Spatial Profiling of Melanocytic Tumors and Their Microenvironment

黑素细胞肿瘤及其微环境的空间分析

• 批准号: 10729434
• 负责人: Maija Helena Tuulia Kiuru
• 金额: $ 8万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10729434
• 关键词: Address; Architecture; Benign; Biological Markers; Biological Sciences; Biology; CDK2 gene; Cells; Cellularity; Characteristics; Chromosome Mapping; Complex; Coupled; Cutaneous Melanoma; Cytokeratin; Data; Dermis; Development; Diagnosis; Diagnostic Errors; Early Diagnosis; Endothelial Cells; Epidermis; Epithelial Cells; Fibroblasts; Gene Combinations; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Goals; Immune; Immunohistochemistry; Knowledge; MART-1 Tumor Antigen; Malignant - descriptor; Malignant Neoplasms; Maps; Melanocytic Neoplasm; Melanocytic nevus; Metastatic Melanoma; Methodology; Mole the mammal; Morphology; Neoplasm Metastasis; Neoplasms; Nevi and Melanomas; Nevus; PTPRC gene; Patient-Focused Outcomes; Pattern; Peripheral; Population; Regulation; Research; Resolution; Role; Skin Cancer; Space Perception; Structure; Survival Rate; Testing; Tissues; Transcript; Tumor Biology; Tumor Markers; Tumor Tissue; biomarker development; biomarker identification; cell type; cellular imaging; diagnostic accuracy; diagnostic biomarker; diagnostic criteria; diagnostic value; differential expression; digital; gene panel; imaging platform; improved; innovation; keratinocyte; melanocyte; melanoma; melanoma biomarkers; neoplastic cell; novel diagnostics; novel marker; preservation; prevent; single cell sequencing; single-cell RNA sequencing; success; transcriptome; tumor; tumor heterogeneity; tumor microenvironment; tumor progression; tumor-immune system interactions

Spatial profiling of melanocytic tumors and their microenvironment Understanding tissue structure is fundamental for biological sciences and for distinguishing benign versus malignant neoplasms, but histopathological assessment alone is inaccurate for the diagnosis of certain tumors, including a subset of melanocytic neoplasms (melanocytic nevi and melanomas), resulting in diagnostic errors and worsened patient outcomes. Therefore, novel biomarkers for the diagnosis of melanoma are needed. To identify such markers, it is imperative to better understand the interaction between melanocytes and neighboring keratinocytes, immune cells, and other components of the complex tumor microenvironment in nevi and melanoma. Nevi and early primary melanoma display intratumoral heterogeneity, often coupled with low cellularity and purity. Therefore, the tumor-microenvironment interactions could be missed by bulk approaches or single-cell sequencing of advanced/metastatic tumors only, which has been the focus of most prior studies. The goal of this research is to build high-resolution spatial maps of gene expression of the tumor and its microenvironment in morphologically preserved nevi and melanomas to identify novel diagnostic biomarkers. The hypothesis is that melanocytic tumors and their microenvironments contain subpopulations of cells with characteristic gene expression patterns that differ between nevi and melanoma. We hypothesize that some of these differentially expressed genes are spatially confined and cell-type specific and could be used as potential diagnostic markers. Our prior data demonstrated differences in CDK2 gene expression between melanocyte- rich regions of nevi and melanoma. In Aim 1, we will assess spatial expression of CDK2 by immunohistochemistry in a tumor panel of over 200 nevi versus melanoma, comparing it to proliferative markers, as well as established melanoma biomarkers, including PRAME. In Aim 2, to identify novel biomarkers, we will establish high-resolution spatial maps of gene expression of tumor and microenvironment subpopulations in nevi versus melanoma by performing a spatial whole transcriptome analysis and a high-plex single-cell imaging. Top differentially expressed genes in these subpopulations will be validated via immunohistochemistry in the tumor panel described above. This study improves current theoretical concepts by investigating tumor and microenvironment populations in nevi and early primary melanoma – the common, yet previously understudied tumor types. Furthermore, this study utilizes improved state-of-the-art approaches, including high-plex single-cell spatial gene expression profiling. This research will improve the understanding of tumor-microenvironment subpopulations in their spatially correct context, relevant for tumor biology and biomarker development, ultimately leading to improved diagnostic accuracy of melanoma and improved patient outcomes.

黑素细胞肿瘤及其微环境的空间分布特征 了解组织结构是生物科学的基础，也是区分良性和非良性组织结构的基础 恶性肿瘤，但仅靠组织病理学评估对某些肿瘤的诊断是不准确的， 包括一组黑素细胞肿瘤(黑色素细胞痣和黑色素瘤)，导致诊断错误 并恶化了患者的预后。因此，需要新的诊断黑色素瘤的生物标志物。至 识别这些标记物，必须更好地了解黑素细胞和邻近细胞之间的相互作用 角质形成细胞，免疫细胞和其他成分的复杂的肿瘤微环境在痣和 黑色素瘤。 色素痣和早期原发黑色素瘤表现为瘤内异质性，通常伴有低细胞密度和低纯度。 因此，肿瘤-微环境的相互作用可能会被整体方法或单细胞方法所忽略。 仅对晚期/转移性肿瘤进行测序，这一直是大多数先前研究的重点。这样做的目的是 研究是建立高分辨率的肿瘤及其微环境基因表达的空间地图 形态保存的色素痣和黑色素瘤，以确定新的诊断生物标记物。 假设黑素细胞肿瘤及其微环境包含亚群的细胞 色素痣和黑色素瘤之间不同的特有基因表达模式。我们假设其中一些人 这些差异表达的基因是空间受限的和特定于细胞类型的，可以作为潜在的 诊断标记物。我们先前的数据表明，在黑素细胞之间CDK2基因表达存在差异。 色素痣和黑色素瘤的丰富区域。在目标1中，我们将通过以下方式评估CDK2的空间表达 在一个由200多名黑色素瘤和痣组成的肿瘤小组中进行免疫组织化学，将其与增殖标记物进行比较， 以及已建立的黑色素瘤生物标记物，包括PRAME。在目标2中，为了确定新的生物标志物，我们将 建立高分辨率肿瘤基因表达和色素痣微环境亚群空间图谱 通过执行空间整体转录组分析和高复合体单细胞成像来对抗黑色素瘤。顶部 这些亚群中差异表达的基因将通过免疫组织化学在肿瘤中得到验证。 上文所述的面板。 这项研究通过研究肿瘤和微环境人群来改进现有的理论概念 色素痣和早期原发黑色素瘤--这是一种常见的、但之前研究不足的肿瘤类型。此外，这一点 研究利用改进的最先进的方法，包括高复合体单细胞空间基因表达 侧写。这项研究将提高对肿瘤微环境亚群的理解。 与肿瘤生物学和生物标记物开发相关的空间正确的背景，最终导致改进 黑色素瘤诊断的准确性和患者预后的改善。