Applications of iTRAQ and TMT Labeling Techniques to the Study of Neurodegenerative Diseases

Li, Kelu; Chen, Zichao; Zhang, Yonggang; Yang, Xinglong

doi:10.2174/1389203721666201103085704

Cited by 11 publications

(5 citation statements)

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“…Proteins display a wide range of variation in abundance, making low-abundant proteins easily masked by high-abundant proteins with similar mass or chemical properties (Smith et al, 2019). Comparative proteomics methods based on mass spectrometry, such as Label-free, iTRAQ, SWATH, PRM, allow us to identify proteins with significantly changed expression levels under specific conditions on a large scale (Bourmaud et al, 2016;Li et al, 2020). Joint analysis of proteomics and other omics provide more useful information for exploring the mechanisms of wool bending and hair follicle development.…”

Section: Introductionmentioning

confidence: 99%

Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending

Liu

Ding

Liu³

et al. 2022

Front. Cell Dev. Biol.

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Zhongwei goat is a unique Chinese native goat breed for excellent lamb fur. The pattern of flower spikes of the lamb fur was significantly reduced due to the reduction of the bending of the hair strands with growth. In order to explore the molecular mechanism underlying hair bending with growth, we performed the comprehensive analysis of transcriptome and proteome of skins from 45-days, 108-days and 365-days goat based on TMT-based quantitative proteomics and RNA-seq methods. In the three comparison groups, 356, 592 and 282 differentially expressed proteins (DEPs) were screened, respectively. KEGG pathway analysis indicated that DEPs were significantly enriched in a set of signaling pathways related to wool growth and bending, such as ECM-receptor interaction, PI3K-Akt signaling pathway, PPAR signaling pathway, protein digestion and absorption, and metabolic pathways. In addition, 20 DEPs abundance of goat skin at three development stages were examined by PRM method, which validated the reliability of proteomic data. Among them, KRT and collagen alpha family may play an important role in the development of goat hair follicle and wool bending. COL6A1, COL6A2, CRNN, TNC and LOC102178129 were identified as candidate genes based on combined analysis of transcriptome and proteome data and PRM quantification. Our results identify the differential expressed proteins as well as pathways related to the wool bending of Zhongwei goats and provide a theoretical basis for further revealing the molecular mechanism underlying wool bending of goats.

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Section: Introductionmentioning

confidence: 99%

Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending

Liu

Ding

Liu³

et al. 2022

Front. Cell Dev. Biol.

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“…Together with the technological advancement on LC-MS and bioinformatics software, it is easier to identify qualified proteins in these days. Regarding the quantification, the Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) has been widely used in mammalian studies [ 46 ]. On the other hand, the application in fishes is still very limited.…”

Section: Resultsmentioning

confidence: 99%

A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration

Ulhaq

Tse

2021

Biomolecules

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Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.

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“…Given that there is a limited understanding of AMH-associated secondary hypertension ( 24 , 25 ), this study mainly investigated the proteome profiles of AMH as well as adjacent control tissues using iTRAQ quantitative analysis, an advanced method with maximum protein coverage and precise quantitation ( 26 – 28 ). It turned out that 782 kinds of differentially expressed proteins were identified in AMH tissue, including 357 types of upregulated proteins and 425 types of downregulated proteins.…”

Section: Discussionmentioning

confidence: 99%

Clinical identification of expressed proteins in adrenal medullary hyperplasia detected with hypertension

Wang

Lai

et al. 2022

Front. Endocrinol.

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BackgroundHypertension remains a challenging public health problem worldwide, and adrenal gland-related diseases are one class of the major causes for secondary hypertension. Among them, one relatively rare pattern is adrenal hyperplastic hypertension caused by adrenal medullary hyperplasia (AMH), leading to excessive secretion of autonomic catecholamine. Given that the pathological changes of adrenal medulla are not well correlated to the onset and even severity of secondary hypertension, the molecular basis why some AMH patients are accompanied with hypertension remains unclear and is worth exploring.AimsFor this reason, this study aims at investigating differentially expressed proteins in clinical AMH tissue, with special focus on the potential contribution of these differentially expressed proteins to AMH development, in order to have a better understanding of mechanisms how AMH leads to secondary hypertension to some extent.Methods and resultsTo this end, AMH specimens were successfully obtained and verified through computed tomography (CT) and haematoxylin-eosin (HE) staining. Proteomic analyses of AMH and control tissues revealed 782 kinds of differentially expressed proteins. Compared with the control tissue, there were 357 types of upregulated proteins and 425 types of downregulated proteins detected in AMH tissue. Of interest, these differentially expressed proteins were significantly enriched in 60 gene ontology terms (P < 0.05), including 28 biological process terms, 14 molecular function terms, and 18 cellular component terms. Pathway analysis further indicated that 306 proteins exert their functions in at least one Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Western blotting showed enhanced expression of phenylethanolamine N- methyltransferase (PNMT), myelin protein zero (MPZ), and Ras-related protein Rab-3C (RAB3C), and reduced expression of cluster of differentiation 36 (CD36) observed in AMH tissue in comparison with controls.ConclusionsClinical AMH specimens display a different proteomic profile compared to control tissue. Of note, PNMT, MPZ, RAB3C, and CD36 are found to differentially expressed and can be potential targets for AMH, providing a theoretical basis for mechanistic exploration of AMH along with hypertension.

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Applications of iTRAQ and TMT Labeling Techniques to the Study of Neurodegenerative Diseases

Cited by 11 publications

References 0 publications

Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending

Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending

A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration

Clinical identification of expressed proteins in adrenal medullary hyperplasia detected with hypertension

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