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Romaniuk-Drapała A, Totoń E, Taube M, Idzik M, Rubiś B, Lisiak N. Breast Cancer Stem Cells and Tumor Heterogeneity: Characteristics and Therapeutic Strategies. Cancers (Basel) 2024; 16:2481. [PMID: 39001543 PMCID: PMC11240630 DOI: 10.3390/cancers16132481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Breast cancer is one of the most frequently detected malignancies worldwide. It is responsible for more than 15% of all death cases caused by cancer in women. Breast cancer is a heterogeneous disease representing various histological types, molecular characteristics, and clinical profiles. However, all breast cancers are organized in a hierarchy of heterogeneous cell populations, with a small proportion of cancer stem cells (breast cancer stem cells (BCSCs)) playing a putative role in cancer progression, and they are responsible for therapeutic failure. In different molecular subtypes of breast cancer, they present different characteristics, with specific marker profiles, prognoses, and treatments. Recent efforts have focused on tackling the Wnt, Notch, Hedgehog, PI3K/Akt/mTOR, and HER2 signaling pathways. Developing diagnostics and therapeutic strategies enables more efficient elimination of the tumor mass together with the stem cell population. Thus, the knowledge about appropriate therapeutic methods targeting both "normal" breast cancer cells and breast cancer stem cell subpopulations is crucial for success in cancer elimination.
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Affiliation(s)
- Aleksandra Romaniuk-Drapała
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
| | - Ewa Totoń
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
| | - Magdalena Taube
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
| | - Malgorzata Idzik
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
| | - Natalia Lisiak
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Collegium Pharmaceuticum, Rokietnicka Str. 3, 60-806 Poznan, Poland
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Regner MJ, Garcia-Recio S, Thennavan A, Wisniewska K, Mendez-Giraldez R, Felsheim B, Spanheimer PM, Parker JS, Perou CM, Franco HL. Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598858. [PMID: 38948758 PMCID: PMC11212881 DOI: 10.1101/2024.06.13.598858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Annotation of the cis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program between in vitro and in vivo cells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.
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Affiliation(s)
- Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Raul Mendez-Giraldez
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brooke Felsheim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Clinical and Translational Cancer Research, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00935
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Choupani E, Mahmoudi Gomari M, Zanganeh S, Nasseri S, Haji-Allahverdipoor K, Rostami N, Hernandez Y, Najafi S, Saraygord-Afshari N, Hosseini A. Newly Developed Targeted Therapies Against the Androgen Receptor in Triple-Negative Breast Cancer: A Review. Pharmacol Rev 2023; 75:309-327. [PMID: 36781219 DOI: 10.1124/pharmrev.122.000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022] Open
Abstract
Among different types of breast cancers (BC), triple-negative BC (TNBC) amounts to 15% to 20% of breast malignancies. Three principal characteristics of TNBC cells are (i) extreme aggressiveness, (ii) absence of hormones, and (iii) growth factor receptors. Due to the lack or poor expression of the estrogen receptor, human epidermal growth factor receptor 2, and progesterone receptor, TNBC is resistant to hormones and endocrine therapies. Consequently, chemotherapy is currently used as the primary approach against TNBC. Expression of androgen receptor (AR) in carcinoma cells has been observed in a subset of patients with TNBC; therefore, inhibiting androgen signaling pathways holds promise for TNBC targeting. The new AR inhibitors have opened up new therapy possibilities for BC patients carrying AR-positive TNBC cells. Our group provides a comprehensive review of the structure and function of the AR and clinical evidence for targeting the cell's nuclear receptor in TNBC. We updated AR agonists, inhibitors, and antagonists. We also presented a new era of genetic manipulating CRISPR/Cas9 and nanotechnology as state-of-the-art approaches against AR to promote the efficiency of targeted therapy in TNBC. SIGNIFICANCE STATEMENT: The lack of effective treatment for triple-negative breast cancer is a health challenge. The main disadvantages of existing treatments are their side effects, due to their nonspecific targeting. Molecular targeting of cellular receptors, such as androgen receptors, increased expression in malignant tissues, significantly improving the survival rate of breast cancer patients.
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Affiliation(s)
- Edris Choupani
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Mohammad Mahmoudi Gomari
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Saeed Zanganeh
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Sherko Nasseri
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Kaveh Haji-Allahverdipoor
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Neda Rostami
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Yaeren Hernandez
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Safa Najafi
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Neda Saraygord-Afshari
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
| | - Arshad Hosseini
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran (E.C., M.M.G., N.S.-A., A.H.); Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran (S.Z.); Department of Molecular Medicine, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran (S.N., K.H.-a.); Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran (N.R.); Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona (Y.H.); and Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (S.N.)
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