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析 了解组织结构对于生物科学和区分良性与 恶性肿瘤，但仅组织病理学评估对于某些肿瘤的诊断不准确， 包括黑素细胞肿瘤的子集（黑色素细胞NEVI和黑色素瘤），导致诊断误差 并恶化了患者的预后。因此，需要新的生物标志物来诊断黑色素瘤。到 识别这样的标记，必须更好地了解黑素细胞和相邻的相互作用 nevi和 黑色素瘤。 NEVI和早期原发性黑色素瘤表现出肿瘤内异质性，通常与细胞低和纯度相结合。 因此，肿瘤 - 微环境相互作用可能会被批量接近或单细胞遗漏 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。目标的目标 研究是建立肿瘤基因表达的高分辨率空间图及其微环境 形态保存的NEVI和黑色素瘤可以鉴定新型的诊断生物标志物。 假设是，黑素细胞肿瘤及其微环境包含与 NEVI和黑色素瘤之间不同的特征基因表达模式。我们假设其中一些 这些表达不同的基因经常被限制并特异性细胞类型，可以用作潜力 诊断标记。我们先前的数据表明，黑色素细胞之间的CDK2基因表达差异 Nevi和黑色素瘤的丰富地区。在AIM 1中，我们将评估CDK2的空间表达 在200多个NEVI与黑色素瘤的肿瘤小组中免疫组织化学，将其与增殖标记物进行比较， 以及既定的黑色素瘤生物标志物，包括普雷姆。在AIM 2中，为了识别新颖的生物标志物，我们将 NEVI中肿瘤和微环境亚群的基因表达的高分辨率空间图 通过进行空间整体转录组分析和高音单细胞成像，与黑色素瘤相对于黑色素瘤。顶部 这些亚群中差异表达的基因将通过肿瘤中的免疫组织化学验证 上面描述的面板。 这项研究通过研究肿瘤和微环境种群来改善当前的理论概念 Nevi和早期原发性黑色素瘤 - 常见但以前了解的肿瘤类型。此外，这个 研究利用了改进的最新方法，包括高音单细胞空间基因表达 分析。这项研究将提高对肿瘤微环境亚种群的理解 在空间上正确的环境，与肿瘤生物学和生物标志物发展有关，最终导致改善 黑色素瘤和改善患者预后的诊断准确性。