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 了解组织结构是生物科学的基础，也是区分良性和恶性肿瘤的基础。 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（黑色素细胞痣和黑色素瘤）的子集，导致诊断错误 并恶化了病人的预后因此，需要用于诊断黑素瘤的新生物标志物。到 为了确定这些标记，必须更好地了解黑素细胞和邻近细胞之间的相互作用。 角化细胞、免疫细胞和痣中复杂肿瘤微环境的其他成分， 黑素瘤 痣和早期原发性黑色素瘤显示瘤内异质性，通常伴有低细胞性和纯度。 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 仅晚期/转移性肿瘤的测序，这一直是大多数先前研究的焦点。这个目标 研究的目的是建立高分辨率的肿瘤及其微环境基因表达的空间图， 形态学上保存的痣和黑色素瘤，以鉴定新的诊断生物标志物。 假设黑素细胞肿瘤及其微环境包含具有以下特征的细胞亚群： 痣和黑色素瘤之间不同的特征基因表达模式。我们假设 这些差异表达的基因具有空间局限性和细胞类型特异性， 诊断标志物。我们先前的数据表明，黑素细胞和正常黑素细胞之间CDK 2基因表达存在差异。 痣和黑色素瘤的丰富区域。在目标1中，我们将通过以下方法评估CDK 2的空间表达： 免疫组织化学在超过200个痣与黑色素瘤的肿瘤组中，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志物，包括PRAME。在目标2中，为了鉴定新的生物标志物，我们将 建立痣中肿瘤和微环境亚群基因表达高分辨率空间图 通过进行空间全转录组分析和高复杂单细胞成像来与黑色素瘤进行比较。顶部 这些亚群中的差异表达基因将通过肿瘤中的免疫组织化学进行验证， 上面描述的面板。 这项研究通过调查肿瘤和微环境群体，改进了当前的理论概念。 痣和早期原发性黑色素瘤-常见的，但以前研究不足的肿瘤类型。而且这 一项研究利用了改进的最先进的方法，包括高复合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志物开发相关的空间上正确的背景，最终导致改善的 黑色素瘤的诊断准确性和改善患者的预后。