Methods for the Analysis of Tumor Extracellular Matrix

描述(申请人提供)：最近的关键研究表明，细胞外基质(ECM)的组成可以决定转移结果，特别是肿瘤细胞是否会从非侵袭性表型转变为侵袭性表型。然而，对细胞外基质-细胞间相互作用的研究一直局限于以一种或几种细胞外基质蛋白为中心的还原方法。到目前为止，负责影响这种细胞表型变化的细胞外生物分子在很大程度上是未知的。对ECM成分进行更全面的描述将有助于更好地理解ECM在促进肿瘤细胞转移中的作用。蛋白质组学研究ECM的方法受到高度交联的基质成分的蛋白质分解和抗溶解特性的阻碍，使得更传统的蛋白质组学技术的研究变得困难，如果不是不可能的话。在这一领域取得进展的一个主要障碍是缺乏合适的样品制备方法来有效地表征ECM的分子特性。这笔赠款的重点是ECM样品制备方法的优化。为了开发有效的样品制备方法，我们将建立一个可重复使用的ECM来源。三维细胞培养模型将用于评估由两对同基因的人乳腺上皮细胞系分泌的ECM的促肿瘤属性。样品制备开发的第一个领域将是优化细胞从其基本的细胞外基质中去除，重点是消除与细胞外基质共同纯化的受污染的细胞内蛋白质。将使用LC-MS/MS(LC-MS/MS)图谱和Western blots来评估细胞污染物的水平。接下来，将以识别的不同ECM蛋白的数量和序列覆盖率为终点，探索ECM的增溶策略和有效的切割方法。利用基于无标记质谱学的定量方法将提供策略的相对排名，并有助于进一步的方法优化。我们假设蛋白质-蛋白质的交联会影响ECM基质样品制备方法的有效性。催化ECM蛋白交联的两类主要蛋白质在肿瘤细胞系和各种癌症组织中显示出异常的表达和活性。我们将使用重组人组织转谷氨酰胺酶及其抑制剂来确定交联物如何影响细胞去除、溶解和消化效率，重点是蛋白质的定量。癌细胞将ECM蛋白沉积到它们的微环境中，可以将非转移细胞编程为与转移相一致的表型。所提出的细胞培养模型和最先进的ECM特异性蛋白质组学技术的发展将提高我们探索和表征细胞外基质在转移中的作用的能力。这些研究将成为转译实验和临床研究的基础，并最终将导致生物标记物和治疗方法的出现，从而改善患者的护理和生存能力。 与公共健康相关：尽管细胞微环境在肿瘤进展中起着基础性作用，但缺乏研究潜在分子机制的方法。这项工作的目的是开发必要的样品制备方法，以表征细胞微环境的基质成分，以便我们最终可能开发新的治疗策略，并识别癌症的早期诊断标记。

DESCRIPTION (provided by applicant): Recent key studies have shown that the composition of the extracellular matrix (ECM) can determine metastatic outcome, specifically whether a tumor cell will transition from a non-invasive to an invasive phenotype. However, the study of ECM-cell interactions has been limited to reductionist methods that focus on one or a few ECM proteins. To date, the extracellular biomolecules that are responsible for influencing this change in cell phenotype are largely unknown. A better understanding of the ECM role in promoting tumor cell metastasis will be facilitated by a more global characterization of ECM composition. Proteomic approaches to study ECM have been hindered by the proteolytic and solubilization resistant properties of highly cross-linked matrix components, making study by more traditional proteomic techniques difficult, if not impossible. A major barrier to progress in this field is the lack of suitable sample preparation methods for effective molecular characterization of ECM. The focus of this grant is the optimization of ECM sample preparation methods. To develop effective sample preparation methods we will establish a reproducible source of ECM. A three- dimensional cell culture model will be used to evaluate the tumor promotional attributes of ECM secreted by two pairs of isogenic human mammary epithelial cell lines. The first areas of sample preparation development will be in the optimization of cell removal from its underlying ECM, with emphasis on eliminating contaminate intracellular proteins that co-purify with the ECM. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) profiling and Western blots will be used to evaluate the level of cellular contaminants. Next, ECM solubilization strategies and effective cleavage methods will be explored using as endpoints the number of distinct ECM protein identified and percent sequence coverage. Utilization of a label-free mass spectrometry based quantification method will provide relative ranking of the strategies and assist in further method optimization. We hypothesize that protein-protein crosslinks influence the effectiveness of matrix sample preparation methods for ECM. The two major classes of proteins that catalyze the cross-linking of ECM proteins show aberrant expression and activity in neoplastic cell lines and various cancerous tissues. We will use recombinant human tissue transglutaminase and its inhibitors to determine how crosslinking influences cell removal, solubilization and digestion efficiencies with emphasis on protein quantification. Cancer cells deposit ECM proteins into their microenvironment that can program non-metastatic cells to a phenotype consistent with metastasis. The development of the proposed cell culture model and state-of the- art ECM specific proteomic techniques will advance our ability to explore and characterize the role of the extracellular matrix in metastasis. These studies will be the foundation for translational experiments, clinical investigations and should ultimately lead to biomarkers and therapeutic approaches that will improve patient care and survivability. PUBLIC HEALTH RELEVANCE: Despite the fundamental role that the cell microenvironment plays in tumor progression, methods to study the underlying molecular mechanisms are lacking. This work is aimed at developing the sample preparation methods necessary to characterize the matrix component of the cell microenvironment so that we may ultimately develop new therapeutic strategies and identify early diagnostic markers of cancer.