<scp>SILAC</scp>‐based quantitative proteomic analysis of gastric cancer secretome

Marimuthu, Arivusudar; Subbannayya, Yashwanth; Sahasrabuddhe, Nandini A.; Balakrishnan, Lavanya; Syed, Nazia; Sekhar, Nirujogi Raja; Katte, Teesta; Pinto, Sneha M.; Srikanth, Srinivas M.; Kumar, Praveen; Pawar, Harsh; Kashyap, Manoj Kumar; Maharudraiah, Jagadeesha; Ashktorab, Hassan; Smoot, Duane T.; Ramaswamy, Girija; Kumar, Rekha V.; Cheng, Yulan; Meltzer, Stephen J.; Roa, Juan Carlos; Chaerkady, Raghothama; Prasad, T. S. Keshava; Harsha, H. C.; Chatterjee, Aditi; Pandey, Akhilesh

doi:10.1002/prca.201200069

Cited by 59 publications

(37 citation statements)

References 64 publications

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“…Given the number of differentially secreted proteins usually found between cancerous cells and their non-neoplastic counterpart cells, it is challenging to select the right candidate biomarkers among the hundreds of candidates for further validation in clinical samples [11,18,19]. First it is not known if otherwise normal cells in the body express these same set of candidates as well.…”

Section: Resultsmentioning

confidence: 99%

The human secretome atlas initiative: Implications in health and disease conditions

Brown

Seol

Pillai

et al. 2013

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts towards secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study.

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Section: Resultsmentioning

confidence: 99%

The human secretome atlas initiative: Implications in health and disease conditions

Brown

Seol

Pillai

et al. 2013

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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“…In most cases, this leads to changes in protein abundances within a limited dynamic range, allowing robust relative quantification of matched precursor ion pairs. Ratios are more extreme, when comparing more heterogeneous samples such as secretomes from cancer cells and their non‐neoplastic counterparts . This effect is exaggerated in our SILAC analysis of different cell types from epithelial and mesenchymal origin, requiring arbitrary ratio cutoffs for assignment of proteins uniquely present in only one of the compared samples.…”

Section: Discussionmentioning

confidence: 99%

Monitoring matrix metalloproteinase activity at the epidermal–dermal interface by SILAC‐iTRAQ‐TAILS

et al. 2015

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Secreted proteases act on interstitial tissue secretomes released from multiple cell types. Thus, substrate proteins might be part of higher molecular complexes constituted by many proteins with diverse and potentially unknown cellular origin. In cell culture, these may be reconstituted by mixing native secretomes from different cell types prior to incubation with a test protease. Although current degradomics techniques could identify novel substrate proteins in these complexes, all information on the cellular origin is lost. To address this limitation, we combined iTRAQ-based terminal amine isotopic labeling of substrates (iTRAQ-TAILS) with SILAC to assign proteins to a specific cell type by MS1- and their cleavage by MS2-based quantification in the same experiment. We demonstrate the power of our newly established workflow by monitoring matrix metalloproteinase (MMP) 10 dependent cleavages in mixtures from light-labeled keratinocyte and heavy-labeled fibroblast secretomes. This analysis correctly assigned extracellular matrix components, such as laminins and collagens, to their respective cellular origins and revealed their processing in an MMP10-dependent manner. Hence, our newly devised degradomics workflow facilitates deeper insight into protease activity in complex intercellular compartments such as the epidermal-dermal interface by integrating multiple modes of quantification with positional proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001643 (http://proteomecentral.proteomexchange.org/dataset/PXD001643).

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“…So a number of studies used SILAC-based quantitative proteomics to identify proteins secreted from different kinds of cancer cells. For example, proteomic comparisons of neoplastic and nonneoplastic pancreatic cells led to the identification of more than 100 proteins that are preferentially secreted by neoplastic cells, with similar results obtained recently for gastric cancer [34,35]. SILAC-based proteomics was also used to characterize proteins secreted from metastatic and non-metastatic colon cancer cells [36].…”

Section: Silac and Biomarkers: Current Applicationsmentioning

confidence: 97%