Recent advances in protein profiling of tissues and tissue fluids

Abstract

Creating protein profiles of tissues and tissue fluids, which contain secreted proteins and peptides released from various cells, is critical for biomarker discovery as well as drug and vaccine target selection. It is extremely difficult to obtain pure samples from tissues or tissue fluids, however, and identification of complex protein mixtures is still a challenge for mass spectrometry analysis. Here, we summarize recent advances in techniques for extracting proteins from tissues for mass spectrometry profiling and imaging. We also introduce a novel technique using a capillary ultrafiltration (CUF) probe to enable in vivo collection of proteins from the tissue microenvironment. The CUF probe technique is compared with existing sampling techniques, including perfusion, saline wash, fine-needle aspiration and microdialysis. In this review, we also highlight quantitative mass spectrometric proteomic approaches with, and without, stable-isotope labels. Advances in quantitative proteomics will significantly improve protein profiling of tissue and tissue fluid samples collected by CUF probes.

Advances in the proteomic investigation of the cell secretome

“…Proteins from the interstitial fluid cannot be identified by studying circulatory fluids, but a few studies have attempted to capture the interstitial fluid at its site of origin using in vivo microdialysis devices [10–14, 64] or a capillary ultrafiltration (CUF) probe [68]. In vivo microdialysis is a versatile technique widely used in neuroscience that has broad clinical and translational applications (for more details, see review Korf et al [69]).…”

“…Some cells such as cancer cell lines are very tolerant to serumfree medium while other cells, such as primary cells, are sensitive to serum-free medium and might result in increased cell death and release of intracellular proteins. Only a few studies have attempted to survey the secretome in vivo or ex vivo , either by analyzing the secretome of tissue explants without isolating individual cells [9], or by using microdialysis devices [10–14]. The most recent advances in cell secretome studies and their applications are outlined in this review.…”

Maternal serum serpin B7 is associated with early spontaneous preterm birth

“…3-6 Mass spectrometry-based shotgun proteomics methodology has become a standard method for characterizing proteomes of biological fluids as well as tissues. 7-9 Further advancements in multidimensional protein separation techniques have made it possible to identify low-abundance proteins and thereby increase the dynamic range of detection in complex biological samples such as plasma and serum. 10, 11 In addition, the application of stable isotope labeling of amino acids in cell culture (SILAC) technology permits the generation of entire labeled proteomes that can be used as internal standards to facilitate accurate quantification of peptides and proteins thereof in biological samples.…”

Secreted proteins as a fundamental source for biomarker discovery

“…Recently, a new method for in vivo secretome sampling was published [53–55] which has been able to dynamically collect the secretome in vivo from tissues and tissue fluids. The method utilized the capillary ultrafiltration (CUF) probe which can be implanted into various tissues to harvest the tissue fluids and extract fluid from the extracellular space that contains secreted and ECM proteins.…”

“…Five secreted proteins (cyclophilin-A, S100A4, profiling-1, thymosin beta 4 and 10) previously associated with progression and five other secreted proteins (fetuin-A, alpha-1 antitrypsin1 and 6, and contrapsin) were detected at the progressive and the regressive stage, respectively. The advantages of CUF probe technique (no tissue damage; concentration of collected sample reflects the concentration in the tissue) were compared to other in vivo methods used for collecting of tissue fluids such as perfusion and saline wash (contamination with other substances from cells damaged in the sampling process; unability to collect the fluids from specific microenvironments of interest), fine-needle aspiration (contamination from blood and needle-damaged tissue) and microdialysis (slow protein diffusion through semipermeable membrane and time-consuming recovery calculations) [55]. …”