4.5 Review

Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Oncology

TLE3 Sustains Luminal Breast Cancer Lineage Fidelity to Suppress Metastasis

Lindsey J. Anstine et al.

Summary: Breast cancer subtypes and their phenotypes correspond to different stages of mammary epithelial cell development. The discovery of mechanisms that control lineage identity may offer new opportunities for reducing disease progression. This study reveals that the transcriptional corepressor TLE3 functions as a guardian of luminal cell fate in breast cancer, independent of the estrogen receptor. TLE3 represses the gene-expression signature associated with aggressive basal-like breast cancers, thereby reducing metastatic capacity and aggressive behaviors.

CANCER RESEARCH (2023)

Article Oncology

Lineage plasticity enables low-ER luminal tumors to evolve and gain basal-like traits

Gadisti Aisha Mohamed et al.

Summary: Stratifying breast cancer into molecular or histologic subtypes helps in making therapy decisions and predicting outcomes. Luminal-like tumors with estrogen receptor (ER) expression have better prognosis than aggressive, triple-negative or basal-like tumors. However, there is a subset of luminal-like tumors with lower ER levels that exhibit basal-like features. The plasticity of luminal-to-basal transition may be responsible for the evolution and emergence of basal-like characteristics, driven by SOX10 expression.

BREAST CANCER RESEARCH (2023)

Review Oncology

Hallmarks of Cancer: New Dimensions

Douglas Hanahan

Summary: The concept of the hallmarks of cancer is a tool for simplifying the complexity of cancer phenotypes and genotypes into basic principles. This article proposes phenotypic plasticity and disrupted differentiation as distinct hallmark capabilities, and discusses nonmutational epigenetic reprogramming and polymorphic microbiomes as enabling characteristics. Additionally, the importance of senescent cells in the tumor microenvironment is highlighted. The integrative concept of the hallmarks of cancer helps in understanding the mechanisms of cancer development and applying that knowledge to cancer medicine.

CANCER DISCOVERY (2022)

Article Oncology

CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression

Kelsey S. Johnson et al.

Summary: EMT facilitates cell migration, invasion, and metastasis in breast cancer, with a global increase in accessible chromatin and enrichment in CTCF binding motifs. The suppression of CTCF alters cellular plasticity, promoting epithelial or mesenchymal phenotypes, highlighting its role in regulating epithelial-mesenchymal plasticity and gene expression dynamics.

CANCERS (2022)

Article Oncology

Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer

Samah El Ghamrasni et al.

Summary: By analyzing primary breast tumors through whole-genome sequencing, we identified transcription factors and cis-regulatory elements associated with the development of breast cancer, providing insights into the driver mechanisms of breast cancer.

MOLECULAR CANCER RESEARCH (2022)

Editorial Material Genetics & Heredity

Cell type-specific chromatin topology and gene regulation

Douglas H. Phanstiel et al.

Summary: In this study, Winick-Ng et al. used immunoGAM to investigate chromatin structure in different brain cell types, revealing cell type-specific chromatin topologies, long gene decompaction, and the involvement of transcription factors.

TRENDS IN GENETICS (2022)

Article Multidisciplinary Sciences

Connecting high-resolution 3D chromatin organization with epigenomics

Fan Feng et al.

Summary: While large-scale 3D genome architecture is well studied, the authors developed a deep learning model CAESAR to map 1D epigenomic profiles to fine-scale 3D chromatin structures, accurately predicting structures that were missed by Hi-C datasets. They successfully imputed high-resolution 3D chromatin contact maps for 91 human tissues and cell lines, demonstrating the potential of CAESAR in coupling transcriptional regulation with 3D chromatin organization at high resolution.

NATURE COMMUNICATIONS (2022)

Article Oncology

Epigenome erosion and SOX10 drive neural crest phenotypic mimicry in triple-negative breast cancer

Jodi M. Saunus et al.

Summary: This study reveals the relevance of SOX10 gene in triple-negative breast cancer (TNBC) and its role in the intratumoral heterogeneity. The researchers found that the reprogramming of SOX10 is associated with genome-wide promoter methylation loss, leading to a more primitive phenotype in TNBC.

NPJ BREAST CANCER (2022)

Review Chemistry, Medicinal

HDAC Inhibitors for the Therapy of Triple Negative Breast Cancer

Cristina Maccallini et al.

Summary: Triple negative breast cancer is a challenging medical condition with poor response to chemotherapy, but recent studies have shown the potential of histone deacetylase inhibitors as a therapeutic strategy.

PHARMACEUTICALS (2022)

Article Multidisciplinary Sciences

Postmitotic differentiation of human monocytes requires cohesin-structured chromatin

Julia Minderjahn et al.

Summary: The study reveals the essential role of cohesin in maintaining genome architecture, controlling long-term differentiation, and activation-associated gene expression programs.

NATURE COMMUNICATIONS (2022)

Review Oncology

Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning

Daniel B. Burkhardt et al.

Summary: Phenotypic plasticity refers to the ability of cancer cells to undergo dynamic non-genetic changes in cell state, which amplifies cancer heterogeneity and promotes metastasis and therapy evasion. With the advancement of technologies to record molecular mechanisms at single-cell resolution, manifold learning techniques can effectively model cell state dynamics, resembling our understanding of the cell state landscape. State-gating therapies targeting phenotypic plasticity are anticipated to limit cancer heterogeneity, metastasis, and therapy resistance.

CANCER DISCOVERY (2022)

Article Multidisciplinary Sciences

3D chromatin remodeling potentiates transcriptional programs driving cell invasion

Benjamin Lebeau et al.

Summary: The relationship between deregulated chromatin structure and cancer progression is still unclear. Loss of CTCF in breast cancer leads to changes in chromatin structure and epigenetic programming, increasing cell invasion. However, this change in chromatin structure also increases susceptibility to mTOR inhibitors.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

Comparative characterization of 3D chromatin organization in triple-negative breast cancers

Taemook Kim et al.

Summary: This study investigated the 3D chromatin organization in different subtypes of breast cancer using in situ Hi-C technology. The results showed that the 3D architectures were significantly disrupted in breast cancer, especially in the triple-negative subtype. The disrupted structures were associated with perturbed chromatin accessibility and transcriptional dysregulation. The study also observed 3D chromatin disorganization in TNBC tissues. Furthermore, distinct tissue-specific chromatin loops were discovered by comparing normal and TNBC tissues.

EXPERIMENTAL AND MOLECULAR MEDICINE (2022)

Article Cell & Tissue Engineering

Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions

Jia Wang et al.

Summary: Studies have shown that there is extensive TAD reorganization during somatic cell reprogramming, which is correlated with gene transcription and changes in cellular identity. Manipulating TAD reorganization can promote reprogramming, with the dynamics of concentrated chromatin loops in OCT4 phase separated condensates playing a crucial role in TAD reorganization.

CELL STEM CELL (2021)

Article Genetics & Heredity

Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+breast cancer cells

Rabi Murad et al.

Summary: The study revealed increased chromatin accessibility within PPP1R1B in trastuzumab-resistant breast cancer cells, associated with its t-Darpp transcript increase, pointing to a possible mechanism for its activation in resistant cells.
Article Multidisciplinary Sciences

CTCF and EGR1 suppress breast cancer cell migration through transcriptional control of Nm23-H1

Ka Ming Wong et al.

Summary: Nm23-H1 is a metastasis suppressor protein whose expression is regulated by transcription factors like CTCF and EGR1, potentially affecting the invasion and metastasis of breast cancer.

SCIENTIFIC REPORTS (2021)

Article Multidisciplinary Sciences

Cell-type specialization is encoded by specific chromatin topologies

Warren Winick-Ng et al.

Summary: The 3D structure of chromatin is crucial for gene regulation and cell function. A new method called immunoGAM has been developed to map 3D chromatin topology in specific brain cell types at a genome-wide scale. The results show that highly specific chromatin conformations in brain cells are closely related to gene regulation mechanisms and specialized functions.

NATURE (2021)

Article Multidisciplinary Sciences

Development of small molecule inhibitors targeting PBX1 transcription signaling as a novel cancer therapeutic strategy

Yao-An Shen et al.

Summary: PBX1 is a crucial transcription factor involved in tumorigenesis, and targeting the PBX-DNA interface can effectively inhibit cancer cells with high PBX1 expression levels while sparing healthy tissues. This study demonstrates a promising strategy for treating tumors reliant on PBX1 for survival.

ISCIENCE (2021)

Article Multidisciplinary Sciences

Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling

Hao Huang et al.

Summary: Triple-negative breast cancer (TNBC) is an aggressive subtype with poor prognosis. This study characterizes super-enhancer heterogeneity and identifies genes specifically regulated by TNBC-specific super-enhancers, including FOXC1, MET, and ANLN.

NATURE COMMUNICATIONS (2021)

Article Oncology

Cancer Cells Retrace a Stepwise Differentiation Program during Malignant Progression

Sadegh Saghafinia et al.

Summary: Pancreatic neuroendocrine tumors consist of two subtypes: relatively benign islet tumors and invasive, metastasis-like primary tumors. The aggressive MLP tumors are revealed to arise from dedifferentiation of IT tumors along the developmental pathway of islet beta cells. This dedifferentiation step, separate from proliferation, leads to increased HMGB3 expression and is associated with higher-grade tumors and worse survival in patients.

CANCER DISCOVERY (2021)

Article Genetics & Heredity

A single-cell and spatially resolved atlas of human breast cancers

Sunny Z. Wu et al.

Summary: This study presents a comprehensive transcriptional atlas of the cellular architecture of breast cancer, identifying recurrent neoplastic cell heterogeneity and new immune cell populations associated with clinical outcomes. A multi-omic atlas integrates single-cell RNA sequencing, spatial transcriptomics, and immunophenotyping to stratify breast cancer into nine ecotypes with unique cellular compositions and clinical outcomes.

NATURE GENETICS (2021)

Article Multidisciplinary Sciences

Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons

Cesar Melendez-Ramirez et al.

Summary: Chromatin architecture plays a key role in influencing transcription during dopaminergic neuron differentiation, with a high abundance of long non-coding RNAs in the most downregulated transcripts. Open chromatin regions decrease during differentiation and are associated with specific functional pathways and gene-sets. The study also identifies potential transcription factors and structural nuclear proteins involved in regulating dopaminergic differentiation.

SCIENTIFIC REPORTS (2021)

Article Multidisciplinary Sciences

OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naive and primed pluripotent states in human

Xin Huang et al.

Summary: This study mapped OCT4 protein interactions in naive and primed human ESCs, revealing specific interactions with BAF subunits that promote an open chromatin architecture at different gene sets. It highlights how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naive and primed ESCs.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Single-cell transcriptional diversity is a hallmark of developmental potential

Gunsagar S. Gulati et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

Revisiting 3D chromatin architecture in cancer development and progression

Yuliang Feng et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Obstetrics & Gynecology

Endocrine therapy resistance: new insights

Jonathan T. Lei et al.

BREAST (2019)

Article Medicine, Research & Experimental

Cooperativity of co-factor NR2F2 with Pioneer Factors GATA3, FOXA1 in promoting ERα function

Guojuan Jiang et al.

THERANOSTICS (2019)

Article Biochemistry & Molecular Biology

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Hector L. Franco et al.

GENOME RESEARCH (2018)

Article Cell Biology

EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration

Nicole M. Aiello et al.

DEVELOPMENTAL CELL (2018)

Review Oncology

The Histone Acetylation Modifications of Breast Cancer and their Therapeutic Implications

Pingping Guo et al.

PATHOLOGY & ONCOLOGY RESEARCH (2018)

Article Multidisciplinary Sciences

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

Tyler Risom et al.

NATURE COMMUNICATIONS (2018)

Review Genetics & Heredity

The Birth of the 3D Genome during Early Embryonic Development

Clemens B. Hug et al.

TRENDS IN GENETICS (2018)

Article Biochemistry & Molecular Biology

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

Aleksandra Pekowska et al.

CELL SYSTEMS (2018)

Article Biochemistry & Molecular Biology

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Sarah C. Hsu et al.

MOLECULAR CELL (2017)

Article Biochemistry & Molecular Biology

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription

Clemens B. Hug et al.

Review Endocrinology & Metabolism

Minireview: The Link Between ERα Corepressors and Histone Deacetylases in Tamoxifen Resistance in Breast Cancer

Stephanie Legare et al.

MOLECULAR ENDOCRINOLOGY (2016)

Article Multidisciplinary Sciences

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Serena Nik-Zainal et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

Elisa Fiorito et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biotechnology & Applied Microbiology

GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler

Motoki Takaku et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

CDK7-Dependent Transcriptional Addiction in Triple-Negative Breast Cancer

Yubao Wang et al.

Article Multidisciplinary Sciences

Chromatin architecture reorganization during stem cell differentiation

Jesse R. Dixon et al.

NATURE (2015)

Article Oncology

JARID1B Is a Luminal Lineage-Driving Oncogene in Breast Cancer

Shoji Yamamoto et al.

CANCER CELL (2014)

Article Biochemistry & Molecular Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S. P. Rao et al.

Article Biochemistry & Molecular Biology

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

Jill M. Dowen et al.

Review Cell Biology

Mammary stem cells and the differentiation hierarchy: current status and perspectives

Jane E. Visvader et al.

GENES & DEVELOPMENT (2014)

Article Biochemistry & Molecular Biology

The pluripotency factor nanog promotes breast cancer tumorigenesis and metastasis

X. Lu et al.

ONCOGENE (2014)

Article Multidisciplinary Sciences

Estrogen Induces Global Reorganization of Chromatin Structure in Human Breast Cancer Cells

Raphael Mourad et al.

PLOS ONE (2014)

Article Cell Biology

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

Christopher J. Kemp et al.

CELL REPORTS (2014)

Review Biochemistry & Molecular Biology

A new genome-driven integrated classification of breast cancer and its implications

Sarah-Jane Dawson et al.

EMBO JOURNAL (2013)

Article Biochemistry & Molecular Biology

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

Vasiliki Theodorou et al.

GENOME RESEARCH (2013)

Article Biochemistry & Molecular Biology

The genomic landscape of cohesin-associated chromatin interactions

Laura E. DeMare et al.

GENOME RESEARCH (2013)

Article Multidisciplinary Sciences

Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

Michael J. Zeitz et al.

PLOS ONE (2013)

Article Biochemistry & Molecular Biology

Slug and Sox9 Cooperatively Determine the Mammary Stem Cell State

Wenjun Guo et al.

Article Biochemistry & Molecular Biology

The Forkhead Box Transcription Factor FOXC1 Promotes Breast Cancer Invasion by Inducing Matrix Metalloprotease 7 (MMP7) Expression

Steven T. Sizemore et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Multidisciplinary Sciences

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Elphege P. Nora et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Sox2 expression in breast tumours and activation in breast cancer stem cells

O. Leis et al.

ONCOGENE (2012)

Article Medicine, Research & Experimental

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

Brian D. Lehmann et al.

JOURNAL OF CLINICAL INVESTIGATION (2011)

Review Endocrinology & Metabolism

Minireview: Basal-Like Breast Cancer: From Molecular Profiles to Targeted Therapies

Daniel J. Toft et al.

MOLECULAR ENDOCRINOLOGY (2011)

Article Genetics & Heredity

FOXA1 is a key determinant of estrogen receptor function and endocrine response

Antoni Hurtado et al.

NATURE GENETICS (2011)

Article Biochemistry & Molecular Biology

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

Daan Peric-Hupkes et al.

MOLECULAR CELL (2010)

Article Biochemistry & Molecular Biology

Biological reprogramming in acquired resistance to endocrine therapy of breast cancer

H. Aguilar et al.

ONCOGENE (2010)

Article Biotechnology & Applied Microbiology

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Guoliang Li et al.

GENOME BIOLOGY (2010)

Article Biophysics

Spatial allelic imbalance of BCL2 genes and chromosome 18 territories in nonneoplastic and neoplastic cervical squamous epithelium

Thorsten Wiech et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2009)

Article Cell Biology

Genome-Wide Reduction in H3K9 Acetylation During Human Embryonic Stem Cell Differentiation

Jana Krejci et al.

JOURNAL OF CELLULAR PHYSIOLOGY (2009)

Review Medicine, Research & Experimental

The basics of epithelial-mesenchymal transition

Raghu Kalluri et al.

JOURNAL OF CLINICAL INVESTIGATION (2009)

Article Multidisciplinary Sciences

An oestrogen-receptor-α-bound human chromatin interactome

Melissa J. Fullwood et al.

NATURE (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

An extended transcriptional network for pluripotency of embryonic stem cells

Jonghwan Kim et al.

News Item Cell & Tissue Engineering

Global transcription in pluripotent embryonic stem cells

Sol Efroni et al.

CELL STEM CELL (2008)

Article Oncology

Epithelial mesenchymal transition traits in human breast cancer cell lines

T. Blick et al.

CLINICAL & EXPERIMENTAL METASTASIS (2008)

Article Biochemistry & Molecular Biology

Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements

You Fu Pan et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Multidisciplinary Sciences

The cohesin ring concatenates sister DNA molecules

Christian H. Haering et al.

NATURE (2008)

Article Multidisciplinary Sciences

CTCF physically links cohesin to chromatin

Eric D. Rubio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Genetics & Heredity

Recruitment to the nuclear periphery can alter expression of genes in human cells

Lee E. Finlan et al.

PLOS GENETICS (2008)

Article Multidisciplinary Sciences

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

Xiaohui Xie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

Tae Hoon Kim et al.

Article Biochemistry & Molecular Biology

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

BE Bernstein et al.

Article Biochemistry & Molecular Biology

Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation

H Niwa et al.

Article Multidisciplinary Sciences

Repeated observation of breast tumor subtypes in independent gene expression data sets

T Sorlie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemistry & Molecular Biology

Chromosomal cohesin forms a ring

S Gruber et al.

Article Multidisciplinary Sciences

Capturing chromosome conformation

J Dekker et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

Molecular portraits of human breast tumours

CM Perou et al.

NATURE (2000)