How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome?Two-dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI-MS, LC-Q-TOF MS and LC-Orbitrap Velos MS for the identification of proteins within one spot. With LC-Orbitrap Velos MS each Coomassie Blue-stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of a human glioblastoma proteome and a human pituitary adenoma proteome, respectively, if a single gel spot was analyzed. If a pool of three matched gel spots was analyzed this number further increased up to an average of 230 and 118 proteins/spot for glioblastoma and pituitary adenoma proteome, respectively. Multiple proteins per spot confirm the necessity of isotopic labeling in large-scale quantification of different protein species in a proteome. Furthermore, a protein abundance analysis revealed that most of the identified proteins in each analyzed 2DE spot were low-abundance proteins. Many proteins were present in several of the analyzed spots showing the ability of 2DE-MS to separate at the protein species level. Therefore, 2DE coupled with high-sensitivity LC-MS has a clearly higher sensitivity as expected until now to detect, identify and quantify low abundance proteins in a complex human proteome with an estimated resolution of about 500 000 protein species. This clearly exceeds the resolution power of bottom-up LC-MS investigations. Keywords:Protein species / Proteome / Resolution / Tandem mass spectrometry / Two-dimensional gel electrophoresis DOI 10.1002/elps.201700330Additional supporting information may be found in the online version of this article at the publisher's web-site Electrophoresis 2018, 39, 965-980

Intrahepatic cholangiocarcinoma (ICC) ranks as the second most malignant type of primary liver cancer with a high degree of incidence and a very poor prognosis. Fat mass and obesity-associated protein (FTO) functions as an eraser of the RNA m 6 A modification, but its roles in ICC tumorigenesis and development remain unknown. We showed here that the protein level of FTO was downregulated in clinical ICC samples and cell lines and that FTO expression was inversely correlated with the expression of CA19-9 and micro-vessel density (MVD). A Kaplan-Meier survival analysis showed that a low expression of FTO predicted poor prognosis in ICC. in vitro , decreased endogenous expression of FTO obviously reduced apoptosis of ICC cells. Moreover, FTO suppressed the anchorage-independent growth and mobility of ICC cells. Through mining the database, FTO was found to regulate the integrin signaling pathway, inflammation signaling pathway, epidermal growth factor receptor (EGFR) signaling pathway, angiogenesis, and the pyrimidine metabolism pathway. RNA decay assay showed that oncogene TEAD2 mRNA stability was impaired by FTO. In addition, the overexpression of FTO suppressed tumor growth in vivo . In conclusion, our study demonstrated the critical roles of FTO in ICC.

N6-methyladenosine (m 6 A) modification has been reported as a critical regulator of gene transcript expression. Although m 6 A modification plays important roles in tumor development, its role in therapeutic resistance remains unknown. In this study, we aimed to examine the expression level of m 6 A-modification related proteins and elucidate the effect of m 6 A-related proteins on radiation response in nasopharyngeal carcinoma (NPC). Among the genes that participated in m 6 A modification, YTHDC2, a m 6 A reader, was found to be consistently highly expressed in radioresistant NPC cells. Knocking down of YTHDC2 expression in radioresistant NPC cells improved the therapeutic effect of radiotherapy in vitro and in vivo, whereas overexpression of YTHDC2 in radiosensitive NPC cells exerted an opposite effect. Bioinformatics and mechanistic studies revealed that YTHDC2 could physically bound to insulin-like growth factor 1 receptor (IGF1R) messenger RNA and promoted translation initiation of IGF1R mRNA, which in turn activated the IGF1R-AKT/S6 signaling pathway. Thus, the present study suggests that YTHDC2 promotes radiotherapy resistance of NPC cells by activating the IGF1R/ATK/S6 signaling axis and may serve as a potential therapeutic target in radiosensitization of NPC cells.

In orchards, measuring crown characteristics is essential for monitoring the dynamics of tree growth and optimizing farm management. However, it lacks a rapid and reliable method of extracting the features of trees with an irregular crown shape such as trained peach trees. Here, we propose an efficient method of segmenting the individual trees and measuring the crown width and crown projection area (CPA) of peach trees with time-series information, based on gathered images. The images of peach trees were collected by unmanned aerial vehicles in an orchard in Okayama, Japan, and then the digital surface model was generated by using a Structure from Motion (SfM) and Multi-View Stereo (MVS) based software. After individual trees were identified through the use of an adaptive threshold and marker-controlled watershed segmentation in the digital surface model, the crown widths and CPA were calculated, and the accuracy was evaluated against manual delineation and field measurement, respectively. Taking manual delineation of 12 trees as reference, the root-mean-square errors of the proposed method were 0.08 m (R2 = 0.99) and 0.15 m (R2 = 0.93) for the two orthogonal crown widths, and 3.87 m2 for CPA (R2 = 0.89), while those taking field measurement of 44 trees as reference were 0.47 m (R2 = 0.91), 0.51 m (R2 = 0.74), and 4.96 m2 (R2 = 0.88). The change of growth rate of CPA showed that the peach trees grew faster from May to July than from July to September, with a wide variation in relative growth rates among trees. Not only can this method save labour by replacing field measurement, but also it can allow farmers to monitor the growth of orchard trees dynamically.

Determination of disease activity in patients with rheumatoid arthritis (RA) has become an important component for RA management. The aim of the present study was to investigate the association between circulating levels of serum amyloid A (SAA) and disease activity in RA patients. The types of disease and the respective number of patients enrolled in the present study were as follows: RA, 88; osteoarthritis (OA), 54; systemic lupus erythematosus (SLE), 43; and other autoimmune diseases, 30, as well as 50 healthy controls (HC). SAA levels were measured using an ELISA assay and western blot analysis was used to detect serum SAA levels. The correlations between SAA levels and disease activity score for 28 joints (DAS28), erythrocyte sedimentation rate (ESR) and C‑reactive protein (CRP), respectively, were evaluated; in addition, the presence and absence of rheumatoid factor (RF) and anti‑cyclic citrullinated peptide antibody (anti‑CCP) were detected in respect to SAA levels. The results of the present study demonstrated that serum levels of SAA in RA patients were significantly increased compared to those of the OA, SLE, others and HC patients (P<0.05). SAA levels were found to be positively correlated with DAS28, ESR and CRP levels (R2=0.6174, 0.4422 and 0.3919, respectively). In addition, anti‑CCP was not correlated with DAS28 (R2=0.0154). Furthermore, increased SAA levels were detected in patients with positive anti‑CCP compared with those in anti‑CCP negative subjects (P<0.01). In conclusion, the results of the present study provided further evidence for possible roles of SAA in RA, which indicated that it may be a useful biomarker for assessing disease severity and may provide additional information about disease activity.