1
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Mattson NM, Chan AKN, Miyashita K, Mukhaleva E, Chang WH, Yang L, Ma N, Wang Y, Pokharel SP, Li M, Liu Q, Xu X, Chen R, Singh P, Zhang L, Elsayed Z, Chen B, Keen D, Pirrotte P, Rosen ST, Chen J, LaBarge MA, Shively JE, Vaidehi N, Rockne RC, Feng M, Chen CW. A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens. Nat Struct Mol Biol 2024; 31:465-475. [PMID: 38316881 PMCID: PMC10948361 DOI: 10.1038/s41594-024-01211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024]
Abstract
The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
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Affiliation(s)
- Nicole M Mattson
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Kazuya Miyashita
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Wen-Han Chang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yingyu Wang
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Priyanka Singh
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Leisi Zhang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zeinab Elsayed
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bryan Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Denise Keen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mark A LaBarge
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John E Shively
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mingye Feng
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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2
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Miyano M, LaBarge MA. ELF5: A Molecular Clock for Breast Aging and Cancer Susceptibility. Cancers (Basel) 2024; 16:431. [PMID: 38275872 PMCID: PMC10813895 DOI: 10.3390/cancers16020431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/25/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Breast cancer is predominantly an age-related disease, with aging serving as the most significant risk factor, compounded by germline mutations in high-risk genes like BRCA1/2. Aging induces architectural changes in breast tissue, particularly affecting luminal epithelial cells by diminishing lineage-specific molecular profiles and adopting myoepithelial-like characteristics. ELF5 is an important transcription factor for both normal breast and breast cancer development. This review focuses on the role of ELF5 in normal breast development, its altered expression throughout aging, and its implications in cancer. It discusses the lineage-specific expression of ELF5, its regulatory mechanisms, and its potential as a biomarker for breast-specific biological age and cancer risk.
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Affiliation(s)
- Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Biomarkers Research, University of Bergen, 5007 Bergen, Norway
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3
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Jokela TA, Dane MA, Smith RL, Devlin KL, Shalabi S, Lopez JC, Miyano M, Stampfer MR, Korkola JE, Gray JW, Heiser LM, LaBarge MA. Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments. Cell Signal 2024; 113:110958. [PMID: 37935340 PMCID: PMC10696611 DOI: 10.1016/j.cellsig.2023.110958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
Microenvironment signals are potent determinants of cell fate and arbiters of tissue homeostasis, however understanding how different microenvironment factors coordinately regulate cellular phenotype has been experimentally challenging. Here we used a high-throughput microenvironment microarray comprised of 2640 unique pairwise signals to identify factors that support proliferation and maintenance of primary human mammary luminal epithelial cells. Multiple microenvironment factors that modulated luminal cell number were identified, including: HGF, NRG1, BMP2, CXCL1, TGFB1, FGF2, PDGFB, RANKL, WNT3A, SPP1, HA, VTN, and OMD. All of these factors were previously shown to modulate luminal cell numbers in painstaking mouse genetics experiments, or were shown to have a role in breast cancer, demonstrating the relevance and power of our high-dimensional approach to dissect key microenvironmental signals. RNA-sequencing of primary epithelial and stromal cell lineages identified the cell types that express these signals and the cognate receptors in vivo. Cell-based functional studies confirmed which effects from microenvironment factors were reproducible and robust to individual variation. Hepatocyte growth factor (HGF) was the factor most robust to individual variation and drove expansion of luminal cells via cKit+ progenitor cells, which expressed abundant MET receptor. Luminal cells from women who are genetically high risk for breast cancer had significantly more MET receptor and may explain the characteristic expansion of the luminal lineage in those women. In ensemble, our approach provides proof of principle that microenvironment signals that control specific cellular states can be dissected with high-dimensional cell-based approaches.
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Affiliation(s)
- Tiina A Jokela
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Mark A Dane
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Rebecca L Smith
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Kaylyn L Devlin
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Sundus Shalabi
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; Faculty of Medicine, Arab American University of Palestine, Jenin, Palestine
| | - Jennifer C Lopez
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James E Korkola
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health Sciences University, Portland, OR, USA.
| | - Mark A LaBarge
- Department of Population Sciences, Center for Cancer and Aging, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA; Center for Cancer Biomarkers Research (CCBIO), University of Bergen, Bergen, Norway; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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4
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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5
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Senapati P, Miyano M, Sayaman RW, Basam M, Leung A, LaBarge MA, Schones DE. Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells. Genome Res 2023; 33:1229-1241. [PMID: 37463750 PMCID: PMC10547379 DOI: 10.1101/gr.277511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
A primary function of DNA methylation in mammalian genomes is to repress transposable elements (TEs). The widespread methylation loss that is commonly observed in cancer cells results in the loss of epigenetic repression of TEs. The aging process is similarly characterized by changes to the methylome. However, the impact of these epigenomic alterations on TE silencing and the functional consequences of this have remained unclear. To assess the epigenetic regulation of TEs in aging, we profiled DNA methylation in human mammary luminal epithelial cells (LEps)-a key cell lineage implicated in age-related breast cancers-from younger and older women. We report here that several TE subfamilies function as regulatory elements in normal LEps, and a subset of these display consistent methylation changes with age. Methylation changes at these TEs occurred at lineage-specific transcription factor binding sites, consistent with loss of lineage specificity. Whereas TEs mainly showed methylation loss, CpG islands (CGIs) that are targets of the Polycomb repressive complex 2 (PRC2) show a gain of methylation in aging cells. Many TEs with methylation loss in aging LEps have evidence of regulatory activity in breast cancer samples. We furthermore show that methylation changes at TEs impact the regulation of genes associated with luminal breast cancers. These results indicate that aging leads to DNA methylation changes at TEs that undermine the maintenance of lineage specificity, potentially increasing susceptibility to breast cancer.
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Affiliation(s)
- Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143-0981, USA
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
- Center for Cancer Biomarker Research, University of Bergen, 5021 Bergen, Norway
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA;
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
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6
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Srivastava V, Hu JL, Garbe JC, Veytsman B, Shalabi SF, Yllanes D, Thomson M, LaBarge MA, Huber G, Gartner ZJ. Configurational entropy is an intrinsic driver of tissue structural heterogeneity. bioRxiv 2023:2023.07.01.546933. [PMID: 37425903 PMCID: PMC10327153 DOI: 10.1101/2023.07.01.546933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Tissues comprise ordered arrangements of cells that can be surprisingly disordered in their details. How the properties of single cells and their microenvironment contribute to the balance between order and disorder at the tissue-scale remains poorly understood. Here, we address this question using the self-organization of human mammary organoids as a model. We find that organoids behave like a dynamic structural ensemble at the steady state. We apply a maximum entropy formalism to derive the ensemble distribution from three measurable parameters - the degeneracy of structural states, interfacial energy, and tissue activity (the energy associated with positional fluctuations). We link these parameters with the molecular and microenvironmental factors that control them to precisely engineer the ensemble across multiple conditions. Our analysis reveals that the entropy associated with structural degeneracy sets a theoretical limit to tissue order and provides new insight for tissue engineering, development, and our understanding of disease progression.
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Affiliation(s)
- Vasudha Srivastava
- Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jennifer L. Hu
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
| | - James C. Garbe
- Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Boris Veytsman
- Chan Zuckerberg Initiative, Redwood City, CA 94963, USA
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | | | - David Yllanes
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Instituto de Biocomputaciòn y Fìsica de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark A. LaBarge
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Greg Huber
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Zev J. Gartner
- Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Center for Cellular Construction, University of California, San Francisco, CA 94158, USA
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7
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Nee K, Ma D, Nguyen QH, Pein M, Pervolarakis N, Insua-Rodríguez J, Gong Y, Hernandez G, Alshetaiwi H, Williams J, Rauf M, Dave KR, Boyapati K, Hasnain A, Calderon C, Markaryan A, Edwards R, Lin E, Parajuli R, Zhou P, Nie Q, Shalabi S, LaBarge MA, Kessenbrock K. Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis. Nat Genet 2023; 55:595-606. [PMID: 36914836 PMCID: PMC10655552 DOI: 10.1038/s41588-023-01298-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 12/28/2022] [Indexed: 03/16/2023]
Abstract
Women with germline BRCA1 mutations (BRCA1+/mut) have increased risk for hereditary breast cancer. Cancer initiation in BRCA1+/mut is associated with premalignant changes in breast epithelium; however, the role of the epithelium-associated stromal niche during BRCA1-driven tumor initiation remains unclear. Here we show that the premalignant stromal niche promotes epithelial proliferation and mutant BRCA1-driven tumorigenesis in trans. Using single-cell RNA sequencing analysis of human preneoplastic BRCA1+/mut and noncarrier breast tissues, we show distinct changes in epithelial homeostasis including increased proliferation and expansion of basal-luminal intermediate progenitor cells. Additionally, BRCA1+/mut stromal cells show increased expression of pro-proliferative paracrine signals. In particular, we identify pre-cancer-associated fibroblasts (pre-CAFs) that produce protumorigenic factors including matrix metalloproteinase 3 (MMP3), which promotes BRCA1-driven tumorigenesis in vivo. Together, our findings demonstrate that precancerous stroma in BRCA1+/mut may elevate breast cancer risk through the promotion of epithelial proliferation and an accumulation of luminal progenitor cells with altered differentiation.
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Affiliation(s)
- Kevin Nee
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Dennis Ma
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Quy H Nguyen
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Maren Pein
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Nicholas Pervolarakis
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | | | - Yanwen Gong
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Grace Hernandez
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Hamad Alshetaiwi
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- Department of Pathology, University of Hail, Hail, Saudi Arabia
| | - Justice Williams
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Maha Rauf
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Kushal Rajiv Dave
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Keerti Boyapati
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Aliza Hasnain
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Christian Calderon
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Anush Markaryan
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Robert Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine Medical Center, Orange, CA, USA
| | - Erin Lin
- Department of Surgery, University of California Irvine Medical Center, Orange, CA, USA
| | - Ritesh Parajuli
- Department of Surgery, University of California Irvine Medical Center, Orange, CA, USA
| | - Peijie Zhou
- Department of Mathematics, University of California, Irvine, CA, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA, USA
| | - Sundus Shalabi
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, CA, USA.
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8
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Miyano M, Sayaman RW, Senapati P, Hinz S, Seewaldt VE, Schones D, LaBarge MA. Abstract A003: Integrating noise into a signal: Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility. Cancer Res 2023. [DOI: 10.1158/1538-7445.agca22-a003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Short Talks from Proffered Abstracts section (PR006) of the Conference Proceedings.
Citation Format: Masaru Miyano, Rosalyn W. Sayaman, Parijat Senapati, Stefan Hinz, Victoria E. Seewaldt, Dustin Schones, Mark A. LaBarge. Integrating noise into a signal: Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A003.
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Affiliation(s)
- Masaru Miyano
- 1Beckman Research Institute at City of Hope, Duarte, CA,
| | | | | | - Stefan Hinz
- 1Beckman Research Institute at City of Hope, Duarte, CA,
| | | | - Dustin Schones
- 1Beckman Research Institute at City of Hope, Duarte, CA,
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9
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Hinz S, Miyano M, Manousopoulou A, Sayaman RW, Aguilera KY, Todhunter ME, Lopez JC, Wang LD, Sohn LL, LaBarge MA. Abstract A016: Aging-dependent emergent mechanical properties of single epithelial cells exploited for detection of breast cancer susceptibility. Cancer Res 2023. [DOI: 10.1158/1538-7445.agca22-a016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
Age is the major risk factor in most carcinomas, yet, little is known about the specific reasons aging increases cancer susceptibility. In the mammary gland, luminal epithelial cells rank high as the putative breast cancer cell of origin. Dysregulation of keratin intermediate filament proteins exemplifies a hallmark age-dependent change in luminal cells, which implicates mechanical states unique to cancer susceptible cells. We implemented mechano-node-pore sensing (mechano-NPS), a multi-parametric single-cell analysis that simultaneously measures cell diameter, resistance to compressive deformation, transverse deformation under constant strain, and recovery time after deformation. We demonstrated that the epithelial lineages, chronological ages, and stages of cancer progression of primary human mammary epithelial cells (HMEC) exhibited discrete mechanical phenotypes. We trained a machine learning model that accurately predicted the chronological age of average risk HMEC cells based exclusively on mechanical properties. Application of the model to cells from women who are germline carriers of high-risk cancer-causing mutations showed that they are mechanically old irrespective of their chronological age, suggesting that mechanical states could be a window into detection and prevention of cancer susceptible states. Indeed, this mechano-age model detected high-risk women with >90% accuracy. Mass spectrometry and cell-based functional assays in mammary epithelia revealed that cytoskeleton related proteins keratin 14 (KRT14) and pseudopodium enriched atypical kinase 1 (PEAK1) were key drivers of age-dependent mechanical signatures. Pharmacological and gene silencing approaches that targeted KRT14 and PEAK1 modulated the mechanical age of HMEC and, in the case of PEAK1 modulation, ablated luminal epithelial cells in an age- and lineage- dependent manner. We define an intersection between mechanical phenotypes and novel age-dependent changes in cytoskeleton-related proteins that we hypothesize can be exploited to assess an individual’s breast cancer susceptibility and provide new targets for cancer-prevention strategies.
Citation Format: Stefan Hinz, Masaru Miyano, Antigoni Manousopoulou, Rosalyn W. Sayaman, Kristina Y. Aguilera, Michael E. Todhunter, Jennifer C. Lopez, Leo D. Wang, Lydia L. Sohn, Mark A. LaBarge. Aging-dependent emergent mechanical properties of single epithelial cells exploited for detection of breast cancer susceptibility [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A016.
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10
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Todhunter ME, Miyano M, Carlson EG, Hinz S, LaBarge MA. Sustained postconfluent culture of human mammary epithelial cells enriches for luminal and c-Kit+ subtypes. Breast Cancer Res 2023; 25:6. [PMID: 36653787 PMCID: PMC9847146 DOI: 10.1186/s13058-022-01595-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND A challenge in human mammary epithelial cell (HMEC) culture is sustaining the representation of competing luminal, myoepithelial, and progenitor lineages over time. As cells replicate in culture, myoepithelial cells come to dominate the composition of the culture with serial passaging. This drift in composition presents a challenge for studying luminal and progenitor cells, which are prospective cells of origin for most breast cancer subtypes. METHODS We demonstrate the use of postconfluent culture on HMECs. Postconfluent culture entails culturing HMECs for 2-5 weeks without passaging but maintaining frequent feedings in low-stress M87A culture medium. In contrast, standard HMEC culture entails enzymatic subculturing every 3-5 days to maintain subconfluent density. RESULTS When compared to standard HMEC culture, postconfluent culture yields increased proportions of luminal cells and c-Kit+ progenitor cells. Postconfluent cultures develop a distinct multilayered morphology with individual cells showing decreased physical deformability as compared to cells in standard culture. Gene expression analysis of postconfluent cells shows increased expression of lineage-specific markers and extracellular matrix components. CONCLUSIONS Postconfluent culture is a novel, useful strategy for altering the lineage composition of HMECs, by increasing the proportional representation of luminal and progenitor cells. We speculate that postconfluent culture creates a microenvironment with cellular composition closer to the physiological state and eases the isolation of scarce cell subtypes. As such, postconfluent culture is a valuable tool for researchers using HMECs for breast cancer research.
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Affiliation(s)
- Michael E. Todhunter
- grid.410425.60000 0004 0421 8357Department of Population Sciences, Beckman Research Institute at City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA
| | - Masaru Miyano
- grid.410425.60000 0004 0421 8357Department of Population Sciences, Beckman Research Institute at City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA
| | - Eric G. Carlson
- grid.410425.60000 0004 0421 8357Department of Population Sciences, Beckman Research Institute at City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA ,grid.410425.60000 0004 0421 8357Irell and Manella Graduate School of Biological Sciences, City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA
| | - Stefan Hinz
- grid.410425.60000 0004 0421 8357Department of Population Sciences, Beckman Research Institute at City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA
| | - Mark A. LaBarge
- grid.410425.60000 0004 0421 8357Department of Population Sciences, Beckman Research Institute at City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010 USA
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11
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Miyano M, Shalabi S, Sayaman RW, Stampfer M, Seewaldt VE, LaBarge MA. Abstract 5682: Accelerated biological age is a driver of cancer susceptibility in genetic high risk breast tissue. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
During aging in the human mammary gland, luminal epithelial cells lose lineage fidelity by expressing markers normally expressed in myoepithelial cells. We hypothesize that loss of lineage fidelity is a general manifestation of epithelia that are susceptible to cancer initiation. We show that histologically normal breast tissue from younger women who are susceptible to breast cancer because they harbor a germline mutation in BRCA1, BRCA2, or PALB2 genes, exhibit hallmarks of accelerated aging. These include proportionately increased luminal epithelial cells that acquired myoepithelial markers, decreased proportions of myoepithelial cells, and a basal differentiation bias or failure of differentiation of cKit+ progenitors. High-risk luminal and myoepithelial cells are transcriptionally enriched for genes of the opposite lineage, inflammatory, and cancer-related pathways. Genetically high risk luminal epithelial cells also show evidence of accelerated age, by as much as four decades compared to their chronological age, using a breast specific biological clock comprised of measurements of methylation and expression of the luminal-specific ELF5 transcription factor. We have identified breast aging hallmarks that reflect a convergent biology of cancer susceptibility, regardless of the specific underlying genetic or age-dependent risk, or the associated breast cancer subtype.
Citation Format: Masaru Miyano, Sundus Shalabi, Rosalyn W. Sayaman, Martha Stampfer, Victoria E. Seewaldt, Mark A. LaBarge. Accelerated biological age is a driver of cancer susceptibility in genetic high risk breast tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5682.
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Affiliation(s)
- Masaru Miyano
- 1Beckman Research Institute at City of Hope, Duarte, CA
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12
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Hinz S, Todhunter ME, LaBarge MA. Protocol for computationally evaluating the loss of stoichiometry and coordinated expression of proteins. STAR Protoc 2022; 3:101182. [PMID: 35313706 PMCID: PMC8933523 DOI: 10.1016/j.xpro.2022.101182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Dysregulation of the transcriptional or translational machinery can alter the stoichiometry of multiprotein complexes and occurs in natural processes such as aging. Loss of stoichiometry has been shown to alter protein complex functions. We provide a protocol and associated code that use omics data to quantify these stoichiometric changes via statistical dispersion utilizing the interquartile range of expression values per grouping variable. This descriptive statistical approach enables the quantification of stoichiometry changes without additional data acquisition. For complete details on the use and execution of this protocol, please refer to Hinz et al. (2021). A protocol to quantify stoichiometry changes of protein complexes Robust and versatile output based on interquartile range of expression Lightweight R functions easily loaded into data pipeline via GitHub Conveniently plot measured stoichiometry changes with ggplot2 wrapper function
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Samson S, Northey JJ, Acerbi I, Goga A, Flink CL, Weaver VM, LaBarge MA. NCI's publication affiliation conundrum: Reframing innovation to incentivize an equitable path for advocate representation. Transl Oncol 2022; 16:101325. [PMID: 34974281 PMCID: PMC8728534 DOI: 10.1016/j.tranon.2021.101325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 11/21/2022] Open
Abstract
Advocacy engagement has been at the forefront of National Cancer Institute (NCI) efforts to advance scientific discoveries and transform medical interventions. Nonetheless, the journey for advocates has been uneven. Case in Point: NCI publication affiliation rules of engagement pose unique equity challenges while raising questions about structural representation in biomedical research. Abiding by the core rationale that publication affiliation should be tailored to employment status, the NCI has systematically denied research advocate volunteers the opportunity to specifically list NCI as an institutional affiliation on academic publications. Unpacking advocate NCI publication affiliation restrictions and its links with advocacy heritage preservation and convergent science goals poses unique diversity, equity, and inclusion challenges and opportunities. Improving the quality of structural representation in biomedical research requires new theories of action and flexible planning to advance, promote and build capacity for strategic advocacy inclusion and equity within publication affiliation initiatives. Here we highlight several opportunities for how leadership might formulate a radically different vision for NCI's approach. This perspective interrogates the best way forward for ensuring that biomedical employee and volunteer advocate workforce publication affiliation intersections are characterized by increased creativity and representation parity. Imbuing the scientist and clinical researcher archetype with social dimensions, we join NCI critical thinkers in urging employees, funded academics, and volunteer citizen scientists to collectively assume the role as paladins of science and integrity who view the triumphs of making a difference in science alongside the social responsibility of promoting transdisciplinary professionalism and the democratization of science.
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Affiliation(s)
- Susan Samson
- Breast Oncology Program, Breast Science Advocacy Core (BSAC), University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94115; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115, United States; Physical Sciences and Oncology Network Program, University of California, San Francisco, CA 94115, United States.
| | - Jason J Northey
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA 94143, United States
| | - Irene Acerbi
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA 94143, United States
| | - Andrei Goga
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115, United States; Department of Cell and Tissue Biology and Medicine, University of California, San Francisco, CA 94143, United States
| | - Carl L Flink
- College of Liberal Arts, Theatre Arts and Dance, University of Minnesota, Minneapolis, MN 55455, United States
| | - Valerie M Weaver
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115, United States; Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA 94143, United States
| | - Mark A LaBarge
- Beckman Research Institute, City of Hope, Duarte, CA 91010, United States
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14
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Jokela TA, Todhunter ME, LaBarge MA. High-Throughput Microenvironment Microarray (MEMA) High-Resolution Imaging. Methods Mol Biol 2022; 2394:47-64. [PMID: 35094321 DOI: 10.1007/978-1-0716-1811-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The interaction between cells and their surrounding microenvironment has a crucial role in determining cell fate. In many pathological conditions, the microenvironment drives disease progression as well as therapeutic resistance. A number of challenges arise for researchers examining these cell-microenvironment interactions: (1) Tissue microenvironments are combinatorial and dynamic systems, and in pathological situations like cancer, microenvironments become infamously chaotic and highly heterogeneous. (2) Cells exhibit heterogeneous phenotypes, and even rare cell subpopulations can have a substantial role in tissue homeostasis and disease progression. This chapter discusses technical aspects relevant to dissecting cell-microenvironment interaction using the Microenvironment Microarray (MEMA) platform, which is a cell-based functional high-throughput screening of interactions between cells and combinatorial microenvironments at the single-cell level. MEMA provides insights into how cell phenotype and function is elicited by microenvironmental components. In this chapter, we describe automating a high-throughput and high-resolution imaging pipeline for single-cell-resolution analysis.
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Affiliation(s)
- Tiina A Jokela
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA.
| | - Michael E Todhunter
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA.
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15
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Li B, Cotner KL, Liu NK, Hinz S, LaBarge MA, Sohn LL. Evaluating sources of technical variability in the mechano-node-pore sensing pipeline and their effect on the reproducibility of single-cell mechanical phenotyping. PLoS One 2021; 16:e0258982. [PMID: 34695165 PMCID: PMC8544830 DOI: 10.1371/journal.pone.0258982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/28/2021] [Accepted: 10/09/2021] [Indexed: 11/19/2022] Open
Abstract
Cellular mechanical properties can reveal physiologically relevant characteristics in many cell types, and several groups have developed microfluidics-based platforms to perform high-throughput single-cell mechanical testing. However, prior work has performed only limited characterization of these platforms' technical variability and reproducibility. Here, we evaluate the repeatability performance of mechano-node-pore sensing, a single-cell mechanical phenotyping platform developed by our research group. We measured the degree to which device-to-device variability and semi-manual data processing affected this platform's measurements of single-cell mechanical properties. We demonstrated high repeatability across the entire technology pipeline even for novice users. We then compared results from identical mechano-node-pore sensing experiments performed by researchers in two different laboratories with different analytical instruments, demonstrating that the mechanical testing results from these two locations are in agreement. Our findings quantify the expectation of technical variability in mechano-node-pore sensing even in minimally experienced hands. Most importantly, we find that the repeatability performance we measured is fully sufficient for interpreting biologically relevant single-cell mechanical measurements with high confidence.
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Affiliation(s)
- Brian Li
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
| | - Kristen L. Cotner
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
| | - Nathaniel K. Liu
- Department of Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California, United States of America
| | - Lydia L. Sohn
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and San Francisco, California, United States of America
- Department of Mechanical Engineering, University of California, Berkeley, California, United States of America
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16
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Hinz S, Manousopoulou A, Miyano M, Sayaman RW, Aguilera KY, Todhunter ME, Lopez JC, Sohn LL, Wang LD, LaBarge MA. Deep proteome profiling of human mammary epithelia at lineage and age resolution. iScience 2021; 24:103026. [PMID: 34522866 PMCID: PMC8426267 DOI: 10.1016/j.isci.2021.103026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/16/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Age is the major risk factor in most carcinomas, yet little is known about how proteomes change with age in any human epithelium. We present comprehensive proteomes comprised of >9,000 total proteins and >15,000 phosphopeptides from normal primary human mammary epithelia at lineage resolution from ten women ranging in age from 19 to 68 years. Data were quality controlled and results were biologically validated with cell-based assays. Age-dependent protein signatures were identified using differential expression analyses and weighted protein co-expression network analyses. Upregulation of basal markers in luminal cells, including KRT14 and AXL, were a prominent consequence of aging. PEAK1 was identified as an age-dependent signaling kinase in luminal cells, which revealed a potential age-dependent vulnerability for targeted ablation. Correlation analyses between transcriptome and proteome revealed age-associated loss of proteostasis regulation. Age-dependent proteome changes in the breast epithelium identified heretofore unknown potential therapeutic targets for reducing breast cancer susceptibility.
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Affiliation(s)
- Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Antigoni Manousopoulou
- Departments of Pediatrics and ImmunoOncology, City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Rosalyn W. Sayaman
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kristina Y. Aguilera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | | | - Jennifer C. Lopez
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
| | - Lydia L. Sohn
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley 94720-1740, USA
| | - Leo D. Wang
- Departments of Pediatrics and ImmunoOncology, City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, Duarte, USA
- Center for Cancer and Aging Research, Duarte, USA
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17
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Zirbes A, Joseph J, Lopez JC, Sayaman RW, Basam M, Seewaldt VL, LaBarge MA. Changes in Immune Cell Types with Age in Breast are Consistent with a Decline in Immune Surveillance and Increased Immunosuppression. J Mammary Gland Biol Neoplasia 2021; 26:247-261. [PMID: 34341887 PMCID: PMC8566425 DOI: 10.1007/s10911-021-09495-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
A majority of breast cancers (BC) are age-related and we seek to determine what cellular and molecular changes occur in breast tissue with age that make women more susceptible to cancer initiation. Immune-epithelial cell interactions are important during mammary gland development and the immune system plays an important role in BC progression. The composition of human immune cell populations is known to change in peripheral blood with age and in breast tissue during BC progression. Less is known about changes in immune populations in normal breast tissue and how their interactions with mammary epithelia change with age. We quantified densities of T cells, B cells, and macrophage subsets in pathologically normal breast tissue from 122 different women who ranged in age from 24 to 74 years old. Donor-matched peripheral blood from a subset of 20 donors was analyzed by flow cytometry. Tissue immune cell densities and localizations relative to the epithelium were quantified in situ with machine learning-based image analyses of multiplex immunohistochemistry-stained tissue sections. In situ results were corroborated with flow cytometry analyses of peri-epithelial immune cells from primary breast tissue preparations and transcriptome analyses of public data from bulk tissue reduction mammoplasties. Proportions of immune cell subsets in breast tissue and donor-matched peripheral blood were not correlated. Density (cells/mm2) of T and B lymphocytes in situ decreased with age. T cells and macrophages preferentially localized near or within epithelial bilayers, rather than the intralobular stroma. M2 macrophage density was higher than M1 macrophage density and this difference was due to higher density of M2 in the intralobular stroma. Transcriptional signature analyses suggested age-dependent decline in adaptive immune cell populations and functions and increased innate immune cell activity. T cells and macrophages are so intimately associated with the epithelia that they are embedded within the bilayer, suggesting an important role for immune-epithelial cell interactions. Age-associated decreased T cell density in peri-epithelial regions, and increased M2 macrophage density in intralobular stroma suggests the emergence of a tissue microenvironment that is simultaneously immune-senescent and immunosuppressive with age.
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Affiliation(s)
- Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Jesuchristopher Joseph
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Cancer Metabolism Training Program, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Mudaser Basam
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Victoria L Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA, 91010, USA.
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.
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18
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Shalabi SF, Miyano M, Sayaman RW, Lopez JC, Jokela TA, Todhunter ME, Hinz S, Garbe JC, Stampfer MR, Kessenbrock K, Seewaldt VE, LaBarge MA. Evidence for accelerated aging in mammary epithelia of women carrying germline BRCA1 or BRCA2 mutations. Nat Aging 2021; 1:838-849. [PMID: 35187501 PMCID: PMC8849557 DOI: 10.1038/s43587-021-00104-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During aging in the human mammary gland, luminal epithelial cells lose lineage fidelity by expressing markers normally expressed in myoepithelial cells. We hypothesize that loss of lineage fidelity is a general manifestation of epithelia that are susceptible to cancer initiation. In the present study, we show that histologically normal breast tissue from younger women who are susceptible to breast cancer, as a result of harboring a germline mutation in BRCA1, BRCA2 or PALB2 genes, exhibits hallmarks of accelerated aging. These include proportionately increased luminal epithelial cells that acquired myoepithelial markers, decreased proportions of myoepithelial cells and a basal differentiation bias or failure of differentiation of cKit+ progenitors. High-risk luminal and myoepithelial cells are transcriptionally enriched for genes of the opposite lineage, inflammatory- and cancer-related pathways. We have identified breast-aging hallmarks that reflect a convergent biology of cancer susceptibility, regardless of the specific underlying genetic or age-dependent risk or the associated breast cancer subtype.
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Affiliation(s)
- Sundus F Shalabi
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA.,Medical Research Center, Al-Quds University, Jerusalem, Palestine
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Cancer Metabolism Training Program, City of Hope, Duarte, CA, USA.,Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Tiina A Jokela
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Michael E Todhunter
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Stefan Hinz
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - James C Garbe
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kai Kessenbrock
- Biological Chemistry Department, University of California, Irvine, CA, USA
| | - Victoria E Seewaldt
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Cancer Metabolism Training Program, City of Hope, Duarte, CA, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.,Center for Cancer and Aging, City of Hope, Duarte, CA, USA.,Center for Cancer Biomarkers Research, University of Bergen, Bergen, Norway
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19
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Miyano M, Sayaman RW, Shalabi SF, Senapati P, Lopez JC, Angarola BL, Hinz S, Zirbes A, Anczukow O, Yee LD, Sedrak MS, Stampfer MR, Seewaldt VL, LaBarge MA. Breast-Specific Molecular Clocks Comprised of ELF5 Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation. Cancer Prev Res (Phila) 2021; 14:779-794. [PMID: 34140348 PMCID: PMC8338914 DOI: 10.1158/1940-6207.capr-20-0635] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 12/09/2020] [Revised: 04/29/2021] [Accepted: 06/07/2021] [Indexed: 01/09/2023]
Abstract
A robust breast cancer prevention strategy requires risk assessment biomarkers for early detection. We show that expression of ELF5, a transcription factor critical for normal mammary development, is downregulated in mammary luminal epithelia with age. DNA methylation of the ELF5 promoter is negatively correlated with expression in an age-dependent manner. Both ELF5 methylation and gene expression were used to build biological clocks to estimate chronological ages of mammary epithelia. ELF5 clock-based estimates of biological age in luminal epithelia from average-risk women were within three years of chronological age. Biological ages of breast epithelia from BRCA1 or BRCA2 mutation carriers, who were high risk for developing breast cancer, suggested they were accelerated by two decades relative to chronological age. The ELF5 DNA methylation clock had better performance at predicting biological age in luminal epithelial cells as compared with two other epigenetic clocks based on whole tissues. We propose that the changes in ELF5 expression or ELF5-proximal DNA methylation in luminal epithelia are emergent properties of at-risk breast tissue and constitute breast-specific biological clocks. PREVENTION RELEVANCE: ELF5 expression or DNA methylation level at the ELF5 promoter region can be used as breast-specific biological clocks to identify women at higher than average risk of breast cancer.
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Affiliation(s)
- Masaru Miyano
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Sundus F Shalabi
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California
| | - Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute at City of Hope, Duarte, California
| | - Jennifer C Lopez
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
| | | | - Stefan Hinz
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
| | - Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Lisa D Yee
- Department of Surgery, City of Hope National Medical Center, Duarte, California
| | - Mina S Sedrak
- Center for Cancer and Aging, City of Hope, Duarte, California
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Victoria L Seewaldt
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, California.
- Center for Cancer and Aging, City of Hope, Duarte, California
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
- Center for Cancer Biomarkers, University of Bergen, Bergen, Norway
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20
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Fresques T, LaBarge MA. <PE-AT>Contributions of Yap and Taz dysfunction to breast cancer initiation, progression, and aging-related susceptibility. ACTA ACUST UNITED AC 2021; 1:5-18. [PMID: 33693435 DOI: 10.1002/aac2.12011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Yap and Taz are co-transcription factors that have been implicated in the development of many cancers. Here, we review the literature that analyzes the function of Yap/Taz in normal breast and breast cancer contexts. Our review of the literature suggests that that Yap and Taz are involved in breast cancer and Taz, in particular, is involved in the triple negative subtype. Nevertheless, the precise contexts in which Yap/Taz contribute to specific breast cancer phenotypes remains unclear. Indeed, Yap/Taz dysregulation acts differentially and in multiple epithelial cell types during early breast cancer progression. We propose Yap/Taz activation promotes breast cancer phenotypes in breast cancer precursor cells. Further, Yap dysregulation as a result of aging in breast tissue may result in microenvironments that increase the fitness of breast cancer precursor cells relative to the normal epithelia. <PE-FRONTEND>.
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Affiliation(s)
- Tara Fresques
- Beckman Research Institute at City of Hope, City of Hope National Medical Center, Duarte, CA USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, City of Hope National Medical Center, Duarte, CA USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Center for Cancer Biomarkers Research, University of Bergen, Norway
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21
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Todhunter ME, Miyano M, Moolamalla DS, Filippov A, Sayaman RW, LaBarge MA. Volume-constrained microcontainers enable myoepithelial functional differentiation in highly parallel mammary organoid culture. iScience 2021; 24:102253. [PMID: 33796842 PMCID: PMC7995530 DOI: 10.1016/j.isci.2021.102253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 01/02/2023] Open
Abstract
A long-standing constraint on organoid culture is the need to add exogenous substances to provide hydrogel matrix, which limits the study of fully human or fully native organoids. This paper introduces an approach to culture reconstituted mammary organoids without the impediment of exogenous matrix. We enclose organoids in nanoliter-scale, topologically enclosed, fluid compartments surrounded by agar. Organoids cultured in these “microcontainers” appear to secrete enough extracellular matrix to yield a self-sufficient microenvironment without exogenous supplements. In microcontainers, mammary organoids exhibit contractility and a high-level, physiological, myoepithelial (MEP) behavior that has not been previously reported in reconstituted organoids. The presence of contractility suggests that microcontainers elicit MEP functional differentiation, an important milestone. Microcontainers yield thousands of substantially identical and individually trackable organoids within a single culture vessel, enabling longitudinal studies and statistically powerful experiments, such as the evaluation of small effect sizes. Microcontainers open new doors for researchers who rely on organoid models. Microcontainers are volume-constrained microwells with hydrogel lids Microcontainers enable statistically robust experimental design with organoids Organoids produce their own extracellular matrix within microcontainers Myoepithelial cells in mammary organoids achieve fully functional differentiation
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Affiliation(s)
- Michael E Todhunter
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Divya S Moolamalla
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Aleksandr Filippov
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
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22
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Srivastava V, Hu JL, Garbe JC, Stampfer MR, LaBarge MA, Thomson M, Gartner ZJ. Identifying Enthalpic Barriers to Entropically-Driven Structural Disruption in Breast Cancers. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Abstract
Purpose of review Cancer stem cells (CSCs) are increasingly understood to play a central role in tumor progression. Growing evidence implicates tumor microenvironments as a source of signals that regulate or even impose CSC states on tumor cells. This review explores points of integration for microenvironment-derived signals that are thought to regulate CSCs in carcinomas. Recent findings CSC states are directly regulated by the mechanical properties and extra cellular matrix (ECM) composition of tumor microenvironments that promote CSC growth and survival, which may explain some modes of therapeutic resistance. CSCs sense mechanical forces and ECM composition through integrins and other cell surface receptors, which then activate a number of intracellular signaling pathways. The relevant signaling events are dynamic and context-dependent. Summary CSCs are thought to drive cancer metastases and therapeutic resistance. Cells that are in CSC states and more differentiated states appear to be reversible and conditional upon the components of the tumor microenvironment. Signals imposed by tumor microenvironment are of a combinatorial nature, ultimately representing the integration of multiple physical and chemical signals. Comprehensive understanding of the tumor microenvironment-imposed signaling that maintains cells in CSC states may guide future therapeutic interventions.
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Affiliation(s)
- Tiina A Jokela
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd, Duarte CA 91010
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, 1500 E. Duarte Rd, Duarte CA 91010
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24
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Engelsen AST, Wnuk-Lipinska K, Bougnaud S, Pelissier Vatter FA, Tiron C, Villadsen R, Miyano M, Lotsberg ML, Madeleine N, Panahandeh P, Dhakal S, Tan TZ, Peters SD, Grøndal S, Aziz SM, Nord S, Herfindal L, Stampfer MR, Sørlie T, Brekken RA, Straume O, Halberg N, Gausdal G, Thiery JP, Akslen LA, Petersen OW, LaBarge MA, Lorens JB. AXL Is a Driver of Stemness in Normal Mammary Gland and Breast Cancer. iScience 2020; 23:101649. [PMID: 33103086 PMCID: PMC7578759 DOI: 10.1016/j.isci.2020.101649] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
The receptor tyrosine kinase AXL is associated with epithelial plasticity in several solid tumors including breast cancer and AXL-targeting agents are currently in clinical trials. We hypothesized that AXL is a driver of stemness traits in cancer by co-option of a regulatory function normally reserved for stem cells. AXL-expressing cells in human mammary epithelial ducts co-expressed markers associated with multipotency, and AXL inhibition abolished colony formation and self-maintenance activities while promoting terminal differentiation in vitro. Axl-null mice did not exhibit a strong developmental phenotype, but enrichment of Axl + cells was required for mouse mammary gland reconstitution upon transplantation, and Axl-null mice had reduced incidence of Wnt1-driven mammary tumors. An AXL-dependent gene signature is a feature of transcriptomes in basal breast cancers and reduced patient survival irrespective of subtype. Our interpretation is that AXL regulates access to epithelial plasticity programs in MaSCs and, when co-opted, maintains acquired stemness in breast cancer cells.
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Affiliation(s)
- Agnete S T Engelsen
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France
| | | | - Sebastien Bougnaud
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Fanny A Pelissier Vatter
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Crina Tiron
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - René Villadsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark
| | - Masaru Miyano
- Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91910, USA
| | - Maria L Lotsberg
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
| | - Noëlly Madeleine
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Pouda Panahandeh
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Sushil Dhakal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Tuan Zea Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | | | - Sturla Grøndal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Sura M Aziz
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Silje Nord
- Department of Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Lars Herfindal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Martha R Stampfer
- Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Therese Sørlie
- Department of Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Rolf A Brekken
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Oddbjørn Straume
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Oncology and Medical Physics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Gro Gausdal
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Jean Paul Thiery
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy Cancer Campus Grand Paris, 94800 Villejuif, France.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, A-STAR, Singapore 138673, Singapore.,Bioland Laboratory, Guangzhou Regenerative Medicine and Health, Bio-island, Guangzhou, 510320, China
| | - Lars A Akslen
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ole W Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, Copenhagen, Copenhagen N 2200, Denmark
| | - Mark A LaBarge
- Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway.,Biolgical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91910, USA
| | - James B Lorens
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway.,Centre for Cancer Biomarkers, University of Bergen, 5021 Bergen, Norway
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25
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Ramos CA, Ouyang C, Qi Y, Chung Y, Cheng CT, LaBarge MA, Seewasldt VL, Ann DK. Abstract 3724: BMAL1 rewires mitochondrial metabolism and promotes tumor progress of triple negative breast cancer during insulin resistance. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Insulin resistance is a hallmark of metabolic diseases and negatively associated with breast cancer outcomes. While much work has dedicated to circadian dysregulation, metabolic diseases in breast cancer progression, the molecular mechanism connecting all these perspectives together has not yet established. To understand this underlying mechanism, we use in vitro and in vivo insulin-resistant triple-negative breast cancer (TNBC) models, illustrating that insulin resistance in TNBC reciprocally alters mitochondrial respiration and the expression of genes in the circadian rhythm pathway. Furthermore, genetic knockdown of BMAL1, an important circadian transcription factor, ablates key adaptations to insulin resistance, such as increased pyruvate flux, oxygen consumption, and lipid storage. Our in vivo study demonstrates that orthotopically transplanted E0771 mouse breast cancer cells with BMAL1 knocked down grow significantly faster than the parental counterpart in mice fed with the high-fat diet. This new understanding of BMAL1 expands our insights into circadian control of tumor metabolism and may lead to novel treatments for breast cancer.
Citation Format: Cassandra A. Ramos, Ching Ouyang, Yue Qi, Yiyin Chung, Chun-Ting Cheng, Mark A. LaBarge, Victoria L. Seewasldt, David K. Ann. BMAL1 rewires mitochondrial metabolism and promotes tumor progress of triple negative breast cancer during insulin resistance [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3724.
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26
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Anglada T, Repullés J, Espinal A, LaBarge MA, Stampfer MR, Genescà A, Martín M. Delayed γH2AX foci disappearance in mammary epithelial cells from aged women reveals an age-associated DNA repair defect. Aging (Albany NY) 2020; 11:1510-1523. [PMID: 30875333 PMCID: PMC6428106 DOI: 10.18632/aging.101849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/09/2019] [Indexed: 01/15/2023]
Abstract
Aging is a degenerative process in which genome instability plays a crucial role. To gain insight into the link between organismal aging and DNA repair capacity, we analyzed DNA double-strand break (DSB) resolution efficiency in human mammary epithelial cells from 12 healthy donors of young and old ages. The frequency of DSBs was measured by quantifying the number of γH2AX foci before and after 1Gy of γ-rays and it was higher in cells from aged donors (ADs) at all times analyzed. At 24 hours after irradiation, ADs retained a significantly higher frequency of residual DSBs than young donors (YDs), which had already reached values close to basal levels. The kinetics of DSB induction and disappearance showed that cells from ADs and YDs repair DSBs with similar speed, although analysis of early times after irradiation indicate that a repair defect may lie within the firing of the DNA repair machinery in AD cells. Indeed, using a mathematical model we calculated a constant factor of delay affecting aged human epithelial cells repair kinetics. This defect manifests with the accumulation of DSBs that might eventually undergo illegitimate repair, thus posing a relevant threat to the maintenance of genome integrity in older individuals.
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Affiliation(s)
- Teresa Anglada
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Repullés
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Microscopy Platform, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, 08041, Spain
| | - Anna Espinal
- Servei d'Estadística Aplicada, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Mark A LaBarge
- Department of Population Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA, 91010, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marta Martín
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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27
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Koll TT, Magnuson A, Dale W, LaBarge MA, Leach CR, Mohile S, Muss H, Sedenquist M, Klepin HD. Developing a clinical and biological measures of aging core: Cancer and Aging Research Group infrastructure. J Geriatr Oncol 2020; 11:343-346. [PMID: 31537478 PMCID: PMC7054170 DOI: 10.1016/j.jgo.2019.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/08/2019] [Accepted: 09/05/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Thuy T Koll
- Division of Geriatrics, Gerontology, Palliative Care Medicine, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America.
| | - Allison Magnuson
- Department of Surgery, University of Rochester Medical Center, Rochester, NY, United States of America; James P. Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, United States of America
| | - William Dale
- Department of Supportive Care Medicine, City of Hope, Duarte, CA, United States of America
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States of America
| | - Corinne R Leach
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, United States of America
| | - Supriya Mohile
- Department of Hematology and Oncology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States of America; Department of Surgery, University of Rochester Medical Center, Rochester, NY, United States of America; James P. Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hyman Muss
- Division of Hematology and Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America; Geriatric Oncology Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Margaret Sedenquist
- SCOREboard Advisory Group, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Heidi D Klepin
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
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28
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Jokela TA, Schones D, LaBarge MA. Abstract P6-03-04: Microenvironment-induced epigenetic reprogramming imposes drug-tolerant states in breast cancer cells. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p6-03-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Development of resistance to breast cancer (BC) therapy is frustratingly common. Multiple mechanisms of resistance have been identified including selection of genetic resistance, redundant signaling, and others. More recently, rare cancer cells were shown to be sporadically reprogrammed by the presence of anti-cancer drugs into transiently resistant states, then to expand later after cessation of therapy. We have demonstrated that the physical character and composition of tumor microenvironment (ME) components are determinants of BC cell drug resistance, however, the mechanism by which this phenomenon occurs is unclear. We hypothesize that epigenetic reprogramming is not rare or sporadic, indeed, that specific tumor ME components impose epigenetic states that beget the expression of gene clusters that put cancer cells into drug-tolerant states. Our current pharmacopeia targets cancer cells, not their ME. Some tumor ME components, e.g. extracellular matrices (ECM), have half-lives that span years, and growth factors with typically short half-lives can be stabilized by direct association with ECM. Thus, a ME-imposed drug tolerance mechanism would explain how resistance can arise rapidly, in multiple locations, without the need for genetic selection. Because ME-cell interactions lead to activation of specific pathways, based on canonical receptor-ligand models, we should be able to circumvent ME-imposed drug tolerance by addition of molecules that alter ME-induced signaling. Clusters of genes that are activated in multidrug resistant breast cancer cells identified potential markers of drug tolerance. ME-drivers of the drug tolerance markers were identified in high-throughput cell-based screens with the MicroEnvironment MicroArray (MEMA) platform. BC cells were exposed in parallel to over 1000 unique combinatorial MEs, which were chosen to mimic normal mammary gland, and luminal or basal BC tumor MEs. Single-cell resolution analysis revealed MEs that induce and maintain drug-tolerance markers. Longer-term functional experiments validated that the identified MEs also increased BC cells drug tolerance. Chromatin accessibility profiling with ATAC-sequencing demonstrated that BC cells cultured in those drug-tolerance inducing MEs exhibit chromatin opening in promoter regions of genes linked to epithelial plasticity (e.g. Axl, SNAI2, Vimentin, TWIST1) within 24h of exposure. These results support the concept that specific MEs drive drug-tolerant cellular phenotypes and suggest a novel interventional avenue for preventing acquired therapy resistance.
Citation Format: Tiina A Jokela, Dustin Schones, Mark A LaBarge. Microenvironment-induced epigenetic reprogramming imposes drug-tolerant states in breast cancer cells [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-03-04.
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Sayaman RW, Wolf DM, Yau C, Wulfkuhle J, Petricoin E, Brown-Swigart L, Asare SM, Hirst GL, Sit L, O'Grady N, Hedistian D, Esserman LJ, LaBarge MA, van 't Veer LJ. Abstract P1-21-08: Application of machine learning to elucidate the biology predicting response in the I-SPY 2 neoadjuvant breast cancer trial. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p1-21-08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Machine learning relies on algorithms that learn patterns in large, complex datasets to predict outcomes. The adaptive, neoadjuvant I-SPY 2 TRIAL evaluates novel agents added to standard therapy, and identifies their most responsive subtype. While previously proposed genes/signatures reflecting an agent’s mechanism of action predicted pathologic complete response (pCR) in some treatment arms/subtypes, not all arms had strong predictive biomarkers. We leverage machine learning to explore the limitations of using only known mechanisms of action in predicting pCR, and the extent to which biology outside known drug action improves response prediction in the first 10 arms of the trial.
Methods: Our study involves 986 patients with pre-treatment gene expression and pCR data across 10 treatment arms including inhibitors of HER2: neratinib (N), pertuzumab (P), TDM1/P; AKT (MK-2206; M); IGF1R (ganitumab); HSP90 (ganetespib); PARP/DNA repair (veliparib/carboplatin; VC); ANG1/2 (AMG386); immune checkpoints (pembrolizumab; Pembro); and a shared control arm (Ctr). Each arm/receptor subtype group was evaluated independently for groups with at least 20 patients (n=19), with 25% of data held out as independent test sets. We implemented a 3-fold cross validation technique with 10 repeats using Random Forest ensemble algorithm with recursive feature elimination. In combination with clinical data, a three-pronged feature-selection approach was employed: (1) restricted to mechanism of action genes: AKT/PI3K/HER (m=10 genes), IGF1 (m=11), HSP90 (m=88), DNA repair (m=79), TIE1/2 (m=11), and immune (m=61), as well as HER2 amplicon genes; (2) expanded to include targeted pathways for all 10 agents/combinations plus ESR1 and proliferation genes (m=339); (3) an unbiased whole genome approach (m=17,990). Models were considered predictive if AUROC ≥ 0.75, Sensitivity ≥ 0.6 and Specificity ≥ 0.6 in cross validation and independent test sets.
Results: Table 1 summarizes the results of our analysis (Yes=predictive; NA=no/insufficient data). Prediction of pCR using only genes reflecting the known mechanism of the drug succeeded in 5 subgroups, with DNA repair genes predicting VC response and immune genes predicting Pembro response in HR+HER2- and HR-HER2- subsets, and AKT/PI3K/HER + HER2 amplicon genes predicting (P) response in HR+HER2+ patients. Expansion of the feature set to include genes associated with all mechanisms of action of all drugs proved sufficient to produce good predictive models in 8 of 19 subgroups. Examples include DNA repair + immune genes predicting response to ganitumab in HR+HER2- and to (N) in HR+HER2+. An unbiased approach using all data yielded predictive power in 8 of 19 subgroups, including 5 with no predictive models from the first two approaches. Examples include HR-HER2- (N) predictors enriched for metabolic, cell division and membrane protein proteolytic processes; HR+HER2+ TDM1/P enriched for metabolic, stress response and cell cycle processes; and HR-HER2- MK-2206 predictors containing Ser/Thr kinases. In total, we identify predictive biomarkers in 14 of 19 subgroups across the three feature selection approaches.
Conclusion: Our results suggests that hypothesis driven analysis restricted to assumed mechanisms of action of the experimental agents may be insufficient, and that exploration of possible off target effects may be needed to understand the underlying biology of response or resistance.
Table 1. Model results across feature selection approachesHR+HER2-HR-HER2-HR+HER2+HR-HER2+Number of PatientsMechanism of ActionAll Mechanisms of ActionUnbiasedNumber of PatientsMechanism of ActionAll Mechanisms of ActionUnbiasedNumber of PatientsMechanism of ActionAll Mechanisms of ActionUnbiasedNumber of PatientsMechanism of ActionAll Mechanisms of ActionUnbiasedneratinib (pan anti-HER)NA32NoNoYes42NoYesYes23NoNoYespertuzumab (anti-HER2)NANA29YesYesNoNATDM1/Pertuzumab (anti-HER2)NANA35NoNoYesNAMK−2206 (AKT inhibitor)28NoNoNo32NoNoYesNANAganitumab (IGFR inhibitor)58NoYesNo48NoNoNoNANAganetespib (HSP90 inhibitor)48NoYesYes45NoNoNoNANAvelirapib/carboplatin (PARP inhibitor/DNA damage)33YesYesNo39YesYesNoNANAAMG386 (ANG1/2 inhibitor)62NoYesYes53NoNoNoNANApembrolizumab (immune checkpoint inhibitor)38YesYesNo29YesNoNoNANAHER2+ controlNANANANAHER2- control94NoNoYes84NoNoNoNANA
Citation Format: Rosalyn W. Sayaman, Denise M. Wolf, Christina Yau, Julie Wulfkuhle, Emanuel Petricoin, Lamorna Brown-Swigart, Smita M. Asare, Gillian L. Hirst, Laura Sit, Nicholas O'Grady, Diane Hedistian, I-SPY 2 TRIAL Consortium, Laura J. Esserman, Mark A. LaBarge, Laura J van 't Veer. Application of machine learning to elucidate the biology predicting response in the I-SPY 2 neoadjuvant breast cancer trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-21-08.
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Affiliation(s)
| | - Denise M. Wolf
- 2University of California, San Francisco, San Francisco, CA
| | - Christina Yau
- 2University of California, San Francisco, San Francisco, CA
| | | | | | | | - Smita M. Asare
- 4Quantum Leap Healthcare Collaborative, San Francisco, CA
| | | | - Laura Sit
- 2University of California, San Francisco, San Francisco, CA
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30
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Ramos CA, Ouyang C, Qi Y, Chung Y, Cheng CT, LaBarge MA, Seewaldt VL, Ann DK. A Non-canonical Function of BMAL1 Metabolically Limits Obesity-Promoted Triple-Negative Breast Cancer. iScience 2020; 23:100839. [PMID: 32058954 PMCID: PMC6997869 DOI: 10.1016/j.isci.2020.100839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/03/2019] [Accepted: 01/09/2020] [Indexed: 01/01/2023] Open
Abstract
The epidemiological association between disrupted circadian rhythms and metabolic diseases is implicated in increased risk of human breast cancer and poor therapeutic outcomes. To define a metabolic phenotype and the underlying molecular mechanism, we applied chronic insulin treatment (CIT) to an in vitro model of triple-negative breast cancer to directly address how BMAL1, a key circadian transcription factor, regulates cancer cell respiration and governs tumor progression. At the cellular level, BMAL1 suppresses the flexibility of mitochondrial substrate usage and the pyruvate-dependent mitochondrial respiration induced by CIT. We established an animal model of diet-induced obesity/hyperinsulinemia and observed that BMAL1 functions as a tumor suppressor in obese, but not lean, mice. Downregulation of BMAL1 is associated with higher risk of metastasis in human breast tumors. In summary, loss of BMAL1 in tumors confers advantages to cancer cells in both intrinsic mitochondrial metabolism and extrinsic inflammatory tumor microenvironment during pre-diabetic obesity/hyperinsulinemia. Circadian regulator BMAL1 rewires metabolism in a chronic insulin-treated TNBC model Pyruvate links BMAL1 to mitochondrial bioenergetics BMAL1 suppresses tumor proliferation and metastasis in hyperinsulinemic obese mice BMAL1 influences tumor microenvironment in high-fat-diet-fed mice
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Affiliation(s)
- Cassandra A Ramos
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Ching Ouyang
- Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA; Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yiyin Chung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Chun-Ting Cheng
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Mark A LaBarge
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA; Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Victoria L Seewaldt
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA; Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA.
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31
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Fresques T, Zirbes A, Shalabi S, Samson S, Preto S, Stampfer MR, LaBarge MA. Breast Tissue Biology Expands the Possibilities for Prevention of Age-Related Breast Cancers. Front Cell Dev Biol 2019; 7:174. [PMID: 31555644 PMCID: PMC6722426 DOI: 10.3389/fcell.2019.00174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022] Open
Abstract
Preventing breast cancer before it is able to form is an ideal way to stop breast cancer. However, there are limited existing options for prevention of breast cancer. Changes in the breast tissue resulting from the aging process contribute to breast cancer susceptibility and progression and may therefore provide promising targets for prevention. Here, we describe new potential targets, immortalization and inflammaging, that may be useful for prevention of age-related breast cancers. We also summarize existing studies of warfarin and metformin, current drugs used for non-cancerous diseases, that also may be repurposed for breast cancer prevention.
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Affiliation(s)
- Tara Fresques
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Arrianna Zirbes
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States
| | - Sundus Shalabi
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Medical Research Center, Al-Quds University, Jerusalem, Palestine
| | - Susan Samson
- Breast Science Advocacy Core, Breast Oncology Program, University of California, San Francisco, San Francisco, CA, United States
| | | | - Martha R Stampfer
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mark A LaBarge
- Department of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, United States.,Center for Cancer and Aging Research, Beckman Research Institute at City of Hope, Duarte, CA, United States
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32
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Sridharan DM, Enerio S, Wang C, LaBarge MA, Stampfer MR, Pluth JM. Genetic variation and radiation quality impact cancer promoting cellular phenotypes in response to HZE exposure. Life Sci Space Res (Amst) 2019; 20:101-112. [PMID: 30797427 DOI: 10.1016/j.lssr.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
There exists a wide degree of genetic variation within the normal human population which includes disease free individuals with heterozygote defects in major DNA repair genes. A lack of understanding of how this genetic variation impacts cellular phenotypes that inform cancer risk post heavy ion exposure poses a major limitation in developing personalized cancer risk assessment astronauts. We initiated a pilot study with Human Mammary Epithelial Cell strains (HMEC) derived from wild type, a p16 silenced derivative of wild type, and various genetic variants that were heterozygote for DNA repair genes; BRCA1, BRCA2 and ATM. Cells strains were exposed to different high and low LET radiation qualities to generate both simple and complex lesions and centrosome aberrations were examined as a surrogate marker of genomic instability and cancer susceptibility post different exposures. Our results indicate that centrosome aberration frequency is higher in the genetic variants under study. The aberration frequency increases with dose, complexity of the lesion generated by different radiation qualities and age of the individual. This increase in genomic instability correlates with elevated check-point activation post radiation exposure. These studies suggest that the influence of individual genetics on cell cycle regulation could modify the degree of early genomic instability in response to complex lesions and potentially define cancer predisposition in response to HZE exposure. These results will have significant implications in estimating cancer susceptibility in genetically variant individuals exposed to HZE particles.
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Affiliation(s)
- Deepa M Sridharan
- Division of Chemical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Shiena Enerio
- Division of Biological Systems and Engineering, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Chris Wang
- Division of Biological Systems and Engineering, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Mark A LaBarge
- Department of Population Sciences, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martha R Stampfer
- Division of Biological Systems and Engineering, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Janice M Pluth
- Department of Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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Abstract
Potential for cancers to form metastases requires cell dissemination utilizing epithelial-to-mesenchymal transition (EMT) program. In this issue of Cancer Cell, Ishay-Ronen et al. show that plasticity intrinsic to the EMT program can be exploited to divert cancer cells into becoming post-mitotic adipocytes, thus preventing formation of metastases.
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Affiliation(s)
- Stefan Hinz
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91010, USA.
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Lee JK, Bloom J, Zubeldia-Plazaola A, Garbe JC, Stampfer MR, LaBarge MA. Different culture media modulate growth, heterogeneity, and senescence in human mammary epithelial cell cultures. PLoS One 2018; 13:e0204645. [PMID: 30273377 PMCID: PMC6166958 DOI: 10.1371/journal.pone.0204645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 09/03/2017] [Accepted: 08/16/2018] [Indexed: 02/07/2023] Open
Abstract
The ability to culture normal human mammary epithelial cells (HMEC) greatly facilitates experiments that seek to understand both normal mammary cell biology and the many differences between normal and abnormal human mammary epithelia. To maximize in vivo relevance, the primary cell culture conditions should maintain cells in states that resemble in vivo as much as possible. Towards this goal, we compared the properties of HMEC strains from two different reduction mammoplasty tissues that were grown in parallel using different media and culture conditions. Epithelial organoids were initiated into three different media: two commonly used serum-free-media, MCDB 170-type (e.g. MEGM) and WIT-P, and a low stress media, M87A. Growth, lineage heterogeneity, p16 protein expression, and population doublings to senescence were measured for each culture condition. MCDB 170 caused rapid senescence and loss of heterogeneity within 2 to 3 passages, but some cultures went through the 1 to 2 month process of selection to generate clonal finite post-selection post-stasis cells. WIT-P caused impressive expansion of luminal cells in 2nd passage followed by their near complete disappearance by passage 4 and senescence shortly thereafter. M87A supported as much as twice the number of population doublings compared to either serum-free medium, and luminal and myoepithelial cells were present for as many as 8 passages. Thus, of the three media compared, WIT-P and MCDB 170 imposed rapid senescence and loss of lineage heterogeneity, phenotypes consistent with cells maintained in high-stress conditions, while M87A supported cultures that maintained multiple lineages and robust growth for up to 60 population doublings. In conjunction with previous studies examining the molecular properties of cultures grown in these media, we conclude that M87A medium is most able to support long-term culture of multiple lineages similar to in vivo conditions, thereby facilitating investigations of normal HMEC biology relevant to the mammary gland in situ.
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Affiliation(s)
- Jonathan K. Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jessica Bloom
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | | | - James C. Garbe
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Martha R. Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail: (MAL); (MRS)
| | - Mark A. LaBarge
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- * E-mail: (MAL); (MRS)
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Todhunter ME, Sayaman RW, Miyano M, LaBarge MA. Tissue aging: the integration of collective and variant responses of cells to entropic forces over time. Curr Opin Cell Biol 2018; 54:121-129. [PMID: 29908481 PMCID: PMC6258070 DOI: 10.1016/j.ceb.2018.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
Abstract
Aging is driven by unavoidable entropic forces, physicochemical in nature, that damage the raw materials that constitute biological systems. Single cells experience and respond to stochastic physicochemical insults that occur either to the cells themselves or to their microenvironment, in a dynamic and reciprocal manner, leading to increased age-related cell-to-cell variation. We will discuss the biological mechanisms that integrate cell-to-cell variation across tissues resulting in stereotypical phenotypes of age.
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Affiliation(s)
- Michael E Todhunter
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Rosalyn W Sayaman
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Masaru Miyano
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA
| | - Mark A LaBarge
- Department of Populations Sciences, and Center for Cancer and Aging, Beckman Research Institute at City of Hope, 1500 E Duarte Rd, Duarte, CA 91011 USA.
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Lin CH, Jokela T, Gray J, LaBarge MA. Combinatorial Microenvironments Impose a Continuum of Cellular Responses to a Single Pathway-Targeted Anti-cancer Compound. Cell Rep 2018; 21:533-545. [PMID: 29020637 DOI: 10.1016/j.celrep.2017.09.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 12/19/2016] [Revised: 07/26/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023] Open
Abstract
Tumor microenvironments are a driver of resistance to anti-cancer drugs. Dissecting cell-microenvironment interactions into tractable units of study presents a challenge. Here, we assess the impact of hundreds of tumor-inspired microenvironments, in parallel, on lapatinib responses in four cancer cell lines. Combinations of ECM and soluble factors were printed on stiffness-tunable substrata to generate a collection of controlled microenvironments in which to explore cell-based functional responses. Proliferation, HER2 protein expression and phosphorylation, and morphology were measured in single cells. Using dimension reduction and linear modeling, the effects of microenvironment constituents were identified and then validated empirically. Each of the cell lines exhibits unique microenvironment-response patterns. Fibronectin, type IV collagen, and matrix rigidity are significant regulators of lapatinib resistance in HER2-amplified breast cancer cells. Small-molecule inhibitors were identified that could attenuate microenvironment-imposed resistance. Thus, we demonstrate a strategy to identify resistance- and sensitivity-driving microenvironments to improve the efficacy of anti-cancer therapeutics.
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Affiliation(s)
- Chun-Han Lin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tiina Jokela
- Department of Population Sciences, City of Hope, Duarte, CA 91010, USA; Center for Cancer Biomarkers, University of Bergen, Bergen 5009, Norway
| | - Joe Gray
- Department of Bioengineering, Oregon Health & Science University, Portland, OR 97201, USA
| | - Mark A LaBarge
- Department of Population Sciences, City of Hope, Duarte, CA 91010, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Center for Cancer Biomarkers, University of Bergen, Bergen 5009, Norway.
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37
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Jokela TA, Engelsen AST, Rybicka A, Pelissier Vatter FA, Garbe JC, Miyano M, Tiron C, Ferariu D, Akslen LA, Stampfer MR, Lorens JB, LaBarge MA. Microenvironment-Induced Non-sporadic Expression of the AXL and cKIT Receptors Are Related to Epithelial Plasticity and Drug Resistance. Front Cell Dev Biol 2018; 6:41. [PMID: 29719832 PMCID: PMC5913284 DOI: 10.3389/fcell.2018.00041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/23/2018] [Indexed: 12/13/2022] Open
Abstract
The existence of rare cancer cells that sporadically acquire drug-tolerance through epigenetic mechanisms is proposed as one mechanism that drives cancer therapy failure. Here we provide evidence that specific microenvironments impose non-sporadic expression of proteins related to epithelial plasticity and drug resistance. Microarrays of robotically printed combinatorial microenvironments of known composition were used to make cell-based functional associations between microenvironments, which were design-inspired by normal and tumor-burdened breast tissues, and cell phenotypes. We hypothesized that specific combinations of microenvironment constituents non-sporadically impose the induction of the AXL and cKIT receptor tyrosine kinase proteins, which are known to be involved in epithelial plasticity and drug-tolerance, in an isogenic human mammary epithelial cell (HMEC) malignant progression series. Dimension reduction analysis reveals type I collagen as a dominant feature, inducing expression of both markers in pre-stasis finite lifespan HMECs, and transformed non-malignant and malignant immortal cell lines. Basement membrane-associated matrix proteins, laminin-111 and type IV collagen, suppress AXL and cKIT expression in pre-stasis and non-malignant cells. However, AXL and cKIT are not suppressed by laminin-111 in malignant cells. General linear models identified key factors, osteopontin, IL-8, and type VIα3 collagen, which significantly upregulated AXL and cKIT, as well as a plasticity-related gene expression program that is often observed in stem cells and in epithelial-to-mesenchymal-transition. These factors are co-located with AXL-expressing cells in situ in normal and breast cancer tissues, and associated with resistance to paclitaxel. A greater diversity of microenvironments induced AXL and cKIT expression consistent with plasticity and drug-tolerant phenotypes in tumorigenic cells compared to normal or immortal cells, suggesting a reduced perception of microenvironment specificity in malignant cells. Microenvironment-imposed reprogramming could explain why resistant cells are seemingly persistent and rapidly adaptable to multiple classes of drugs. These results support the notion that specific microenvironments drive drug-tolerant cellular phenotypes and suggest a novel interventional avenue for preventing acquired therapy resistance.
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Affiliation(s)
- Tiina A. Jokela
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Population Sciences, Center for Cancer and Aging, City of Hope, Duarte, CA, United States
| | - Agnete S. T. Engelsen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Agata Rybicka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - James C. Garbe
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Masaru Miyano
- Department of Population Sciences, Center for Cancer and Aging, City of Hope, Duarte, CA, United States
| | - Crina Tiron
- Regional Institute of Oncology, Iasi, Romania
| | - Dan Ferariu
- Regional Institute of Oncology, Iasi, Romania
| | - Lars A. Akslen
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Martha R. Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - James B. Lorens
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Mark A. LaBarge
- Department of Population Sciences, Center for Cancer and Aging, City of Hope, Duarte, CA, United States
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Samson S, Northey JJ, Plaks V, Baas C, Dean I, LaBarge MA, Goga A, Van't Veer LJ, Weaver VM. New Horizons in Advocacy Engaged Physical Sciences and Oncology Research. Trends Cancer 2018; 4:260-264. [PMID: 29606307 DOI: 10.1016/j.trecan.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 01/09/2018] [Accepted: 02/12/2018] [Indexed: 11/28/2022]
Abstract
To address cancer as a multifaceted adaptive system, the increasing momentum for cross-disciplinary connectivity between cancer biologists, physical scientists, mathematicians, chemists, biomedical engineers, computer scientists, clinicians, and advocates is fueling the emergence of new scientific frontiers, principles, and opportunities within physical sciences and oncology. In parallel to highlighting the advances, challenges, and acceptance of advocates as credible contributors, we offer recommendations for addressing real world hurdles in advancing equitable partnerships among advocacy stakeholders.
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Affiliation(s)
- Susan Samson
- Breast Science Advocacy Core (BSAC), Breast Oncology Program, University of California, San Francisco, CA, 94115, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA.
| | - Jason J Northey
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, 94143, USA
| | - Vicki Plaks
- Department of Orofacial Sciences, University of California, San Francisco, CA, 94143, USA
| | - Carole Baas
- Division of Cancer Biology, National Cancer Institute, National Institutes of Health, Rockville, MD, 20892
| | - Ivory Dean
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, 94143, USA
| | - Mark A LaBarge
- Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Andrei Goga
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA; Department of Cell and Tissue Biology and Medicine, University of California, San Francisco, CA, 94143, USA
| | - Laura J Van't Veer
- Breast Science Advocacy Core (BSAC), Breast Oncology Program, University of California, San Francisco, CA, 94115, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, 94115, USA
| | - Valerie M Weaver
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA; Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, CA, 94143, USA; Departments of Anatomy and Bioengineering and Therapeutic Sciences and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA
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Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MR, Gartner ZJ, LaBarge MA, Sohn LL. Characterizing cellular mechanical phenotypes with mechano-node-pore sensing. Microsyst Nanoeng 2018; 4:17091. [PMID: 29780657 PMCID: PMC5958920 DOI: 10.1038/micronano.2017.91] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The mechanical properties of cells change with their differentiation, chronological age, and malignant progression. Consequently, these properties may be useful label-free biomarkers of various functional or clinically relevant cell states. Here, we demonstrate mechano-node-pore sensing (mechano-NPS), a multi-parametric single-cell-analysis method that utilizes a four-terminal measurement of the current across a microfluidic channel to quantify simultaneously cell diameter, resistance to compressive deformation, transverse deformation under constant strain, and recovery time after deformation. We define a new parameter, the whole-cell deformability index (wCDI), which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell types. The wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant, MCF-10A and BEAS-2B cell lines, and distinguishes between cells treated or untreated with cytoskeleton-perturbing small molecules. We categorize cell recovery time, ΔTr, as instantaneous (ΔTr ~ 0 ms), transient (ΔTr ≤ 40ms), or prolonged (ΔTr > 40ms), and show that the composition of recovery types, which is a consequence of changes in cytoskeletal organization, correlates with cellular transformation. Through the wCDI and cell-recovery time, mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells with accuracy comparable to flow cytometry, but without antibody labeling. Mechano-NPS identifies mechanical phenotypes that distinguishes lineage, chronological age, and stage of malignant progression in human epithelial cells.
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Affiliation(s)
- Junghyun Kim
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
| | - Sewoon Han
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
| | - Andy Lei
- Department of Bioengineering, University of California at Berkeley, Berkeley, 94720-1762 CA USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
| | - Jessica Bloom
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 94143 CA USA
| | - Martha R. Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, 94720 USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, 94143 CA USA
- Graduate Program in Bioengineering, University of California, Berkeley, and
University of California, San Francisco, Berkeley, 94720 CA USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, 91010 CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, 94720 USA
| | - Lydia L. Sohn
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, 94720-1740 CA USA
- Graduate Program in Bioengineering, University of California, Berkeley, and
University of California, San Francisco, Berkeley, 94720 CA USA
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40
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Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. Opportunities for organoids as new models of aging. J Cell Biol 2017; 217:39-50. [PMID: 29263081 PMCID: PMC5748992 DOI: 10.1083/jcb.201709054] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023] Open
Abstract
The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research.
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Affiliation(s)
- Jennifer L Hu
- University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA
| | - Michael E Todhunter
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Mark A LaBarge
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA .,National Science Foundation Center for Cellular Construction, University of California San Francisco, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
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41
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Sridharan DM, Enerio S, LaBarge MA, Stampfer MM, Pluth JM. Lesion complexity drives age related cancer susceptibility in human mammary epithelial cells. Aging (Albany NY) 2017; 9:665-686. [PMID: 28245431 PMCID: PMC5391225 DOI: 10.18632/aging.101183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/19/2017] [Indexed: 01/11/2023]
Abstract
Exposures to various DNA damaging agents can deregulate a wide array of critical mechanisms that maintain genome integrity. It is unclear how these processes are impacted by one's age at the time of exposure and the complexity of the DNA lesion. To clarify this, we employed radiation as a tool to generate simple and complex lesions in normal primary human mammary epithelial cells derived from women of various ages. We hypothesized that genomic instability in the progeny of older cells exposed to complex damages will be exacerbated by age-associated deterioration in function and accentuate age-related cancer predisposition. Centrosome aberrations and changes in stem cell numbers were examined to assess cancer susceptibility. Our data show that the frequency of centrosome aberrations proportionately increases with age following complex damage causing exposures. However, a dose-dependent increase in stem cell numbers was independent of both age and the nature of the insult. Phospho-protein signatures provide mechanistic clues to signaling networks implicated in these effects. Together these studies suggest that complex damage can threaten the genome stability of the stem cell population in older people. Propagation of this instability is subject to influence by the microenvironment and will ultimately define cancer risk in the older population.
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Affiliation(s)
- Deepa M Sridharan
- Division of Biological Systems and Engineering, Department of Organismal Systems and Bioresilience, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Shiena Enerio
- Division of Biological Systems and Engineering, Department of Organismal Systems and Bioresilience, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Mark A LaBarge
- Department of Population Sciences, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martha M Stampfer
- Division of Biological Systems and Engineering, Department of Organismal Systems and Bioresilience, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
| | - Janice M Pluth
- Division of Biological Systems and Engineering, Department of Organismal Systems and Bioresilience, Lawrence Berkeley National Laboratory, Berkeley, CA 94803, USA
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42
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Cornish-Bowden A, Cornish-Bowden A, Rasnick D, Heng HH, Horne S, Abdallah B, Liu G, Ye CJ, Bloomfield M, Vincent MD, Aldaz CM, Karlsson J, Valind A, Jansson C, Gisselsson D, Graves JAM, Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Huleyuk NL, Baklaushev VP, Kovaleva OA, Chekhonin VP, Vassetzky YS, Avdieiev SS, Bakker B, Taudt AS, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Tatché MC, Foijer F, Liehr T, Baudoin NC, Nicholson JM, Soto K, Quintanilla I, Camps J, Cimini D, Dürrbaum M, Donnelly N, Passerini V, Kruse C, Habermann B, Storchová Z, Mandrioli D, Belpoggi F, Silbergeld EK, Perry MJ, Skotheim RI, Løvf M, Johannessen B, Hoff AM, Zhao S, SveeStrømme JM, Sveen A, Lothe RA, Hehlmann R, Voskanyan A, Fabarius A, Böcking A, Biesterfeld S, Berynskyy L, Börgermann C, Engers R, Dietz J, Fritz A, Sehgal N, Vecerova J, Stojkovicz B, Ding H, Page N, Tye C, Bhattacharya S, Xu J, Stein G, Stein J, Berezney R, Gong X, Grasedieck S, Swoboda J, Rücker FG, Bullinger L, Pollack JR, Roumelioti FM, Chiourea M, Raftopoulou C, Gagos S, Duesberg P, Bloomfield M, Hwang S, Gustafsson HT, O’Sullivan C, Acevedo-Colina A, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM, Stampfer MR, Vrba L, LaBarge MA, Futscher B, Garbe JC, Zhou YH, Trinh AL, Zhou YH, Digman M. Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects. Mol Cytogenet 2017. [PMCID: PMC5499067 DOI: 10.1186/s13039-017-0320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
A novel microsphere-based flow cytometry approach to study adherent cell signaling responses in different microenvironmental contexts at the single cell level.
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Affiliation(s)
| | - Garry P. Nolan
- Baxter Laboratory in Stem Cell Biology
- Department of Microbiology and Immunology
- Stanford University
- Stanford
- USA
| | - Mark A. LaBarge
- Life Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - James B. Lorens
- Department of Biomedicine
- Center for Cancer Biomarkers
- University of Bergen
- Bergen
- Norway
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44
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Weber RJ, Cerchiari AE, Delannoy LS, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ. Rapid Organoid Reconstitution by Chemical Micromolding. ACS Biomater Sci Eng 2016; 2:1851-1855. [DOI: 10.1021/acsbiomaterials.6b00421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Robert J. Weber
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Chemistry
and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, Room 522, San Francisco, California 94158, United States,
- Medical
Scientist Training Program, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Alec E. Cerchiari
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
- UCSF Bioengineering and Therapeutic Sciences, 1700 Fourth Street, Room 216B, San Francisco, California 94158, United States
| | - Lucas S. Delannoy
- Laboratory
of Stem Cell Bioengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Station
15, Building Al 1106, CH-1015 Lausanne, Switzerland
| | - James C. Garbe
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Mark A. LaBarge
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Tejal A. Desai
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
- UCSF Bioengineering and Therapeutic Sciences, 1700 Fourth Street, Room 216B, San Francisco, California 94158, United States
| | - Zev J. Gartner
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States,
- Chemistry
and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, Room 522, San Francisco, California 94158, United States,
- UC Berkeley−UCSF Group in Bioengineering, 1700 Fourth Street, Room 216, San Francisco, California 94158, United States,
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45
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LaBarge MA, Mora-Blanco EL, Samson S, Miyano M. Breast Cancer beyond the Age of Mutation. Gerontology 2015; 62:434-42. [PMID: 26539838 DOI: 10.1159/000441030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/11/2015] [Indexed: 12/26/2022] Open
Abstract
Age is the greatest risk factor for breast cancer, but the reasons underlying this association are unclear. While there is undeniably a genetic component to all cancers, the accumulation of mutations with age is insufficient to explain the age-dependent increase in breast cancer incidence. In this viewpoint, we propose a multilevel framework to better understand the respective roles played by somatic mutation, microenvironment, and epigenetics making women more susceptible to breast cancer with age. The process of aging is associated with gradual breast tissue changes that not only corrupt the tumor-suppressive activity of normal tissue but also impose age-specific epigenetic changes that alter gene expression, thus reinforcing cellular phenotypes that are associated with a continuum of age-related tissue microenvironments. The evidence discussed here suggests that while the riddle of whether epigenetics drives microenvironmental changes, or whether changes in the microenvironment alter heritable cellular memory has not been solved, a path has been cleared enabling functional analysis leading to the prediction of key nodes in the network that link the microenvironment with the epigenome. The hypothesis that the accumulation of somatic mutations with age drives the age-related increase in breast cancer incidence, if correct, has a somewhat nihilistic conclusion, namely that cancers will be impossible to avoid. Alternatively, if microenvironment-driven epigenetic changes are the key to explaining susceptibility to age-related breast cancers, then there is hope that primary prevention is possible because epigenomes are relatively malleable.
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Affiliation(s)
- Mark A LaBarge
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, Calif., USA
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46
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Lin CH, Pelissier FA, Zhang H, Lakins J, Weaver VM, Park C, LaBarge MA. Microenvironment rigidity modulates responses to the HER2 receptor tyrosine kinase inhibitor lapatinib via YAP and TAZ transcription factors. Mol Biol Cell 2015; 26:3946-53. [PMID: 26337386 PMCID: PMC4710228 DOI: 10.1091/mbc.e15-07-0456] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [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: 07/01/2015] [Revised: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 12/31/2022] Open
Abstract
Stiffness is a biophysical property of the extracellular matrix that modulates cellular functions, including proliferation, invasion, and differentiation, and it also may affect therapeutic responses. Therapeutic durability in cancer treatments remains a problem for both chemotherapies and pathway-targeted drugs, but the reasons for this are not well understood. Tumor progression is accompanied by changes in the biophysical properties of the tissue, and we asked whether matrix rigidity modulated the sensitive versus resistant states in HER2-amplified breast cancer cell responses to the HER2-targeted kinase inhibitor lapatinib. The antiproliferative effect of lapatinib was inversely proportional to the elastic modulus of the adhesive substrata. Down-regulation of the mechanosensitive transcription coactivators YAP and TAZ, either by siRNA or with the small-molecule YAP/TEAD inhibitor verteporfin, eliminated modulus-dependent lapatinib resistance. Reduction of YAP in vivo in mice also slowed the growth of implanted HER2-amplified tumors, showing a trend of increasing sensitivity to lapatinib as YAP decreased. Thus we address the role of stiffness in resistance to and efficacy of a HER2 pathway-targeted therapeutic via the mechanotransduction arm of the Hippo pathway.
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Affiliation(s)
- Chun-Han Lin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Fanny A Pelissier
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Hui Zhang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Jon Lakins
- Center for Bioengineering, Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143
| | - Valerie M Weaver
- Center for Bioengineering, Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143
| | - Catherine Park
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143
| | - Mark A LaBarge
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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47
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Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ. Programmed synthesis of three-dimensional tissues. Nat Methods 2015; 12:975-81. [PMID: 26322836 PMCID: PMC4589502 DOI: 10.1038/nmeth.3553] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/17/2015] [Indexed: 12/31/2022]
Abstract
Reconstituting tissues from their cellular building blocks facilitates the modeling of morphogenesis, homeostasis and disease in vitro. Here we describe DNA-programmed assembly of cells (DPAC), a method to reconstitute the multicellular organization of organoid-like tissues having programmed size, shape, composition and spatial heterogeneity. DPAC uses dissociated cells that are chemically functionalized with degradable oligonucleotide 'Velcro', allowing rapid, specific and reversible cell adhesion to other surfaces coated with complementary DNA sequences. DNA-patterned substrates function as removable and adhesive templates, and layer-by-layer DNA-programmed assembly builds arrays of tissues into the third dimension above the template. DNase releases completed arrays of organoid-like microtissues from the template concomitant with full embedding in a variety of extracellular matrix (ECM) gels. DPAC positions subpopulations of cells with single-cell spatial resolution and generates cultures several centimeters long. We used DPAC to explore the impact of ECM composition, heterotypic cell-cell interactions and patterns of signaling heterogeneity on collective cell behaviors.
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Affiliation(s)
- Michael E Todhunter
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Noel Y Jee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Chemistry &Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Alex J Hughes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Maxwell C Coyle
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alec Cerchiari
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Graduate Program in Bioengineering, University of California, Berkeley, and University of California, San Francisco, Berkeley, California, USA
| | - Justin Farlow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - James C Garbe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mark A LaBarge
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tejal A Desai
- Chemistry &Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Graduate Program in Bioengineering, University of California, Berkeley, and University of California, San Francisco, Berkeley, California, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Chemistry &Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Graduate Program in Bioengineering, University of California, Berkeley, and University of California, San Francisco, Berkeley, California, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, California, USA
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48
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Garbe JC, Vrba L, Sputova K, Fuchs L, Novak P, Brothman AR, Jackson M, Chin K, LaBarge MA, Watts G, Futscher BW, Stampfer MR. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross genomic alterations. Cell Cycle 2015; 13:3423-35. [PMID: 25485586 PMCID: PMC4613853 DOI: 10.4161/15384101.2014.954456] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Telomerase reactivation and immortalization are critical for human carcinoma progression. However, little is known about the mechanisms controlling this crucial step, due in part to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the 2 main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier was bypassed using shRNA to p16INK4; replicative senescence due to critically shortened telomeres was bypassed in post-stasis HMEC by c-MYC transduction. Thus, 2 pathologically relevant oncogenic agents are sufficient to immortally transform normal HMEC. The resultant non-clonal immortalized lines exhibited normal karyotypes. Most human carcinomas contain genomically unstable cells, with widespread instability first observed in vivo in pre-malignant stages; in vitro, instability is seen as finite cells with critically shortened telomeres approach replicative senescence. Our results support our hypotheses that: (1) telomere-dysfunction induced genomic instability in pre-malignant finite cells may generate the errors required for telomerase reactivation and immortalization, as well as many additional “passenger” errors carried forward into resulting carcinomas; (2) genomic instability during cancer progression is needed to generate errors that overcome tumor suppressive barriers, but not required per se; bypassing the senescence barriers by direct targeting eliminated a need for genomic errors to generate immortalization. Achieving efficient HMEC immortalization, in the absence of “passenger” genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression, and exploration of agents that could prevent immortalization.
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Key Words
- BaP, benzo(a)pyrene
- CT, cholera toxin
- DDR, DNA damage response
- DMR, differentially methylated regions
- HMEC, human mammary epithelial cells
- OIS, oncogene-induced senescence
- PD, population doublings
- RB, retinoblastoma protein
- TTS, transcription start site
- X, oxytocin
- c-Myc
- carcinogenesis
- genomic instability
- human mammary epithelial cells
- immortalization
- p, passage
- p16INK4a
- p16sh, shRNA to p16INK4A
- senescence
- telomerase
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Affiliation(s)
- James C Garbe
- a Life Sciences Division ; Lawrence Berkeley National Laboratory ; Berkeley , CA USA
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49
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Lee JK, Garbe JC, Vrba L, Miyano M, Futscher BW, Stampfer MR, LaBarge MA. Age and the means of bypassing stasis influence the intrinsic subtype of immortalized human mammary epithelial cells. Front Cell Dev Biol 2015; 3:13. [PMID: 25815289 PMCID: PMC4356162 DOI: 10.3389/fcell.2015.00013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/17/2015] [Indexed: 11/23/2022] Open
Abstract
Based on molecular features, breast cancers are grouped into intrinsic subtypes that have different prognoses and therapeutic response profiles. With increasing age, breast cancer incidence increases, with hormone receptor-positive and other luminal-like subtype tumors comprising a majority of cases. It is not known at what stage of tumor progression subtype specification occurs, nor how the process of aging affects the intrinsic subtype. We examined subtype markers in immortalized human mammary epithelial cell lines established following exposure of primary cultured cell strains to a two-step immortalization protocol that targets the two main barriers to immortality: stasis (stress-associated senescence) and replicative senescence. Cell lines derived from epithelial cells obtained from non-tumorous pre- and post-menopausal breast surgery tissues were compared. Additionally, comparisons were made between lines generated using two different genetic interventions to bypass stasis: transduction of either an shRNA that down-regulated p16INK4A, or overexpressed constitutive active cyclin D1/CDK2. In all cases, the replicative senescence barrier was bypassed by transduction of c-Myc. Cells from all resulting immortal lines exhibited normal karyotypes. Immunofluorescence, flow cytometry, and gene expression analyses of lineage-specific markers were used to categorize the intrinsic subtypes of the immortalized lines. Bypassing stasis with p16 shRNA in young strains generated cell lines that were invariably basal-like, but the lines examined from older strains exhibited some luminal features such as keratin 19 and estrogen receptor expression. Overexpression of cyclin D1/CDK2 resulted in keratin 19 positive, luminal-like cell lines from both young and old strains, and the lines examined from older strains exhibited estrogen receptor expression. Thus age and the method of bypassing stasis independently influence the subtype of immortalized human mammary epithelial cells.
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Affiliation(s)
- Jonathan K Lee
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - James C Garbe
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Lukas Vrba
- Arizona Cancer Center, The University of Arizona Tucson, AZ, USA ; College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona Tucson, AZ, USA
| | - Masaru Miyano
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Bernard W Futscher
- Arizona Cancer Center, The University of Arizona Tucson, AZ, USA ; College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona Tucson, AZ, USA
| | - Martha R Stampfer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Arizona Cancer Center, The University of Arizona Tucson, AZ, USA
| | - Mark A LaBarge
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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50
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Cerchiari AE, Garbe JC, Jee NY, Todhunter ME, Broaders KE, Peehl DM, Desai TA, LaBarge MA, Thomson M, Gartner ZJ. A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity. Proc Natl Acad Sci U S A 2015; 112:2287-92. [PMID: 25633040 PMCID: PMC4343104 DOI: 10.1073/pnas.1410776112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Developing tissues contain motile populations of cells that can self-organize into spatially ordered tissues based on differences in their interfacial surface energies. However, it is unclear how self-organization by this mechanism remains robust when interfacial energies become heterogeneous in either time or space. The ducts and acini of the human mammary gland are prototypical heterogeneous and dynamic tissues comprising two concentrically arranged cell types. To investigate the consequences of cellular heterogeneity and plasticity on cell positioning in the mammary gland, we reconstituted its self-organization from aggregates of primary cells in vitro. We find that self-organization is dominated by the interfacial energy of the tissue-ECM boundary, rather than by differential homo- and heterotypic energies of cell-cell interaction. Surprisingly, interactions with the tissue-ECM boundary are binary, in that only one cell type interacts appreciably with the boundary. Using mathematical modeling and cell-type-specific knockdown of key regulators of cell-cell cohesion, we show that this strategy of self-organization is robust to severe perturbations affecting cell-cell contact formation. We also find that this mechanism of self-organization is conserved in the human prostate. Therefore, a binary interfacial interaction with the tissue boundary provides a flexible and generalizable strategy for forming and maintaining the structure of two-component tissues that exhibit abundant heterogeneity and plasticity. Our model also predicts that mutations affecting binary cell-ECM interactions are catastrophic and could contribute to loss of tissue architecture in diseases such as breast cancer.
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Affiliation(s)
- Alec E Cerchiari
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, University of California, Berkeley, CA 94720; Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, and
| | - James C Garbe
- Departments of Bioengineering and Therapeutic Sciences and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
| | | | | | | | - Donna M Peehl
- Stanford University School of Medicine, Stanford University, Palo Alto, CA 94305
| | - Tejal A Desai
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, University of California, Berkeley, CA 94720; Departments of Bioengineering and Therapeutic Sciences and
| | - Mark A LaBarge
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
| | - Matthew Thomson
- Center for Systems and Synthetic Biology, University of California, San Francisco, CA 94143
| | - Zev J Gartner
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, University of California, Berkeley, CA 94720; Pharmaceutical Chemistry, and Center for Systems and Synthetic Biology, University of California, San Francisco, CA 94143;
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