Identification of Upstream Kinases by Fluorescence Complementation Mass Spectrometry

A ratiometric fluorescent probe with dual-targeting capability for heat shock imaging

HSO3- is an important reactive sulfur species that maintains the normal physiological activities of living organisms and participates in a variety of redox homeostatic processes. It has been found that changes in HSO3- levels is closely related to the heat stroke phenomenon of the organism. Heat stroke causes damage to normal cells, which in turn causes damage to the body and even death. It is crucial to accurately monitor and track the physiological behavior of HSO3- during heat stroke. Herein, a ratiometric multifunctional fluorescent probe DRM-SO2 with dual-targeting ability to rapidly and precisely recognize HSO3- being constructed based on the FRET mechanism. DRM-SO2 has extra Large Stokes shift (216 nm), very high sensitivity (DL = 12.2 nM), fast response time and good specificity. When DRM-SO2 undergoes Michael addition with HSO3-, the fluorescence emission peak was blue-shifted from 616 nm to 472 nm, and a clear ratiometric signal appeared. The interaction between lysosomes and mitochondria in maintaining cellular homeostasis was investigated by the dual-targeting ability of the probe using HSO3- as a mediator. DRM-SO2 achieved successful targeting and real-time monitoring of exogenous and endogenous HSO3- in the cells. More importantly, imaging experiments in heat stroke mice revealed high HSO3- expression in intestinal tissues. This provides new ideas and research tools for early prevention of heat stroke-induced diseases such as intestinal injuries. In addition, the semi-quantitative monitoring experiments for paper-based visualization of HSO3- make the probe promising for the design of portable detectors.

Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS)

Hyperphosphorylation of the microtubule-associated protein Tau is a major hallmark of Alzheimer's disease and other tauopathies. Understanding the protein kinases that phosphorylate Tau is critical for the development of new drugs that target Tau phosphorylation. At present, the repertoire of the Tau kinases remains incomplete, and methods to uncover novel upstream protein kinases are still limited. Here, we apply our newly developed proteomic strategy, fluorescence complementation mass spectrometry, to identify novel kinase candidates of Tau. By constructing Tau- and kinase-fluorescent fragment library, we detected 59 Tau-associated kinases, including 23 known kinases of Tau and 36 novel candidate kinases. In the validation phase using in vitro phosphorylation, among 15 candidate kinases we attempted to purify and test, four candidate kinases, OXSR1 (oxidative-stress responsive gene 1), DAPK2 (death-associated protein kinase 2), CSK (C-terminal SRC kinase), and ZAP70 (zeta chain of T-cell receptor-associated protein kinase 70), displayed the ability to phosphorylate Tau in time-course experiments. Furthermore, coexpression of these four kinases along with Tau increased the phosphorylation of Tau in human neuroglioma H4 cells. We demonstrate that fluorescence complementation mass spectrometry is a powerful proteomic strategy to systematically identify potential kinases that can phosphorylate Tau in cells. Our discovery of new candidate kinases of Tau can present new opportunities for developing Alzheimer's disease therapeutic strategies.

Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles

We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.

An Integrated Proteomic Strategy to Identify SHP2 Substrates

Protein phosphatases play an essential role in normal cell physiology and the development of diseases such as cancer. The innate challenges associated with studying protein phosphatases have limited our understanding of their substrates, molecular mechanisms, and unique functions within highly coordinated networks. Here, we introduce a novel strategy using substrate-trapping mutants coupled with quantitative proteomics methods to identify physiological substrates of Src homology 2 containing protein tyrosine phosphatase 2 (SHP2) in a high-throughput manner. The technique integrates three parallel mass spectrometry-based proteomics experiments, including affinity isolation of substrate-trapping mutant complex using wild-type and SHP2 KO cells, in vivo global quantitative phosphoproteomics, and in vitro phosphatase reaction. We confidently identified 18 direct substrates of SHP2 in the epidermal growth factor receptor signaling pathways, including both known and novel SHP2 substrates. Docking protein 1 was further validated using biochemical assays as a novel SHP2 substrate, providing a mechanism for SHP2-mediated Ras activation. This advanced workflow improves the systemic identification of direct substrates of protein phosphatases, facilitating our understanding of the equally important roles of protein phosphatases in cellular signaling.

Recent Advances in CRISPR/Cas-Based Biosensors for Protein Detection

CRISPR is an acquired immune system found in prokaryotes that can accurately recognize and cleave foreign nucleic acids, and has been widely explored for gene editing and biosensing. In the past, CRISPR/Cas-based biosensors were mainly applied to detect nucleic acids in the field of biosensing, and their applications for the detection of other types of analytes were usually overlooked such as small molecules and disease-related proteins. The recent work shows that CRISPR/Cas biosensors not only provide a new tool for protein analysis, but also improve the sensitivity and specificity of protein detections. However, it lacks the latest review to summarize CRISPR/Cas-based biosensors for protein detection and elucidate their mechanisms of action, hindering the development of superior biosensors for proteins. In this review, we summarized CRISPR/Cas-based biosensors for protein detection based on their mechanism of action in three aspects: antibody-assisted CRISPR/Cas-based protein detection, aptamer-assisted CRISPR/Cas-based protein detection, and miscellaneous CRISPR/Cas-based methods for protein detection, respectively. Moreover, the prospects and challenges for CRISPR/Cas-based biosensors for protein detection are also discussed.

In Vitro Tracking of Intracellular Metabolism-Derived Cancer Volatiles via Isotope Labeling

Cancer detection relying on the release of volatile biomarkers has been extensively studied, but the individual biochemical processes of the cells from which biogenic volatiles originate have not been thoroughly elucidated to date. Inadequate determination of the metabolic origin of the volatile biomarkers has limited the progress of the scientific and practical applications of volatile biomarkers. To overcome the current limitations, we developed a metabolism tracking approach combining stable isotope labeling and flux analysis of volatiles to trace the intracellular metabolism-derived volatiles and to reveal their relation to cancer metabolic pathways. Specifically, after the ¹³C labeling of lung cancer cell, the isotopic ratio of whole cellular carbon was measured by nanoscale secondary ion mass spectrometry-based imaging. The kinetic modeling with the time-dependent isotopic ratio determined the period during which cancer cells reach the metabolic steady state, at which time all of the potential volatiles derived from intracellular metabolism were fully enriched isotopically. By measuring the isotopic enrichment of volatiles at the end-stage of isotopic flux, we found that 2-pentadecanone appeared to be derived from the metabolic cascade starting from glucose to fatty acid synthesis. Furthermore, this biosynthetic pathway was determined to be distinct in cancer, as it was upregulated in colon, breast, and pancreatic cancer cells but not in normal cells. The investigation of the metabolic footprint of 2-pentadecanone demonstrates that our novel approach could be applied to trace the metabolic origin of biogenic volatile organic compounds. This analytical strategy represents a potential cutting-edge tool in elucidating the biochemical authenticity of cancer volatiles and further expanding our understanding of the metabolic network of airborne metabolites in vitro.