多種氧化還原相關半胱氨酸後修飾作用之定量蛋白質體學質譜分析法

Abstract

許多研究已指出，細胞可藉由形成多種可逆性的蛋白半胱胺酸修飾，傳遞外界訊息或平衡細胞內之氧化還原狀態。諸如次磺酸化、硫基亞硝酸化、麩胱甘肽化等氧化還原相關修飾，皆已證實在各種生理或病理狀態中扮演重要角色。心肌細胞在缺氧下的損傷以及一氧化氮相關的保護作用便是一重要例證。近期研究更明確指出，蛋白半胱胺酸修飾之間的交互影響與轉換是調控細胞功能不可或缺的手段。若能同時測量所有細胞之蛋白半胱胺酸修飾，並追蹤其動態變化，將可針對細胞內氧化還原調控與訊息傳遞提供全面性、系統性之瞭解。但即使在當今質譜分析技術的快速發展中，同時定量分析所有可逆性之蛋白半胱胺酸修飾仍十分困難。在本研究中，我們利用多次連續的專一性還原反應，搭配不可逆的烷基化作用，以具硫醇基反應性的穩定同位素或是同量異構物標誌取代不同之半胱胺酸修飾，並經由親和性純化與定量質譜技術，成功地建立多種半胱胺酸修飾的蛋白體分析平台。我們首先利用生物體外蛋白酪氨酸磷酸酶1B (PTP1B)與亞硝基麩胱甘肽(GSNO)的反應作用，證實我們建立的分析平台可精準地針對特定半胱胺酸位置所發生之氧化還原修飾進行化學計量分析。我們更將此方法應用於探討在一氧化氮對缺氧心肌細胞的保護作用中整個蛋白體的可逆性的蛋白半胱胺酸修飾的變化。在該病理環境中，我們鑑定到超過260個半胱胺酸發生可逆性之氧化還原修飾，並提供其相對應之定量分析。我們更進一步探討缺氧心肌細胞內面對一氧化氮相關之保護作用時可能之氧化還原調控與訊號傳遞。這是目前已知第一個分析平台可同時在蛋白體規模下，定量分析一種以上的可逆性的蛋白半胱胺酸修飾。 然而，面對易受氧化狀態影響之關鍵酵素，包含蛋白酪氨酸磷酸酶與天冬胺酸特異性半胱胺酸蛋白酶，因受限其於細胞中含量較低，大規模蛋白體分析技術仍難以解析其半胱胺酸催化區之修飾變化。因此，我們利用原先建立的多次烷基化標定不同可逆性半胱胺酸修飾，搭配後續之免疫純化以及標靶式液相層析串聯質譜分析技術，成功完成蛋白酪氨酸磷酸酶SHP2在缺氧心肌細胞以及一氧化氮保護作用下不同半胱胺酸位置的亞硝基化化學計量分析。未來我們更將持續拓展可專一性分析的半胱胺酸修飾種類，以及針對其他氧化還原調控關鍵蛋白的標靶分析。預期這些分析方法的建立，將使未來可更深入地探討細胞如何經歷氧化還原環境的改變而走向不同之細胞命運，並對半胱胺酸修飾的轉換循環在其中調控的關聯提出更明確的佐證。

Distinctive states of redox-dependent cysteine (Cys) modifications, such as sulfenation (SOH), S-nitrosylation (SNO) and S-glutathionylation (SSG), are known to regulate signaling homeostasis under various pathophysiological conditions, including myocardial injury or protection in response to ischemic stress. Recent evidence further implicates a dynamic interplay among these modified forms following changes in cellular redox environment. Simultaneous monitoring of the dynamics of various reversible cysteine modifications is required to obtain a systems view of how cells response to changing redox status. However, a precise delineation of multiplexed Cys-modifications in a cellular context remains technically challenging. In this thesis, we reported the development, optimization, and applications of mass spectrometry (MS)-based quantitative approaches for global and targeted redox proteomic studies that mostly based on sequential cycles of selective reduction and irreversible alkylation with isotope-coded or isobaric mass tags endowed with Cys-reactivities. By applying the sequential alkylation switch workflow, all Cys thiols in the samples were differentially labeled with designated tags depending on their initial redox status and were then quantitatively measured by following MS analysis with or without immunoenrichment. We first demonstrated the capabilities of this approach by proving the accurate and site-specific measurement of the fold change and the stoichiometry of multiplexed reversible Cys modifications on purified PTP1B treated with S-nitrosoglutathione (GSNO). Next, we applied the workflow to differentially quantify the multiple redox-modified forms of a Cys site in the original cellular context. In one single analysis, we have identified over 260 Cys sites showing quantitative differences in multiplexed redox-modifications from the total lysates of H9c2 cardiomyocytes experiencing hypoxia in the absence and presence of GSNO, indicative of a distinct pattern of individual susceptibility to S-nitrosylation or S-glutathionylation. Among those most significantly affected are proteins functionally implicated in hypoxic damage from which we showed that GSNO would protect. We thus demonstrate for the first time how quantitative analysis of various Cys-redox modifications occurring in biological samples can be performed precisely and simultaneously at proteomic levels. Finally, selected reaction monitoring (SRM) assays coupled with complete immunoprecipitation were developed to quantitatively follow the dynamics of Cys modifications on targeted proteins as effected through external NO donors and/or physiologically relevant stimuli. We showed that, by this targeted approach, significant increase of SNO was occurred site-specifically on catalytic Cys of endogenous SHP-2 in NO-protected cardiomyocyte under hypoxic insult, which was not detectable in global redox-proteomic analysis. In conclusion, we have not only developed a new approach to map global Cys-redoxomic regulation in vivo, but also provided new evidences implicating Cys-redox modifications of key molecules in NO-mediated ischemic cardioprotection.