Use Of Proteomics Research Articles

Use of Proteomics in the Study of Mastitis in Ewes.

The objective of this review is to describe the usage and applicability of proteomics technologies in the study of mastitis in ewes. In ewes, proteomics technologies have been employed for furthering knowledge in mastitis caused by various agents (Staphylococcus aureus, Staphylococcus chromogenes, Mannheimia haemolytica, Streptococcus uberis, Mycoplasma agalactiae). Studies have focused on improving knowledge regarding pathogenesis of the infections and identifying biomarkers for its diagnosis. Findings have revealed that ewes with mastitis mount a defence response, controlled by many proteins and over various mechanisms and pathways, which are interdependent at various points. Many proteins can participate in this process. Moreover, as the result of proteomics studies, cathelicidins and serum amyloid A have been identified as proteins that can be used as biomarkers for improved diagnosis of the disease. In the long term, proteomics will contribute to improvements in the elucidation of the pathogenesis of mastitis. Further in-depth investigations into the various proteomes and application of new methodological strategies in experimental and clinical studies will provide information about mastitis processes, which will be of benefit in controlling the disease. Improvement of diagnostic techniques, establishment of prognostic tools and development of vaccines are key areas for targeted research.

Circadian rhythms and proteomics: It's all about posttranslational modifications!

The circadian clock is a molecular endogenous timekeeping system and allows organisms to adjust their physiology and behavior to the geophysical time. Organized hierarchically, the master clock in the suprachiasmatic nuclei, coordinates peripheral clocks, via direct, or indirect signals. In peripheral organs, such as the liver, the circadian clock coordinates gene expression, notably metabolic gene expression, from transcriptional to posttranslational level. The metabolism in return feeds back on the molecular circadian clock via posttranslational-based mechanisms. During the last two decades, circadian gene expression studies have mostly been relying primarily on genomics or transcriptomics approaches and transcriptome analyses of multiple organs/tissues have revealed that the majority of protein-coding genes display circadian rhythms in a tissue specific manner. More recently, new advances in mass spectrometry offered circadian proteomics new perspectives, that is, the possibilities of performing large scale proteomic studies at cellular and subcellular levels, but also at the posttranslational modification level. With important implications in metabolic health, cell signaling has been shown to be highly relevant to circadian rhythms. Moreover, comprehensive characterization studies of posttranslational modifications are emerging and as a result, cell signaling processes are expected to be more deeply characterized and understood in the coming years with the use of proteomics. This review summarizes the work studying diurnally rhythmic or circadian gene expression performed at the protein level. Based on the knowledge brought by circadian proteomics studies, this review will also discuss the role of posttranslational modification events as an important link between the molecular circadian clock and metabolic regulation. This article is categorized under: Laboratory Methods and Technologies > Proteomics Methods Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Signaling.

Molecular insights into an ancient form of Paget’s disease of bone

Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.

Proteomics and Its Application in Forensic Pathology.

Proteomics has become one of the hot topics in modern life sciences. Its application prospects have been confirmed in clinical medical research, such as the discovery of new disease biomarkers, identification of disease-related proteins, and development of new drug targets. However, in the field of forensic science, especially in forensic pathology, it is still in the stage of exploration. This paper reviews the research techniques and the use of proteomics in forensic pathology in domestic and foreign scholars, in order to provide new ideas for the research and application of forensic pathology.

A REVIEW ON APPLICATIONS OF PROBIOTICS IN HUMAN HEALTH AND DISEASE

The emergence of resistance and tolerance to the existing drugs has created a decreased efficacy of these drugs in use. Along with the advancement in other fields of medicine, the problem of resistance has been tried to be overcome by increasing the drug delivery to the target site by the use of polymers or through nanotechnology, synthesis of new drugs, either by the use of proteomics or synthesis from lactic acid bacteria, or marine microorganisms. Recent research has revealed a potential therapeutic role for the manipulation of the microbiota in the maintenance of human health and treatment of various mucosal disorders. Probiotic microorganisms can shape the immune system both at the local and systemic level which will allow future probiotics as treatments for many diseases. The benefits include either a shortened duration of infections or decreased susceptibility to pathogens.
 Probiotic bacteria have multiple and various influences onthe host. Different organisms can influence the intestinal luminal environment, epithelial and mucosal barrier function, and the mucosal immune system. The numerous cell types affected by probiotics involve epithelial cells, dendritic cells, monocytes/macrophages, B cells, T cells. Probiotics do not always colonize the intestinal tract to exert their effects. Some probiotics like Bifidobacterium longum become part of the human intestinal microflora, whereas others like Lactobacillus casei indirectly exert their effects in a transient manner as they pass through by remodeling or influencing the existing microbial community. 
 Probiotics seem to have promising role in shortening duration of infections or decreasing susceptibility to the pathogens. Incorporation of probiotics in nutrition as a means of derivation of health benefits. The best documented effects include bowel disorders such as lactose intolerance, antibiotic-associated diarrhea and infectious diarrhea, emerging evidence accumulates concerning their potential role in various other conditions. In the same time as relevant consumer awareness grows, such products are becoming increasingly popular and tend to represent one of the largest functional food markets.
 Key words: probiotics, Antibiotic associated diarrhea, microorganisms, Antibiotic resistance, Lactic acid bacteria.

Proteomics and Metabolomics in Pregnancy-An Overview.

Pregnancy is getting more and more complex due to increasing number of complications that may affect fetal outcomes. The introduction of newer "proteomics and metabolomics" technologies in the field of obstetrics and gynecology may allow physicians to identify possible associated etiologies that affect the mother during pregnancy and lead to associated complications affecting the offspring. The principal objective of this review article is to provide a comprehensive evaluation of the use of proteomics and metabolomics in complicated pregnancies. Future studies that incorporate data from multiple technologies may allow the development of an integrated biological system approach to maternal genomes, proteomes, and metabolomes in pregnancy. We conducted a substantial MEDLINE, EBSCOhost, and Cochrane database search for all the relevant articles containing use of "omics" technologies in pregnancy. We identified 197 relevant articles, following standardized systematic review process along with grading systems; 69 eligible articles were identified. We sought to provide a comprehensive review in this emerging field of "omics" in pregnancy and associated complications. This article focuses mainly on use of proteomics and metabolomics identification techniques and possible interventions for early pregnancy complications to improve neonatal outcomes.

Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics.

Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.

Vascular Proteomics Reveals Critical Roles of ADAMTS18 in Stroke Associated with Imbalanced Level of Von Willebrand Factor Versus ADAMTS13

Background and Purpose-Stroke is the second leading cause of death worldwide. Acute ischemic stroke (AIS) is frequently induced by internal carotid artery thrombosis. Clinically, most arterial thrombus formation is initiated by platelets adhering to the damaged vessel wall. The adherent platelets become activated and bind with fibrinogen and von Willebrand factor (vWF), allowing formation of a platelet aggregate or mural thrombus. Identifying new mechanism involved in this pathogenesis is critical for understanding the molecular basis of thrombus formation and ultimately developing new therapeutic interventions for stroke. The ADAMTS (A disintegrin and metalloproteinase with thrombospondin motifs) family comprises 19 secreted metalloproteinases that cleave extracellular matrix components and have diverse functions in numerous disease and physiological contexts. Several ADAMTS genes (ADAMTS -7,-8, 12, and 13) have been shown to be involved in cardiovascular disease and pediatric stroke. ADAMTS18 remains “orphan” protease. We have previously shown that ADAMTS18 deficiency causes abnormal remodeling of the common carotid artery (CCA) and an increase in carotid thrombosis and size of cerebral infarct in mice. Thus, the stroke-prone Adamts18 KO mice could be valuable for identification of molecular signatures of accelerated carotid thrombosis related to stroke. One of the major steps yet to be taken by the field is the widespread use of proteomics to uncover the critical molecular events and signaling pathway involved in ADAMTS gene-related stroke.Methods and Results-Here, we carried out the first proteomics comparison of protein expression patterns in CCA and abdominal artery (AA) between Adamts18 knockout (KO) mice and their wild-type (WT) littermates. A total of 1654 proteins were identified in four separate CCA samples (0.4-1 mg/wet weight each), and 1810 proteins were detected in four separate AA samples (2.3-3.6 mg/wet weight each). The abundances of 154 proteins in CCA and 55 proteins in AA were significantly different between KO and WT mice. Ingenuity® Pathway Analysis revealed that ADAMTS18 deficiency predisposes mice to stroke by altering the abundance of many proteins related to cytoskeleton, prothrombotic activity, coagulation, angiogenesis, oxidative homeostasis, and energy metabolism. Western blotting and qRT-PCR analyses further revealed the imbalanced level of von Willebrand factor and ADAMTS13, the pivotal pathogenic factors of ischemic stroke, in CCA of KO mice.Conclusion and Significance-Results of this first vascular proteomic study of Adamts18 KO mice establish a substantial new resource for investigation of how ADAMTS gene affects cellular phenotypes of stroke. These new findings contribute to inform novel prevention strategies and direct therapeutic development for stroke. DisclosuresNo relevant conflicts of interest to declare.

Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review.

The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.

A1166 Use of proteomics to investigate blood pressure progress in the elderly

Objectives: Hypertension increases cardiovascular risks. Apart from established clinical risk factors for hypertension, biomarkers were identified as potential risk factors for hypertension but not well-established. We therefore investigated association between cardiovascular proteins and blood pressure (BP) change in prospective cohorts. Methods: We used a proteomic profiling approach in two independent cohorts, Prospective Investigation of the Vasculature in Uppsala Seniors study (PIVUS; n = 566, mean age of 70.2 years, 50.4% female) and Uppsala Longitudinal Study of Adult Men (ULSAM; n = 238, mean age of 77.6 years) of elderly individuals at baseline and follow-up data on BP for 5 years. Proteomic chips, which used two antibodies for each protein and a PCR step to achieve a high-specific binding, was measured 92 plasma proteins simultaneously. Malmö Diet and Cancer Study (MDC) was validated the finding. Results: In PIVUS and ULSAM, renin protein significantly predicted BP progression. The odds ratio of renin and BP progression was 1.09 (95% CI, 1.02–1.15; p-value, 0.006) after adjusted for baseline characteristics using mixed models on PIVUS, ULSAM, and MDC cohort. Using linear regression models, the baseline renin level was associated with MAP (mean arterial pressure) change in composite ULSAM and PIVUS cohort (β, 1.21; 95% CI, 0.41 to 2.01), and MDC cohort (β, 0.80; 95% CI, 0.07 to 1.53). However, meta-analysis of three cohorts showed insignificantly associated between renin and MAP change (β, 0.11; 95% CI, −0.10 to 0.33). Conclusion: Using proteomics approach, we discovered and replicated the association between renin protein and BP change but weak associated with BP progression. Further studies are needed to confirm the findings.

Expanding the Use of Spectral Libraries in Proteomics.

The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.

Predicting Concussion Recovery in Children and Adolescents in the Emergency Department

Concussion, or mild traumatic brain injury (mTBI), represents the majority of pediatric Emergency Department (ED) presentations of TBI. While most children and adolescents will recover within 4weeks of injury, approximately one third will continue to experience persisting symptoms. This review aimed to provide an overview of literature from the past 5years examining predictors of recovery in the ED. Predictors could be characterized into three categories; (i) cognition, (ii) proteomics, and (iii) pre-injury/injury-related factors. There is preliminary support for the use of computerized neuropsychological testing. The prognostic use of proteomics is a promising area of future research. Pre-injury and injury-related characteristics have been thoroughly examined and developed into a clinical risk score for predicting delayed recovery. Substantial progress has been made in identifying risk factors for delayed recovery at ED presentation. The current evidence provides a platform for additional research that can refine and validate these predictors.

Proteomic approaches in kidney disease biomarker discovery.

Biomarkers have the potential to greatly facilitate diagnosis and treatment of patients with various forms of kidney disease. State-of-the-art mass spectrometry-based methods possess the capability, on a proteome scale and in an unbiased manner, to detect alterations in protein abundances and/or posttranslational modifications in plasma, urine, or tissue. Such approaches can provide a large, unbiased database to facilitate identification of potential biomarkers. In the diagnosis of kidney diseases, urine is usually a more favorable specimen than plasma and kidney tissue due to its noninvasive collection and simplicity of processing. However, whether analysis of proteins in urine faithfully reflects their changes in the kidney tissue remains unclear. The use of proteomics to analyze kidney tissue samples collected during late-stage kidney diseases has also recently gathered pace. The goal of this minireview is to provide an overview of the proteomic technologies currently applied to studies of kidney and their limitations, present existing kidney and urine proteome databases, and highlight a few applications of such approaches in kidney disease biomarker discovery.

Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains

African swine fever (ASF) is a pathology of pigs against which there is no treatment or vaccine. Understanding the equilibrium between innate and adaptive protective responses and immune pathology might contribute to the development of strategies against ASFV. Here we compare, using a proteomic approach, the course of the in vivo infection caused by two homologous strains: the virulent E75 and the attenuated E75CV1. Our results show a progressive loss of proteins by day 7 post-infection (pi) with E75, reflecting tissue destruction. Many signal pathways were affected by both infections but in different ways and extensions. Cytoskeletal remodelling and clathrin-endocytosis were affected by both isolates, while a greater number of proteins involved on inflammatory and immunological pathways were altered by E75CV1. 14-3-3 mediated signalling, related to immunity and apoptosis, was inhibited by both isolates. The implication of the Rho GTPases by E75CV1 throughout infection is also evident. Early events reflected the lack of E75 recognition by the immune system, an evasion strategy acquired by the virulent strains, and significant changes at 7 days post-infection (dpi), coinciding with the peak of infection and the time of death. The protein signature at day 31 pi with E75CV1 seems to reflect events observed at 1 dpi, including the upregulation of proteosomal subunits and molecules described as autoantigens (vimentin, HSPB1, enolase and lymphocyte cytosolic protein 1), which allow the speculation that auto-antibodies could contribute to chronic ASFV infections. Therefore, the use of proteomics could help understand ASFV pathogenesis and immune protection, opening new avenues for future research.

Meet the Editors: David R. Goodlett

Meet the Editors: David R. Goodlett

Proteomics in Human Reproduction.

Assisted Reproduction Techniques (ART) have significantly advanced since the first successful In Vitro Fertilization (IVF). However, most in vitro-produced embryos fail to implant. Key steps in ART are the correct infertility diagnosis, in order to manage the individualised treatments, and the assessment of gamete and embryo viability, to identify the embryo with the best implantation potential. The goal for this manuscript was to present a brief review of proteomics in Assisted Reproduction Technologies (ART) and raises the question of whether proteomics is a good alternative for the future of ART. A literature review concerning proteomics and assisted reproduction was conducted. Non-invasive approaches to correctly diagnose infertility and to access embryo development potential have the advantages of increasing our knowledge about embryo physiology, therefore allowing the development of methods to predict developmental competence and viability. These approaches include proteomic profiling and other omics technologies. The use of proteomics in clinical practice goes beyond the identification of the oocytes and embryos with the best developmental potentials, it may add to the diagnosis of both male and female infertility and in the future, it may be a laboratory tool that will contribute to the birth of a healthy child.

Perspectives in the Use of Peptidomics in Ham.

The use of proteomics in food science has permitted both a better characterization of the food products and the control of their final quality despite the fact that food systems are under continuous changes during processing and consumption. Ham is a very popular meat product frequently consumed in Mediterranean countries after a dry-curing processing that results in the generation of large amounts of peptides that contribute to its texture, flavor, and final quality. Proteolysis is the main biochemical mechanism occurring throughout the dry-cured ham processing and a better knowledge of this phenomenon is essential to give an extra value to the product and produce regular batches. In this regard, peptidomics has become an important tool for the characterization of dry-cured hams in order to identify and quantify bioactive peptides and potential biomarkers, study their stability under processing conditions or gastrointestinal digestion, and search for post-translational modifications that could affect the quality of dry-cured hams. This manuscript is reviewing from the first uses of comparative proteomics in dry-cured ham approaches to the most modern peptidomic studies and their contribution to the advance in meat science.

Proteomics and phosphoproteomics in precision medicine: applications and challenges.

Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.

Use of Proteomics To Investigate Kidney Function Decline over 5 Years.

Using a discovery/replication approach, we investigated associations between a multiplex panel of 80 circulating proteins associated with cardiovascular pathology or inflammation, and eGFR decline per year and CKD incidence. We used two cohorts, the Prospective Investigation of the Vasculature in Uppsala Seniors Study (PIVUS; n=687, mean age of 70 years, 51% women) and the Uppsala Longitudinal Study of Adult Men (ULSAM; n=360 men, mean age of 78 years), with 5-year follow-up data on eGFR. There were 231 and 206 incident cases of CKD during follow-up in the PIVUS and ULSAM studies, respectively. Proteomic profiling of 80 proteins was assessed by a multiplex assay (proximity extension assay). The assay uses two antibodies for each protein and a PCR step to achieve a high-specific binding and the possibility to measure multiple proteins in parallel, but gives no absolute concentrations. In the discovery cohort from the PIVUS Study, 28 plasma proteins were significantly associated with eGFR decline per year, taking into account the multiple testing. Twenty of these proteins were significantly associated with eGFR decline per year in the replication cohort from the ULSAM Study after adjustment for age, sex, cardiovascular risk factors, medications, and urinary albumin-to-creatinine ratio (in order of significance: TNF-related apoptosis-inducing ligand receptor 2*, CD40L receptor, TNF receptor 1*, placenta growth factor*, thrombomodulin*, urokinase plasminogen activator surface receptor*, growth/differentiation factor 15*, macrophage colony-stimulating factor 1, fatty acid-binding protein*, cathepsin D, resistin, kallikrein 11*, C-C motif chemokine 3, proteinase-activated receptor 1*, cathepsin L, chitinase 3-like protein 1, TNF receptor 2*, fibroblast growth factor 23*, monocyte chemotactic protein 1, and kallikrein 6). Moreover, 11 of the proteins predicted CKD incidence (marked with * above). No protein consistently predicted eGFR decline per year independently of baseline eGFR in both cohorts. Several circulating proteins involved in phosphate homeostasis, inflammation, apoptosis, extracellular matrix remodeling, angiogenesis, and endothelial dysfunction were associated with worsening kidney function. Multiplex proteomics appears to be a promising way of discovering novel aspects of kidney disease pathology.

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models.

Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies. Our aim is to review the information and lessons acquired so far from the use of proteomics in animal models of colitis. These studies helped understand the importance of different proteins at different stages of the disease and unraveled the different pathways that are activated or inhibited during the inflammatory process. Expressed proteins related to inflammation, cellular structure, endoplasmic reticulum stress, and energy depletion advanced the knowledge about the reaction of intestinal cells to inflammation and repair. The role of mesenteric lymphocytes, exosomes, and the intestinal mucosal barrier was emphasized in the inflammatory process. In addition, studies in animal models revealed mechanisms of the beneficial effects of some therapeutic interventions and foods or food components on intestinal inflammation by monitoring changes in protein expression and paved the way for some new possible inflammatory pathways to target in the future. Advances in proteomics technology will further clarify the interaction between intestinal microbiota and IBD pathogenesis and investigate the gene-environmental axis of IBD etiology.