Proteomes

14 pages, 4644 KiB

Open AccessArticle

A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1–10/11

by Aditi S. Kesari, Uma K. Aryal and Douglas J. LaCount

Proteomes 2020, 8(4), 37; https://doi.org/10.3390/proteomes8040037 - 2 Dec 2020

Cited by 2 | Viewed by 4006

Proximity biotinylation was developed to detect physiologically relevant protein–protein interactions in living cells. In this method, the protein of interest is tagged with a promiscuous biotin ligase, such as BioID or BioID2, which produces activated biotin that reacts with nearby proteins; these proteins [...] Read more.

Proximity biotinylation was developed to detect physiologically relevant protein–protein interactions in living cells. In this method, the protein of interest is tagged with a promiscuous biotin ligase, such as BioID or BioID2, which produces activated biotin that reacts with nearby proteins; these proteins can subsequently be purified and identified by mass spectrometry. Here we report a novel modification of this technique by combining it with a self-associating split-GFP system in which we exploit the high-affinity interaction between GFP1–10 and GFP11 to recruit BioID2 to the protein of interest. As a test case, we fused GFP11 to clathrin light chain (CLTB) and BioID2 to GFP1–10. Co-expression of GFP11-CLTB and BioID2-GFP1–10 yielded a green fluorescent complex that co-localized with clathrin heavy chain. To facilitate removal of non-specifically biotinylated proteins, we generated an inducible cell line expressing BioID2-GFP1–10. Proximity biotinylation in this cell line with GFP11-CLTB yielded a higher percentage of biologically relevant interactions than direct fusion of BioID2 to CLTB. Thus, this system can be used to monitor expression and localization of BioID bait proteins and to identify protein–protein interactions. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Quantitative Proteomics)

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12 pages, 1673 KiB

Open AccessCommunication

Discovery of Candidate Stool Biomarker Proteins for Biliary Atresia Using Proteome Analysis by Data-Independent Acquisition Mass Spectrometry

by Eiichiro Watanabe, Yusuke Kawashima, Wataru Suda, Tomo Kakihara, Shinya Takazawa, Daisuke Nakajima, Ren Nakamura, Akira Nishi, Kan Suzuki, Osamu Ohara and Jun Fujishiro

Proteomes 2020, 8(4), 36; https://doi.org/10.3390/proteomes8040036 - 27 Nov 2020

Cited by 4 | Viewed by 4499

Abstract

Biliary atresia (BA) is a destructive inflammatory obliterative cholangiopathy of the neonate that affects various parts of the bile duct. If early diagnosis followed by Kasai portoenterostomy is not performed, progressive liver cirrhosis frequently leads to liver transplantation in the early stage of [...] Read more.

Biliary atresia (BA) is a destructive inflammatory obliterative cholangiopathy of the neonate that affects various parts of the bile duct. If early diagnosis followed by Kasai portoenterostomy is not performed, progressive liver cirrhosis frequently leads to liver transplantation in the early stage of life. Therefore, prompt diagnosis is necessary for the rescue of BA patients. However, the prompt diagnosis of BA remains challenging because specific and reliable biomarkers for BA are currently unavailable. In this study, we discovered potential biomarkers for BA using deep proteome analysis by data-independent acquisition mass spectrometry (DIA–MS). Four patients with BA and three patients with neonatal cholestasis of other etiologies (non-BA) were recruited for stool proteome analysis. Among the 2110 host-derived proteins detected in their stools, 49 proteins were significantly higher in patients with BA and 54 proteins were significantly lower. These varying stool protein levels in infants with BA can provide potential biomarkers for BA. As demonstrated in this study, the deep proteome analysis of stools has great potential not only in detecting new stool biomarkers for BA but also in elucidating the pathophysiology of BA and other pediatric diseases, especially in the field of pediatric gastroenterology. Full article

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6 pages, 904 KiB

Open AccessCommentary

Reporting of Hybrid Data and the Difficulties with Cross-Discipline Research Techniques

by Matthew B. O’Rourke and Matthew P. Padula

Proteomes 2020, 8(4), 35; https://doi.org/10.3390/proteomes8040035 - 23 Nov 2020

Cited by 2 | Viewed by 2481

Abstract

Peer review is the way in which we, as scientists, criticise, check, and confirm the findings of our colleagues. The process of peer review relies on individuals in all fields applying their particular expertise and determining if they agree with the findings submitted [...] Read more.

Peer review is the way in which we, as scientists, criticise, check, and confirm the findings of our colleagues. The process of peer review relies on individuals in all fields applying their particular expertise and determining if they agree with the findings submitted for publication. In recent years, there has been a significant rise in the number of manuscripts submitted for publication that draw from a range of disparate and complementary fields. This has created the curious situation where an expert may be requested to review a manuscript that is only partially within their immediate field of expertise. The issue that arises is that, without full knowledge of the data, techniques, methodologies, and principles that are presented, it is difficult for reviewers to make properly informed decisions, especially when it can take an entire career to reach that specific level of expertise in a single field. From this perspective, we explore these issues and also provide a commentary on how peer review could evolve in the context of a changing cross-disciplinarily-focused scientific landscape. Full article

(This article belongs to the Special Issue Feature Review Papers in Proteomes)

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18 pages, 4349 KiB

Open AccessArticle

The Constitutive Proteome of Human Aqueous Humor and Race Specific Alterations

by Sai Karthik Kodeboyina, Tae Jin Lee, Lara Churchwell, Lane Ulrich, Kathryn Bollinger, David Bogorad, Amy Estes, Wenbo Zhi, Shruti Sharma and Ashok Sharma

Proteomes 2020, 8(4), 34; https://doi.org/10.3390/proteomes8040034 - 18 Nov 2020

Cited by 12 | Viewed by 4383

Abstract

Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging, mainly due to low sample volume and protein concentration. In this study, by utilizing state [...] Read more.

Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging, mainly due to low sample volume and protein concentration. In this study, by utilizing state of the art technology, we performed Liquid-Chromatography Mass spectrometry (LC-MS/MS) analysis of 88 aqueous humor samples from subjects undergoing cataract surgery. A total of 2263 unique proteins were identified, which were sub-divided into four categories that were based on their detection in the number of samples: High (n = 152), Medium (n = 91), Low (n = 128), and Rare (n = 1892). A total of 243 proteins detected in at least 50% of the samples were considered as the constitutive proteome of human aqueous humor. The biological processes and pathways enriched in the AH proteins mainly include vesicle mediated transport, acute phase response signaling, LXR/RXR activation, complement system, and secretion. The enriched molecular functions are endopeptidase activity, and various binding functions, such as protein binding, lipid binding, and ion binding. Additionally, this study provides a novel insight into race specific differences in the AH proteome. A total of six proteins were upregulated, and five proteins were downregulated in African American subjects as compared to Caucasians. Full article

(This article belongs to the Special Issue Human Proteomics)

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9 pages, 1024 KiB

Open AccessArticle

Quantitative Proteomic Analysis of Biogenesis-Based Classification for Extracellular Vesicles

by Linwen Zhang, Jeremie Parot, Vincent A. Hackley and Illarion V. Turko

Proteomes 2020, 8(4), 33; https://doi.org/10.3390/proteomes8040033 - 6 Nov 2020

Cited by 8 | Viewed by 3167

Abstract

Extracellular vesicles (EVs) are traditionally divided into two major groups: (i) large vesicles originating from plasma membrane and called microvesicles, and (ii) small vesicles originating from the endoplasmic membrane and called exosomes. However, it is increasingly clear that the actual composition of a [...] Read more.

Extracellular vesicles (EVs) are traditionally divided into two major groups: (i) large vesicles originating from plasma membrane and called microvesicles, and (ii) small vesicles originating from the endoplasmic membrane and called exosomes. However, it is increasingly clear that the actual composition of a particular EV preparation cannot be adequately described with these two simple terms and is much more complex. Since the cell membrane origin of EVs predetermines their biological functions, the understanding of EV biogenesis is important for accurate interpretation of observed results. In the present study, we propose to take advantage of selective expression of some proteins in plasma or endosomal membranes and to use these proteins as plasma membrane-specific or endosomal membrane-specific markers. We have demonstrated that a quantitative mass spectrometry analysis allows simultaneous measurement of plasma membrane-specific and endosomal membrane-specific proteins in microvesicles and exosomes obtained after differential ultracentrifugation. Before mass spectrometry analysis, we also used sonicated platelets as a model of mixed EVs and multidetector asymmetrical-flow field-flow fractionation as an analytical method to verify a possible cross contamination of obtained microvesicles and exosomes. Based on the quantitative appearance of membrane-specific protein markers in EV preparations from human plasma and from human ARPE-19 cell medium, we concluded that there is no actual size limitation and both microvesicles and exosomes can be represented by large and small vesicles. Full article

(This article belongs to the Special Issue Targeted Analyses of Proteomes)

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8 pages, 721 KiB

Open AccessArticle

Ovarian Cancer: Tumor-Specific Urinary Micro-Peptides Profiling as Potential Biomarkers for Early Diagnosis

by Sulafa S. Murgan, Faisal J. Abd Elaziz, Abubakr M. A. Nasr, Mona E. E. Elfaki and Eltahir A. G. Khalil

Proteomes 2020, 8(4), 32; https://doi.org/10.3390/proteomes8040032 - 29 Oct 2020

Cited by 6 | Viewed by 2689

Abstract

Ovarian cancer is the second major lethal gynecologic malignancy in developing countries. This study aimed to characterize urinary micro-peptides as potential diagnostic biomarkers for ovarian cancer. In a prospective, longitudinal and case-controlled study and following informed consent, urine and plasma samples were collected [...] Read more.

Ovarian cancer is the second major lethal gynecologic malignancy in developing countries. This study aimed to characterize urinary micro-peptides as potential diagnostic biomarkers for ovarian cancer. In a prospective, longitudinal and case-controlled study and following informed consent, urine and plasma samples were collected from 112 women with histologically-proven ovarian cancer and 200 apparently healthy age-matched volunteers. Urinary micro-peptides were detected and sequenced using SDS-PAGE and Edman degradation technique. Serum CA125 was detected in less than a quarter (23.2%, 26/112) of patients. One or more urinary micro-peptides were detected in about two thirds of the patients (62.5%, 70/112). A total of 40 patients had three bands (57.1%, 40/70), while two bands (15 and 35 kDa) were detected in 28.6% (20/70) of the patients. Isolated 45 kDa band was seen in 14.3% (10/70). No urinary micro-peptide was detected in the volunteers. The 15 and 35 kDa bands disappeared after 6 months of regular chemotherapy, while the 45 kDa band persisted in 2.9% (2/70) of the patients after treatment. The micro-peptides were identified as: Catalase (45 kDa), α-1 Acid Glycoprotein (35 kDa) and Peroxiredoxin-2 (15 kDa). Urinary catalase, α-1 Acid Glycoprotein and Peroxiredoxin-2 can be useful biomarkers for early detection and treatment response of ovarian cancer. Full article

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14 pages, 2104 KiB

Open AccessArticle

The New and the Old: Platform Cross-Validation of Immunoaffinity MASS Spectrometry versus ELISA for PromarkerD, a Predictive Test for Diabetic Kidney Disease

by Scott Bringans, Kirsten Peters, Tammy Casey, Jason Ito and Richard Lipscombe

Proteomes 2020, 8(4), 31; https://doi.org/10.3390/proteomes8040031 - 28 Oct 2020

Cited by 7 | Viewed by 3246

Abstract

PromarkerD is a proteomics derived test for predicting diabetic kidney disease that measures the concentrations of three plasma protein biomarkers, APOA4, CD5L and IBP3. Antibodies against these proteins were developed and applied to a multiplexed immunoaffinity capture mass spectrometry assay. In parallel, and [...] Read more.

PromarkerD is a proteomics derived test for predicting diabetic kidney disease that measures the concentrations of three plasma protein biomarkers, APOA4, CD5L and IBP3. Antibodies against these proteins were developed and applied to a multiplexed immunoaffinity capture mass spectrometry assay. In parallel, and facilitating current clinical laboratory workflows, a standard ELISA was also developed to measure each protein. The performance characteristics of the two technology platforms were compared using a cohort of 100 samples, with PromarkerD test scores demonstrating a high correlation (R = 0.97). These technologies illustrate the potential for large scale, high throughput clinical applications of proteomics now and into the future. Full article

(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)

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17 pages, 2745 KiB

Open AccessArticle

Radiation Response of Human Cardiac Endothelial Cells Reveals a Central Role of the cGAS-STING Pathway in the Development of Inflammation

by Jos Philipp, Ronan Le Gleut, Christine von Toerne, Prabal Subedi, Omid Azimzadeh, Michael J. Atkinson and Soile Tapio

Proteomes 2020, 8(4), 30; https://doi.org/10.3390/proteomes8040030 - 26 Oct 2020

Cited by 19 | Viewed by 4125

Abstract

Radiation-induced inflammation leading to the permeability of the endothelial barrier may increase the risk of cardiovascular disease. The aim of this study was to investigate potential mechanisms in vitro at the level of the proteome in human coronary artery endothelial cells (HCECest2) that [...] Read more.

Radiation-induced inflammation leading to the permeability of the endothelial barrier may increase the risk of cardiovascular disease. The aim of this study was to investigate potential mechanisms in vitro at the level of the proteome in human coronary artery endothelial cells (HCECest2) that were exposed to radiation doses of 0, 0.25, 0.5, 2.0 and 10 Gy (60Co-γ). Proteomics analysis was performed using mass spectrometry in a label-free data-independent acquisition mode. The data were validated using bioinformatics and immunoblotting. The low- and moderate-dose-irradiated samples (0.25 Gy, 0.5 Gy) showed only scarce proteome changes. In contrast, an activation of DNA-damage repair, inflammation, and oxidative stress pathways was seen after the high-dose treatments (2 and 10 Gy). The level of the DNA damage response protein DDB2 was enhanced early at the 10 Gy dose. The expression of proteins belonging to the inflammatory response or cGAS-STING pathway (STING, STAT1, ICAM1, ISG15) increased in a dose-dependent manner, showing the strongest effects at 10 Gy after one week. This study suggests a connection between the radiation-induced DNA damage and the induction of inflammation which supports the inhibition of the cGAS-STING pathway in the prevention of radiation-induced cardiovascular disease. Full article

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19 pages, 2018 KiB

Open AccessArticle

Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures

by Mamosa G. Ngcala, Tatenda Goche, Adrian P. Brown, Stephen Chivasa and Rudo Ngara

Proteomes 2020, 8(4), 29; https://doi.org/10.3390/proteomes8040029 - 22 Oct 2020

Cited by 19 | Viewed by 3347

Abstract

Plants reprogram gene expression as an adaptive response to survive high temperatures. While the identity and functions of intracellular heat stress-responsive proteins have been extensively studied, the heat response of proteins secreted to the extracellular matrix is unknown. Here, we used Sorghum bicolor [...] Read more.

Plants reprogram gene expression as an adaptive response to survive high temperatures. While the identity and functions of intracellular heat stress-responsive proteins have been extensively studied, the heat response of proteins secreted to the extracellular matrix is unknown. Here, we used Sorghum bicolor, a species adapted for growth in hot climates, to investigate the extracellular heat-induced responses. When exposed to 40 °C for 72 h, heat-sensitive Arabidopsis cell suspension cultures died, while ICSB338 sorghum cell cultures survived by activation of a transcriptional response characterized by the induction of HSP70 and HSP90 genes. Quantitative proteomic analysis of proteins recovered from cell culture medium revealed specific heat stress-induced protein accumulation within the sorghum secretome. Of the 265 secreted proteins identified, 31 responded to heat (≥2-fold change), with 84% possessing a predicted signal peptide for targeting to the classical secretory pathway. The differentially accumulated proteins have putative functions in metabolism, detoxification, and protein modifications. A germin (SORBI_3003G427700) was highly heat-inducible at both protein and gene level. Overall, our study reveals new insights into sorghum responses to heat and provides a useful resource of extracellular proteins that could serve as targets for developing thermotolerant crops. Data are available via ProteomeXchange with identifier PXD021536. Full article

(This article belongs to the Special Issue Proteomics to Unravel Plant Adaptation, Acclimation or Vulnerability to Stress and Diseases)

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17 pages, 1768 KiB

Open AccessArticle

Short-Chain Fatty Acids Modulate Metabolic Pathways and Membrane Lipids in Prevotella bryantii B₁4

by Andrej Trautmann, Lena Schleicher, Simon Deusch, Jochem Gätgens, Julia Steuber and Jana Seifert

Proteomes 2020, 8(4), 28; https://doi.org/10.3390/proteomes8040028 - 16 Oct 2020

Cited by 19 | Viewed by 4204

Abstract

Short-chain fatty acids (SCFAs) are bacterial products that are known to be used as energy sources in eukaryotic hosts, whereas their role in the metabolism of intestinal microbes is rarely explored. In the present study, acetic, propionic, butyric, isobutyric, valeric, and isovaleric acid, [...] Read more.

Short-chain fatty acids (SCFAs) are bacterial products that are known to be used as energy sources in eukaryotic hosts, whereas their role in the metabolism of intestinal microbes is rarely explored. In the present study, acetic, propionic, butyric, isobutyric, valeric, and isovaleric acid, respectively, were added to a newly defined medium containing Prevotella bryantii B₁4 cells. After 8 h and 24 h, optical density, pH and SCFA concentrations were measured. Long-chain fatty acid (LCFA) profiles of the bacterial cells were analyzed via gas chromatography-time of flight-mass spectrometry (GC-ToF MS) and proteins were quantified using a mass spectrometry-based, label-free approach. Cultures supplemented with single SCFAs revealed different growth behavior. Structural features of the respective SCFAs were identified in the LCFA profiles, which suggests incorporation into the bacterial membranes. The proteomes of cultures supplemented with acetic and valeric acid differed by an increased abundance of outer membrane proteins. The proteome of the isovaleric acid supplementation showed an increase of proteins in the amino acid metabolism. Our findings indicate a possible interaction between SCFAs, the lipid membrane composition, the abundance of outer membrane proteins, and a modulation of branched chain amino acid biosynthesis by isovaleric acid. Full article

(This article belongs to the Special Issue Microbial Proteomics II)

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18 pages, 2894 KiB

Open AccessArticle

Differential Protein Expression in Striatal D1- and D2-Dopamine Receptor-Expressing Medium Spiny Neurons

by M. Shahid Mansuri, Gang Peng, Rashaun S. Wilson, TuKiet T. Lam, Hongyu Zhao, Kenneth R. Williams and Angus C. Nairn

Proteomes 2020, 8(4), 27; https://doi.org/10.3390/proteomes8040027 - 13 Oct 2020

Cited by 6 | Viewed by 4852

Abstract

Many neurological disorders and diseases including drug addiction are associated with specific neuronal cell types in the brain. The striatum, a region that plays a critically important role in the development of addictive drug-related behavior, provides a good example of the cellular heterogeneity [...] Read more.

Many neurological disorders and diseases including drug addiction are associated with specific neuronal cell types in the brain. The striatum, a region that plays a critically important role in the development of addictive drug-related behavior, provides a good example of the cellular heterogeneity challenges associated with analyses of specific neuronal cell types. Such studies are needed to identify the adaptive changes in neuroproteomic signaling that occur in response to diseases such as addiction. The striatum contains two major cell types, D1 and D2 type dopaminoceptive medium spiny neurons (MSNs), whose cell bodies and processes are intermingled throughout this region. Since little is known about the proteomes of these two neuronal cell populations, we have begun to address this challenge by using fluorescence-activated nuclear sorting (FANS) to isolate nuclei-containing fractions from striatum from D1 and D2 “Translating Ribosome Affinity Purification” (TRAP) mice. This approach enabled us to devise and implement a robust and reproducible workflow for preparing samples from specific MSN cell types for mass spectrometry analyses. These analyses quantified at least 685 proteins in each of four biological replicates of 50 K sorted nuclei from two D1 mice/replicate and from each of four biological replicates of 50 K sorted nuclei from two D2 mice/replicate. Proteome analyses identified 87 proteins that were differentially expressed in D1 versus D2 MSN nuclei and principal component analysis (PCA) of these proteins separated the 8 biological replicates into specific cell types. Central network analysis of the 87 differentially expressed proteins identified Hnrnpd and Hnmpa2b1 in D1 and Cct2 and Cct7 in D2 as potential central interactors. This workflow can now be used to improve our understanding of many neurological diseases including characterizing the short and long-term impact of drugs of abuse on the proteomes of these two dopaminoceptive neuronal populations. Full article

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Proteomes, Volume 8, Issue 4 (December 2020) – 11 articles

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