Alteration of the protein tyrosine phosphatome in cancer

Moskal, D., Tonks, N. K., Lucito, R. (August 2015) Alteration of the protein tyrosine phosphatome in cancer. Cancer Research, 75 (Supple). Abstract 1933. ISSN 0008-5472

URL: http://cancerres.aacrjournals.org/content/75/15_Su...
DOI: 10.1158/1538-7445.am2015-1933

Abstract

While the importance of receptor tyrosine kinase pathways in cancer has and continues to be carefully studied there are more than 100 tyrosine phosphatases, either receptor or non receptor, that also play an important role in cancer development. However there has been no comprehensive study of all PTPs or the protein tyrosine phosphatome (PTPome), to identify which have a role in cancer. We as a cancer community are fortunate to have access to a wide array of data types from a number of data sources such as TCGA, where we can determine if the PTPs are mis regulated in more than 20 types of cancers, totaling close to 4,000 samples. We utilized TCGA data for all tumor types with mature data sub setting the data to analyze the PTPome for all data types including expression, methylation, copy number and sequence data where available. Our intention was to use the genomic data to identify PTPs that were important to specific cancers as well as to understand which PTPs play an important role in multiple tumor types. Presently we have studied copy number variations, expression and methylation changes in 20 different tumor types. Thus far, copy number variations, as could be expected were extremely useful to determine the primary mutations in specific tumor types as well as PTPs that are found recurrently in multiple tumor types but not as useful to identify a number of PTPs that are co-altered or altered in the same individual tumors. We were surprised to find that the methylation data was not very useful to identify alterations but could use the methylation data to corroborate other alterations found. Presently we are also using the methylation data to determine if it can be used to identify possible clinical correlations. The expression data has been very useful to identify co-altered PTPs. Interestingly we found several PTPs that are altered together (for example, PTPN6, PTPN7, PTPN18, PTPN22, PTPRC, DUSP2 and DUSP22 with an overall pvalue of 0.02 and much lower if measured between any two PTPs in this list). In addition we have found PTPs that are co-altered in a specific tumor type but possibly more interesting PTPs that are co-altered in a number of tumor types. We are now studying if our results can be used to determine if these PTPs represent multiple specific pathways that are advantageously altered in carcinogenesis.

Item Type: Paper
Additional Information: Meeting Abstract
Subjects: diseases & disorders > cancer
Publication Type > Meeting Abstract
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > kinase > tyrosine kinase
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > protein tyrosine phosphatase
CSHL Authors:
Communities: CSHL labs > Tonks lab
Depositing User: Matt Covey
Date: 1 August 2015
Date Deposited: 01 Apr 2016 20:59
Last Modified: 06 Feb 2018 15:06
URI: http://repository.cshl.edu/id/eprint/32470

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