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 了解组织结构是生物科学和区分良性与良性的基础 恶性肿瘤，但单独的组织病理学评估对于某些肿瘤的诊断是不准确的， 包括黑色素细胞肿瘤的子集（黑色素细胞痣和黑色素瘤），导致诊断错误 并恶化患者的治疗效果。因此，需要用于诊断黑色素瘤的新生物标志物。到 识别此类标记物后，必须更好地了解黑素细胞与邻近细胞之间的相互作用 角质形成细胞、免疫细胞和痣中复杂肿瘤微环境的其他成分 黑色素瘤。 痣和早期原发性黑色素瘤表现出瘤内异质性，通常伴有低细胞结构和纯度。 因此，批量方法或单细胞方法可能会错过肿瘤与微环境的相互作用。 仅对晚期/转移性肿瘤进行测序，这是大多数先前研究的重点。此举的目标 研究目的是建立肿瘤基因表达及其微环境的高分辨率空间图 形态学上保留的痣和黑色素瘤，以确定新的诊断生物标志物。 该假设是黑素细胞肿瘤及其微环境包含具有以下特征的细胞亚群： 痣和黑色素瘤之间的特征性基因表达模式不同。我们假设其中一些 这些差异表达基因具有空间限制和细胞类型特异性，可用作潜在的 诊断标记。我们之前的数据证明了黑素细胞之间 CDK2 基因表达的差异 痣和黑色素瘤丰富的区域。在目标 1 中，我们将通过以下方式评估 CDK2 的空间表达： 对 200 多个痣与黑色素瘤的肿瘤组进行免疫组织化学分析，将其与增殖标记物进行比较， 以及已确定的黑色素瘤生物标志物，包括 PRAME。在目标 2 中，为了识别新的生物标志物，我们将 建立痣肿瘤和微环境亚群基因表达的高分辨率空间图 通过进行空间全转录组分析和高复数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肿瘤中的免疫组织化学进行验证 面板如上所述。 这项研究通过研究肿瘤和微环境群体改进了当前的理论概念 痣和早期原发性黑色素瘤——常见但之前尚未得到充分研究的肿瘤类型。此外，这 研究利用改进的最先进方法，包括高复杂单细胞空间基因表达 分析。这项研究将增进对肿瘤微环境亚群的理解 空间正确的背景，与肿瘤生物学和生物标志物开发相关，最终导致改进 黑色素瘤的诊断准确性并改善患者的治疗结果。