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Zabala M, Lobo NA, Antony J, Heitink LS, Gulati GS, Lam J, Parashurama N, Sanchez K, Adorno M, Sikandar SS, Kuo AH, Qian D, Kalisky T, Sim S, Li L, Dirbas FM, Somlo G, Newman A, Quake SR, Clarke MF. LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis. Cell Stem Cell 2020; 27:284-299.e8. [DOI: 10.1016/j.stem.2020.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 03/25/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022]
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Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 2020; 367:405-411. [PMID: 31974247 PMCID: PMC7694873 DOI: 10.1126/science.aax0249] [Citation(s) in RCA: 377] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/03/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential-the number of expressed genes per cell-and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.
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Affiliation(s)
- Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shaheen S Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anoop Manjunath
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anjan Bharadwaj
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark J Berger
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Francisco Ilagan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angera H Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert W Hsieh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shang Cai
- School of Life Sciences, Westlake University, Zhejiang Province, China
| | - Maider Zabala
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ferenc A Scheeren
- Department of Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Neethan A Lobo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94305, USA
| | - Frederick M Dirbas
- Department of Surgery, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael F Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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Sikandar SS, Kuo AH, Kalisky T, Cai S, Zabala M, Hsieh RW, Lobo NA, Scheeren FA, Sim S, Qian D, Dirbas FM, Somlo G, Quake SR, Clarke MF. Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis. Nat Commun 2017; 8:1669. [PMID: 29162812 PMCID: PMC5698470 DOI: 10.1038/s41467-017-01666-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/06/2017] [Indexed: 12/12/2022] Open
Abstract
Previous studies have proposed that epithelial to mesenchymal transition (EMT) in breast cancer cells regulates metastasis, stem cell properties and chemo-resistance; most studies were based on in vitro culture of cell lines and mouse transgenic cancer models. However, the identity and function of cells expressing EMT-associated genes in normal murine mammary gland homeostasis and human breast cancer still remains under debate. Using in vivo lineage tracing and triple negative breast cancer (TNBC) patient derived xenografts we demonstrate that the repopulating capacity in normal mammary epithelial cells and tumorigenic capacity in TNBC is independent of expression of EMT-associated genes. In breast cancer, while a subset of cells with epithelial and mesenchymal phenotypes have stem cell activity, in many cells that have lost epithelial characteristics with increased expression of mesenchymal genes, have decreased tumor-initiating capacity and plasticity. These findings have implications for the development of effective therapeutic agents targeting tumor-initiating cells.
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Affiliation(s)
- Shaheen S Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Angera H Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Tomer Kalisky
- Department of Bioengineering, 318 Campus Drive, Stanford, CA, 94305, USA
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Shang Cai
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Maider Zabala
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Robert W Hsieh
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Neethan A Lobo
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Ferenc A Scheeren
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
- Department of Medical Oncology, Leiden University Medical Center, Leiden, RC, 2300, The Netherlands
| | - Sopheak Sim
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Frederick M Dirbas
- Department of Surgery, Stanford University School of Medicine, Stanford Cancer Institute, 875 Blake Wilbur Drive, Rm CC2235, Stanford, CA, 94305, USA
| | - George Somlo
- City of Hope Comprehensive Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Stephen R Quake
- Department of Bioengineering, 318 Campus Drive, Stanford, CA, 94305, USA
| | - Michael F Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
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Chen YK, Bonaldi T, Cuomo A, Del Rosario JR, Hosfield DJ, Kanouni T, Kao SC, Lai C, Lobo NA, Matuszkiewicz J, McGeehan A, O’Connell SM, Shi L, Stafford JA, Stansfield RK, Veal JM, Weiss MS, Yuen NY, Wallace MB. Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS Med Chem Lett 2017; 8:869-874. [PMID: 28835804 DOI: 10.1021/acsmedchemlett.7b00220] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in the regulation of chromatin-related processes. Herein, we describe our discovery of a series of potent KDM4 inhibitors that are both cell permeable and antiproliferative in cancer models. The modulation of histone H3K9me3 and H3K36me3 upon compound treatment was verified by homogeneous time-resolved fluorescence assay and by mass spectroscopy detection. Optimization of the series using structure-based drug design led to compound 6 (QC6352), a potent KDM4 family inhibitor that is efficacious in breast and colon cancer PDX models.
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Affiliation(s)
- Young K. Chen
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Tiziana Bonaldi
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Alessandro Cuomo
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Joselyn R. Del Rosario
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - David J. Hosfield
- Ben
May Department for Cancer Research, University of Chicago, 929 East
57th Street, Chicago, Illinois 60637, United States
| | - Toufike Kanouni
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Shih-chu Kao
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Chon Lai
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Neethan A. Lobo
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Jennifer Matuszkiewicz
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Andrew McGeehan
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Shawn M. O’Connell
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Lihong Shi
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Jeffrey A. Stafford
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Ryan K. Stansfield
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - James M. Veal
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Michael S. Weiss
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Natalie Y. Yuen
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Michael B. Wallace
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
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Parashurama N, Lobo NA, Ito K, Mosley AR, Habte FG, Zabala M, Smith BR, Lam J, Weissman IL, Clarke MF, Gambhir SS. Remodeling of endogenous mammary epithelium by breast cancer stem cells. Stem Cells 2013; 30:2114-27. [PMID: 22899386 DOI: 10.1002/stem.1205] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Poorly regulated tissue remodeling results in increased breast cancer risk, yet how breast cancer stem cells (CSC) participate in remodeling is unknown. We performed in vivo imaging of changes in fluorescent, endogenous duct architecture as a metric for remodeling. First, we quantitatively imaged physiologic remodeling of primary branches of the developing and regenerating mammary tree. To assess CSC-specific remodeling events, we isolated CSC from MMTV-Wnt1 (mouse mammary tumor virus long-term repeat enhancer driving Wnt1 oncogene) breast tumors, a well studied model in which tissue remodeling affects tumorigenesis. We confirm that CSC drive tumorigenesis, suggesting a link between CSC and remodeling. We find that normal, regenerating, and developing gland maintain a specific branching pattern. In contrast, transplantation of CSC results in changes in the branching patterns of endogenous ducts while non-CSC do not. Specifically, in the presence of CSC, we identified an increased number of branches, branch points, ducts which have greater than 40 branches (5/33 for CSC and 0/39 for non-CSC), and histological evidence of increased branching. Moreover, we demonstrate that only CSC implants invade into surrounding stroma with structures similar to developing mammary ducts (nine for CSC and one for non-CSC). Overall, we demonstrate a novel approach for imaging physiologic and pathological remodeling. Furthermore, we identify unique, CSC-specific, remodeling events. Our data suggest that CSC interact with the microenvironment differently than non-CSC, and that this could eventually be a therapeutic approach for targeting CSC.
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Affiliation(s)
- Natesh Parashurama
- Molecular Imaging Program @Stanford, Department of Radiology, Division of Nuclear Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR. Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab Chip 2009; 9:1365-70. [PMID: 19417902 PMCID: PMC4123551 DOI: 10.1039/b819648f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful assay used to probe DNA-protein interactions. Traditional methods of implementing this assay are lengthy, cumbersome and require a large number of cells, making it difficult to study rare cell types such as certain cancer and stem cells. We have designed a microfluidic device to perform sensitive ChIP analysis on low cell numbers in a rapid, automated fashion while preserving the specificity of the assay. Comparing ChIP results for two modified histone protein targets, we showed our automated microfluidic ChIP (AutoChIP) from 2,000 cells to be comparable to that of conventional ChIP methods using 50,000-500,000 cells. This technology may provide a solution to the need for a high sensitivity, rapid, and automated ChIP assay, and in doing so facilitate the use of ChIP for many interesting and valuable applications.
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Affiliation(s)
- Angela R Wu
- Dept. of Bioengineering, Stanford University, Stanford and Howard Hughes Medical Institute, CA 94305, USA
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Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas FM, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature 2009; 458:780-3. [PMID: 19194462 DOI: 10.1038/nature07733] [Citation(s) in RCA: 1818] [Impact Index Per Article: 121.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 04/09/2009] [Accepted: 12/18/2008] [Indexed: 02/08/2023]
Abstract
The metabolism of oxygen, although central to life, produces reactive oxygen species (ROS) that have been implicated in processes as diverse as cancer, cardiovascular disease and ageing. It has recently been shown that central nervous system stem cells and haematopoietic stem cells and early progenitors contain lower levels of ROS than their more mature progeny, and that these differences are critical for maintaining stem cell function. We proposed that epithelial tissue stem cells and their cancer stem cell (CSC) counterparts may also share this property. Here we show that normal mammary epithelial stem cells contain lower concentrations of ROS than their more mature progeny cells. Notably, subsets of CSCs in some human and murine breast tumours contain lower ROS levels than corresponding non-tumorigenic cells (NTCs). Consistent with ROS being critical mediators of ionizing-radiation-induced cell killing, CSCs in these tumours develop less DNA damage and are preferentially spared after irradiation compared to NTCs. Lower ROS levels in CSCs are associated with increased expression of free radical scavenging systems. Pharmacological depletion of ROS scavengers in CSCs markedly decreases their clonogenicity and results in radiosensitization. These results indicate that, similar to normal tissue stem cells, subsets of CSCs in some tumours contain lower ROS levels and enhanced ROS defences compared to their non-tumorigenic progeny, which may contribute to tumour radioresistance.
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Affiliation(s)
- Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
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Abstract
Cancers originally develop from normal cells that gain the ability to proliferate aberrantly and eventually turn malignant. These cancerous cells then grow clonally into tumors and eventually have the potential to metastasize. A central question in cancer biology is, which cells can be transformed to form tumors? Recent studies elucidated the presence of cancer stem cells that have the exclusive ability to regenerate tumors. These cancer stem cells share many characteristics with normal stem cells, including self-renewal and differentiation. With the growing evidence that cancer stem cells exist in a wide array of tumors, it is becoming increasingly important to understand the molecular mechanisms that regulate self-renewal and differentiation because corruption of genes involved in these pathways likely participates in tumor growth. This new paradigm of oncogenesis has been validated in a growing list of tumors. Studies of normal and cancer stem cells from the same tissue have shed light on the ontogeny of tumors. That signaling pathways such as Bmi1 and Wnt have similar effects in normal and cancer stem cell self-renewal suggests that common molecular pathways regulate both populations. Understanding the biology of cancer stem cells will contribute to the identification of molecular targets important for future therapies.
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Affiliation(s)
- Neethan A Lobo
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA.
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