Secretome proteomics for discovery of cancer biomarkers

“Secretome” is referred to as the rich, complex set of molecules secreted from living cells. In a less strict definition frequently followed in “secretome” studies, the term also includes molecules shed from the surface of living cells. Proteins of secretome (will be referred to as secreted) play a key role in cell signaling, communication and migration. The need for developing more effective cancer biomarkers and therapeutic modalities has led to the study of cancer cell secretome as a means to identify and characterize diagnostic and prognostic markers and potential drug and therapeutic targets. Significant technological advances in the field of proteomics during the last two decades have greatly facilitated research towards this direction. Nevertheless, secretome analysis still faces some difficulties mainly related to sample collection and preparation. The goal of this article is to provide an overview of the main findings from the analysis of cancer cell secretome. Specifically, we focus on the presentation of main methodological approaches that have been developed for the study of secreted proteins and the results thereof from the analysis of secretome in different types of malignancies; special emphasis is given on correlation of findings with protein expression in body fluids.     

Is a gene‐centric human proteome project the best way for proteomics to serve biology?

With the recent developments in proteomic technologies, a complete human proteome project (HPP) appears feasible for the first time. However, there is still debate as to how it should be designed and what it should encompass. In “proteomics speak”, the debate revolves around the central question as to whether a gene‐centric or a protein‐centric proteomics approach is the most appropriate way forward. In this paper, we try to shed light on what these definitions mean, how large‐scale proteomics such as a HPP can insert into the larger omics chorus, and what we can reasonably expect from a HPP in the way it has been proposed so far.     

Next issue (February 2008): Focus on Protein Production

Edited by Dr. Alois Jungbauer, Vienna, Austria – Special Articles on Protein Synthesis Pharmacological agents against protein aggregation Amaranth seed protein expression Direct infusion LC-MS for macrotetrolide biosynthesis Silk protein based matrix for the enzymatic conversion of tyrosine to L-DOPA Spectroscopy analysis of inclusion bodies – Regular Articles Antioxidant and free radical scavenging Procyanidins in apple juice – Methods and Advances in Biotech Dielectric measurement of short DNA Enhancement of immunity in mice Use of proteomics in biotechnology Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”.     

Applications of cell-based phage display panning to proteomic analysis

In the post-genomic era, proteomics together with genomic tools have led to powerful new strategies in basic and clinical research. These combined “omics” technologies are being integrated into the drug target discovery process. Unlike the genome, the proteome is a highly dynamic entity that requires techniques capable of analyzing on selected populations of proteins in specific biological conditions that reflect the proteins’ functional characteristics. Antibodies have become one of the most important reagents for the analysis of selected populations of proteins, and the application of phage-display antibody libraries to high-throughput antibody generation against large numbers of various antigens provides a tool for proteome-wide protein expression analysis. In this review, we will discuss the utility of phage-display antibodies in proteomics applications, specifically for the discovery of novel disease markers and therapeutic targets.     

Enabling cryo-EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures

In the cellular context, proteins participate in communities to perform their function. The detection and identification of these communities as well as in-community interactions has long been the subject of investigation, mainly through proteomics analysis with mass spectrometry. With the advent of cryogenic electron microscopy and the “resolution revolution,” their visualization has recently been made possible, even in complex, native samples. The advances in both fields have resulted in the generation of large amounts of data, whose analysis requires advanced computation, often employing machine learning approaches to reach the desired outcome. In this work, we first performed a robust proteomics analysis of mass spectrometry (MS) data derived from a yeast native cell extract and used this information to identify protein communities and inter-protein interactions. Cryo-EM analysis of the cell extract provided a reconstruction of a biomolecule at medium resolution (∼8 Å (FSC = 0.143)). Utilizing MS-derived proteomics data and systematic fitting of AlphaFold-predicted atomic models, this density was assigned to the 2.6 MDa complex of yeast fatty acid synthase. Our proposed workflow identifies protein complexes in native cell extracts from Saccharomyces cerevisiae by combining proteomics, cryo-EM, and AI-guided protein structure prediction.     

Quantitative proteomic analysis of hepatic tissue in allotetraploid hybridized from red crucian carp and common carp identified crucial proteins and pathways associated with metabolism and growth rate

Allotetraploid is a new species produced by distant hybridization between red crucian carp (Carassius auratus red var., abbreviated as RCC) and common carp (Cyprinus carpio L., abbreviated as CC). There is a significant difference in growth rate between allotetraploid and its parents. However, the underlying molecular mechanism is largely unknown. In this study, to find direct evidence associated with metabolism and growth rate in protein level, we performed quantitative proteomics analysis on liver tissues between allotetraploid and its parents. A total of 2502 unique proteins were identified and quantified by SWATH-MS in our proteomics profiling. Subsequently, comprehensive bioinformatics analyses including gene ontology enrichment analysis, pathway and network analysis, and protein–protein interaction analysis (PPI) were conducted based on differentially expressed proteins (DEPs) between allotetraploid and its parents. The results revealed several significant DEPs involved in metabolism pathways in liver. More specifically, the integrative analysis highlighted that the DEPs ACSBG1, OAT, and LDHBA play vital roles in metabolism pathways including “pentose phosphate pathway,” “TCA cycle,” and “glycolysis and gluconeogenesis.” These could directly affect the growth rate in fresh water fishes by regulating the metabolism, utilization, and exchange of substance and energy. Since the liver is the central place for metabolism activity in animals, we firstly established the comprehensive and quantitative proteomics knowledge base for liver tissue from freshwater fishes, our study may serve as an irreplaceable reference for further studies regarding fishes’ culture and growth.     

《生物多样性公约》中“土著和地方社区”术语在中国的适用性和评价指标体系

《生物多样性公约》第8(j)条提出了术语“土著和地方社区”, 《名古屋议定书》关于遗传资源特别是传统知识获取与惠益分享的很多重要条款中都涉及该术语。然而, 二者均未对该术语予以定义, 国际社会对该术语的适用范围至今尚未达成一致, 缔约方只能根据公约文本内涵和各国具体国情予以推断和解读。当前的普遍理解包括殖民主义特征的“狭义土著和地方社区”和仅具有原住民特征的“广义土著和地方社区”两种情况。对于中国而言, “土著和地方社区”是否与中国少数民族社区概念上等同或完全不同, 对于全面履行《生物多样性公约》和《名古屋议定书》具有重要意义。本文通过词源分析、定性和定量化等理论和实证研究, 构建了以少数民族具体地方社区为评估单元的“土著和地方社区特征”评价指标体系, 进而对部分少数民族具体地方社区进行了实际评估。结果表明, 一些至今仍然维持传统生产和生活方式及保留传统文化的少数民族地方社区具有明显的“土著和地方社区”特征, 适用于国际公约的相关规定。这为理解国际上的“土著和地方社区”和中国“少数民族”提供了思路, 为中国履行《生物多样性公约》《名古屋议定书》中涉及“土著和地方社区”的条款提供了技术支持, 也为维护中国少数民族地方社区在遗传资源及相关传统知识获取与公平惠益分享中的应有权益提供了理论基础。     

Proteomic Analysis of Kinase Inhibitor Selectivity and Function

Small molecule inhibitors of protein kinases have become highly popular tools in signal transduction research, despite the fact that rather limited data about their respective selectivities have been available. We established an efficient chemical proteomics method to characterize the cellular targets of the widely used inhibitor SB203580, which was deemed to be rather specific for p38 kinase. Our results revealed several protein kinases as high affinity targets of SB 203580 and therefore imply a far more complicated cellular mode of action of this inhibitor than previously assumed. This raises the important question whether a lack of selectivity is inherent to many other “specific” inhibitors of protein kinases and warrants their evaluation employing experimental approaches adapted from our described proteomic technique.     

Total variance should drive data handling strategies in third generation proteomic studies

Quantitative proteomics is entering its “third generation,” where intricate experimental designs aim to increase the spatial and temporal resolution of protein changes. This paper re‐analyses multiple internally consistent proteomic datasets generated from whole cell homogenates and fractionated brain tissue samples providing a unique opportunity to explore the different factors influencing experimental outcomes. The results clearly indicate that improvements in data handling are required to compensate for the increased mean CV associated with complex study design and intricate upstream tissue processing. Furthermore, applying arbitrary inclusion thresholds such as fold change in protein abundance between groups can lead to unnecessary exclusion of important and biologically relevant data.     

The roles of moonlight ribosomal proteins in the development of human cancers

“Moonlighting protein” is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.     

PROTEOMER: A workflow‐optimized laboratory information management system for 2‐D electrophoresis‐centered proteomics

In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large‐scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract meaningful results from large datasets and therefore limit the exploitation of the generated biological information. In our proteomic core facility, which almost exclusively focuses on 2‐DE/MS‐based proteomics, we developed a proteomic database custom tailored to our needs aiming at connecting MS protein identification information to 2‐DE derived protein expression profiles. The tools developed should not only enable an automatic evaluation of single experiments, but also link multiple 2‐DE experiments with MS‐data on different levels and thereby helping to create a comprehensive network of our proteomics data. Therefore the key feature of our “PROTEOMER” database is its high cross‐referencing capacity, enabling integration of a wide range of experimental data. To illustrate the workflow and utility of the system, two practical examples are provided to demonstrate that proper data cross‐referencing can transform information into biological knowledge.     

Glucosyltransferase‐dependent and ‐independent effects of TcdB on the proteome of HEp‐2 cells

Toxin B (TcdB) of the nosocomial pathogen C. difficile has been reported to exhibit a glucosyltransferase‐dependent and ‐independent effect on treated HEp‐2 cells at toxin concentration above 0.3 nM. In order to investigate and further characterize both effects epithelial cells were treated with wild type TcdB and glucosyltransferase‐deficient TcdB_NXN and their proteomes were analyzed by LC‐MS. Triplex SILAC labeling was used for quantification. Identification of 5212 and quantification of 4712 protein groups was achieved. Out of these 257 were affected by TcdB treatment, 92 by TcdB_NXN treatment and 49 by both. TcdB mainly led to changes in proteins that are related to “GTPase mediated signaling” and the “cytoskeleton” while “chromatin” and “cell cycle” related proteins were altered by both, TcdB and TcdB_NXN. The obtained dataset of HEp‐2 cell proteome helps us to better understand glucosyltransferase‐dependent and ‐independent mechanisms of TcdB and TcdB_NXN, particularly those involved in pyknotic cell death. All proteomics data have been deposited in the ProteomeXchange with the dataset identifier PXD006658 ( https://proteomecentral.proteomexchange.org/dataset/PXD006658 ).     

When is a cladist not a cladist?

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the term.     

Next issue (April 2008): Novel Approaches to Drug Discovery in Signal Transduction

Edited by Lodewijk Dekker, Nottingham, UK – Computational chemistry approaches – Cell-based assays for G-Protein-coupled Receptors – Cell-based label-free technologies Methods and Advances in Biotech – Application of proteomics in biotechnology – Mining marine biological wastes for bioactive molecules – PCR-based strategy to express endogenous protein levels in yeast – Method for tracking nanogel particles – Gene expression studies on bio-electrosprayed primary cardiac myocytes Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”. http://www.biotechnology-journal.com     

Lipid Rafts Disruption Increases Ochratoxin A Cytotoxicity to Hepatocytes

Lipid rafts are microdomains in plasma membrane and can mediate cytotoxicity. In this study, the role of lipid rafts in ochratoxin A‐induced toxicity was investigated using Hepatoblastoma Cell Line HepG‐2 cells. Disruption of cholesterol‐containing lipid rafts enhanced Ochratoxin A (OTA) toxicity, as shown by increased lactate dehydrogenase leakage, increased reactive oxygen species level and reduction of superoxide dismutase activity in a time‐dependent manner. Isobaric tags for relative and absolute quantitation‐based proteomics of the cell membranes showed that nearly 85.5% proteins were downregulated by OTA, indicating that OTA inhibited the membrane protein synthesis. Most of altered proteins were involved in Gene Ontology “transport”, “cell adhesion” and “vesicle‐mediated transport”. In conclusion, lipid rafts play a key role in OTA‐induced cytotoxicity. This study provides insight into how OTA toxicity is regulated by the plasma membrane, especially the lipid rafts.     

Is a community still a community? Reviewing definitions of key terms in community ecology

Community ecology is an inherently complicated field, confounded by the conflicting use of fundamental terms. Nearly two decades ago, Fauth et al. (1996) demonstrated that imprecise language led to the virtual synonymy of important terms and so attempted to clearly define four keywords in community ecology; “community,” “assemblage,” “guild,” and “ensemble”. We revisit Fauth et al.'s conclusion and discuss how the use of these terms has changed over time since their review. An updated analysis of term definition from a selection of popular ecological textbooks suggests that definitions have drifted away from those encountered pre‐1996, and slightly disagreed with results from a survey of 100 ecology professionals (comprising of academic professors, nonacademic PhDs, graduate and undergraduate biology students). Results suggest that confusion about these terms is still widespread in ecology. We conclude with clear suggestions for definitions of each term to be adopted hereafter to provide greater cohesion among research groups.     

Proteolytic ectodomain shedding of membrane proteins in mammals—hardware,concepts, and recent developments

Proteolytic removal of membrane protein ectodomains (ectodomain shedding) is a post‐translational modification that controls levels and function of hundreds of membrane proteins. The contributing proteases, referred to as sheddases, act as important molecular switches in processes ranging from signaling to cell adhesion. When deregulated, ectodomain shedding is linked to pathologies such as inflammation and Alzheimer's disease. While proteases of the “a disintegrin and metalloprotease” (ADAM) and “beta‐site APP cleaving enzyme” (BACE) families are widely considered as sheddases, in recent years a much broader range of proteases, including intramembrane and soluble proteases, were shown to catalyze similar cleavage reactions. This review demonstrates that shedding is a fundamental process in cell biology and discusses the current understanding of sheddases and their substrates, molecular mechanisms and cellular localizations, as well as physiological functions of protein ectodomain shedding. Moreover, we provide an operational definition of shedding and highlight recent conceptual advances in the field. While new developments in proteomics facilitate substrate discovery, we expect that shedding is not a rare exception, but rather the rule for many membrane proteins, and that many more interesting shedding functions await discovery.     

Tropicality and abjection: What do we really mean by “Neglected Tropical Diseases”?

Neglected tropical diseases are defined operationally as diseases that prevail in “tropical” regions and are under‐researched, under‐funded, and under‐treated compared with their disease burden. By analysing the adjectives “tropical” and “neglected,” I expose and interrogate the discourses within which the term “neglected tropical disease” derives its meaning. First, I argue that the term “tropical” conjures the notion of “tropicality,” a form of Othering which erroneously explains the disease‐prevalence of “tropical” regions by reference to environmental determinism, rather than colonialism and neocolonialism. Second, I examine the way in which this Othering enables the abjection of tropical regions and their peoples, leading to neglect. I recommend that the term “neglected tropical diseases” be more carefully contextualised within health scholarship, education, and policy.