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Article

Searchable High-Resolution 2D Gel Proteome of the Human Colon Crypt

Supporting Info

Bhavinkumar B. Patel,^†^# Xin-Ming Li,^†^# Maketa P. Dixon,^† Elena L. Blagoi,^† Steven H. Seeholzer,^† Yibai Chen,^† C. Glenn Miller,^† Yin A. He,^† Mazell Tetruashvily,^† Anam H. Chaudhry,^† Eileen Ke,^† Joan Xie,^† Harry Cooper,^‡ Alfonso Bellacosa,^§ Margie L. Clapper,^§ Bruce M. Boman, Tao Zhang, Samuel Litwin,^§ Eric A. Ross,^§ Peggy Conrad, James A. Crowell, Levy Kopelovich, Alfred Knudson,^§ and Anthony T. Yeung*^†

Division of Basic Science, Medical Science, and Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania, 19111, Division of Genetic and Preventive Medicine, Thomas Jefferson University, 1025 Walnut Street, Philadelphia, Pennsylvania, 19107 UCSF Colorectal Cancer Prevention Program, University of California at San Francisco, San Francisco, California 94115, and Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892

J. Proteome Res., 2007, 6 (6), pp 2232–2238

DOI: 10.1021/pr060641e

Publication Date (Web): April 20, 2007

†

Division of Basic Science, Fox Chase Cancer Center.

These authors contributed equally to this manuscript.

‡

Division of Medical Science, Fox Chase Cancer Center.

Division of Population Science, Fox Chase Cancer Center.

Thomas Jefferson University.

University of California at San Francisco.

National Cancer Institute.

To whom correspondence should be addressed: Anthony T. Yeung, Ph.D., Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497. Phone, 215-728-2488; fax, 215-728-3647; e-mail, AT_Yeung@fccc.edu.

Abstract

We seek alterations in protein patterns at the earliest possible step on the path to cancer, namely, in cells of the target tissue from normal persons versus the corresponding normally appearing cells from persons who are heterozygous for mutation in a tumor suppressor gene that predisposes strongly to carcinoma in that tissue. To begin a systematic comparison of the proteomes of cells from normal and from neoplastic colons, we have undertaken the isolation of human colon crypts that are derived from the normal-appearing mucosa of left (descending) colon of patients with sporadic colorectal cancer. Two-dimensional (2D) gel electrophoresis is a proteomic approach that excels in the resolution of protein isoforms. Here, we document the practicality of this approach with human samples using gels of three overlapping pH ranges. For the first time, about 800 nonredundant proteins and 900 isoforms from purified human colonic crypts were identified, permitting an assessment of the contributions of protein isoforms. These interactive, searchable, hyperlink-enabled proteome maps and gene ontology analyses will facilitate future studies to discover the earliest markers and intervention targets during progression to colon cancer.

Keywords: proteomics • colonic crypts • morphologically normal

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