Blog
About

  • Record: found
  • Abstract: found
  • Article: not found

Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon

Read this article at

ScienceOpenPublisherPMC
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Alpha-methylacyl-coenzyme A racemase (AMACR) regulates peroxisomal β-oxidation of phytol-derived, branched-chain fatty acids from red meat and dairy products — suspected risk factors for colon carcinoma (CCa). AMACR was first found overexpressed in prostate cancer but not in benign glands and is now an established diagnostic marker for prostate cancer. Aberrant expression of AMACR was recently reported in Cca; however, little is known about how this gene is abnormally activated in cancer. By using a panel of immunostained-laser-capture-microdissected clinical samples comprising the entire colon adenoma–carcinoma sequence, we show that deregulation of AMACR during colon carcinogenesis involves two nonrandom events, resulting in the mutually exclusive existence of double-deletion at CG3 and CG10 and deletion of CG12-16 in a newly identified CpG island within the core promoter of AMACR. The double-deletion at CG3 and CG10 was found to be a somatic lesion. It existed in histologically normal colonic glands and tubular adenomas with low AMACR expression and was absent in villous adenomas and all CCas expressing variable levels of AMACR. In contrast, deletion of CG12-16 was shown to be a constitutional allele with a frequency of 43% in a general population. Its prevalence reached 89% in moderately differentiated CCas strongly expressing AMACR but only existed at 14% in poorly differentiated CCas expressing little or no AMACR. The DNA sequences housing these deletions were found to be putative cis-regulatory elements for Sp1 at CG3 and CG10, and ZNF202 at CG12-16. Chromatin immunoprecipitation, siRNA knockdown, gel shift assay, ectopic expression, and promoter analyses supported the regulation by Sp1 and ZNF202 of AMACR gene expression in an opposite manner. Our findings identified key in vivo events and novel transcription factors responsible for AMACR regulation in CCas and suggested these AMACR deletions may have diagnostic/prognostic value for colon carcinogenesis.

      Author Summary

      Men consuming high amounts of red meat and dairy products are at a higher risk of developing colon and prostate cancer. Alpha-methylacyl-coenzyme A racemase (AMACR) is an enzyme that helps to break down fat from these foods to produce energy. An increase in the utilization of energy from fat is a hallmark of many cancers including colon and prostate cancers. Indeed, the AMACR gene was first found to be abnormally active in prostate cancers, and its abnormal expression has become a diagnostic marker for the cancer. However, little is known about how AMACR becomes activated in cancer cells. Here, we show that AMACR is also highly expressed in certain stages of colon cancer, though not all stages. A close examination of the AMACR gene in a panel of normal and progressively malignant colon tissues reveals that deletions of specific sequences in the AMACR gene may trigger its abnormal expression during the evolution of colon cancer. We also identify unique proteins known as “transcription factors” that normally bind to these deleted sequences to maintain normal expression of the gene. Finally, we report a new deletion variant of the AMACR gene in the general population that may influence the course of colon carcinogenesis.

      Related collections

      Most cited references 49

      • Record: found
      • Abstract: not found
      • Article: not found

      Primer3 on the WWW for general users and for biologist programmers.

       H Skaletsky,  S Rozen (1999)
        Bookmark
        • Record: found
        • Abstract: not found
        • Article: not found

        A genetic model for colorectal tumorigenesis.

          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          MatInspector and beyond: promoter analysis based on transcription factor binding sites.

          Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
            Bookmark

            Author and article information

            Affiliations
            [1 ]Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
            [2 ]Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
            [3 ]Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
            [4 ]Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
            [5 ]Department of Pathology and Laboratory Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
            [6 ]Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
            [7 ]Center for Genome Information, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
            [8 ]Cancer Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
            University of Illinois at Urbana-Champaign, United States of America
            Author notes
            [¤]

            Current address: Department of Pathology and Laboratory Medicine, University of Utah, Salt Lake City, Utah, United States of America

            Conceived and designed the experiments: XZ SMH. Performed the experiments: XZ IL. Analyzed the data: XZ IL RD MM SMH. Contributed reagents/materials/analysis tools: IL MPR RD ZJ SMH. Wrote the paper: XZ IL SMH.

            Contributors
            Role: Editor
            Journal
            PLoS Genet
            plos
            plosgen
            PLoS Genetics
            Public Library of Science (San Francisco, USA )
            1553-7390
            1553-7404
            January 2009
            January 2009
            16 January 2009
            : 5
            : 1
            2613032
            19148275
            08-PLGE-RA-0801R3
            10.1371/journal.pgen.1000334
            (Editor)
            Zhang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Counts
            Pages: 15
            Categories
            Research Article
            Cell Biology/Gene Expression
            Genetics and Genomics/Gene Expression
            Molecular Biology
            Oncology
            Pathology/Immunology

            Genetics

            Comments

            Comment on this article