Proteomes

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19 pages, 15617 KiB

Open AccessArticle

Proteomics Analysis to Assess the Role of Mitochondria in BRCA1-Mediated Breast Tumorigenesis

by Antonio Concolino, Erika Olivo, Laura Tammè, Claudia Vincenza Fiumara, Maria Teresa De Angelis, Barbara Quaresima, Valter Agosti, Francesco Saverio Costanzo, Giovanni Cuda and Domenica Scumaci

Proteomes 2018, 6(2), 16; https://doi.org/10.3390/proteomes6020016 - 27 Mar 2018

Cited by 14 | Viewed by 6769

Abstract

Mitochondria are the organelles deputed to energy production, but they are also involved in carcinogenesis, cancer progression, and metastasis, playing a role in altered energy metabolism in cancer cells. Mitochondrial metabolism is connected with several mitochondrial pathways such as ROS signaling, Ca²⁺ [...] Read more.

Mitochondria are the organelles deputed to energy production, but they are also involved in carcinogenesis, cancer progression, and metastasis, playing a role in altered energy metabolism in cancer cells. Mitochondrial metabolism is connected with several mitochondrial pathways such as ROS signaling, Ca²⁺ homeostasis, mitophagy, and mitochondrial biogenesis. These pathways are merged in an interactive super-network that seems to play a crucial role in cancer. Germline mutations of the BRCA1 gene account for 5–10% of breast cancers and confer a risk of developing the disease 10- to 20-fold much higher than in non-carriers. By considering metabolic networks that could reconcile both genetic and non-genetic causal mechanisms in BRCA1 driven tumorigenesis, we herein based our study on the hypothesis that BRCA1 haploinsufficiency might drive metabolic rewiring in breast epithelial cells, acting as a push toward malignant transformation. Using 2D-DIGE we analyzed and compared the mitochondrial proteomic profile of sporadic breast cancer cell line (MCF7) and BRCA1 mutated breast cancer cell line (HCC1937). Image analysis was carried out with Decider Software, and proteins differentially expressed were identified by LC-MS/MS on a quadrupole-orbitrap mass spectrometer Q-Exactive. Ingenuity pathways analysis software was used to analyze the fifty-three mitochondrial proteins whose expression resulted significantly altered in response to BRCA1 mutation status. Mitochondrial Dysfunction and oxidative phosphorylation, and energy production and nucleic acid metabolism were, respectively, the canonical pathway and the molecular function mainly affected. Western blotting analysis was done to validate the expression and the peculiar mitochondrial compartmentalization of specific proteins such us HSP60 and HIF-1α. Particularly intriguing is the correlation between BRCA1 mutation status and HIF-1α localization into the mitochondria in a BRCA1 dependent manner. Data obtained led us to hypothesize an interesting connection between BRCA1 and mitochondria pathways, capable to trigger metabolic changes, which, in turn, sustain the high energetic and anabolic requirements of the malignant phenotype. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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8 pages, 2235 KiB

Open AccessFeature PaperArticle

Proteome Profiling of Diabetic Mellitus Patient Urine for Discovery of Biomarkers by Comprehensive MS-Based Proteomics

by Yoshitoshi Hirao, Suguru Saito, Hidehiko Fujinaka, Shigeru Miyazaki, Bo Xu, Ali F. Quadery, Amr Elguoshy, Keiko Yamamoto and Tadashi Yamamoto

Proteomes 2018, 6(1), 9; https://doi.org/10.3390/proteomes6010009 - 6 Feb 2018

Cited by 11 | Viewed by 5113

Abstract

Diabetic mellitus (DM) is a disease that affects glucose homeostasis and causes complications, such as diabetic nephropathy (DN). For early diagnosis of DN, microalbuminuria is currently one of the most frequently used biomarkers. However, more early diagnostic biomarkers are desired in addition to [...] Read more.

Diabetic mellitus (DM) is a disease that affects glucose homeostasis and causes complications, such as diabetic nephropathy (DN). For early diagnosis of DN, microalbuminuria is currently one of the most frequently used biomarkers. However, more early diagnostic biomarkers are desired in addition to microalbuminuria. In this study, we performed comprehensive proteomics analysis of urine proteomes of diabetic mellitus patients without microalbuminuria and healthy volunteers to compare the protein profiles by mass spectrometry. With high confidence criteria, 942 proteins in healthy volunteer urine and 645 proteins in the DM patient urine were identified with label-free semi-quantitation, respectively. Gene ontology and pathway analysis were performed with the proteins, which were up- or down-regulated in the DM patient urine to elucidate significant changes in pathways. The discovery of a useful biomarker for early DN discovery is expected. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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1266 KiB

Open AccessArticle

Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry

by Sebastian Malchow, Christina Loosse, Albert Sickmann and Christin Lorenz

Proteomes 2017, 5(4), 31; https://doi.org/10.3390/proteomes5040031 - 15 Nov 2017

Cited by 13 | Viewed by 6159

Abstract

Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or [...] Read more.

Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or inhibitory effects. A variety of factors, e.g., collagen, fibrinogen, ADP, vWF, thrombin, and thromboxane promote platelet adhesion and aggregation by utilizing multiple intracellular signal cascades. To quantify platelet proteins for this work, a targeted proteomics workflow was applied. In detail, platelets are isolated and lyzed, followed by a tryptic protein digest. Subsequently, a mix of stable isotope-labeled peptides of interesting biomarker proteins in concentrations ranging from 0.1 to 100 fmol is added to 3 μg digest. These peptides are used as an internal calibration curve to accurately quantify endogenous peptides and corresponding proteins in a pooled platelet reference sample by nanoLC-MS/MS with parallel reaction monitoring. In order to assure a valid quantification, limit of detection (LOD) and limit of quantification (LOQ), as well as linear range, were determined. This quantification of platelet activation and proteins by targeted mass spectrometry may enable novel diagnostic strategies in the detection and prevention of cardiovascular diseases. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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1461 KiB

Open AccessArticle

Performance of a Multiplex Serological Helicobacter pylori Assay on a Novel Microfluidic Assay Platform

by Angela Filomena, Anna Guenther, Hannes Planatscher, Francois Topin, Joseph She, Luca Formichella, Laurent Terradot, Markus Gerhard, Thomas O. Joos, Hannelore Meyer and Nicole Schneiderhan-Marra

Proteomes 2017, 5(4), 24; https://doi.org/10.3390/proteomes5040024 - 3 Oct 2017

Cited by 11 | Viewed by 5411

Abstract

Infection with Helicobacter pylori (H. pylori) occurs in 50% of the world population, and is associated with the development of ulcer and gastric cancer. Serological diagnostic tests indicate an H. pylori infection by detecting antibodies directed against H. pylori proteins. In [...] Read more.

Infection with Helicobacter pylori (H. pylori) occurs in 50% of the world population, and is associated with the development of ulcer and gastric cancer. Serological diagnostic tests indicate an H. pylori infection by detecting antibodies directed against H. pylori proteins. In addition to line blots, multiplex assay platforms provide smart solutions for the simultaneous analysis of antibody responses towards several H. pylori proteins. We used seven H. pylori proteins (FliD, gGT, GroEL, HpaA, CagA, VacA, and HP0231) and an H. pylori lysate for the development of a multiplex serological assay on a novel microfluidic platform. The reaction limited binding regime in the microfluidic channels allows for a short incubation time of 35 min. The developed assay showed very high sensitivity (99%) and specificity (100%). Besides sensitivity and specificity, the technical validation (intra-assay CV = 3.7 ± 1.2% and inter-assay CV = 5.5 ± 1.2%) demonstrates that our assay is also a robust tool for the analysis of the H. pylori-specific antibody response. The integration of the virulence factors CagA and VacA allow for the assessment of the risk for gastric cancer development. The short assay time and the performance of the platform shows the potential for implementation of such assays in a clinical setting. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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Review

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17 pages, 1184 KiB

Open AccessReview

Integrated Chemometrics and Statistics to Drive Successful Proteomics Biomarker Discovery

by Anouk Suppers, Alain J. van Gool and Hans J. C. T. Wessels

Proteomes 2018, 6(2), 20; https://doi.org/10.3390/proteomes6020020 - 26 Apr 2018

Cited by 25 | Viewed by 6076

Abstract

Protein biomarkers are of great benefit for clinical research and applications, as they are powerful means for diagnosing, monitoring and treatment prediction of different diseases. Even though numerous biomarkers have been reported, the translation to clinical practice is still limited. This mainly due [...] Read more.

Protein biomarkers are of great benefit for clinical research and applications, as they are powerful means for diagnosing, monitoring and treatment prediction of different diseases. Even though numerous biomarkers have been reported, the translation to clinical practice is still limited. This mainly due to: (i) incorrect biomarker selection, (ii) insufficient validation of potential biomarkers, and (iii) insufficient clinical use. In this review, we focus on the biomarker selection process and critically discuss the chemometrical and statistical decisions made in proteomics biomarker discovery to increase to selection of high value biomarkers. The characteristics of the data, the computational resources, the type of biomarker that is searched for and the validation strategy influence the decision making of the chemometrical and statistical methods and a decision made for one component directly influences the choice for another. Incorrect decisions could increase the false positive and negative rate of biomarkers which requires independent confirmation of outcome by other techniques and for comparison between different related studies. There are few guidelines for authors regarding data analysis documentation in peer reviewed journals, making it hard to reproduce successful data analysis strategies. Here we review multiple chemometrical and statistical methods for their value in proteomics-based biomarker discovery and propose to include key components in scientific documentation. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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17 pages, 2840 KiB

Open AccessReview

Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases

by Jessica Y. Lee, Valerie C. Wasinger, Yunki Y. Yau, Emil Chuang, Vijay Yajnik and Rupert WL. Leong

Proteomes 2018, 6(2), 17; https://doi.org/10.3390/proteomes6020017 - 31 Mar 2018

Cited by 66 | Viewed by 9935

Abstract

Over the years, the scientific community has explored myriads of theories in search of the etiology and a cure for inflammatory bowel disease (IBD). The cumulative evidence has pointed to the key role of the intestinal barrier and the breakdown of these mechanisms [...] Read more.

Over the years, the scientific community has explored myriads of theories in search of the etiology and a cure for inflammatory bowel disease (IBD). The cumulative evidence has pointed to the key role of the intestinal barrier and the breakdown of these mechanisms in IBD. More and more scientists and clinicians are embracing the concept of the impaired intestinal epithelial barrier and its role in the pathogenesis and natural history of IBD. However, we are missing a key tool that bridges these scientific insights to clinical practice. Our goal is to overcome the limitations in understanding the molecular physiology of intestinal barrier function and develop a clinical tool to assess and quantify it. This review article explores the proteins in the intestinal tissue that are pivotal in regulating intestinal permeability. Understanding the molecular pathophysiology of impaired intestinal barrier function in IBD may lead to the development of a biochemical method of assessing intestinal tissue integrity which will have a significant impact on the development of novel therapies targeting the intestinal mucosa. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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8 pages, 421 KiB

Open AccessFeature PaperReview

Exploring the Psoriatic Arthritis Proteome in Search of Novel Biomarkers

by Shalini M. Mahendran and Vinod Chandran

Proteomes 2018, 6(1), 5; https://doi.org/10.3390/proteomes6010005 - 24 Jan 2018

Cited by 20 | Viewed by 6302

Abstract

Psoriatic arthritis (PsA) is an inflammatory arthritis which develops in up to one-third of patients suffering from the cutaneous disorder, psoriasis. The complex and heterogeneous nature of PsA renders it difficult to diagnose, leading to poor outcomes and, therefore, warrants an examination into [...] Read more.

Psoriatic arthritis (PsA) is an inflammatory arthritis which develops in up to one-third of patients suffering from the cutaneous disorder, psoriasis. The complex and heterogeneous nature of PsA renders it difficult to diagnose, leading to poor outcomes and, therefore, warrants an examination into soluble biomarkers, which may facilitate early detection of the disease. Protein biomarkers are a dynamic resource of pathophysiological information able to provide an immediate reflection of pathological changes caused by disease. Investigations of the serum and synovial fluid of PsA patients has provided new insights into the molecular basis of this disease and led to the identification of sensitive diagnostic and prognostic biomarkers. The collection of novel PsA biomarkers identified through proteomic studies has been reviewed below. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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188 KiB

Open AccessReview

Mass Spectrometric Studies of Apolipoprotein Proteoforms and Their Role in Lipid Metabolism and Type 2 Diabetes

by Dobrin Nedelkov

Proteomes 2017, 5(4), 27; https://doi.org/10.3390/proteomes5040027 - 15 Oct 2017

Cited by 15 | Viewed by 4430

Abstract

Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies [...] Read more.

Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies correlating apolipoproteins proteoforms with the specific clinical measures of lipid metabolism and cardiometabolic risk. Targeted mass spectrometric immunoassays toward apolipoproteins A-I, A-II, and C-III were applied on large cross-sectional and longitudinal clinical cohorts. Several correlations were observed, including greater apolipoprotein A-I and A-II oxidation in patients with diabetes and cardiovascular disease, and a divergent apoC-III proteoforms association with plasma triglycerides, indicating significant differences in the metabolism of the individual apoC-III proteoforms. These are the first studies of their kind, correlating specific proteoforms with clinical measures in order to determine their utility as potential clinical biomarkers for disease diagnosis, risk stratification, and therapy decisions. Such studies provide the impetus for the further development and clinical translation of MS-based protein tests. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

993 KiB

Open AccessReview

Role of Salivary Biomarkers in Detection of Cardiovascular Diseases (CVD)

by Saad Abdul Rehman, Zohaib Khurshid, Fayez Hussain Niazi, Mustafa Naseem, Hamed Al Waddani, Haafsa Arshad Sahibzada and Rabia Sannam Khan

Proteomes 2017, 5(3), 21; https://doi.org/10.3390/proteomes5030021 - 7 Aug 2017

Cited by 51 | Viewed by 9649

Abstract

Human whole mouth saliva (WMS) is secreted by salivary glands, namely parotid, submandibular/sublingual and other minor glands of the oral cavity. It is secreted in a systematic way, and contain informative proteins and peptides for the early detection of contagious diseases and organ-related [...] Read more.

Human whole mouth saliva (WMS) is secreted by salivary glands, namely parotid, submandibular/sublingual and other minor glands of the oral cavity. It is secreted in a systematic way, and contain informative proteins and peptides for the early detection of contagious diseases and organ-related diseases. The role of WMS as a liquid biopsy for the detection of cardiovascular diseases (CVD) through Myoglobin (MYO), Cardiac troponin I (cTnI), Creatine phosphokinase MB (CK-MB), Myeloperoxidase (MPO), brain natriuretic peptide (NT-proBNP), Exosomal miRNA, C-Reactive Protein (CRP), Matrix metalloproteinase-8 (MMP-8), MMP-9 and tissue inhibitor of MMP-8 (TIMP-1), leukotriene B4 has been well reported in last decade, that have been reviewed in the literature comprehensively below. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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