Proteomic Strategies to Characterize Signaling Pathways

Harsha, H. C.; Pinto, Sneha M.; Pandey, Akhilesh

doi:10.1007/978-1-62703-392-3_16

Cited by 11 publications

(8 citation statements)

References 95 publications

(53 reference statements)

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“…Another SILAC-based study led to the discovery that CXCL10, a cytokine, was upregulated in TbetaRII knockout mammary fibroblasts involved in breast tumour cell proliferation and migration 36 . This proteomic technique has also been used in the study of signalling 37 and drug resistance 38 . Recently Tyanova et al discovered a signature of 12 proteins in different breast cancer subtypes in their SILAC-based comprehensive breast cancer study 14 .…”

Section: Quantitative Mass Spectrometry-based Proteomic Strategies Inmentioning

confidence: 99%

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer

et al. 2017

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Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us to identify protein signatures or protein biomarkers, which can be used to improve cancer diagnosis, prognosis and treatment. For example, mass spectrometry-based proteomics has been used in breast cancer research for over two decades to elucidate protein function. Breast cancer is a heterogeneous group of diseases with distinct molecular features that are reflected in tumour characteristics and clinical outcomes. Compared with all other subtypes of breast cancer, triple-negative breast cancer is perhaps the most distinct in nature and heterogeneity. In this review, we provide an introductory overview of the application of advanced proteomic technologies to triple-negative breast cancer research.

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Section: Quantitative Mass Spectrometry-based Proteomic Strategies Inmentioning

confidence: 99%

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer

et al. 2017

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“…Peptides were mixed with beads in a 1:1 ratio and incubated at RT for 30 min. Further, peptides were washed with 80% ACN in 3% TFA, then eluted using a 4% ammonia solution and immediately neutralized with 4% TFA . Eluted peptides were vacuum dried, resuspended in 30 μL 0.1% TFA, and desalted using C 18 Stage Tips .…”

Section: Methodsmentioning

confidence: 99%

Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats

et al. 2015

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To gain insights into the toxicity induced by the nerve agent VX, an MS-based phosphoproteomic analysis was carried out on the piriform cortex region of brains from VX-treated rats. Using isobaric tag based TMT labeling followed by titanium dioxide enrichment strategy, we identified 9975 unique phosphosites derived from 3287 phosphoproteins. Temporal changes in the phosphorylation status of peptides were observed over a time period of 24 h in rats exposed to a 1× LD50, intravenous (i.v.) dose with the most notable changes occurring at the 1 h postexposure time point. Five major functional classes of proteins exhibited changes in their phosphorylation status: (i) ion channels/transporters, including ATPases, (ii) kinases/phosphatases, (iii) GTPases, (iv) structural proteins, and (v) transcriptional regulatory proteins. This study is the first quantitative phosphoproteomic analysis of VX toxicity in the brain. Understanding the toxicity and compensatory signaling mechanisms will improve the understanding of the complex toxicity of VX in the brain and aid in the elucidation of novel molecular targets that would be important for development of improved countermeasures. All MS data have been deposited in the ProteomeXchange with identifier PXD001184 (http://proteomecentral.proteomexchange.org/dataset/PXD001184).

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“…Bununla birlikte doku ve biyolojik sıvılar gibi farklı biyolojik numunelerde uygulanabilir olması önemli bir avantaj sağlar. SILAC ve diğer etiketli yöntemler ilaç hedeflerinin, ilaç direncinin, hücre döngüsü gelişiminin ya da sinyal yolaklarının araştırıldığı çalışmalarda kullanılabilmektedir (6,98).…”

Section: Etiketli Yöntemlerunclassified

An Overview of The Phosphoproteomic Workflow

Sürmen¹,

Sürmen²,

Pençe³

2018

Experimed

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İnsan genom projesinin tamamlanmasıyla birlikte-protein kodlayan yaklaşık 20.000 gen ortaya çıkarılmış, bu genlere ait mutasyonlar ve ekspresyon farklılıkları ortaya konulmuştur (1). İnsan genomunun haritalanması hastalıkların moleküler mekanizmasının anlaşılmasında, erken tespitinde ve tedavisinde büyük umut kaynağı olmuştur. Kapsamlı genomik çalışmalarla tespit edilen mutasyonlar ve ekspresyon farklılıkları çeşitli hastalıklarda rol oynayan sinyal yolaklarına olan bakış açımızın gelişmesini sağlarken kanser gibi moleküler mekanizması kompleks olan heterojen hastalıkların araştırılmasında sadece genomik analizlerin yeterli olmadığı da anlaşılmıştır. Bununla birlikte yaşanan genomik devrim; protein, transkript, metabolit veya lipid profillerinin biyoniformatik destekle topluca değerlendirildiği genom sonrası "omik" platformlarının gelişmesine zemin hazırlamıştır (2, 3). Hücrenin fonksiyonel makromolekülleri olan proteinlerin; fizyolojik ve patolojik süreçlerdeki rolünü daha iyi anlamaya yönelik yapılan proteomik çalışmalar son onbeş yıl içerisinde özellikle kanser araştırmalarında önem kazanmıştır (4, 5). Post translasyonel değişiklikler (PTM'ler) ve izoform varyasyon nedeniyle genomun aksine çok daha çeşitli olan proteom aynı zamanda dinamik yapıdadır. Genellikle geri dönüşümlü modifikasyonlar olan fosforilasyonlar, proteinleri aktif ya da inaktif formlarına dönüştürürler. Buna bağlı olarak sinyal iletimi, büyüme ve apoptoz gibi hücresel süreçlerin düzenlenmesinde rol oynayan fosforilasyonlar,

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Proteomic Strategies to Characterize Signaling Pathways

Cited by 11 publications

References 95 publications

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer

Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats

An Overview of The Phosphoproteomic Workflow

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