1
|
Zhang T, Zhao C, Li Y, Wu J, Wang F, Yu J, Wang Z, Gao Y, Zhao L, Liu Y, Yan Y, Li X, Gao H, Hu Z, Cui B, Li K. FGD5 in basal cells induces CXCL14 secretion that initiates a feedback loop to promote murine mammary epithelial growth and differentiation. Dev Cell 2024; 59:2085-2100.e9. [PMID: 38821057 DOI: 10.1016/j.devcel.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2023] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
The interactions of environmental compartments with epithelial cells are essential for mammary gland development and homeostasis. Currently, the direct crosstalk between the endothelial niche and mammary epithelial cells remains poorly understood. Here, we show that faciogenital dysplasia 5 (FGD5) is enriched in mammary basal cells (BCs) and mediates critical interactions between basal and endothelial cells (ECs) in the mammary gland. Conditional deletion of Fgd5 reduced, whereas conditional knockin of Fgd5 increased, the engraftment and expansion of BCs, regulating ductal morphogenesis in the mammary gland. Mechanistically, murine mammary BC-expressed FGD5 inhibited the transcriptional activity of activating transcription factor 3 (ATF3), leading to subsequent transcriptional activation and secretion of CXCL14. Furthermore, activation of CXCL14/CXCR4/ERK signaling in primary murine mammary stromal ECs enhanced the expression of HIF-1α-regulated hedgehog ligands, which initiated a positive feedback loop to promote the function of BCs. Collectively, these findings identify functionally important interactions between BCs and the endothelial niche that occur through the FGD5/CXCL14/hedgehog axis.
Collapse
Affiliation(s)
- Tingting Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Chenxi Zhao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yunxuan Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Feng Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinmei Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, Chinese Academy of Medical Sciences & Peking Union Medical College, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhenhe Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, Chinese Academy of Medical Sciences & Peking Union Medical College, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yang Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Luyao Zhao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ying Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yechao Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xia Li
- Marine College, Shandong University, Weihai 264200, China
| | - Huan Gao
- Marine College, Shandong University, Weihai 264200, China
| | - Zhuowei Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, Chinese Academy of Medical Sciences & Peking Union Medical College, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Bing Cui
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, Chinese Academy of Medical Sciences & Peking Union Medical College, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Ke Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
2
|
Nightingale R, Reehorst CM, Vukelic N, Papadopoulos N, Liao Y, Guleria S, Bell C, Vaillant F, Paul S, Luk IY, Dhillon AS, Jenkins LJ, Morrow RJ, Jackling FC, Chand AL, Chisanga D, Chen Y, Williams DS, Anderson RL, Ellis S, Meikle PJ, Shi W, Visvader JE, Pal B, Mariadason JM. Ehf controls mammary alveolar lineage differentiation and is a putative suppressor of breast tumorigenesis. Dev Cell 2024; 59:1988-2004.e11. [PMID: 38781975 DOI: 10.1016/j.devcel.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/03/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The transcription factor EHF is highly expressed in the lactating mammary gland, but its role in mammary development and tumorigenesis is not fully understood. Utilizing a mouse model of Ehf deletion, herein, we demonstrate that loss of Ehf impairs mammary lobuloalveolar differentiation at late pregnancy, indicated by significantly reduced levels of milk genes and milk lipids, fewer differentiated alveolar cells, and an accumulation of alveolar progenitor cells. Further, deletion of Ehf increased proliferative capacity and attenuated prolactin-induced alveolar differentiation in mammary organoids. Ehf deletion also increased tumor incidence in the MMTV-PyMT mammary tumor model and increased the proliferative capacity of mammary tumor organoids, while low EHF expression was associated with higher tumor grade and poorer outcome in luminal A and basal human breast cancers. Collectively, these findings establish EHF as a non-redundant regulator of mammary alveolar differentiation and a putative suppressor of mammary tumorigenesis.
Collapse
Affiliation(s)
- Rebecca Nightingale
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Natalia Vukelic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nikolaos Papadopoulos
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Shalini Guleria
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Caroline Bell
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - François Vaillant
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sudip Paul
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Amardeep S Dhillon
- The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Laura J Jenkins
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Riley J Morrow
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Felicity C Jackling
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Ashwini L Chand
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - David Chisanga
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yunshun Chen
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - David S Williams
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Pathology, Austin Health, Heidelberg, VIC 3084, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah Ellis
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC 3086, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jane E Visvader
- Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Bhupinder Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia.
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia; Department of Medicine, University of Melbourne, Parkville, VIC 3052, Australia.
| |
Collapse
|
3
|
Treekitkarnmongkol W, Shah V, Kai K, Katayama H, Wong J, Ladha FA, Nguyen T, Menegaz B, Lu W, Yang F, Mino B, Tang X, Gagea M, Batra H, Raso MG, Wistuba II, Krishnamurthy S, Pinder SE, Sawyer EJ, Thompson AM, Sen S. Epigenetic activation of SOX11 is associated with recurrence and progression of ductal carcinoma in situ to invasive breast cancer. Br J Cancer 2024; 131:171-183. [PMID: 38760444 PMCID: PMC11231151 DOI: 10.1038/s41416-024-02697-5] [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: 05/26/2023] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Risk of recurrence and progression of ductal carcinoma in situ (DCIS) to invasive cancer remains uncertain, emphasizing the need for developing predictive biomarkers of aggressive DCIS. METHODS Human cell lines and mouse models of disease progression were analyzed for candidate risk predictive biomarkers identified and validated in two independent DCIS cohorts. RESULTS RNA profiling of normal mammary and DCIS tissues (n = 48) revealed that elevated SOX11 expression correlates with MKI67, EZH2, and DCIS recurrence score. The 21T human cell line model of DCIS progression to invasive cancer and two mouse models developing mammary intraepithelial neoplasia confirmed the findings. AKT activation correlated with chromatin accessibility and EZH2 enrichment upregulating SOX11 expression. AKT and HER2 inhibitors decreased SOX11 expression along with diminished mammosphere formation. SOX11 was upregulated in HER2+ and basal-like subtypes (P < 0.001). Longitudinal DCIS cohort (n = 194) revealed shorter recurrence-free survival in SOX11+ than SOX11- patients (P = 0.0056 in all DCIS; P < 0.0001 in HER2+ subtype) associated with increased risk of ipsilateral breast event/IBE (HR = 1.9, 95%CI = 1.2-2.9; P = 0.003). DISCUSSION Epigenetic activation of SOX11 drives recurrence of DCIS and progression to invasive cancer, suggesting SOX11 as a predictive biomarker of IBE.
Collapse
MESH Headings
- Humans
- Female
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Animals
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- SOXC Transcription Factors/genetics
- SOXC Transcription Factors/metabolism
- Mice
- Disease Progression
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Epigenesis, Genetic
- Cell Line, Tumor
- Neoplasm Invasiveness
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Gene Expression Regulation, Neoplastic
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Enhancer of Zeste Homolog 2 Protein/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
Collapse
Affiliation(s)
- Warapen Treekitkarnmongkol
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Kazuharu Kai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroshi Katayama
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin Wong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farah A Ladha
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tristian Nguyen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Menegaz
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fei Yang
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mihai Gagea
- Department of Veterinary Medicine & Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Savitri Krishnamurthy
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Alastair M Thompson
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
4
|
Carabaña C, Sun W, Veludo Ramos C, Huyghe M, Perkins M, Maillot A, Journot R, Hartani F, Faraldo MM, Lloyd-Lewis B, Fre S. Spatially distinct epithelial and mesenchymal cell subsets along progressive lineage restriction in the branching embryonic mammary gland. EMBO J 2024; 43:2308-2336. [PMID: 38760574 PMCID: PMC11183262 DOI: 10.1038/s44318-024-00115-3] [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: 07/25/2023] [Revised: 04/06/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024] Open
Abstract
How cells coordinate morphogenetic cues and fate specification during development remains a fundamental question in organogenesis. The mammary gland arises from multipotent stem cells (MaSCs), which are progressively replaced by unipotent progenitors by birth. However, the lack of specific markers for early fate specification has prevented the delineation of the features and spatial localization of MaSC-derived lineage-committed progenitors. Here, using single-cell RNA sequencing from E13.5 to birth, we produced an atlas of matched mouse mammary epithelium and mesenchyme and reconstructed the differentiation trajectories of MaSCs toward basal and luminal fate. We show that murine MaSCs exhibit lineage commitment just prior to the first sprouting events of mammary branching morphogenesis at E15.5. We identify early molecular markers for committed and multipotent MaSCs and define their spatial distribution within the developing tissue. Furthermore, we show that the mammary embryonic mesenchyme is composed of two spatially restricted cell populations, and that dermal mesenchyme-produced FGF10 is essential for embryonic mammary branching morphogenesis. Altogether, our data elucidate the spatiotemporal signals underlying lineage specification of multipotent MaSCs, and uncover the signals from mesenchymal cells that guide mammary branching morphogenesis.
Collapse
Affiliation(s)
- Claudia Carabaña
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, C/Tajo, s/n, Villaviciosa de Odón, 28670, Madrid, Spain
| | - Wenjie Sun
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Camila Veludo Ramos
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Mathilde Huyghe
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Meghan Perkins
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Aurélien Maillot
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Robin Journot
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Fatima Hartani
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Marisa M Faraldo
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France
| | - Bethan Lloyd-Lewis
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol, BS8 1TD, UK.
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, 75248, Paris, France.
| |
Collapse
|
5
|
Tayyebi Z, Pine AR, Leslie CS. Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace. Nat Methods 2024; 21:1014-1022. [PMID: 38724693 PMCID: PMC11166566 DOI: 10.1038/s41592-024-02274-x] [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: 05/02/2022] [Accepted: 04/11/2024] [Indexed: 06/13/2024]
Abstract
Standard scATAC sequencing (scATAC-seq) analysis pipelines represent cells as sparse numeric vectors relative to an atlas of peaks or genomic tiles and consequently ignore genomic sequence information at accessible loci. Here we present CellSpace, an efficient and scalable sequence-informed embedding algorithm for scATAC-seq that learns a mapping of DNA k-mers and cells to the same space, to address this limitation. We show that CellSpace captures meaningful latent structure in scATAC-seq datasets, including cell subpopulations and developmental hierarchies, and can score transcription factor activities in single cells based on proximity to binding motifs embedded in the same space. Importantly, CellSpace implicitly mitigates batch effects arising from multiple samples, donors or assays, even when individual datasets are processed relative to different peak atlases. Thus, CellSpace provides a powerful tool for integrating and interpreting large-scale scATAC-seq compendia.
Collapse
Affiliation(s)
- Zakieh Tayyebi
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Allison R Pine
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
6
|
Gao ZJ, Fang H, Sun S, Liu SQ, Fang Z, Liu Z, Li B, Wang P, Sun SR, Meng XY, Wu Q, Chen CS. Single-cell analyses reveal evolution mimicry during the specification of breast cancer subtype. Theranostics 2024; 14:3104-3126. [PMID: 38855191 PMCID: PMC11155410 DOI: 10.7150/thno.96163] [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: 03/11/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024] Open
Abstract
Background: The stem or progenitor antecedents confer developmental plasticity and unique cell identities to cancer cells via genetic and epigenetic programs. A comprehensive characterization and mapping of the cell-of-origin of breast cancer using novel technologies to unveil novel subtype-specific therapeutic targets is still absent. Methods: We integrated 195,144 high-quality cells from normal breast tissues and 406,501 high-quality cells from primary breast cancer samples to create a large-scale single-cell atlas of human normal and cancerous breasts. Potential heterogeneous origin of malignant cells was explored by contrasting cancer cells against reference normal epithelial cells. Multi-omics analyses and both in vitro and in vivo experiments were performed to screen and validate potential subtype-specific treatment targets. Novel biomarkers of identified immune and stromal cell subpopulations were validated by immunohistochemistry in our cohort. Results: Tumor stratification based on cancer cell-of-origin patterns correlated with clinical outcomes, genomic aberrations and diverse microenvironment constitutions. We found that the luminal progenitor (LP) subtype was robustly associated with poor prognosis, genomic instability and dysfunctional immune microenvironment. However, the LP subtype patients were sensitive to neoadjuvant chemotherapy (NAC), PARP inhibitors (PARPi) and immunotherapy. The LP subtype-specific target PLK1 was investigated by both in vitro and in vivo experiments. Besides, large-scale single-cell profiling of breast cancer inspired us to identify a range of clinically relevant immune and stromal cell subpopulations, including subsets of innate lymphoid cells (ILCs), macrophages and endothelial cells. Conclusion: The present single-cell study revealed the cellular repertoire and cell-of-origin patterns of breast cancer. Combining single-cell and bulk transcriptome data, we elucidated the evolution mimicry from normal to malignant subtypes and expounded the LP subtype with vital clinical implications. Novel immune and stromal cell subpopulations of breast cancer identified in our study could be potential therapeutic targets. Taken together, Our findings lay the foundation for the precise prognostic and therapeutic stratification of breast cancer.
Collapse
Affiliation(s)
- Zhi-Jie Gao
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huan Fang
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Si-Qing Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Fang
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhou Liu
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bei Li
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei. China
| | - Ping Wang
- Medical College, Anhui University of Science and Technology, Huainan, AnHui. China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sheng-Rong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiang-Yu Meng
- Health Science Center, Hubei Minzu University, Enshi, Hubei, China
| | - Qi Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ce-Shi Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences. Kunming, Yunnan, China
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, Yunnan, China
- The Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
| |
Collapse
|
7
|
Li K, Wang B, Hu H. Research progress of SWI/SNF complex in breast cancer. Epigenetics Chromatin 2024; 17:4. [PMID: 38365747 PMCID: PMC10873968 DOI: 10.1186/s13072-024-00531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
In the past decade, numerous epigenetic mechanisms have been discovered to be associated with cancer. The mammalian SWI/SNF complex is an ATP-dependent chromatin remodeling complex whose mutations are associated with various malignancies including breast cancer. As the SWI/SNF complex has become one of the most commonly mutated complexes in cancer, targeting epigenetic mutations acquired during breast cancer progress is a potential means of improving clinical efficacy in treatment strategies. This article reviews the composition of the SWI/SNF complex, its main roles and research progress in breast cancer, and links these findings to the latest discoveries in cancer epigenomics to discuss the potential mechanisms and therapeutic potential of SWI/SNF in breast cancer.
Collapse
Affiliation(s)
- Kexuan Li
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Haolin Hu
- Breast Center, Zhongda Hospital, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing, 210009, Jiangsu, China.
| |
Collapse
|
8
|
Stanger BZ, Wahl GM. Cancer as a Disease of Development Gone Awry. ANNUAL REVIEW OF PATHOLOGY 2024; 19:397-421. [PMID: 37832945 DOI: 10.1146/annurev-pathmechdis-031621-025610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
In the 160 years since Rudolf Virchow first postulated that neoplasia arises by the same law that regulates embryonic development, scientists have come to recognize the striking overlap between the molecular and cellular programs used by cancers and embryos. Advances in cancer biology and molecular techniques have further highlighted the similarities between carcinogenesis and embryogenesis, where cellular growth, differentiation, motility, and intercellular cross talk are mediated by common drivers and regulatory networks. This review highlights the many connections linking cancer biology and developmental biology to provide a deeper understanding of how a tissue's developmental history may both enable and constrain cancer cell evolution.
Collapse
Affiliation(s)
- Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, Abramson Family Cancer Research Institute, and Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA;
| |
Collapse
|
9
|
Cui J, Christin JR, Reisz JA, Cendali FI, Sanawar R, Coutinho De Miranda M, D’Alessandro A, Guo W. Targeting ABCA12-controlled ceramide homeostasis inhibits breast cancer stem cell function and chemoresistance. SCIENCE ADVANCES 2023; 9:eadh1891. [PMID: 38039374 PMCID: PMC10691781 DOI: 10.1126/sciadv.adh1891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023]
Abstract
Cancer stem cells (CSCs) drive tumor growth, metastasis, and chemoresistance. While emerging evidence suggests that CSCs have a unique dependency on lipid metabolism, the functions and regulation of distinct lipid species in CSCs remain poorly understood. Here, we developed a stem cell factor SOX9-based reporter for isolating CSCs in primary tumors and metastases of spontaneous mammary tumor models. Transcriptomic analyses uncover that SOX9high CSCs up-regulate the ABCA12 lipid transporter. ABCA12 down-regulation impairs cancer stemness and chemoresistance. Lipidomic analyses reveal that ABCA12 maintains cancer stemness and chemoresistance by reducing intracellular ceramide abundance, identifying a CSC-associated function of ABCA subfamily transporter. Ceramide suppresses cancer stemness by inhibiting the YAP-SOX9 signaling pathway in CSCs. Increasing ceramide levels in tumors enhances their sensitivity to chemotherapy and prevents the enrichment of SOX9high CSCs. In addition, SOX9high and ABCA12high cancer cells contribute to chemoresistance in human patient-derived xenografts. These findings identify a CSC-suppressing lipid metabolism pathway that can be exploited to inhibit CSCs and overcome chemoresistance.
Collapse
Affiliation(s)
- Jihong Cui
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - John R. Christin
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Francesca Isabelle Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Rahul Sanawar
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Marcelo Coutinho De Miranda
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
10
|
Milevskiy MJ, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan WF, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. CELL GENOMICS 2023; 3:100424. [PMID: 38020976 PMCID: PMC10667557 DOI: 10.1016/j.xgen.2023.100424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
Abstract
Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.
Collapse
Affiliation(s)
- Michael J.G. Milevskiy
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hannah D. Coughlan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Serena R. Kane
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Timothy M. Johanson
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Somayeh Kordafshari
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Wing Fuk Chan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Wilcox
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rhys S. Allan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Yunshun Chen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Geoffrey J. Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E. Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
11
|
Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
Collapse
|
12
|
Gray GK, Girnius N, Kuiken HJ, Henstridge AZ, Brugge JS. Single-cell and spatial analyses reveal a tradeoff between murine mammary proliferation and lineage programs associated with endocrine cues. Cell Rep 2023; 42:113293. [PMID: 37858468 PMCID: PMC10840493 DOI: 10.1016/j.celrep.2023.113293] [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: 05/25/2023] [Revised: 08/25/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Although distinct epithelial cell types have been distinguished in glandular tissues such as the mammary gland, the extent of heterogeneity within each cell type and the degree of endocrine control of this diversity across development are incompletely understood. By combining mass cytometry and cyclic immunofluorescence, we define a rich array of murine mammary epithelial cell subtypes associated with puberty, the estrous cycle, and sex. These subtypes are differentially proliferative and spatially segregate distinctly in adult versus pubescent glands. Further, we identify systematic suppression of lineage programs at the protein and RNA levels as a common feature of mammary epithelial expansion during puberty, the estrous cycle, and gestation and uncover a pervasive enrichment of ribosomal protein genes in luminal cells elicited specifically during progesterone-dominant expansionary periods. Collectively, these data expand our knowledge of murine mammary epithelial heterogeneity and connect endocrine-driven epithelial expansion with lineage suppression.
Collapse
Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; The Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hendrik J Kuiken
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aylin Z Henstridge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
13
|
Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
Collapse
Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| |
Collapse
|
14
|
Thakur S, Haider S, Natrajan R. Implications of tumour heterogeneity on cancer evolution and therapy resistance: lessons from breast cancer. J Pathol 2023; 260:621-636. [PMID: 37587096 DOI: 10.1002/path.6158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 08/18/2023]
Abstract
Tumour heterogeneity is pervasive amongst many cancers and leads to disease progression, and therapy resistance. In this review, using breast cancer as an exemplar, we focus on the recent advances in understanding the interplay between tumour cells and their microenvironment using single cell sequencing and digital spatial profiling technologies. Further, we discuss the utility of lineage tracing methodologies in pre-clinical models of breast cancer, and how these are being used to unravel new therapeutic vulnerabilities and reveal biomarkers of breast cancer progression. © 2023 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Shefali Thakur
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| |
Collapse
|
15
|
van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MDM. Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. J Mammary Gland Biol Neoplasia 2023; 28:17. [PMID: 37450065 PMCID: PMC10349020 DOI: 10.1007/s10911-023-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.
Collapse
Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Robert B Clarke
- Manchester Breast Centre, Division of Cancer Sciences, School of Medical Sciences, University of Manchester, Manchester, UK
| | - Silvia Fre
- Institut Curie, Genetics and Developmental Biology Department, PSL Research University, CNRS UMR3215, U93475248, InsermParis, France
| | - Eva Gonzalez Suarez
- Transformation and Metastasis Laboratory, Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Iggo
- INSERM U1312, University of Bordeaux, 33076, Bordeaux, France
| | - Martin Jechlinger
- Cell Biology and Biophysics Department, EMBL, Heidelberg, Germany
- Molit Institute of Personalized Medicine, Heilbronn, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O.B. 56, 00014, Helsinki, Finland
| | - Zuzana Sumbalova Koledova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria dM Vivanco
- Cancer Heterogeneity Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Technological Park Bizkaia, 48160, Derio, Spain
| |
Collapse
|
16
|
de la O S, Yao X, Chang S, Liu Z, Sneddon JB. Single-cell chromatin accessibility of developing murine pancreas identifies cell state-specific gene regulatory programs. Mol Metab 2023; 73:101735. [PMID: 37178817 PMCID: PMC10230264 DOI: 10.1016/j.molmet.2023.101735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Numerous studies have characterized the existence of cell subtypes, along with their corresponding transcriptional profiles, within the developing mouse pancreas. The upstream mechanisms that initiate and maintain gene expression programs across cell states, however, remain largely unknown. Here, we generate single-nucleus ATAC-Sequencing data of developing murine pancreas and perform an integrated, multi-omic analysis of both chromatin accessibility and RNA expression to describe the chromatin landscape of the developing pancreas at both E14.5 and E17.5 at single-cell resolution. We identify candidate transcription factors regulating cell fate and construct gene regulatory networks of active transcription factor binding to regulatory regions of downstream target genes. This work serves as a valuable resource for the field of pancreatic biology in general and contributes to our understanding of lineage plasticity among endocrine cell types. In addition, these data identify which epigenetic states should be represented in the differentiation of stem cells to the pancreatic beta cell fate to best recapitulate in vitro the gene regulatory networks that are critical for progression along the beta cell lineage in vivo.
Collapse
Affiliation(s)
- Sean de la O
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Xinkai Yao
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sean Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Zhe Liu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Julie B Sneddon
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.
| |
Collapse
|
17
|
Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023; 164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
The advent of sequencing technologies for assessing chromosome conformations has provided a wealth of information on the organization of the 3-dimensional genome and its role in cancer progression. It is now known that changes in chromatin folding and accessibility can promote aberrant activation or repression of transcriptional programs that can drive tumorigenesis and progression in diverse cancers. This includes breast cancer, which comprises several distinct subtypes defined by their unique transcriptomes that dictate treatment response and patient outcomes. Of these, basal-like breast cancer is an aggressive subtype controlled by a pluripotency-enforcing transcriptome. Meanwhile, the more differentiated luminal subtype of breast cancer is driven by an estrogen receptor-dominated transcriptome that underlies its responsiveness to antihormone therapies and conveys improved patient outcomes. Despite the clear differences in molecular signatures, the genesis of each subtype from normal mammary epithelial cells remains unclear. Recent technical advances have revealed key distinctions in chromatin folding and organization between subtypes that could underlie their transcriptomic and, hence, phenotypic differences. These studies also suggest that proteins controlling particular chromatin states may be useful targets for treating aggressive disease. In this review, we explore the current state of understanding of chromatin architecture in breast cancer subtypes and its potential role in defining their phenotypic characteristics.
Collapse
Affiliation(s)
- Jessica R Bobbitt
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| |
Collapse
|
18
|
Single-cell chromatin landscapes of mouse skin development. Sci Data 2022; 9:741. [PMID: 36460683 PMCID: PMC9718782 DOI: 10.1038/s41597-022-01839-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
Collapse
|
19
|
Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D. Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer. Cancer Discov 2022; 12:2930-2953. [PMID: 36108220 PMCID: PMC9812400 DOI: 10.1158/2159-8290.cd-21-0865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2022] [Accepted: 09/13/2022] [Indexed: 01/21/2023]
Abstract
Systematically investigating the scores of genes mutated in cancer and discerning disease drivers from inconsequential bystanders is a prerequisite for precision medicine but remains challenging. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to study 215 recurrent "long-tail" breast cancer genes, which revealed epigenetic regulation as a major tumor-suppressive mechanism. We report that components of the BAP1 and COMPASS-like complexes, including KMT2C/D, KDM6A, BAP1, and ASXL1/2 ("EpiDrivers"), cooperate with PIK3CAH1047R to transform mouse and human breast epithelial cells. Mechanistically, we find that activation of PIK3CAH1047R and concomitant EpiDriver loss triggered an alveolar-like lineage conversion of basal mammary epithelial cells and accelerated formation of luminal-like tumors, suggesting a basal origin for luminal tumors. EpiDriver mutations are found in ∼39% of human breast cancers, and ∼50% of ductal carcinoma in situ express casein, suggesting that lineage infidelity and alveogenic mimicry may significantly contribute to early steps of breast cancer etiology. SIGNIFICANCE Infrequently mutated genes comprise most of the mutational burden in breast tumors but are poorly understood. In vivo CRISPR screening identified functional tumor suppressors that converged on epigenetic regulation. Loss of epigenetic regulators accelerated tumorigenesis and revealed lineage infidelity and aberrant expression of alveogenesis genes as potential early events in tumorigenesis. This article is highlighted in the In This Issue feature, p. 2711.
Collapse
Affiliation(s)
- Ellen Langille
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Zhibo Ma
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Minggao Liang
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Roderic Espin
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Katie Teng
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Somaieh Afiuni-Zadeh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sana Alvi
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robin H. Oh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Katelyn J. Kozma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Masahiro Narimatsu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeff C. Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Nguyen
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Seda Barutcu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rod Bremner
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sean E. Egan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - David W. Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway
| | - Jeffrey L. Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hartland W. Jackson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Erik S. Knudsen
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Miguel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Geoffrey M. Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
20
|
Aylon Y, Furth N, Mallel G, Friedlander G, Nataraj NB, Dong M, Hassin O, Zoabi R, Cohen B, Drendel V, Salame TM, Mukherjee S, Harpaz N, Johnson R, Aulitzky WE, Yarden Y, Shema E, Oren M. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis. Nat Commun 2022; 13:7199. [PMID: 36443319 PMCID: PMC9705295 DOI: 10.1038/s41467-022-34863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
Collapse
Affiliation(s)
- Yael Aylon
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Noa Furth
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Giuseppe Mallel
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gilgi Friedlander
- grid.13992.300000 0004 0604 7563Department of Life Sciences Core Facilities, The Nancy & Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nishanth Belugali Nataraj
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Meng Dong
- grid.502798.10000 0004 0561 903XDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology and University of Tuebingen, Stuttgart, Germany
| | - Ori Hassin
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Rawan Zoabi
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Benjamin Cohen
- grid.13992.300000 0004 0604 7563Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Vanessa Drendel
- grid.416008.b0000 0004 0603 4965Department of Pathology, Robert Bosch Hospital, Stuttgart, Germany
| | - Tomer Meir Salame
- grid.13992.300000 0004 0604 7563Flow Cytometry Unit, Department of Life Sciences Core Facilities, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Saptaparna Mukherjee
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nofar Harpaz
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Randy Johnson
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Walter E. Aulitzky
- grid.416008.b0000 0004 0603 4965Department of Hematology, Oncology and Palliative Medicine, Robert Bosch Hospital, Stuttgart, Germany
| | - Yosef Yarden
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Efrat Shema
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Moshe Oren
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| |
Collapse
|
21
|
Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nat Commun 2022; 13:6747. [PMID: 36347848 PMCID: PMC9643508 DOI: 10.1038/s41467-022-34413-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.
Collapse
|
22
|
Zhou J, Chen Y, Ma L, Zhou C, Zhe R. Correlation of liver and kidney indicators with foetal vital organ function. J OBSTET GYNAECOL 2022; 42:2912-2916. [PMID: 35998258 DOI: 10.1080/01443615.2022.2112939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This study aimed to investigate the correlation between indicators of liver and kidney function and foetal vital organ function. One hundred and eighty-five pregnant women who underwent cordocentesis and whose foetuses were diagnosed with abnormal foetal organ function were enrolled. The indicators of liver and kidney function were compared between foetuses with abnormal vital organ function and healthy foetuses. There was a significant difference between foetuses with and those without normal cardiovascular systems in terms of total protein, albumin, total bile acid, and creatinine levels (P < .05). A significant difference in aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) levels was observed in foetuses with and those without normal foetal urinary systems (P < .05). A difference between foetuses with normal and those without normal musculoskeletal systems was noted when comparing LDH levels. Further, there was a significant difference in gestational age and AST, alanine aminotransferase, albumin, total bilirubin, alkaline phosphatase, LDH, adenosine dehydrogenase, fibronectin, and creatinine levels between foetuses with normal versus abnormal blood systems (P < .05). Thus, hepatic and renal function indicators may be associated with abnormal foetal vital organ function.Impact statementWhat is already known on this subject? Foetal cardiac function is currently evaluated using colour Doppler ultrasound and magnetic resonance imaging in clinical practice, but there are few predictive indicators of the function of other vital organs. It is difficult to determine whether children have abnormalities in the urinary system, digestive system, nervous system, or other vital organs.What do the results of this study add? In this study, it was found that total protein, albumin, total bile acid, creatinine, aspartate aminotransferase, lactate dehydrogenase, fibronectin, alanine aminotransferase, total bilirubin, alkaline phosphatase, adenosine dehydrogenase, and other liver and kidney function indicators may be associated with foetal vital organ dysfunction. However, the forecast range of specific indicators must be further improved upon.What are the implications of these findings for clinical practice and/or further research? This study provides an additional reference for predicting foetal cardiac function.
Collapse
Affiliation(s)
- Jun Zhou
- Department of Obstetrics, Shenzhen People's Hospital, Shenzhen, China
| | - Yuying Chen
- Department of Obstetrics, Shenzhen People's Hospital, Shenzhen, China
| | - Li Ma
- Department of Obstetrics, Shenzhen People's Hospital, Shenzhen, China
| | - Cuixiang Zhou
- Department of Obstetrics, Shenzhen People's Hospital, Shenzhen, China
| | - Ruilian Zhe
- Department of Obstetrics, Shenzhen People's Hospital, Shenzhen, China
| |
Collapse
|
23
|
McMullen JRW, Soto U. Newly identified breast luminal progenitor and gestational stem cell populations likely give rise to HER2-overexpressing and basal-like breast cancers. Discov Oncol 2022; 13:38. [PMID: 35633393 PMCID: PMC9148339 DOI: 10.1007/s12672-022-00500-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022] Open
Abstract
Breast Cancer (BrC) is a common malignancy with genetically diverse subtypes. There is evidence that specific BrC subtypes originate from particular normal mammary cell populations. However, the cell populations that give rise to most BrC subtypes are unidentified. Several human breast scRNAseq datasets are available. In this research, we utilized a robust human scRNAseq dataset to identify population-specific marker genes and then identified the expression of these marker genes in specific BrC subtypes. In humans, several BrC subtypes, HER2-enriched, basal-like, and triple-negative (TN), are more common in women who have had children. This observation suggests that cell populations that originate during pregnancy give rise to these BrCs. The current human datasets have few normal parous samples, so we supplemented this research with mouse datasets, which contain mammary cells from various developmental stages. This research identified two novel normal breast cell populations that may be the origin of the basal-like and HER2-overexpressing subtypes, respectively. A stem cell-like population, SC, that expresses gestation-specific genes has similar gene expression patterns to basal-like BrCs. A novel luminal progenitor cell population and HER2-overexpressing BrCs are marked by S100A7, S100A8, and S100A9 expression. We bolstered our findings by examining SC gene expression in TN BrC scRNAseq datasets and S100A7-A9 gene expression in BrC cell lines. We discovered that several potential cancer stem cell populations highly express most of the SC genes in TN BrCs and confirmed S100A8 and A9 overexpression in a HER2-overexpressing BrC cell line. In summary, normal SC and the novel luminal progenitor cell population likely give rise to basal-like and HER2-overexpressing BrCs, respectively. Characterizing these normal cell populations may facilitate a better understanding of specific BrCs subtypes.
Collapse
Affiliation(s)
- James R W McMullen
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Ubaldo Soto
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA.
| |
Collapse
|
24
|
Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell 2022; 57:1400-1420.e7. [PMID: 35617956 DOI: 10.1016/j.devcel.2022.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.
Collapse
Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Jia-Ren Lin
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Walter L Goh
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Kaitlin Moore
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Hana K Shapiro
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Shaolin Mei
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Kurt D'Andrea
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter K Sorger
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Sandro Santagata
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA.
| |
Collapse
|
25
|
Alveolar cells in the mammary gland: lineage commitment and cell death. Biochem J 2022; 479:995-1006. [PMID: 35551601 PMCID: PMC9162463 DOI: 10.1042/bcj20210734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022]
Abstract
The mammary gland provides a spectacular example of physiological cell death whereby the cells that produce milk during lactation are removed swiftly, efficiently, and without inducing inflammation upon the cessation of lactation. The milk-producing cells arise primarily during pregnancy and comprise the alveolar lineage that is specified by signalling pathways and factors that are activated in response to pregnancy hormones. There are at least two alveolar sub-lineages, one of which is marked by the presence of binucleate cells that are especially susceptible to programmed cell death during involution. This process of post-lactational regression, or involution, is carefully orchestrated and occurs in two phases, the first results in a rapid switch in cell fate with the secretory epithelial cells becoming phagocytes whereupon they destroy dead and dying cells from milk. This reversible phase is followed by the second phase that is marked by an influx of immune cells and a remodelling of the gland to replace the alveolar cells with re-differentiated adipocytes, resulting in a return to the pre-pregnant state in preparation for any subsequent pregnancies. The mouse mammary gland provides an excellent experimental tool with which to investigate lineage commitment and the mechanisms of programmed cell death that occur in a normal physiological process. Importantly, involution has highlighted a role for lysoptosis, a mechanism of cell death that is mediated by lysosomal cathepsins and their endogenous inhibitors, serpins. In this review, I discuss alveolar lineage commitment during pregnancy and the programmed cell death pathways that destroy these cells during involution.
Collapse
|
26
|
The Mammary Gland: Basic Structure and Molecular Signaling during Development. Int J Mol Sci 2022; 23:ijms23073883. [PMID: 35409243 PMCID: PMC8998991 DOI: 10.3390/ijms23073883] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/22/2022] [Accepted: 03/30/2022] [Indexed: 01/27/2023] Open
Abstract
The mammary gland is a compound, branched tubuloalveolar structure and a major characteristic of mammals. The mammary gland has evolved from epidermal apocrine glands, the skin glands as an accessory reproductive organ to support postnatal survival of offspring by producing milk as a source of nutrition. The mammary gland development begins during embryogenesis as a rudimentary structure that grows into an elementary branched ductal tree and is embedded in one end of a larger mammary fat pad at birth. At the onset of ovarian function at puberty, the rudimentary ductal system undergoes dramatic morphogenetic change with ductal elongation and branching. During pregnancy, the alveolar differentiation and tertiary branching are completed, and during lactation, the mature milk-producing glands eventually develop. The early stages of mammary development are hormonal independent, whereas during puberty and pregnancy, mammary gland development is hormonal dependent. We highlight the current understanding of molecular regulators involved during different stages of mammary gland development.
Collapse
|
27
|
Spina E, Simundza J, Incassati A, Chandramouli A, Kugler MC, Lin Z, Khodadadi-Jamayran A, Watson CJ, Cowin P. Gpr125 is a unifying hallmark of multiple mammary progenitors coupled to tumor latency. Nat Commun 2022; 13:1421. [PMID: 35302059 PMCID: PMC8931046 DOI: 10.1038/s41467-022-28937-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
Gpr125 is an orphan G-protein coupled receptor, with homology to cell adhesion and axonal guidance factors, that is implicated in planar polarity and control of cell movements. By lineage tracing we demonstrate that Gpr125 is a highly specific marker of bipotent mammary stem cells in the embryo and of multiple long-lived unipotent basal mammary progenitors in perinatal and postnatal glands. Nipple-proximal Gpr125+ cells express a transcriptomic profile indicative of chemo-repulsion and cell movement, whereas Gpr125+ cells concentrated at invasive ductal tips display a hybrid epithelial-mesenchymal phenotype and are equipped to bind chemokine and growth factors and secrete a promigratory matrix. Gpr125 progenitors acquire bipotency in the context of transplantation and cancer and are greatly expanded and massed at the pushing margins of short latency MMTV-Wnt1 tumors. High Gpr125 expression identifies patients with particularly poor outcome within the basal breast cancer subtype highlighting its potential utility as a factor to stratify risk. Gpr125 has emerged as a specific marker of mammary stem cells and basal progenitors. Here they show that Gpr125 cells congregate at ductal tips during morphogenesis and amass at tumor margins, and that high Gpr125 predicts early tumor onset and poor outcome in basal breast cancer.
Collapse
Affiliation(s)
- Elena Spina
- Department of Cell Biology, New York University School of Medicine, New York, USA.
| | - Julia Simundza
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Angela Incassati
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Anupama Chandramouli
- Department of Cell Biology, New York University School of Medicine, New York, USA.,Department of Dermatology, New York University School of Medicine, New York, USA
| | - Matthias C Kugler
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, USA
| | - Ziyan Lin
- Department of Applied Bioinformatics, New York University School of Medicine, New York, USA
| | | | | | - Pamela Cowin
- Department of Cell Biology, New York University School of Medicine, New York, USA. .,Department of Dermatology, New York University School of Medicine, New York, USA.
| |
Collapse
|
28
|
Janghorban M, Yang Y, Zhao N, Hamor C, Nguyen TM, Zhang XHF, Rosen JM. Single-Cell Analysis Unveils the Role of the Tumor Immune Microenvironment and Notch Signaling in Dormant Minimal Residual Disease. Cancer Res 2022; 82:885-899. [PMID: 34965936 PMCID: PMC8898263 DOI: 10.1158/0008-5472.can-21-1230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/15/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022]
Abstract
Tumor dormancy is a stage in which residual cancer cells remain inactive, but regrowth of dormant cancer cells contributes to recurrence. The complex ecosystem in cancer that promotes cell survival and the factors that eventually overcome growth constraints and result in proliferation remain to be fully elucidated. Doing so may provide new insights and help identify novel strategies to prolong cancer dormancy and prevent disease recurrence. To dissect the molecular pathways and the microenvironments involved in regulation of dormancy, we utilized a novel immunocompetent transgenic model to study minimal residual disease and relapse. This model revealed a significant reorganization of cancer cell structures, stroma, and immune cells, with cancer cells showing dormant cell signatures. Single-cell RNA sequencing uncovered remodeling of myeloid and lymphoid compartments. In addition, the Jagged-1/Notch signaling pathway was shown to regulate many aspects of tumorigenesis, including stem cell development, epithelial-to-mesenchymal transition, and immune cell homeostasis during minimal residual disease. Treatment with an anti-Jagged-1 antibody inhibited the Jagged-1/Notch signaling pathway in tumor cells and the microenvironment, delaying tumor recurrence. These findings uncover a cascade of regulatory changes in the microenvironment during dormancy and identify a therapeutic strategy to undercut these changes. SIGNIFICANCE Single-cell RNA-sequencing analysis reveals dormancy-associated changes in immune and stromal cells and demonstrates a rationale to pursue Jagged-1/Notch pathway inhibition as a viable therapeutic strategy to reduce disease recurrence.
Collapse
Affiliation(s)
- Mahnaz Janghorban
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, United States
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Na Zhao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Clark Hamor
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, United States
| | - Tuan M. Nguyen
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Divisions of Renal Medicine and Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Xiang H.-F. Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, United States
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, United States
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Jeffrey M. Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
29
|
Han Y, Villarreal-Ponce A, Gutierrez G, Nguyen Q, Sun P, Wu T, Sui B, Berx G, Brabletz T, Kessenbrock K, Zeng YA, Watanabe K, Dai X. Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1. Cell Rep 2022; 38:110240. [PMID: 35021086 PMCID: PMC9894649 DOI: 10.1016/j.celrep.2021.110240] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 02/04/2023] Open
Abstract
Maintenance of undifferentiated, long-lived, and often quiescent stem cells in the basal compartment is important for homeostasis and regeneration of multiple epithelial tissues, but the molecular mechanisms that coordinately control basal cell fate and stem cell quiescence are elusive. Here, we report an epithelium-intrinsic requirement for Zeb1, a core transcriptional inducer of epithelial-to-mesenchymal transition, for mammary epithelial ductal side branching and for basal cell regenerative capacity. Our findings uncover an evolutionarily conserved role of Zeb1 in promoting basal cell fate over luminal differentiation. We show that Zeb1 loss results in increased basal cell proliferation at the expense of quiescence and self-renewal. Moreover, Zeb1 cooperates with YAP to activate Axin2 expression, and inhibition of Wnt signaling partially restores stem cell function to Zeb1-deficient basal cells. Thus, Zeb1 is a transcriptional regulator that maintains both basal cell fate and stem cell quiescence, and it functions in part through suppressing Wnt signaling.
Collapse
Affiliation(s)
- Yingying Han
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Alvaro Villarreal-Ponce
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Ting Wu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Benjamin Sui
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Geert Berx
- Molecular and Cellular Oncology Lab, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium,Cancer Research Institute Ghent, Ghent, Belgium
| | - Thomas Brabletz
- Department of Experimental Medicine, Nikolaus-Fiebiger-Center for Molecular Medicine I, University, Erlangen-Nuernberg Glueckstr. 6, 91054 Erlangen, Germany
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Yi Arial Zeng
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,Lead contact,Correspondence:
| |
Collapse
|
30
|
Liu XZ, Rulina A, Choi MH, Pedersen L, Lepland J, Takle ST, Madeleine N, Peters SD, Wogsland CE, Grøndal SM, Lorens JB, Goodarzi H, Lønning PE, Knappskog S, Molven A, Halberg N. C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer. Nat Commun 2022; 13:69. [PMID: 35013251 PMCID: PMC8748947 DOI: 10.1038/s41467-021-27734-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Epidemiological studies have established a positive association between obesity and the incidence of postmenopausal breast cancer. Moreover, it is known that obesity promotes stem cell-like properties of breast cancer cells. However, the cancer cell-autonomous mechanisms underlying this correlation are not well defined. Here we demonstrate that obesity-associated tumor formation is driven by cellular adaptation rather than expansion of pre-existing clones within the cancer cell population. While there is no correlation with specific mutations, cellular adaptation to obesity is governed by palmitic acid (PA) and leads to enhanced tumor formation capacity of breast cancer cells. This process is governed epigenetically through increased chromatin occupancy of the transcription factor CCAAT/enhancer-binding protein beta (C/EBPB). Obesity-induced epigenetic activation of C/EBPB regulates cancer stem-like properties by modulating the expression of key downstream regulators including CLDN1 and LCN2. Collectively, our findings demonstrate that obesity drives cellular adaptation to PA drives tumor initiation in the obese setting through activation of a C/EBPB dependent transcriptional network. Obesity is linked to cancer risk in post-menopausal breast cancer. At the molecular level this is governed by cellular adaption to palmitic acid through epigenetic activation of a C/EBPB-dependent transcriptional network that drives tumor formation.
Collapse
Affiliation(s)
- Xiao-Zheng Liu
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Anastasiia Rulina
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Man Hung Choi
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Line Pedersen
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Johanna Lepland
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Sina T Takle
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Noelly Madeleine
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | | | | | | | - James B Lorens
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Hani Goodarzi
- Department of Biophysics and Biochemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Per E Lønning
- Department of Clinical Science, Faculty of Medicine, University of Bergen, N-5020, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Stian Knappskog
- Department of Clinical Science, Faculty of Medicine, University of Bergen, N-5020, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway.
| |
Collapse
|
31
|
Ma Z, Lytle NK, Ramos C, Naeem RF, Wahl GM. Single-Cell Transcriptomic and Epigenetic Analyses of Mouse Mammary Development Starting with the Embryo. Methods Mol Biol 2022; 2471:49-82. [PMID: 35175591 PMCID: PMC9663269 DOI: 10.1007/978-1-0716-2193-6_3] [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] [Indexed: 06/14/2023]
Abstract
Cancers are caricatures of normal development. Yet, for most organs we are only beginning to learn about the molecular events underlying the embryonic antecedents of organogenesis and when differentiation into the cell types found in the adult actually begins. Here, we will focus on the powerful single-cell RNA sequencing and Assay for Transposase Accessible DNA by DNA sequencing (ATAC-seq) that we and others have been using to decipher the key regulators and signal transduction pathways involved in normal mammary development. We will first describe the techniques we use to identify, dissect, and isolate embryonic mammary rudiments and their constituent cells. We then describe the methods we have employed to perform single-cell RNA-seq and single-nucleus ATAC-seq using the small number of cells obtainable from mouse embryos. Finally, we will discuss the bioinformatic techniques we have used to interpret the vast amount of data obtained with these methods.
Collapse
Affiliation(s)
- Zhibo Ma
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nikki K Lytle
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Ramos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Razia F Naeem
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
32
|
Hanasoge Somasundara AV, Moss MA, Feigman MJ, Chen C, Cyrill SL, Ciccone MF, Trousdell MC, Vollbrecht M, Li S, Kendall J, Beyaz S, Wilkinson JE, Dos Santos CO. Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell Rep 2021; 37:110099. [PMID: 34879282 PMCID: PMC8719356 DOI: 10.1016/j.celrep.2021.110099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/25/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
Pregnancy reprograms mammary epithelial cells (MECs) to control their responses to pregnancy hormone re-exposure and carcinoma progression. However, the influence of pregnancy on the mammary microenvironment is less clear. Here, we used single-cell RNA sequencing to profile the composition of epithelial and non-epithelial cells in mammary tissue from nulliparous and parous female mice. Our analysis indicates an expansion of γδ natural killer T-like immune cells (NKTs) following pregnancy and upregulation of immune signaling molecules in post-pregnancy MECs. We show that expansion of NKTs following pregnancy is due to elevated expression of the antigen-presenting molecule CD1d on MECs. Loss of CD1d expression on post-pregnancy MECs, or overall lack of activated NKTs, results in mammary oncogenesis. Collectively, our findings illustrate how pregnancy-induced changes modulate the communication between MECs and the immune microenvironment and establish a causal link between pregnancy, the immune microenvironment, and mammary oncogenesis.
Collapse
MESH Headings
- Animals
- Antigens, CD1d/metabolism
- Cell Communication
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Epithelial Cells/immunology
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Genes, BRCA1
- Genes, myc
- Lymphocyte Activation
- Mammary Glands, Animal/immunology
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/immunology
- Mammary Neoplasms, Experimental/metabolism
- Mammary Neoplasms, Experimental/pathology
- Mice, Inbred BALB C
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Natural Killer T-Cells/immunology
- Natural Killer T-Cells/metabolism
- Parity
- Pregnancy
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Signal Transduction
- Tumor Microenvironment
- Mice
Collapse
Affiliation(s)
| | - Matthew A Moss
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Mary J Feigman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chen Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Macy Vollbrecht
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Siran Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - John E Wilkinson
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | | |
Collapse
|
33
|
Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| |
Collapse
|
34
|
Sinha VC, Rinkenbaugh AL, Xu M, Zhou X, Zhang X, Jeter-Jones S, Shao J, Qi Y, Zebala JA, Maeda DY, McAllister F, Piwnica-Worms H. Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast. Nat Commun 2021; 12:5024. [PMID: 34408137 PMCID: PMC8373912 DOI: 10.1038/s41467-021-25240-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
There is an unmet clinical need for stratification of breast lesions as indolent or aggressive to tailor treatment. Here, single-cell transcriptomics and multiparametric imaging applied to a mouse model of breast cancer reveals that the aggressive tumor niche is characterized by an expanded basal-like population, specialization of tumor subpopulations, and mixed-lineage tumor cells potentially serving as a transition state between luminal and basal phenotypes. Despite vast tumor cell-intrinsic differences, aggressive and indolent tumor cells are functionally indistinguishable once isolated from their local niche, suggesting a role for non-tumor collaborators in determining aggressiveness. Aggressive lesions harbor fewer total but more suppressed-like T cells, and elevated tumor-promoting neutrophils and IL-17 signaling, disruption of which increase tumor latency and reduce the number of aggressive lesions. Our study provides insight into tumor-immune features distinguishing indolent from aggressive lesions, identifies heterogeneous populations comprising these lesions, and supports a role for IL-17 signaling in aggressive progression.
Collapse
Affiliation(s)
- Vidya C. Sinha
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Amanda L. Rinkenbaugh
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Mingchu Xu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xinhui Zhou
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xiaomei Zhang
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Sabrina Jeter-Jones
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jiansu Shao
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Yuan Qi
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | | | | | - Florencia McAllister
- grid.240145.60000 0001 2291 4776Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Helen Piwnica-Worms
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| |
Collapse
|
35
|
Ranjan M, Lee O, Cottone G, Mirzaei Mehrabad E, Spike BT, Zeng Z, Yadav S, Chatterton R, Kim JJ, Clare SE, Khan SA. Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland. Breast Cancer Res 2021; 23:78. [PMID: 34344445 PMCID: PMC8330021 DOI: 10.1186/s13058-021-01455-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background The ovarian hormones estrogen and progesterone (EP) are implicated in breast cancer causation. A specific consequence of progesterone exposure is the expansion of the mammary stem cell (MSC) and luminal progenitor (LP) compartments. We hypothesized that this effect, and its molecular facilitators, could be abrogated by progesterone receptor (PR) antagonists administered in a mouse model. Methods Ovariectomized FVB mice were randomized to 14 days of treatment: sham, EP, EP + telapristone (EP + TPA), EP + mifepristone (EP + MFP). Mice were then sacrificed, mammary glands harvested, and mammary epithelial cell lineages separated by flow cytometry using cell surface markers. RNA from each lineage was sequenced and differential gene expression was analyzed using DESeq. Quantitative PCR was performed to confirm the candidate genes discovered in RNA seq. ANOVA with Tukey post hoc analysis was performed to compare relative expression. Alternative splicing events were examined using the rMATs multivariate analysis tool. Results Significant increases in the MSC and luminal mature (LM) cell fractions were observed following EP treatment compared to control (p < 0.01 and p < 0.05, respectively), whereas the LP fraction was significantly reduced (p < 0.05). These hormone-induced effects were reversed upon exposure to TPA and MFP (p < 0.01 for both). Gene Ontology analysis of RNA-sequencing data showed EP-induced enrichment of several pathways, with the largest effect on Wnt signaling in MSC, significantly repressed by PR inhibitors. In LP cells, significant induction of Wnt4 and Rankl, and Wnt pathway intermediates Lrp2 and Axin2 (confirmed by qRTPCR) were reversed by TPA and MFP (p < 0.0001). Downstream signaling intermediates of these pathways (Lrp5, Mmp7) showed similar effects. Expression of markers of epithelial-mesenchymal transition (Cdh1, Cdh3) and the induction of EMT regulators (Zeb1, Zeb2, Gli3, Snai1, and Ptch2) were significantly responsive to progesterone. EP treatment was associated with large-scale alternative splicing events, with an enrichment of motifs associated with Srsf, Esrp, and Rbfox families. Exon skipping was observed in Cdh1, Enah, and Brd4. Conclusions PR inhibition reverses known tumorigenic pathways in the mammary gland and suppresses a previously unknown effect of progesterone on RNA splicing events. In total, our results strengthen the case for reconsideration of PR inhibitors for breast cancer prevention. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01455-2.
Collapse
Affiliation(s)
- Manish Ranjan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Oukseub Lee
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Gannon Cottone
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Benjamin T Spike
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Zexian Zeng
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Shivangi Yadav
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Robert Chatterton
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - J Julie Kim
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
| | - Susan E Clare
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Seema A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
| |
Collapse
|
36
|
Zhao N, Rosen JM. Breast cancer heterogeneity through the lens of single-cell analysis and spatial pathologies. Semin Cancer Biol 2021; 82:3-10. [PMID: 34274486 DOI: 10.1016/j.semcancer.2021.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
Breast cancer ecosystems are composed of complex cell types, including tumor, stromal and immune cells, each of which can assume diverse phenotypes. Both the heterogeneous composition and spatially distinct tumor microenvironment impact breast cancer progression, treatment response and therapeutic resistance. Thus, a deeper understanding of breast cancer heterogeneity may help facilitate the development of novel therapies and improve outcomes for patients. The advent of paradigm shifting single-cell analysis and spatial pathologies allows for a comprehensive analysis of the tumor ecosystem as well as the interactions between its components at unprecedented resolution. In this review, we discuss the insights gained through single-cell analysis and spatial pathologies on breast cancer heterogeneity.
Collapse
Affiliation(s)
- Na Zhao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
37
|
Saeki K, Chang G, Kanaya N, Wu X, Wang J, Bernal L, Ha D, Neuhausen SL, Chen S. Author Correction: Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis. Commun Biol 2021; 4:892. [PMID: 34267300 PMCID: PMC8282780 DOI: 10.1038/s42003-021-02424-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Kohei Saeki
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Noriko Kanaya
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lauren Bernal
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Desiree Ha
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| |
Collapse
|
38
|
Single cell transcriptome atlas of mouse mammary epithelial cells across development. Breast Cancer Res 2021; 23:69. [PMID: 34187545 PMCID: PMC8243869 DOI: 10.1186/s13058-021-01445-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01445-4.
Collapse
|
39
|
Saeki K, Chang G, Kanaya N, Wu X, Wang J, Bernal L, Ha D, Neuhausen SL, Chen S. Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis. Commun Biol 2021; 4:660. [PMID: 34079055 PMCID: PMC8172904 DOI: 10.1038/s42003-021-02201-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/11/2021] [Indexed: 01/01/2023] Open
Abstract
The female mammary epithelium undergoes reorganization during development, pregnancy, and menopause, linking higher risk with breast cancer development. To characterize these periods of complex remodeling, here we report integrated 50 K mouse and 24 K human mammary epithelial cell atlases obtained by single-cell RNA sequencing, which covers most lifetime stages. Our results indicate a putative trajectory that originates from embryonic mammary stem cells which differentiates into three epithelial lineages (basal, luminal hormone-sensing, and luminal alveolar), presumably arising from unipotent progenitors in postnatal glands. The lineage-specific genes infer cells of origin of breast cancer using The Cancer Genome Atlas data and single-cell RNA sequencing of human breast cancer, as well as the association of gland reorganization to different breast cancer subtypes. This comprehensive mammary cell gene expression atlas ( https://mouse-mammary-epithelium-integrated.cells.ucsc.edu ) presents insights into the impact of the internal and external stimuli on the mammary epithelium at an advanced resolution.
Collapse
Affiliation(s)
- Kohei Saeki
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Noriko Kanaya
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Lauren Bernal
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Desiree Ha
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| |
Collapse
|
40
|
Slepicka PF, Somasundara AVH, Dos Santos CO. The molecular basis of mammary gland development and epithelial differentiation. Semin Cell Dev Biol 2021; 114:93-112. [PMID: 33082117 PMCID: PMC8052380 DOI: 10.1016/j.semcdb.2020.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of the molecular events underpinning the development of mammalian organ systems has been increasing rapidly in recent years. With the advent of new and improved next-generation sequencing methods, we are now able to dig deeper than ever before into the genomic and epigenomic events that play critical roles in determining the fates of stem and progenitor cells during the development of an embryo into an adult. In this review, we detail and discuss the genes and pathways that are involved in mammary gland development, from embryogenesis, through maturation into an adult gland, to the role of pregnancy signals in directing the terminal maturation of the mammary gland into a milk producing organ that can nurture the offspring. We also provide an overview of the latest research in the single-cell genomics of mammary gland development, which may help us to understand the lineage commitment of mammary stem cells (MaSCs) into luminal or basal epithelial cells that constitute the mammary gland. Finally, we summarize the use of 3D organoid cultures as a model system to study the molecular events during mammary gland development. Our increased investigation of the molecular requirements for normal mammary gland development will advance the discovery of targets to predict breast cancer risk and the development of new breast cancer therapies.
Collapse
Affiliation(s)
- Priscila Ferreira Slepicka
- Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
41
|
Twigger AJ, Khaled WT. Mammary gland development from a single cell 'omics view. Semin Cell Dev Biol 2021; 114:171-185. [PMID: 33810979 PMCID: PMC8158430 DOI: 10.1016/j.semcdb.2021.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/09/2021] [Accepted: 03/21/2021] [Indexed: 02/06/2023]
Abstract
Understanding the complexity and heterogeneity of mammary cell subpopulations is vital to delineate the mechanisms behind breast cancer development, progression and prevention. Increasingly sophisticated tools for investigating these cell subtypes has led to the development of a greater understanding of these cell subtypes, complex interplay of certain subtypes and their developmental potential. Of note, increasing accessibility and affordability of single cell technologies has led to a plethora of studies being published containing data from mammary cell subtypes and their differentiation potential in both mice and human data sets. Here, we review the different types of single cell technologies and how they have been used to improve our understanding of mammary gland development.
Collapse
Affiliation(s)
- Alecia-Jane Twigger
- Department of Pharmacology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
| | - Walid T Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
| |
Collapse
|
42
|
Regan JL, Schumacher D, Staudte S, Steffen A, Lesche R, Toedling J, Jourdan T, Haybaeck J, Mumberg D, Henderson D, Győrffy B, Regenbrecht CRA, Keilholz U, Schäfer R, Lange M. RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence. iScience 2021; 24:102618. [PMID: 34142064 PMCID: PMC8185225 DOI: 10.1016/j.isci.2021.102618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Recent data suggest that therapy-resistant quiescent cancer stem cells (qCSCs) are the source of relapse in colon cancer. Here, using colon cancer patient-derived organoids and xenografts, we identify rare long-term label-retaining qCSCs that can re-enter the cell cycle to generate new tumors. RNA sequencing analyses demonstrated that these cells display the molecular hallmarks of quiescent tissue stem cells, including expression of p53 signaling genes, and are enriched for transcripts common to damage-induced quiescent revival stem cells of the regenerating intestine. In addition, we identify negative regulators of cell cycle, downstream of p53, that we show are indicators of poor prognosis and may be targeted for qCSC abolition in both p53 wild-type and mutant tumors. These data support the temporal inhibition of downstream targets of p53 signaling, in combination with standard-of-care treatments, for the elimination of qCSCs and prevention of relapse in colon cancer. Colon tumors contain therapy-resistant quiescent cancer stem cells (qCSCs) qCSC gene expression mirrors that of quiescent stem cells of the regenerating gut qCSCs are enriched for p53 signaling genes qCSC elimination may be achieved by inhibiting downstream targets of p53 signaling
Collapse
Affiliation(s)
- Joseph L Regan
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Dirk Schumacher
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Stephanie Staudte
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany.,Department of Radiation Oncology and Radiotherapy, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Andreas Steffen
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Ralf Lesche
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Joern Toedling
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Thibaud Jourdan
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria.,Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - David Henderson
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary.,TTK Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Christian R A Regenbrecht
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,CELLphenomics GmbH, 13125 Berlin, Germany.,Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| |
Collapse
|
43
|
Tsang SM, Kim H, Oliemuller E, Newman R, Boateng NA, Guppy N, Howard BA. Sox11 regulates mammary tumour-initiating and metastatic capacity in Brca1-deficient mouse mammary tumour cells. Dis Model Mech 2021; 14:261799. [PMID: 33969421 PMCID: PMC8188883 DOI: 10.1242/dmm.046037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Little is known about the role of Sox11 in the regulation of mammary progenitor cells. Sox11 is expressed by mammary bud epithelial cells during embryonic mammary gland development and is not detected in mammary epithelial cells after birth. As Sox11 is an oncofetal gene, we investigated the effects of reducing Sox11 levels in embryonic mammary progenitor cells and found that Sox11 regulates proliferative state, stem cell activity and lineage marker expression. We also investigated the effect of reducing Sox11 levels in two transplantable Brca1-deficient oestrogen receptor-negative mouse mammary tumour cell lines, to assess whether Sox11 regulates similar functions in tumour progenitor cells. When Sox11 levels were reduced in one Brca1-deficient mammary tumour cell line that expressed both epithelial and mesenchymal markers, similar effects on proliferation, stem cell activity and expression of lineage markers to those seen in the embryonic mammary progenitor cells were observed. Orthotopic grafting of mammary tumour cells with reduced Sox11 levels led to alterations in tumour-initiating capacity, latency, expression of lineage markers and metastatic burden. Our results support a model in which tumours expressing higher levels of Sox11 have more stem and tumour-initiating cells, and are less proliferative, whereas tumours expressing lower levels of Sox11 become more proliferative and capable of morphogenetic/metastatic growth, similar to what occurs during embryonic mammary developmental progression. Summary:Brca1−/− mammary tumours expressing Sox11 at high levels have more stem- and tumour-initiating cells, and are less proliferative, whereas tumours expressing Sox11 at lower levels become more proliferative and are capable of morphogenetic/metastatic growth.
Collapse
Affiliation(s)
- Siu Man Tsang
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Hyojin Kim
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Erik Oliemuller
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naa-Anyima Boateng
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| |
Collapse
|
44
|
Watson CJ. How should we define mammary stem cells? Trends Cell Biol 2021; 31:621-627. [PMID: 33902986 DOI: 10.1016/j.tcb.2021.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/10/2023]
Abstract
Mammary stem cells (MaSCs) have been defined by cell surface marker expression and their ability to repopulate a cleared fat pad, a capacity now known to result from reprogramming upon transplantation. Furthermore, lineage-tracing studies have provoked controversy as to whether MaSCs are unipotent or bi/multipotent. Various innovative experimental approaches, including single-cell RNA sequencing (scRNA-Seq), epigenetic analyses, deep tissue and live imaging, and advanced mouse models, have provided new and unexpected insights into stem and progenitor cells; thus, it is now timely to reappraise our concept of the MaSC hierarchy. Here, I highlight misconceptions, suggest definitions of stem and progenitor cells, and propose a way forward in our search for an understanding of MaSCs.
Collapse
Affiliation(s)
- Christine J Watson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| |
Collapse
|
45
|
Muto Y, Wilson PC, Ledru N, Wu H, Dimke H, Waikar SS, Humphreys BD. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Nat Commun 2021; 12:2190. [PMID: 33850129 PMCID: PMC8044133 DOI: 10.1038/s41467-021-22368-w] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differentially accessible chromatin regions are localized to promoters and a significant proportion are closely associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF-κB that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb.
Collapse
Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Parker C Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Henrik Dimke
- Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Nephrology, Odense University Hospital, Odense, Denmark
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
46
|
Wan X, Guan S, Hou Y, Qin Y, Zeng H, Yang L, Qiao Y, Liu S, Li Q, Jin T, Qiu Y, Liu M. FOSL2 promotes VEGF-independent angiogenesis by transcriptionnally activating Wnt5a in breast cancer-associated fibroblasts. Am J Cancer Res 2021; 11:4975-4991. [PMID: 33754039 PMCID: PMC7978317 DOI: 10.7150/thno.55074] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/24/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs), a predominant component of the tumor microenvironment, contribute to aggressive angiogenesis progression. In clinical practice, traditional anti-angiogenic therapy, mainly anti-VEGF, provides extremely limited beneficial effects to breast cancer. Here, we reveal that FOS-like 2 (FOSL2), a transcription factor in breast CAFs, plays a critical role in VEGF-independent angiogenesis in stromal fibroblasts. Methods: FOSL2 and Wnt5a expression was assessed by qRT-PCR, western blotting and immunohistochemistry in primary and immortalized CAFs and clinical samples. FOSL2- or Wnt5a-silenced CAFs and FOSL2-overexpressing NFs were established to explore their proangiogenic effects. Invasion, tubule formation, three-dimensional sprouting assays, and orthotopic xenografts were conducted as angiogenesis experiments. FZD5/NF-κB/ERK signaling activation was evaluated by western blotting after blocking VEGF/VEGFR with an anti-VEGF antibody and axitinib. Dual luciferase reporter assays and chromatin immunoprecipitation were performed to test the role of FOSL2 in regulating Wnt5a expression, and Wnt5a in the serum of the patients was measured to assess its clinical diagnostic value for breast cancer patients. Results: Enhanced FOSL2 in breast CAFs was significantly associated with angiogenesis and clinical progression in patients. The supernatant from CAFs highly expressing FOSL2 strongly promoted tube formation and sprouting of human umbilical vein endothelial cells (HUVECs) in a VEGF-independent manner and angiogenesis as well as tumor growth in vivo. Mechanistically, the enhanced FOSL2 in CAFs was regulated by estrogen/cAMP/PKA signaling. Wnt5a, a direct target of FOSL2, specifically activated FZD5/NF-κB/ERK signaling in HUVECs to promote VEGF-independent angiogenesis. In addition, a high level of Wnt5a was commonly detected in the serum of breast cancer patients and closely correlated with microvessel density in breast tumor tissues, suggesting a promising clinical value of Wnt5a for breast cancer diagnostics. Conclusion: FOSL2/Wnt5a signaling plays an essential role in breast cancer angiogenesis in a VEGF-independent manner, and targeting the FOSL2/Wnt5a signaling axis in CAFs may offer a potential option for antiangiogenesis therapy.
Collapse
|
47
|
Liu Y, Guo W. SOX factors as cell-state regulators in the mammary gland and breast cancer. Semin Cell Dev Biol 2021; 114:126-133. [PMID: 33583737 DOI: 10.1016/j.semcdb.2021.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 12/27/2022]
Abstract
Emerging evidence has shown that several SOX family transcription factors are key regulators of stem/progenitor cell fates in the mammary gland. These cell-fate regulators are often upregulated in breast cancer and contribute to tumor initiation and progression. They induce lineage plasticity and the epithelial-mesenchymal transition, which promotes tumor invasion, metastasis, and therapeutic resistance. SOX factors act through modulating multiple oncogenic signaling pathways in breast cancer. In addition to the cell-autonomous functions, new evidence suggests they can shape the tumor immune microenvironment. Here, we will review the molecular and functional evidence linking SOX factors with mammary gland development and discuss how these cell-fate regulators are co-opted in breast cancer.
Collapse
Affiliation(s)
- Yu Liu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|
48
|
Chen D, Parker TM, Bhat-Nakshatri P, Chu X, Liu Y, Wang Y, Nakshatri H. Nonlinear relationship between chromatin accessibility and estradiol-regulated gene expression. Oncogene 2021; 40:1332-1346. [PMID: 33420376 DOI: 10.1038/s41388-020-01607-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022]
Abstract
Chromatin accessibility is central to basal and inducible gene expression. Through ATAC-seq experiments in estrogen receptor-positive (ER+) breast cancer cell line MCF-7 and integration with multi-omics data, we found estradiol (E2) induced chromatin accessibility changes in a small number of breast cancer-relevant E2-regulated genes. As expected, open chromatin regions associated with E2-inducible gene expression showed enrichment of estrogen response element (ERE) and those associated with E2-repressible gene expression were enriched for ERE, PBX1, and PBX3. While a significant number of open chromatin regions showed pioneer factor FOXA1 occupancy in the absence of E2, E2-treatment further enhanced FOXA1 occupancy suggesting that ER-E2 enhances chromatin occupancy of FOXA1 to a subset of E2-regulated genes. Surprisingly, promoters of 80% and enhancers of 60% of E2-inducible genes displayed closed chromatin configuration both in the absence and presence of E2. Integration of ATAC-seq data with ERα ChIP-seq data revealed that ~40% ERα binding sites in the genome are found in chromatin regions that are not accessible as per ATAC-seq. Such ERα binding regions were enriched for binding sites of multiple nuclear receptors including ER, ESRRB, ERRγ, COUP-TFII (NR2F2), RARα, EAR2 as well as traditional pioneer factors FOXA1 and GATA3. Similar data were also obtained when ERα ChIP-seq data were integrated with MNase-seq and DNase-seq data sets. In summation, our results reveal complex mechanisms of ER-E2 interaction with nucleosomes. Notably, "closed chromatin" configuration as defined by ATAC-seq or by other techniques is not necessarily associated with lack of gene expression and technical limitations may preclude ATAC-seq to demonstrate accessibility of chromatin regions that are bound by ERα.
Collapse
Affiliation(s)
- Duojiao Chen
- Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Taylor M Parker
- Departments of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Xiaona Chu
- Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yue Wang
- Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Harikrishna Nakshatri
- Departments of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Departments of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Roudebush VA Medical Center, Indianapolis, IN, 46202, USA.
| |
Collapse
|
49
|
van de Grift YBC, Heijmans N, van Amerongen R. How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b. J Mammary Gland Biol Neoplasia 2020; 25:319-335. [PMID: 33625717 PMCID: PMC7960620 DOI: 10.1007/s10911-020-09474-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
An increasing number of '-omics' datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific '-omics' datasets and thereby expand the in silico toolbox.
Collapse
Affiliation(s)
- Yorick Bernardus Cornelis van de Grift
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Nika Heijmans
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| |
Collapse
|
50
|
Dietrich N, Hoffman JA, Archer TK. BAF Complexes and the Glucocorticoid Receptor in Breast Cancers. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2020; 15:8-14. [PMID: 35128145 PMCID: PMC8813045 DOI: 10.1016/j.coemr.2020.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Breast cancers are a diverse group of diseases and are often characterized by their expression of receptors for hormones such as estrogen and progesterone. Recently another steroid hormone receptor, the glucocorticoid receptor (GR) has been shown to be a key player in breast cancer progression, metastasis, and treatment. These receptors bind to chromatin to elicit transcriptional changes within cells, which are often inhibited by the structure of chromatin itself. Chromatin remodeling proteins, such as Brahma-related gene 1 (BRG1), function to overcome this physical inhibition of transcription factor function and have been linked to many cancers including breast cancer. Recent efforts to understand the interactions of BRG1 and GR, including genomic and single cell analyses, within breast cancers may give insight into personalized medicine and other potential treatments.
Collapse
Affiliation(s)
- Nicholas Dietrich
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| | - Jackson A. Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| | - Trevor K. Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, North Carolina, United States
| |
Collapse
|