinoma; Cell Communication; Cell physiology; Cells; Code; Communities; Computing Methodologies; Data; Data Analyses; Data Set; Detection; Development; Dissociation; Drug resistance; Epithelium; Event; Evolution; Fibroblasts; Genes; Genomics; Goals; Growth; Human; Immune; In Vitro; Individual; Infrastructure; Intervention; Knowledge; Length; Ligands; Link; Malignant Neoplasms; Mammary Gland Parenchyma; Mammary Neoplasms; Maps; Measures; Mediating; Molecular; Morphology; Mus; Pathology; Pattern; Phase; Phenotype; Population; Prevention; Protein Isoforms; Proteins; RNA; RNA Splicing; Research; Research Personnel; Resources; Risk Factors; Role; Sampling; Screening for cancer; Spatial Distribution; Standardization; Systems Biology; Technology; Tissues; Transcript; Tumor Subtype; Up-Regulation; Visualization; Visualization software; Woman; Work; age related; cancer cell; cancer initiation; cancer subtypes; cell type; computerized tools; data infrastructure; data mining; data resource; data sharing; data visualization; early detection biomarkers; human old age (65+); in vivo; innovation; insight; malignant breast neoplasm; mammary; neoplastic; novel marker; novel strategies; older women; online resource; receptor; response; success; tool; transcriptome; transcriptome sequencing; transcriptomics; treatment response; tumor; tumor initiation; tumorigenesis; young woman

PROJECT SUMMARY/ABSTRACT Aging is the greatest risk factor for cancer, but it is not known which age-dependent cellular and molecular events drive cancer initiation. Spatial transcriptomic approaches are revolutionizing our understanding of cancer initiation, progression, and drug resistance by revealing expression patterns with tissue morphological context. However, these approaches have not yet been applied to the interdisciplinary biology of aging-driven cancers, despite the likelihood that intratissue and microenvironmental evolution mediate the aging phenotype. Moreover, the majority of current single cell spatial projects are based on 3' short read RNA-sequencing (RNA-seq) and therefore lack the ability to detect full-length spliced isoforms, which are frequently observed in tumors and are known to impact tumor initiation and treatment response. Work from us and others has revealed widespread alterations in alternative RNA splicing in human tumors, including in breast cancer, and that half of all spliced isoforms detected in human breast tumors using long-read sequencing (LR-seq) are missed by RNA-seq and absent from reference transcriptomes. In addition, we have causally linked the upregulation of specific splicing factors with breast tumor initiation both in vitro and in vivo and identified age-dependent changes in spliced isoforms in cancer-associated genes in mammary epithelial cells. Together, these results suggest that alternative splicing is a critical mechanism underlying tumor initiation with age, and that spatial LR-seq approaches are required to resolve these mechanisms. However, standardized approaches and resources to measure, quantify, and visualize expression of full-length isoforms within tissues are lacking. This gap in infrastructure impedes the field's ability to identify cell populations that express age-dependent isoforms, how such isoforms impact cancer initiation for example through changes in receptor-ligand interactions. To address these infrastructure and knowledge gaps, we will first develop approaches to map and analyze full-length RNA isoforms spatially within tissue sections (R21 phase, Aim 1). These tools, which merge LR-seq and spatial transcriptomics, will be applicable across sample types and will therefore be of broad, sustainable utility to the research community. We will then apply these technologies to generate a spatial map of full-length RNA isoforms in healthy breast tissues and tumors during aging (R33 phase, Aims 2 and 3). Finally, we will develop data sharing and visualization tools for spatial isoform expression to enable others to mine our data via a web resource (R33 phase, Aim 4). To achieve these goals, this project will leverage the complementary and interdisciplinary expertise of the Anczukow lab in alternative splicing and breast cancer, and of the Chuang lab in systems biology and spatial transcriptomics analysis. In response to NOT-CA-22-002, Notice of NCI's Participation in PAR-20- 070, this project will deliver a spatial transcriptomic infrastructure for isoform profiling and a critical interdisciplinary data resource for aging and cancer researchers to understand the role of splicing in tissue aging and oncogenesis, thereby advancing approaches for cancer early detection, intervention, and prevention.

项目摘要/摘要 衰老是癌症的最大危险因素，但尚不清楚哪些年龄依赖性细胞和分子事件 驱动癌症开始。空间转录组方法正在彻底改变我们对癌症的理解 通过组织形态环境揭示表达模式，起始，进展和耐药性。 但是，这些方法尚未应用于衰老驱动的癌症的跨学科生物学， 尽管内部和微环境进化可能介导衰老表型。而且， 当前的大多数单细胞空间项目基于3'简短读取RNA测序（RNA-Seq）和 因此缺乏检测全长剪接同工型的能力，这些剪接同工型经常在肿瘤中观察到，并且是 已知会影响肿瘤的启动和治疗反应。我们和其他人的工作揭示了广泛的 人类肿瘤中替代RNA剪接的改变，包括乳腺癌，所有剪接的一半 RNA-Seq和 参考转录组不存在。另外，我们还将特定剪接的上调联系起来 体外和体内乳腺肿瘤启动的因素，并确定了剪接的年龄变化 乳腺上皮细胞中癌症相关基因的同工型。这些结果在一起表明替代 剪接是随着年龄的年龄开始肿瘤开始的关键机制，空间LR-Seq方法是 需要解决这些机制。但是，标准化方法和资源以衡量，量化， 并且缺乏可视化组织中全长同工型的表达。基础设施中的这一差距阻碍了 场鉴定表达年龄依赖同工型的细胞群体的能力，这种同工型如何影响癌症 例如，通过受体配体相互作用的变化来启动。解决这些基础架构和 知识差距，我们将首先开发用于映射和分析全长RNA同工型的方法 在组织切片中（R21期，AIM 1）。这些工具合并了LR-seq和空间转录组学，将 跨样本类型适用，因此将对研究界具有广泛，可持续的实用性。 然后，我们将应用这些技术来生成健康中全长RNA的空间图 衰老期间的乳腺组织和肿瘤（R33期，目标2和3）。最后，我们将开发数据共享 和空间同工型表达的可视化工具，使其他人通过Web资源挖掘我们的数据 （R33阶段，目标4）。为了实现这些目标，该项目将利用互补和跨学科 ANCZUKOW实验室在替代剪接和乳腺癌中的专业知识，以及系统生物学中的Chuang Lab的专业知识 和空间转录组学分析。为了响应非CA-22-002，NCI参与Par-20-的通知 070，该项目将提供同工型分析和关键的空间转录基础架构 衰老和癌症研究人员了解剪接在组织衰老中的作用的跨学科数据资源 和肿瘤发生，从而提高了癌症早期检测，干预和预防的方法。