ArticlePloS one2013
Genomic interaction profiles in breast cancer reveal altered chromatin architecture.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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Who cites it
28 citing papers in PubMed, 42 citations in OpenAlex.
- A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Single-Sample Networks Reveal Intra-Cytoband Co-Expression Hotspots in Breast Cancer Subtypes.International journal of molecular sciences · 2024Article
- Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.International journal of molecular sciences · 2024Article
- Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity.Endocrinology · 2023Review
- Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications.Genes · 2023Review
- Comparative characterization of 3D chromatin organization in triple-negative breast cancers.Experimental & molecular medicine · 2022Article
- Nuclear Actin Dynamics in Gene Expression, DNA Repair, and Cancer.Results and problems in cell differentiation · 2022Article
- Review
- Article
- Profound alterations of the chromatin architecture at chromosome 11p15.5 in cells from Beckwith-Wiedemann and Silver-Russell syndromes patients.Scientific reports · 2020Article
- Article
- Hypoxia induces cancer cell-specific chromatin interactions and increases MALAT1 expression in breast cancer cells.The Journal of biological chemistry · 2019Article
- The role of 3D genome organization in disease: From compartments to single nucleotides.Seminars in cell & developmental biology · 2019Review
- Interchromosomal Translocations as a Means to Map Chromosome Territories in Breast Cancer.Cancer informatics · 2019Article
- Novel insights into chromosomal conformations in cancer.Molecular cancer · 2017Review
- Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization.BMC bioinformatics · 2017Article
- Tissue-of-origin-specific gene repositioning in breast and prostate cancer.Histochemistry and cell biology · 2016Article
- Locus-specific gene repositioning in prostate cancer.Molecular biology of the cell · 2016Article
- Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool.Frontiers in genetics · 2016Review
- C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization.Journal of cellular physiology · 2016Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene transcription can be regulated by remote enhancer regions through chromosome looping either in cis or in trans. Cancer cells are characterized by wholesale changes in long-range gene interactions, but the role that these long-range interactions play in cancer progression and metastasis is not well understood. In this study, we used IGFBP3, a gene involved in breast cancer pathogenesis, as bait in a 4C-seq experiment comparing normal breast cells (HMEC) with two breast cancer cell lines (MCF7, an ER positive cell line, and MDA-MB-231, a triple negative cell line). The IGFBP3 long-range interaction profile was substantially altered in breast cancer. Many interactions seen in normal breast cells are lost and novel interactions appear in cancer lines. We found that in HMEC, the breast carcinoma amplified sequence gene family (BCAS) 1-4 were among the top 10 most significantly enriched regions of interaction with IGFBP3. 3D-FISH analysis indicated that the translocation-prone BCAS genes, which are located on chromosomes 1, 17, and 20, are in close physical proximity with IGFBP3 and each other in normal breast cells. We also found that epidermal growth factor receptor (EGFR), a gene implicated in tumorigenesis, interacts significantly with IGFBP3 and that this interaction may play a role in their regulation. Breakpoint analysis suggests that when an IGFBP3 interacting region undergoes a translocation an additional interaction detectable by 4C is gained. Overall, our data from multiple lines of evidence suggest an important role for long-range chromosomal interactions in the pathogenesis of cancer.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.