ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2022
Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 25 citations in OpenAlex.
- AI-guided design of plectin-1-targetedJournal of nanobiotechnology · 2026Article
- GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.PLoS computational biology · 2026Article
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.Cell death discovery · 2025Review
- Chromosome compartmentalization: causes, changes, consequences, and conundrums.Trends in cell biology · 2024Review
- DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression.Cell death & disease · 2024Article
- Article
- Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken.Communications biology · 2024Article
- Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation.Nucleic acids research · 2024Article
- 3C methods in cancer research: recent advances and future prospects.Experimental & molecular medicine · 2024Review
- Alteration of chromosome structure impacts gene expressions implicated in pancreatic ductal adenocarcinoma cells.BMC genomics · 2024Article
- A comparative analysis of transcriptomics of newly diagnosed multiple myeloma: exploring drug repurposing.Frontiers in oncology · 2024Article
- Improving the prognosis of pancreatic cancer: insights from epidemiology, genomic alterations, and therapeutic challenges.Frontiers of medicine · 2023Review
- Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis.International journal of molecular sciences · 2023Article
- Three-dimensional genome structure and function.MedComm · 2023Review
- ITGA3 acts as a purity-independent biomarker of both immunotherapy and chemotherapy resistance in pancreatic cancer: bioinformatics and experimental analysis.Functional & integrative genomics · 2023Article
- 3D genomic organization in cancers.Quantitative biology (Beijing, China) · 2023Review
- Neoantigens: promising targets for cancer therapy.Signal transduction and targeted therapy · 2023Review
- Chromosome conformation capture technologies as tools to detect structural variations and their repercussion in chromatin 3D configuration.Frontiers in cell and developmental biology · 2023Review
- Developing and validating a survival prediction model based on blood exosomal ceRNA network in patients with PAAD.BMC medical genomics · 2022Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Structural variations (SVs) are the greatest source of variations in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human cancer remain technologically challenging. Here, long-read sequencing is first employed to depict the signatures of structural variations in carcinogenesis of human pancreatic ductal epithelium. Then widespread reprogramming of the 3D chromatin architecture is revealed by an in situ Hi-C technique. Integrative analyses indicate that the distribution pattern of SVs among the 3D genome is highly cell-type specific and the bulk remodeling effects of SVs in the chromatin organization partly depend on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability. Notably, complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4 are identified, and their influence on the expression of oncogenes MIR31HG, MYO5B, etc., are further elucidated from both a linear view and 3D perspective. Overall, this work provides a genome-wide resource and highlights the impact, complexity, and dynamicity of the interplay between structural variations and high-order chromatin organization, which expands the current understanding of the pathogenesis of SVs in human 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.