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Zhou Y, Li T, Choppavarapu L, Fang K, Lin S, Jin VX. Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations. Nat Commun 2024; 15:8310. [PMID: 39333113 PMCID: PMC11436782 DOI: 10.1038/s41467-024-52440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 09/06/2024] [Indexed: 09/29/2024] Open
Abstract
An integration of 3D chromatin structure and gene expression at single-cell resolution has yet been demonstrated. Here, we develop a computational method, a multiomic data integration (MUDI) algorithm, which integrates scHi-C and scRNA-seq data to precisely define the 3D-regulated and biological-context dependent cell subpopulations or topologically integrated subpopulations (TISPs). We demonstrate its algorithmic utility on the publicly available and newly generated scHi-C and scRNA-seq data. We then test and apply MUDI in a breast cancer cell model system to demonstrate its biological-context dependent utility. We find the newly defined topologically conserved associating domain (CAD) is the characteristic single-cell 3D chromatin structure and better characterizes chromatin domains in single-cell resolution. We further identify 20 TISPs uniquely characterizing 3D-regulated breast cancer cellular states. We reveal two of TISPs are remarkably resemble to high cycling breast cancer persister cells and chromatin modifying enzymes might be functional regulators to drive the alteration of the 3D chromatin structures. Our comprehensive integration of scHi-C and scRNA-seq data in cancer cells at single-cell resolution provides mechanistic insights into 3D-regulated heterogeneity of developing drug-tolerant cancer cells.
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Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Lavanya Choppavarapu
- Division of Biostatistics, The Medical College of Wisconsin, Milwaukee, WI, USA
- MCW Cancer Center, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kun Fang
- Division of Biostatistics, The Medical College of Wisconsin, Milwaukee, WI, USA
- MCW Cancer Center, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, USA
| | - Victor X Jin
- Division of Biostatistics, The Medical College of Wisconsin, Milwaukee, WI, USA.
- MCW Cancer Center, The Medical College of Wisconsin, Milwaukee, WI, USA.
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Das P, San Martin R, Hong T, McCord RP. Rearrangement of 3D genome organization in breast cancer epithelial - mesenchymal transition and metastasis organotropism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609227. [PMID: 39229150 PMCID: PMC11370564 DOI: 10.1101/2024.08.23.609227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Breast cancer cells exhibit organotropism during metastasis, showing preferential homing to certain organs such as bone, lung, liver, and brain. One potential explanation for this organotropic behavior is that cancer cells gain properties that enable thriving in certain microenvironments. Such specific metastatic traits may arise from gene regulation at the primary tumor site. Spatial genome organization plays a crucial role in oncogenic transformation and progression, but the extent to which chromosome architecture contributes to organ-specific metastatic traits is unclear. This work characterizes chromosome architecture changes associated with organotropic metastatic traits. By comparing a collection of genomic data from different subtypes of localized and lung metastatic breast cancer cells with both normal and cancerous lung cells, we find important trends of genomic reorganization. The most striking differences in 3D genome compartments segregate cell types according to their epithelial vs. mesenchymal status. This EMT compartment signature occurs at genomic regions distinct from transcription-defined EMT signatures, suggesting a separate layer of regulation. Specifically querying organotropism, we find 3D genome changes consistent with adaptations needed to survive in a new microenvironment, with lung metastatic breast cells exhibiting compartment switch signatures that shift the genome architecture to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state. TCGA patient data reveals gene expression changes concordant with these organ-permissive compartment changes. These results suggest that genome architecture provides an additional level of cell fate specification informing organotropism and enabling survival at the metastatic site.
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Zhou Y, He Z, Li T, Choppavarapu L, Hu X, Cao R, Leone GW, Kahn M, Jin VX. 3D Chromatin Alteration by Disrupting β-Catenin/CBP Interaction Is Enriched with Insulin Signaling in Pancreatic Cancer. Cancers (Basel) 2024; 16:2202. [PMID: 38927910 PMCID: PMC11201718 DOI: 10.3390/cancers16122202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/02/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The therapeutic potential of targeting the β-catenin/CBP interaction has been demonstrated in a variety of preclinical tumor models with a small molecule inhibitor, ICG-001, characterized as a β-catenin/CBP antagonist. Despite the high binding specificity of ICG-001 for the N-terminus of CBP, this β-catenin/CBP antagonist exhibits pleiotropic effects. Our recent studies found global changes in three-dimensional (3D) chromatin architecture in response to disruption of the β-catenin/CBP interaction in pancreatic cancer cells. However, an understanding of how the functional crosstalk between the antagonist and the β-catenin/CBP interaction affects changes in 3D chromatin architecture and, thereby, gene expression and downstream effects remains to be elucidated. Here, we perform Hi-C analyses on canonical and patient-derived pancreatic cancer cells before and after treatment with ICG-001. In addition to global alteration of 3D chromatin domains, we unexpectedly identify insulin signaling genes enriched in the altered chromatin domains. We further demonstrate that the chromatin loops associated with insulin signaling genes are significantly weakened after ICG-001 treatment. We finally elicit the deletion of a looping of IRS1-a key insulin signaling gene-significantly impeding pancreatic cancer cell growth, indicating that looping-mediated insulin signaling might act as an oncogenic pathway to promote pancreatic cancer progression. Our work shows that targeting aberrant insulin chromatin looping in pancreatic cancer might provide a therapeutic benefit.
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Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (Y.Z.); (Z.H.); (T.L.)
| | - Zhijing He
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (Y.Z.); (Z.H.); (T.L.)
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (Y.Z.); (Z.H.); (T.L.)
| | - Lavanya Choppavarapu
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaohui Hu
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
| | - Ruifeng Cao
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Gustavo W. Leone
- MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael Kahn
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA;
| | - Victor X. Jin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Choppavarapu L, Fang K, Liu T, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584872. [PMID: 38559097 PMCID: PMC10979939 DOI: 10.1101/2024.03.13.584872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Current knowledge in three-dimensional (3D) chromatin regulation in normal and disease states was mostly accumulated through Hi-C profiling in in vitro cell culture system. The limitations include failing to recapitulate disease-specific physiological properties and often lacking clinically relevant disease microenvironment. In this study, we conduct tissue-specific Hi-C profiling in a pilot cohort of 12 breast tissues comprising of two normal tissues (NTs) and ten ER+ breast tumor tissues (TTs) including five primary tumors (PTs), and five tamoxifen-treated recurrent tumors (RTs). We find largely preserved compartments, highly heterogeneous topological associated domains (TADs) and intensively variable chromatin loops among breast tumors, demonstrating 3D chromatin-regulated breast tumor heterogeneity. Further cross-examination identifies RT-specific looping-mediated biological pathways and suggests CA2, an enhancer-promoter looping (EPL)-mediated target gene within the bicarbonate transport metabolism pathway, might play a role in driving the tamoxifen resistance. Remarkably, the inhibition of CA2 not only impedes tumor growth both in vitro and in vivo , but also reverses chromatin looping. Our study thus yields significant mechanistic insights into the role and clinical relevance of 3D chromatin architecture in breast cancer endocrine resistance.
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Abdulaziz O, Khan FR, Alharthi NS, Alhuthali HM, Hazazi A, Alzahrani HA, Gharib AF, Alsalmi OA, Hawsawi NM, Alhazmi AY. Computational insights into overcoming resistance mechanisms in targeted therapies for advanced breast cancer: focus on EGFR and HER2 co-inhibition. J Biomol Struct Dyn 2024:1-12. [PMID: 38234016 DOI: 10.1080/07391102.2024.2301766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024]
Abstract
In the present study, the formation of a heterodimer involving both epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) has been explored as a potential therapeutic mechanism to inhibit the progression of breast cancer. Virtual screening using molecular docking resulted in the three hit compounds (ZINC08382411, ZINC08382438, and ZINC08382292) with minimum binding scores and commonly binding to both receptors. Further, MD simulation analysis of these complexes illustrated the high stability of these compounds with EGFR and HER2. RMSD showed that ZINC08382411 displayed the most stable RMSD of 2 - 3 Å when bound to both receptors, suggesting to have strong compatibility with the active site of the receptor. Hydrogen bond analysis showed that ZINC08382411 forms the maximum number of H-bonds (2 to 3) in both EGFR and HER2 bound complexes, with the highest occupancy of 62% and 79%, respectively. Binding free energy calculation showed that ZINC08382411 possesses maximum affinity towards both the receptors with ΔGbind = -129.628 and -164.063 kJ/mol, respectively. This approach recognizes the significance of EGFR and HER2 in breast cancer development and aims to disrupt their collaborative signaling, which is known to promote the antagonistic behavior of cancer cells. By focusing on this EGFR/HER2 heterodimer, the study offers a promising avenue for identifying a potential candidate (ZINC08382411) that may inhibit breast cancer cell growth and potentially improve patient outcomes. The study's findings may contribute to the ongoing efforts to advance breast cancer treatment strategies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Osama Abdulaziz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Taif University, Taif Province, Kingdom of Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Science,College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Nahed S Alharthi
- Department of Medical Laboratory, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Kingdom of Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | - Hind A Alzahrani
- Department of Basic Sciences, College of Applied of Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Amal F Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Ohud A Alsalmi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Nahed M Hawsawi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Abdulfattah Y Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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Zhou Y, Li T, He Z, Choppavarapu L, Hu X, Cao R, Leone GW, Kahn M, Jin VX. Reprogramming of 3D chromatin domains by antagonizing the β-catenin/CBP interaction attenuates insulin signaling in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566585. [PMID: 38013997 PMCID: PMC10680786 DOI: 10.1101/2023.11.10.566585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The therapeutic potential of targeting the β-catenin/CBP interaction has been demonstrated in a variety of preclinical tumor models with a small molecule inhibitor, ICG-001, characterized as a β-catenin/CBP antagonist. Despite the high binding specificity of ICG-001 for the N-terminus of CBP, this β-catenin/CBP antagonist exhibits pleiotropic effects. Our recent studies found global changes in three-dimensional (3D) chromatin architecture in response to disruption of the β-catenin/CBP interaction in pancreatic cancer cells. However, an understanding of the functional crosstalk between antagonizing the β-catenin/CBP interaction effect changes in 3D chromatin architecture and thereby gene expression and downstream effects remains to be elucidated. Here we perform Hi-C analyses on canonical and patient-derived pancreatic cancer cells before and after the treatment with ICG-001. In addition to global alteration of 3D chromatin domains, we unexpectedly identify insulin signaling genes enriched in the altered chromatin domains. We further demonstrate the chromatin loops associated with insulin signaling genes are significantly weakened after ICG-001 treatment. We finally elicit the deletion of a looping of IRS1, a key insulin signaling gene, significantly impede pancreatic cancer cell growth, indicating that looping-mediated insulin signaling might act as an oncogenic pathway to promote pancreatic cancer progression. Our work shows that targeting aberrant insulin chromatin looping in pancreatic cancer might provide a therapeutic benefit.
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Jiang C, Zhu Y, Chen H, Lin J, Xie R, Li W, Xue J, Chen L, Chen X, Xu S. Targeting c-Jun inhibits fatty acid oxidation to overcome tamoxifen resistance in estrogen receptor-positive breast cancer. Cell Death Dis 2023; 14:653. [PMID: 37803002 PMCID: PMC10558541 DOI: 10.1038/s41419-023-06181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
Tamoxifen-based endocrine therapy remains a major adjuvant therapy for estrogen receptor (ER)-positive breast cancer (BC). However, many patients develop tamoxifen resistance, which results in recurrence and poor prognosis. Herein, we show that fatty acid oxidation (FAO) was activated in tamoxifen-resistant (TamR) ER-positive BC cells by performing bioinformatic and functional studies. We also reveal that CPT1A, the rate-limiting enzyme of FAO, was significantly overexpressed and that its enzymatic activity was enhanced in TamR cells. Mechanistically, the transcription factor c-Jun was activated by JNK kinase-mediated phosphorylation. Activated c-Jun bound to the TRE motif in the CPT1A promoter to drive CPT1A transcription and recruited CBP/P300 to chromatin, catalysing histone H3K27 acetylation to increase chromatin accessibility, which ensured more effective transcription of CPT1A and an increase in the FAO rate, eliminating the cytotoxic effects of tamoxifen in ER-positive BC cells. Pharmacologically, inhibiting CPT1A enzymatic activity with the CPT1 inhibitor etomoxir or blocking c-Jun phosphorylation with a JNK inhibitor restored the tamoxifen sensitivity of TamR cells. Clinically, high levels of phosphorylated c-Jun and CPT1A were observed in ER-positive BC tissues in patients with recurrence after tamoxifen therapy and were associated with poor survival. These results indicate that the assessment and targeting of the JNK/c-Jun-CPT1A-FAO axis will provide promising insights for clinical management, increased tamoxifen responses and improved outcomes for ER-positive BC patients.
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Affiliation(s)
- Cen Jiang
- Central Laboratory, Fujian Medical University Union Hospital, 350001, Fuzhou, China
| | - Youzhi Zhu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 350212, Fuzhou, China
| | - Huaying Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
| | - Junyu Lin
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
| | - Ruiwang Xie
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
| | - Weiwei Li
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
| | - Jiajie Xue
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 350212, Fuzhou, China
| | - Ling Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 350212, Fuzhou, China
| | - Xiangjin Chen
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China.
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 350212, Fuzhou, China.
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, 350005, Fuzhou, China.
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 350212, Fuzhou, China.
- Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Fuzhou, China.
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Zhou Y, Li T, Choppavarapu L, Jin VX. Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560193. [PMID: 37873257 PMCID: PMC10592853 DOI: 10.1101/2023.09.29.560193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
An integration of 3D chromatin structure and gene expression at single-cell resolution has yet been demonstrated. Here, we develop a computational method, a multiomic data integration (MUDI) algorithm, which integrates scHi-C and scRNA-seq data to precisely define the 3D-regulated and biological-context dependent cell subpopulations or topologically integrated subpopulations (TISPs). We demonstrate its algorithmic utility on the publicly available and newly generated scHi-C and scRNA-seq data. We then test and apply MUDI in a breast cancer cell model system to demonstrate its biological-context dependent utility. We found the newly defined topologically conserved associating domain (CAD) is the characteristic single-cell 3D chromatin structure and better characterizes chromatin domains in single-cell resolution. We further identify 20 TISPs uniquely characterizing 3D-regulated breast cancer cellular states. We reveal two of TISPs are remarkably resemble to high cycling breast cancer persister cells and chromatin modifying enzymes might be functional regulators to drive the alteration of the 3D chromatin structures. Our comprehensive integration of scHi-C and scRNA-seq data in cancer cells at single-cell resolution provides mechanistic insights into 3D-regulated heterogeneity of developing drug-tolerant cancer cells.
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Massa C, Seliger B. Combination of multiple omics techniques for a personalized therapy or treatment selection. Front Immunol 2023; 14:1258013. [PMID: 37828984 PMCID: PMC10565668 DOI: 10.3389/fimmu.2023.1258013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023] Open
Abstract
Despite targeted therapies and immunotherapies have revolutionized the treatment of cancer patients, only a limited number of patients have long-term responses. Moreover, due to differences within cancer patients in the tumor mutational burden, composition of the tumor microenvironment as well as of the peripheral immune system and microbiome, and in the development of immune escape mechanisms, there is no "one fit all" therapy. Thus, the treatment of patients must be personalized based on the specific molecular, immunologic and/or metabolic landscape of their tumor. In order to identify for each patient the best possible therapy, different approaches should be employed and combined. These include (i) the use of predictive biomarkers identified on large cohorts of patients with the same tumor type and (ii) the evaluation of the individual tumor with "omics"-based analyses as well as its ex vivo characterization for susceptibility to different therapies.
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Affiliation(s)
- Chiara Massa
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Brandenburg an der Havel, Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Brandenburg an der Havel, Germany
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
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Comparative characterization of 3D chromatin organization in triple-negative breast cancers. Exp Mol Med 2022; 54:585-600. [PMID: 35513575 PMCID: PMC9166756 DOI: 10.1038/s12276-022-00768-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a malignant cancer subtype with a high risk of recurrence and an aggressive phenotype compared to other breast cancer subtypes. Although many breast cancer studies conducted to date have investigated genetic variations and differential target gene expression, how 3D chromatin architectures are reorganized in TNBC has been poorly elucidated. Here, using in situ Hi-C technology, we characterized the 3D chromatin organization in cells representing five distinct subtypes of breast cancer (including TNBC) compared to that in normal cells. We found that the global and local 3D architectures were severely disrupted in breast cancer. TNBC cell lines (especially BT549 cells) showed the most dramatic changes relative to normal cells. Importantly, we detected CTCF-dependent TNBC-susceptible losses/gains of 3D chromatin organization and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulation. In TNBC tissue, 3D chromatin disorganization was also observed relative to the 3D chromatin organization in normal tissues. We observed that the perturbed local 3D architectures found in TNBC cells were partially conserved in TNBC tissues. Finally, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. In this study, we elucidated the characteristics of the 3D chromatin organization in breast cancer relative to normal cells/tissues at multiple scales and identified associations between disrupted structures and various epigenetic features and transcriptomes. Collectively, our findings reveal important 3D chromatin structural features for future diagnostic and therapeutic studies of TNBC. The 3D architecture of the genome is dramatically altered in an aggressive form of breast cancer, leading to changes in the regulation of gene expression that can fuel tumor growth. A team from South Korea, led by Hyeong-Gon Moon of Seoul National University College of Medicine and Daeyoup Lee of the Korea Advanced Institute of Science and Technology, Daejeon, detailed how chromosomes are positioned and folded within the nucleus of cell liness from five different subtypes of breast cancer. They found that triple-negative breast cancers displayed the most extreme reorganization of their genomes, a pattern also observed in biopsy tissues taken from patients with this subtype of cancer. Knowledge of these conformational changes could inform future efforts to develop therapies and diagnostics for patients with triple-negative breast tumors.
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11
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Mapping nucleosome and chromatin architectures: A survey of computational methods. Comput Struct Biotechnol J 2022; 20:3955-3962. [PMID: 35950186 PMCID: PMC9340519 DOI: 10.1016/j.csbj.2022.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
With ever-growing genomic sequencing data, the data variabilities and the underlying biases of the sequencing technologies pose significant computational challenges ranging from the need for accurately detecting the nucleosome positioning or chromatin interaction to the need for developing normalization methods to eliminate systematic biases. This review mainly surveys the computational methods for mapping the higher-resolution nucleosome and higher-order chromatin architectures. While a detailed discussion of the underlying algorithms is beyond the scope of our survey, we have discussed the methods and tools that can detect the nucleosomes in the genome, then demonstrated the computational methods for identifying 3D chromatin domains and interactions. We further illustrated computational approaches for integrating multi-omics data with Hi-C data and the advance of single-cell (sc)Hi-C data analysis. Our survey provides a comprehensive and valuable resource for biomedical scientists interested in studying nucleosome organization and chromatin structures as well as for computational scientists who are interested in improving upon them.
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Li J, Fang K, Choppavarapu L, Yang K, Yang Y, Wang J, Cao R, Jatoi I, Jin VX. Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance. Clin Epigenetics 2021; 13:175. [PMID: 34535185 PMCID: PMC8447690 DOI: 10.1186/s13148-021-01167-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. METHODS In this study, we conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. Furthermore, we performed in silico functional analysis on 3D-growth-specific looping genes and to compare patient outcomes with or without endocrinal therapy. Finally, we performed 3C/RT-qPCR validations in 3D spheroids and 3D-FISH confirmations in organoids of breast cancer patient tissues. RESULTS We found that chromatin structures have experienced drastic changes during the 3D culture growth of BC cells although there is not much change in the quantity of chromatin domains. We also observed that the strengths of looping genes were statistically different between 2D monolayers and 3D spheroids. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected genes in Hippo relevant pathways with enhanced looping in organoids of breast cancer patient tissues. CONCLUSIONS Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer. Our analyses suggest that the strengthened looping-mediated Hippo relevant pathways may contribute to endocrine therapy resistance in breast cancer patients.
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Affiliation(s)
- Jingwei Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, 410006, Hunan, People's Republic of China
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Kun Fang
- Program of Biomedical Engineering, UTHSA-UTSA Joint Graduate Program, San Antonio, TX, 78229, USA
| | - Lavanya Choppavarapu
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Ke Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Yini Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Minimally Invasive Surgical Center, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, 0310, Montebello, Oslo, Norway
| | - Ruifeng Cao
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Ismail Jatoi
- Department of Surgery, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
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