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Chen X, Yu Y, Zheng H, Yang M, Wang C, Cai Q, Zhang W, Jiang F, Zhu Y, Yang H, Zhang T, Zhou Z. Single-cell transcriptome analysis reveals dynamic changes of the preclinical A549 cancer models, and the mechanism of dacomitinib. Eur J Pharmacol 2023; 960:176046. [PMID: 37708985 DOI: 10.1016/j.ejphar.2023.176046] [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: 05/09/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The in vitro A549 cells, and A549 xenografts in nude mouse, were two commonly used models for anti-cancer drug discovery. However, the biological and molecular characteristics of these two classic models, and also the dynamic transcriptome changes after dacomitinib exposure remains elusive. We performed single-cell RNA sequencing to define the transcriptome profile at single-cell resolution, and processed tumor samples for bulk RNA and protein analysis to validate the differently expressed genes. Transcriptome profiling revealed that the in vitro A549 cells are heterogeneous. The minimal subpopulation of the in vitro A549 cells, which were characterized by the signature of response to unfolded protein, became the overriding subpopulation of the xenografts. The EGFR non-activating A549 cells were resistant to dacomitinib in vitro, while A549 xenografts were comparatively sensitive as EGFR-activating HCC827 xenografts. Dacomitinib inhibited MAPK signaling pathway, and increased the immune response in the A549 xenografts. A phagocytosis checkpoint stanniocalcin-1 (STC1) was significantly inhibited in dacomitinib-treated xenografts. So here our study gives the first insight of the heterogeneity of the two classic models, and the translational potential of dacomitinib being used into a broader patient population rather than EGFR common activating mutation.
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Affiliation(s)
- Xiaoyan Chen
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; The College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yangziwei Yu
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Haoyang Zheng
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Mengjing Yang
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Chuqiao Wang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, 110122, China
| | - Qianqian Cai
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Weiguo Zhang
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Feixiang Jiang
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yanmei Zhu
- Department of Pathology, Affiliated Cancer Hospital of Dalian University of Technology, Shenyang, 110042, China; Liaoning Cancer Hospital and Institute, Shenyang, 110042, China; Cancer Hospital of China Medical University, Shenyang, 110042, China
| | - Hedi Yang
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Tianbiao Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, 110122, China
| | - Zhaoli Zhou
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
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2
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Thankamony AP, Ramkomuth S, Ramesh ST, Murali R, Chakraborty P, Karthikeyan N, Varghese BA, Jaikumar VS, Jolly MK, Swarbrick A, Nair R. Phenotypic heterogeneity drives differential disease outcome in a mouse model of triple negative breast cancer. Front Oncol 2023; 13:1230647. [PMID: 37841442 PMCID: PMC10570535 DOI: 10.3389/fonc.2023.1230647] [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: 05/29/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
The triple negative breast cancer (TNBC) subtype is one of the most aggressive forms of breast cancer that has poor clinical outcome and is an unmet clinical challenge. Accumulating evidence suggests that intratumoral heterogeneity or the presence of phenotypically distinct cell populations within a tumor play a crucial role in chemoresistance, tumor progression and metastasis. An increased understanding of the molecular regulators of intratumoral heterogeneity is crucial to the development of effective therapeutic strategies in TNBC. To this end, we used an unbiased approach to identify a molecular mediator of intratumoral heterogeneity in breast cancer by isolating two tumor cell populations (T1 and T2) from the 4T1 TNBC model. Phenotypic characterization revealed that the cells are different in terms of their morphology, proliferation and self-renewal ability in vitro as well as primary tumor formation and metastatic potential in vivo. Bioinformatic analysis followed by Kaplan Meier survival analysis in TNBC patients identified Metastasis associated colon cancer 1 (Macc1) as one of the top candidate genes mediating the aggressive phenotype in the T1 tumor cells. The role of Macc1 in regulating the proliferative phenotype was validated and taken forward in a therapeutic context with Lovastatin, a small molecule transcriptional inhibitor of Macc1 to target the T1 cell population. This study increases our understanding of the molecular underpinnings of intratumoral heterogeneity in breast cancer that is critical to improve the treatment of women currently living with the highly aggressive TNBC subtype.
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Affiliation(s)
- Archana P. Thankamony
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Sonny Ramkomuth
- The Kinghorn Cancer Centre and Cancer Research Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Shikha T. Ramesh
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Reshma Murali
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | | | | | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Radhika Nair
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
- Centre for Human Genetics, Bangalore, India
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3
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Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. Nature 2023; 620:651-659. [PMID: 37468627 PMCID: PMC10628994 DOI: 10.1038/s41586-023-06342-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells1-7. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy7-9; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.
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Affiliation(s)
- Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Gianna T Busch
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jingxin Li
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan H Boe
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emanuelle I Grody
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Manoj Chelvanambi
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jonas Braun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Amanpreet Kaur
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Naveen Jain
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pavithran T Ravindran
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Mellis
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karun Kiani
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Syeda Subia Ahmed
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Haiyin Li
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Cedric Chai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Reproductive Science, Northwestern University, Chicago, IL, USA
| | | | - Russell G Witt
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah B Johnson
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalida Wani
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Harryman WL, Marr KD, Nagle RB, Cress AE. Integrins and Epithelial-Mesenchymal Cooperation in the Tumor Microenvironment of Muscle-Invasive Lethal Cancers. Front Cell Dev Biol 2022; 10:837585. [PMID: 35300411 PMCID: PMC8921537 DOI: 10.3389/fcell.2022.837585] [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] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 11/18/2022] Open
Abstract
Muscle-invasive lethal carcinomas traverse into and through this specialized biophysical and growth factor enriched microenvironment. We will highlight cancers that originate in organs surrounded by smooth muscle, which presents a barrier to dissemination, including prostate, bladder, esophageal, gastric, and colorectal cancers. We propose that the heterogeneity of cell-cell and cell-ECM adhesion receptors is an important driver of aggressive tumor networks with functional consequences for progression. Phenotype heterogeneity of the tumor provides a biophysical advantage for tumor network invasion through the tensile muscle and survival of the tumor network. We hypothesize that a functional epithelial-mesenchymal cooperation (EMC)exists within the tumor invasive network to facilitate tumor escape from the primary organ, invasion and traversing of muscle, and navigation to metastatic sites. Cooperation between specific epithelial cells within the tumor and stromal (mesenchymal) cells interacting with the tumor is illustrated using the examples of laminin-binding adhesion molecules—especially integrins—and their response to growth and inflammatory factors in the tumor microenvironment. The cooperation between cell-cell (E-cadherin, CDH1) and cell-ECM (α6 integrin, CD49f) expression and growth factor receptors is highlighted within poorly differentiated human tumors associated with aggressive disease. Cancer-associated fibroblasts are examined for their role in the tumor microenvironment in generating and organizing various growth factors. Cellular structural proteins are potential utility markers for future spatial profiling studies. We also examine the special characteristics of the smooth muscle microenvironment and how invasion by a primary tumor can alter this environment and contribute to tumor escape via cooperation between epithelial and stromal cells. This cooperative state allows the heterogenous tumor clusters to be shaped by various growth factors, co-opt or evade immune system response, adapt from hypoxic to normoxic conditions, adjust to varying energy sources, and survive radiation and chemotherapeutic interventions. Understanding the epithelial-mesenchymal cooperation in early tumor invasive networks holds potential for both identifying early biomarkers of the aggressive transition and identification of novel agents to prevent the epithelial-mesenchymal cooperation phenotype. Epithelial-mesenchymal cooperation is likely to unveil new tumor subtypes to aid in selection of appropriate therapeutic strategies.
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Affiliation(s)
- William L Harryman
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona Cancer Center, Tucson, AZ, United States
| | - Kendra D Marr
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona Cancer Center, Tucson, AZ, United States.,Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States.,Medical Scientist Training Program, College of Medicine, University of Arizona, Tucson, AZ, United States
| | - Ray B Nagle
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona Cancer Center, Tucson, AZ, United States.,Department of Pathology, College of Medicine, University of Arizona, Tucson, AZ, United States
| | - Anne E Cress
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona Cancer Center, Tucson, AZ, United States.,Department of Cellular and Molecular Medicine and Department of Radiation Oncology, College of Medicine, University of Arizona, Tucson, AZ, United States
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