Nanoproteomics deciphers the prognostic value of EGFR family proteins-based liquid biopsy.

Monitoring tumor-associated protein status in serum can effectively track tumors and avoid time-consuming, costly, and invasive tissue biopsy. Epidermal growth factor receptor (EGFR) family proteins are often recommended in the clinical management of multiple solid tumors. However, the low-abundance of serum EGFR (sEGFR) family proteins hinders the depth-understanding of their function and tumor management. Herein, a nanoproteomics approach coupling with aptamer-modified MOFs (NMOFs-Apt) with mass spectrometry was developed for the enrichment and quantitative analysis of sEGFR family proteins. This nanoproteomics approach exhibited high sensitivity and specificity for sEGFR family protein quantification, with the limit of quantification as low as 1.00 nM. After detecting 626 patients' sEGFR family proteins with various malignant tumors, we concluded that the levels of serum proteins had a moderate concordance with tissue counterparts. Metastatic breast cancer patients with a high level of serum human epidermal growth factor receptor 2 (sHER2) and a low level of sEGFR had a poor prognosis, and patients with a sHER2 decrease of more than 20% had longer disease-free time after receiving chemotherapy. This nanoproteomics method provided a simple and effective approach for low-abundant serum protein detection and our results clarified the potential of sHER2 and sEGFR as cancer markers.

Simultaneous Detection of Six Isoforms of Tau Protein in Human Cerebrospinal Fluid by Multidimensional Mass Spectrometry-Based Targeted Proteomics.

Abnormal expression of Tau protein can cause the development of Alzheimer's disease (AD). So far, much evidence has demonstrated that Tau has multiple isoforms. These isoforms are suggested to have distinct physiological roles and contribute unequally to the progress of AD. Thus, detection of individual Tau isoforms may be helpful to better understand the link between clinical outcome and Tau status and to further improve AD diagnosis and treatment. However, few studies have been conducted on absolute quantification of Tau isoforms, probably due to high sequence homology and also low abundance of these isoforms in biofluids such as cerebrospinal fluid (CSF). Therefore, mass spectrometry-based targeted proteomics was attempted here. This targeted proteomics approach can principally measure a protein of interest at the surrogate peptide level, yet little has been done to detect protein isoforms, probably due to lack of isoform-specific surrogate peptides in mass spectrometry. In this study, separations in more dimensions were added, including immunoprecipitation (IP) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for sample pretreatment and systems of linear equations for post-lab data extraction. Moreover, the reliability of the approach including IP enrichment, gel separation, and linear algebra algorithms was discussed. As a result, each isoform of Tau protein can be individually detected and quantified. Using IP enrichment, ∼250-fold enhancement of sensitivity was achieved. The ultimate LOQ was 0.50 nM. Finally, this multidimensional mass spectrometry-based targeted proteomics assay was validated and applied to simultaneous quantitative analysis of six Tau isoforms in CSF of AD patients.

Simultaneous and quantitative monitoring transcription factors in human embryonic stem cell differentiation using mass spectrometry-based targeted proteomics.

Human embryonic stem cells (hESCs) can be self-propagated indefinitely in culture while holding the capacity to generate almost all cell types. Although this powerful differentiation ability of hESCs has become a potential source of cell replacement therapies, application of stem cells in clinical practice relies heavily on the exquisite control of their developmental fate. In general, an essential first step in differentiation is to exit the pluripotent state, which is precariously balanced and depends on a variety of factors, mainly centering on the core transcriptional mechanism. To date, much evidence has indicated that transcription factors such as Sox2, Oct4, and Nanog control the self-renewal and pluripotency of hESCs. Their expression displays a restricted spatial-temporal pattern and their small changes in level can significantly affect directed differentiation and the cell type derived. So far, few assays have been developed to monitor this process. Herein, we provided a mass spectrometry (MS)-based approach for simultaneous and quantitative monitoring of these transcription factors, in an attempt to provide insight into their contributions in hESC differentiation.