Identification of proteins that are differentially expressed in brains with Alzheimer's disease using iTRAQ labeling and tandem mass spectrometry

Minjarez, Benito; Calderón-González, Karla Grisel; Rustarazo, Ma Luz Valero; Herrera-Aguirre, María Esther; Labra-Barrios, María Luisa; Rincón-Limas, Diego E.; Pino, Manuel M. Sánchez del; Mena, Raúl; Luna-Arias, Juan Pedro

doi:10.1016/j.jprot.2016.03.022

Cited by 56 publications

(56 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The iTRAQ is a reliable and accurate technique for quantitative analysis in proteomics study (Wiese, 2007). This technique uses stable isotopically-labeled molecules that can be covalently bonded to the N-terminus and side chain amines of proteins, and have been increasingly applied to investigate the proteome in different organisms (Liu et al, 2016a;Minjarez et al, 2016;Xiong et al, 2016;Campos et al, 2017). In this study, we performed iTRAQ-based proteomics analysis using embryonic muscle samples, and identified differentially expressed proteins during skeletal muscle development in chickens.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

et al. 2017

View full text Add to dashboard Cite

Embryonic growth and development of skeletal muscle is a major determinant of muscle mass, and has a significant effect on meat production in chicken. To assess the protein expression profiles during embryonic skeletal muscle development, we performed a proteomics analysis using isobaric tags for relative and absolute quantification (iTRAQ) in leg muscle tissues of female Xinghua chicken at embryonic age (E) 11, E16, and 1-day post hatch (D1). We identified 3,240 proteins in chicken embryonic muscle and 491 of them were differentially expressed (fold change ≥ 1.5 or ≤ 0.666 and p < 0.05). There were 19 up- and 32 down-regulated proteins in E11 vs. E16 group, 238 up- and 227 down-regulated proteins in E11 vs. D1 group, and 13 up- and 5 down-regulated proteins in E16 vs. D1 group. Protein interaction network analyses indicated that these differentially expressed proteins were mainly involved in the pathway of protein synthesis, muscle contraction, and oxidative phosphorylation. Integrative analysis of proteome and our previous transcriptome data found 189 differentially expressed proteins that correlated with their mRNA level. The interactions between these proteins were also involved in muscle contraction and oxidative phosphorylation pathways. The lncRNA-protein interaction network found four proteins DMD, MYL3, TNNI2, and TNNT3 that are all involved in muscle contraction and may be lncRNA regulated. These results provide several candidate genes for further investigation into the molecular mechanisms of chicken embryonic muscle development, and enable us to better understanding their regulation networks and biochemical pathways.

show abstract

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

et al. 2017

View full text Add to dashboard Cite

show abstract

“…This could be due to the limited availability of CSF in healthy controls. All these proteomic studies were mainly case-control and, more importantly, the protein recognition by MS was made on enzyme digested protein samples following a “bottom-up” proteomic strategy [7, 9]. …”

Section: Introductionmentioning

confidence: 99%

Protein signature in cerebrospinal fluid and serum of Alzheimer’s disease patients: The case of apolipoprotein A-1 proteoforms

et al. 2017

View full text Add to dashboard Cite

In the diagnosis of Alzheimer’s disease (AD) total tau (T-tau), tau phosphorylated at threonine 181 (P-tau181), and the 42 amino acid isoform of alpha β-amyloid (Aβ) are well established surrogate CSF markers. However, there is a constant need for new diagnostic markers to identify the disease at a very early stage. The identification of new molecules for AD diagnosis and monitoring in CSF is hampered by several “confounding” factors including intra- and inter-individual, pre-analytical and analytical variabilities. In an attempt to partially overcome patient’s variability and to determine new molecules significantly dysregulated in CSF, we assessed the proteome profile of low molecular weight protein species in CSF and serum of the same patients. CSFs and sera from 36 ADs, 32 iNPHs (idiopathic normal pressure hydrocephalus) and 12 controls were compared by MALDI profiling (non-parametric statistics, CV<20%, AUC>0.750). After protein identification by mass spectrometry, the proteoform composition was assessed by 2-D DIGE/MS. Results indicated that CSF of iNPH can be used as control. Serum and CSF of AD patients shows a specific protein profile compared to iNPH samples. A variation (p<0.01) of Apo A-1 levels in AD, together with a specific dysregulation of Apo A-1 proteoforms was observed. The profiling of CSF and serum of the same patients, suggests that the decrement of total Apo A-1 occurs specifically in CSF. Serum and CSF of AD shows a characteristic Apo A-1 proteoform pattern suggesting it as potential marker which can support the clinical workflow adopted for AD diagnosis and progression.

show abstract

“…Given the successful application of MS technologies to neurodegenerative studies [152,153,165], similar strategies should readily be adopted to probe for biomarkers and putative therapeutic targets in psychiatric disorders. In our view, several MS platforms for proteome investigation in neurological disorders especially with a focus on quantitation, will gain a major impetus in the near future and are critically discussed here.…”

Section: Five-year Perspectivementioning

confidence: 99%

“…Thus far, the majority of neurological studies employed global proteomic profiling towards identification of differentially expressed proteins between health and disease states [153,165]. In this respect, shotgun proteomics was particularly well suited for qualitative studies of complex proteomes, but it is limited in reproducibility and sensitivity [166,167].…”

Section: Five-year Perspectivementioning

confidence: 99%

Recent advances in applying mass spectrometry and systems biology to determine brain dynamics

Scifo

Calza

Fuhrmann

et al. 2017

Expert Review of Proteomics

View full text Add to dashboard Cite

Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.

show abstract

Identification of proteins that are differentially expressed in brains with Alzheimer's disease using iTRAQ labeling and tandem mass spectrometry

Cited by 56 publications

References 90 publications

Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development

Protein signature in cerebrospinal fluid and serum of Alzheimer’s disease patients: The case of apolipoprotein A-1 proteoforms

Recent advances in applying mass spectrometry and systems biology to determine brain dynamics

Contact Info

Product

Resources

About