1
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Kiianitsa K, Lukes ME, Hayes BJ, Brutman JN, Valdmanis PN, Bird TD, Raskind WH, Korvatska O. TREM2 variants that cause early dementia and increase Alzheimer's disease risk affect gene splicing. Brain 2024; 147:2368-2383. [PMID: 38226698 PMCID: PMC11224616 DOI: 10.1093/brain/awae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Loss-of-function variants in the triggering receptor expressed on myeloid cells 2 (TREM2) are responsible for a spectrum of neurodegenerative disorders. In the homozygous state, they cause severe pathologies with early onset dementia, such as Nasu-Hakola disease and behavioural variants of frontotemporal dementia (FTD), whereas heterozygous variants increase the risk of late-onset Alzheimer's disease (AD) and FTD. For over half of TREM2 variants found in families with recessive early onset dementia, the defect occurs at the transcript level via premature termination codons or aberrant splicing. The remaining variants are missense alterations thought to affect the protein; however, the underlying pathogenic mechanism is less clear. In this work, we tested whether these disease-associated TREM2 variants contribute to the pathology via altered splicing. Variants scored by SpliceAI algorithm were tested by a full-size TREM2 splicing reporter assay in different cell lines. The effect of variants was quantified by qRT-/RT-PCR and western blots. Nanostring nCounter was used to measure TREM2 RNA in the brains of NHD patients who carried spliceogenic variants. Exon skipping events were analysed from brain RNA-Seq datasets available through the Accelerating Medicines Partnership for Alzheimer's Disease Consortium. We found that for some Nasu-Hakola disease and early onset FTD-causing variants, splicing defects were the primary cause (D134G) or likely contributor to pathogenicity (V126G and K186N). Similar but milder effects on splicing of exons 2 and 3 were demonstrated for A130V, L133L and R136W enriched in patients with dementia. Moreover, the two most frequent missense variants associated with AD/FTD risk in European and African ancestries (R62H, 1% in Caucasians and T96K, 12% in Africans) had splicing defects via excessive skipping of exon 2 and overproduction of a potentially antagonistic TREM2 protein isoform. The effect of R62H on exon 2 skipping was confirmed in three independent brain RNA-Seq datasets. Our findings revealed an unanticipated complexity of pathogenic variation in TREM2, in which effects on post-transcriptional gene regulation and protein function often coexist. This necessitates the inclusion of computational and experimental analyses of splicing and mRNA processing for a better understanding of genetic variation in disease.
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Affiliation(s)
- Kostantin Kiianitsa
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maria E Lukes
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Brian J Hayes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Julianna N Brutman
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Paul N Valdmanis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
- Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, WA 98108, USA
| | - Wendy H Raskind
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
- Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Medical Center, Seattle, WA 98108, USA
| | - Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
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2
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Voeltzel T, Fossard G, Degaud M, Geistlich K, Gadot N, Jeanpierre S, Mikaelian I, Brevet M, Anginot A, Le Bousse-Kerdilès MC, Trichet V, Lefort S, Maguer-Satta V. A minimal standardized human bone marrow microphysiological system to assess resident cell behavior during normal and pathological processes. Biomater Sci 2021; 10:485-498. [PMID: 34904143 DOI: 10.1039/d1bm01098k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bone marrow is a complex and dynamic microenvironment that provides essential cues to resident cells. We developed a standardized three-dimensional (3D) model to decipher mechanisms that control human cells during hematological and non-hematological processes. Our simple 3D-model is constituted of a biphasic calcium phosphate-based scaffold and human cell lines to ensure a high reproducibility. We obtained a minimal well-organized bone marrow-like structure in which various cell types and secreted extracellular matrix can be observed and characterized by in situ imaging or following viable cell retrieval. The complexity of the system can be increased and customized, with each cellular component being independently modulated according to the issue investigated. Introduction of pathological elements in this 3D-system accurately reproduced changes observed in patient bone marrow. Hence, we have developed a handy and flexible standardized microphysiological system that mimics human bone marrow, allowing histological analysis and functional assays on collected cells.
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Affiliation(s)
- Thibault Voeltzel
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,CNRS GDR 3697 MicroNiT, Tours, France.
| | - Gaëlle Fossard
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,Hospices Civils de Lyon, Hematology Department, Centre Hospitalier Lyon Sud, F-69495 Pierre Bénite, France
| | - Michaël Degaud
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,Hospices Civils de Lyon, Hematology Department, Centre Hospitalier Lyon Sud, F-69495 Pierre Bénite, France
| | - Kevin Geistlich
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Nicolas Gadot
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Research Pathology Platform, Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Sandrine Jeanpierre
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Ivan Mikaelian
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France
| | - Marie Brevet
- Pathology Department, Hospices Civils de Lyon, Bron F-69500, France
| | - Adrienne Anginot
- UMR1197, Université Paris-Saclay, 94800 Villejuif, France.,CNRS GDR 3697 MicroNiT, Tours, France.
| | | | - Valérie Trichet
- INSERM, UMR 1238, PHYOS, Faculty of Medicine, University of Nantes, Nantes, France.,CNRS GDR 3697 MicroNiT, Tours, France.
| | - Sylvain Lefort
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,CNRS GDR 3697 MicroNiT, Tours, France.
| | - Véronique Maguer-Satta
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France.,Université de Lyon, 69000, Lyon, France.,Department of Cancer Initiation and Tumor cell Identity and Lyon, France.,CNRS GDR 3697 MicroNiT, Tours, France. .,Centre Léon Bérard, Lyon, France
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3
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Adamo A, Delfino P, Gatti A, Bonato A, Takam Kamga P, Bazzoni R, Ugel S, Mercuri A, Caligola S, Krampera M. HS-5 and HS-27A Stromal Cell Lines to Study Bone Marrow Mesenchymal Stromal Cell-Mediated Support to Cancer Development. Front Cell Dev Biol 2020; 8:584232. [PMID: 33251214 PMCID: PMC7674674 DOI: 10.3389/fcell.2020.584232] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022] Open
Abstract
In this study, we compared the overall gene and pathway expression profiles of HS-5 and HS-27A stromal cell lines with those of primary bone marrow MSCs to verify if they can be considered a reliable alternative tool for evaluating the contribution of MSCs in tumor development and immunomodulation. Indeed, due to their easier manipulation in vitro as compared to primary MSC cultures, several published studies took advantage of stromal cell lines to assess the biological mechanisms mediated by stromal cells in influencing tumor biology and immune responses. However, the process carried out to obtain immortalized cell lines could profoundly alter gene expression profile, and consequently their biological characteristics, leading to debatable results. Here, we evaluated the still undisclosed similarities and differences between HS-5, HS-27A cell lines and primary bone marrow MSCs in the context of tumor development and immunomodulation. Furthermore, we assessed by standardized immunological assays the capability of the cell lines to reproduce the general mechanisms of MSC immunoregulation. We found that only HS-5 cell line could be suitable to reproduce not only the MSC capacity to influence tumor biology, but also to evaluate the molecular mechanisms underlying tumor immune escape mediated by stroma cells. However, HS-5 pre-treatment with inflammatory cytokines, that normally enhances the immunosuppressive activity of primary MSCs, did not reproduce the same MSCs behavior, highlighting the necessity to accurately set up in vitro assays when HS-5 cell line is used instead of its primary counterpart.
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Affiliation(s)
- Annalisa Adamo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy.,Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Alessandro Gatti
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alice Bonato
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Paul Takam Kamga
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy.,EA4340-BCOH, Biomarker in Cancerology and Onco-Haematology, UVSQ, Université Paris Saclay, Boulogne-Billancourt, France
| | - Riccardo Bazzoni
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Angela Mercuri
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Mauro Krampera
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
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4
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Buschhaus JM, Humphries BA, Eckley SS, Robison TH, Cutter AC, Rajendran S, Haley HR, Bevoor AS, Luker KE, Luker GD. Targeting disseminated estrogen-receptor-positive breast cancer cells in bone marrow. Oncogene 2020; 39:5649-5662. [PMID: 32678295 PMCID: PMC7442734 DOI: 10.1038/s41388-020-01391-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/08/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
Estrogen receptor-positive (ER+) breast cancer can recur up to 20 years after initial diagnosis. Delayed recurrences arise from disseminated tumors cells (DTCs) in sites such as bone marrow that remain quiescent during endocrine therapy and subsequently proliferate to produce clinically detectable metastases. Identifying therapies that eliminate DTCs and/or effectively target cells transitioning to proliferation promises to reduce risk of recurrence. To tackle this problem, we utilized a 3D co-culture model incorporating ER+ breast cancer cells and bone marrow mesenchymal stem cells to represent DTCs in a bone marrow niche. 3D co-cultures maintained cancer cells in a quiescent, viable state as measured by both single-cell and population-scale imaging. Single-cell imaging methods for metabolism by fluorescence lifetime (FLIM) of NADH and signaling by kinases Akt and ERK revealed that breast cancer cells utilized oxidative phosphorylation and signaling by Akt to a greater extent both in 3D co-cultures and a mouse model of ER+ breast cancer cells in bone marrow. Using our 3D co-culture model, we discovered that combination therapies targeting oxidative phosphorylation via the thioredoxin reductase (TrxR) inhibitor, D9, and the Akt inhibitor, MK-2206, preferentially eliminated breast cancer cells without altering viability of bone marrow stromal cells. Treatment of mice with disseminated ER+ human breast cancer showed that D9 plus MK-2206 blocked formation of new metastases more effectively than tamoxifen. These data establish an integrated experimental system to investigate DTCs in bone marrow and identify combination therapy against metabolic and kinase targets as a promising approach to effectively target these cells and reduce risk of recurrence in breast cancer.
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Affiliation(s)
- Johanna M Buschhaus
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI, 48109-2099, USA
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Brock A Humphries
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Samantha S Eckley
- Unit for Laboratory Animal Medicine, University of Michigan, 412 Victor Vaughan, Ann Arbor, MI, 48109-2200, USA
- Office of Animal Resources, University of Iowa, Iowa City, IA, USA
| | - Tanner H Robison
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI, 48109-2099, USA
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Alyssa C Cutter
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Shrila Rajendran
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Henry R Haley
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Avinash S Bevoor
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Kathryn E Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Gary D Luker
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI, 48109-2099, USA.
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA.
- Department of Microbiology and Immunology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA.
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5
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Deynoux M, Sunter N, Ducrocq E, Dakik H, Guibon R, Burlaud-Gaillard J, Brisson L, Rouleux-Bonnin F, le Nail LR, Hérault O, Domenech J, Roingeard P, Fromont G, Mazurier F. A comparative study of the capacity of mesenchymal stromal cell lines to form spheroids. PLoS One 2020; 15:e0225485. [PMID: 32484831 PMCID: PMC7266346 DOI: 10.1371/journal.pone.0225485] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/17/2020] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSC)-spheroid models favor maintenance of stemness, ex vivo expansion and transplantation efficacy. Spheroids may also be considered as useful surrogate models of the hematopoietic niche. However, accessibility to primary cells, from bone marrow (BM) or adipose tissues, may limit their experimental use and the lack of consistency in methods to form spheroids may affect data interpretation. In this study, we aimed to create a simple model by examining the ability of cell lines, from human (HS-27a and HS-5) and murine (MS-5) BM origins, to form spheroids, compared to primary human MSCs (hMSCs). Our protocol efficiently allowed the spheroid formation from all cell types within 24 hours. Whilst hMSC-spheroids began to shrink after 24 hours, the size of spheroids from cell lines remained constant during three weeks. The difference was partially explained by the balance between proliferation and cell death, which could be triggered by hypoxia and induced oxidative stress. Our results demonstrate that, like hMSCs, MSC cell lines make reproductible spheroids that are easily handled. Thus, this model could help in understanding mechanisms involved in MSC functions and may provide a simple model by which to study cell interactions in the BM niche.
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Affiliation(s)
- Margaux Deynoux
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
| | - Nicola Sunter
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
| | - Elfi Ducrocq
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
| | - Hassan Dakik
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
| | - Roseline Guibon
- Anatomie et cytologie pathologique, CHRU de Tours, Tours, France
- INSERM UMR1069, Nutrition, Croissance et Cancer, Université de Tours, Tours, France
| | - Julien Burlaud-Gaillard
- Plateforme IBiSA de Microscopie Electronique, Université et CHRU de Tours, Tours, France
- INSERM U1259 MAVIVH, Université et CHRU de Tours, Tours, France
| | - Lucie Brisson
- INSERM UMR1069, Nutrition, Croissance et Cancer, Université de Tours, Tours, France
| | | | | | - Olivier Hérault
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
- Service d'hématologie biologique, CHRU de Tours, Tours, France
| | - Jorge Domenech
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
- Service d'hématologie biologique, CHRU de Tours, Tours, France
| | - Philippe Roingeard
- Plateforme IBiSA de Microscopie Electronique, Université et CHRU de Tours, Tours, France
- INSERM U1259 MAVIVH, Université et CHRU de Tours, Tours, France
| | - Gaëlle Fromont
- Anatomie et cytologie pathologique, CHRU de Tours, Tours, France
- INSERM UMR1069, Nutrition, Croissance et Cancer, Université de Tours, Tours, France
| | - Frédéric Mazurier
- EA 7501 GICC, CNRS ERL 7001 LNOx, Université de Tours, Tours, France
- * E-mail:
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6
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Witherel CE, Abebayehu D, Barker TH, Spiller KL. Macrophage and Fibroblast Interactions in Biomaterial-Mediated Fibrosis. Adv Healthc Mater 2019; 8:e1801451. [PMID: 30658015 PMCID: PMC6415913 DOI: 10.1002/adhm.201801451] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/07/2018] [Indexed: 01/08/2023]
Abstract
Biomaterial-mediated inflammation and fibrosis remain a prominent challenge in designing materials to support tissue repair and regeneration. Despite the many biomaterial technologies that have been designed to evade or suppress inflammation (i.e., delivery of anti-inflammatory drugs, hydrophobic coatings, etc.), many materials are still subject to a foreign body response, resulting in encapsulation of dense, scar-like extracellular matrix. The primary cells involved in biomaterial-mediated fibrosis are macrophages, which modulate inflammation, and fibroblasts, which primarily lay down new extracellular matrix. While macrophages and fibroblasts are implicated in driving biomaterial-mediated fibrosis, the signaling pathways and spatiotemporal crosstalk between these cell types remain loosely defined. In this review, the role of M1 and M2 macrophages (and soluble cues) involved in the fibrous encapsulation of biomaterials in vivo is investigated, with additional focus on fibroblast and macrophage crosstalk in vitro along with in vitro models to study the foreign body response. Lastly, several strategies that have been used to specifically modulate macrophage and fibroblast behavior in vitro and in vivo to control biomaterial-mediated fibrosis are highlighted.
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Affiliation(s)
- Claire E. Witherel
- Drexel University, School of Biomedical Engineering, Science and Health Systems, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
| | - Daniel Abebayehu
- University of Virginia, Department of Biomedical Engineering, School of Engineering & School of Medicine, 415 Lane Road, Charlottesville, Virginia 22904, USA
| | - Thomas H. Barker
- University of Virginia, Department of Biomedical Engineering, School of Engineering & School of Medicine, 415 Lane Road, Charlottesville, Virginia 22904, USA
| | - Kara L. Spiller
- Drexel University, School of Biomedical Engineering, Science and Health Systems, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA,
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7
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Diaz Bessone MI, Gattas MJ, Laporte T, Tanaka M, Simian M. The Tumor Microenvironment as a Regulator of Endocrine Resistance in Breast Cancer. Front Endocrinol (Lausanne) 2019; 10:547. [PMID: 31440208 PMCID: PMC6694443 DOI: 10.3389/fendo.2019.00547] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Estrogen receptor positive breast neoplasias represent over 70% of diagnosed breast cancers. Depending on the stage at which the tumor is detected, HER2 status and genomic risk, endocrine therapy is combined with either radio, chemo and/or targeted therapy. A growing amount of evidence supports the notion that components of the tumor microenvironment play specific roles in response to treatment and that strategies targeting these key interactions with tumor cells could pave the way to a new generation of therapies. In this review, we analyze the evidence suggesting different components of the tumor microenvironment play a role in hormone receptor positive breast cancer progression. In particular we focus on the immune system, carcinoma associated fibroblasts and the extracellular matrix. Further insight into the cross talk between these constituents of the microenvironment and the tumor cells may lead to therapies that eliminate disseminated metastatic cells early on, and thus reduce distant disease relapse which is the leading cause of death for patients who are diagnosed with this illness.
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Affiliation(s)
- María Inés Diaz Bessone
- Laboratory of NanoBiology, Instituto de Nanosistemas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - María José Gattas
- Laboratory of NanoBiology, Instituto de Nanosistemas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Tomás Laporte
- Laboratory of NanoBiology, Instituto de Nanosistemas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Max Tanaka
- Laboratory of NanoBiology, Instituto de Nanosistemas, Universidad Nacional de San Martín, Buenos Aires, Argentina
- Amsterdam UMC, VUmc School of Medical Sciences, University of Vrije, Amsterdam, Netherlands
| | - Marina Simian
- Laboratory of NanoBiology, Instituto de Nanosistemas, Universidad Nacional de San Martín, Buenos Aires, Argentina
- *Correspondence: Marina Simian
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8
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Rose WA, Okragly AJ, Hu NN, Daniels MR, Martin AP, Koh YT, Kikly K, Benschop RJ. Interleukin-33 Contributes Toward Loss of Tolerance by Promoting B-Cell-Activating Factor of the Tumor-Necrosis-Factor Family (BAFF)-Dependent Autoantibody Production. Front Immunol 2018; 9:2871. [PMID: 30574145 PMCID: PMC6292404 DOI: 10.3389/fimmu.2018.02871] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/21/2018] [Indexed: 01/13/2023] Open
Abstract
Breaking tolerance is a key event leading to autoimmunity, but the exact mechanisms responsible for this remain uncertain. Here we show that the alarmin IL-33 is able to drive the generation of autoantibodies through induction of the B cell survival factor BAFF. A temporary, short-term increase in IL-33 results in a primary (IgM) response to self-antigens. This transient DNA-specific autoantibody response was dependent on the induction of BAFF. Notably, radiation resistant cells and not myeloid cells, such as neutrophils or dendritic cells were the major source of BAFF and were critical in driving the autoantibody response. Chronic exposure to IL-33 elicited dramatic increases in BAFF levels and resulted in elevated numbers of B and T follicular helper cells as well as germinal center formation. We also observed class-switching from an IgM to an IgG DNA-specific autoantibody response. Collectively, the results provide novel insights into a potential mechanism for breaking immune-tolerance via IL-33-mediated induction of BAFF.
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Affiliation(s)
- William A Rose
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Angela J Okragly
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Ningjie N Hu
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Montanea R Daniels
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Andrea P Martin
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Yi Ting Koh
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Kristine Kikly
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Robert J Benschop
- Immunology Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
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9
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Kotha SS, Hayes BJ, Phong KT, Redd MA, Bomsztyk K, Ramakrishnan A, Torok-Storb B, Zheng Y. Engineering a multicellular vascular niche to model hematopoietic cell trafficking. Stem Cell Res Ther 2018; 9:77. [PMID: 29566751 PMCID: PMC5865379 DOI: 10.1186/s13287-018-0808-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/10/2018] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The marrow microenvironment and vasculature plays a critical role in regulating hematopoietic cell recruitment, residence, and maturation. Extensive in vitro and in vivo studies have aimed to understand the marrow cell types that contribute to hematopoiesis and the stem cell environment. Nonetheless, in vitro models are limited by a lack of complex multicellular interactions, and cellular interactions are not easily manipulated in vivo. Here, we develop an engineered human vascular marrow niche to examine the three-dimensional cell interactions that direct hematopoietic cell trafficking. METHODS Using soft lithography and injection molding techniques, fully endothelialized vascular networks were fabricated in type I collagen matrix, and co-cultured under flow with embedded marrow fibroblast cells in the matrix. Marrow fibroblast (mesenchymal stem cells (MSCs), HS27a, or HS5) interactions with the endothelium were imaged via confocal microscopy and altered endothelial gene expression was analyzed with RT-PCR. Monocytes, hematopoietic progenitor cells, and leukemic cells were perfused through the network and their adhesion and migration was evaluated. RESULTS HS27a cells and MSCs interact directly with the vessel wall more than HS5 cells, which are not seen to make contact with the endothelial cells. In both HS27a and HS5 co-cultures, endothelial expression of junctional markers was reduced. HS27a co-cultures promote perfused monocytes to adhere and migrate within the vessel network. Hematopoietic progenitors rely on monocyte-fibroblast crosstalk to facilitate preferential recruitment within HS27a co-cultured vessels. In contrast, leukemic cells sense fibroblast differences and are recruited preferentially to HS5 and HS27a co-cultures, but monocytes are able to block this sensitivity. CONCLUSIONS We demonstrate the use of a microvascular platform that incorporates a tunable, multicellular composition to examine differences in hematopoietic cell trafficking. Differential recruitment of hematopoietic cell types to distinct fibroblast microenvironments highlights the complexity of cell-cell interactions within the marrow. This system allows for step-wise incorporation of cellular components to reveal the dynamic spatial and temporal interactions between endothelial cells, marrow-derived fibroblasts, and hematopoietic cells that comprise the marrow vascular niche. Furthermore, this platform has potential for use in testing therapeutics and personalized medicine in both normal and disease contexts.
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Affiliation(s)
- Surya S Kotha
- Department of Bioengineering, University of Washington, Brotman Building, 850 Republican Street, Seattle, WA, 98109, USA
| | - Brian J Hayes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kiet T Phong
- Department of Bioengineering, University of Washington, Brotman Building, 850 Republican Street, Seattle, WA, 98109, USA
| | | | - Karol Bomsztyk
- Department of Pharmacology, University of Washington, Seattle, WA, 98109, USA
| | - Aravind Ramakrishnan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Beverly Torok-Storb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ying Zheng
- Department of Bioengineering, University of Washington, Brotman Building, 850 Republican Street, Seattle, WA, 98109, USA.
- Center for Cardiovascular Biology, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
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10
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Human Cord Blood and Bone Marrow CD34+ Cells Generate Macrophages That Support Erythroid Islands. PLoS One 2017; 12:e0171096. [PMID: 28135323 PMCID: PMC5279789 DOI: 10.1371/journal.pone.0171096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/16/2017] [Indexed: 02/05/2023] Open
Abstract
Recently, we developed a small molecule responsive hyperactive Mpl-based Cell Growth Switch (CGS) that drives erythropoiesis associated with macrophages in the absence of exogenous cytokines. Here, we compare the physical, cellular and molecular interaction between the macrophages and erythroid cells in CGS expanded CD34+ cells harvested from cord blood, marrow or G-CSF-mobilized peripheral blood. Results indicated that macrophage based erythroid islands could be generated from cord blood and marrow CD34+ cells but not from G-CSF-mobilized CD34+ cells. Additional studies suggest that the deficiency resides with the G-CSF-mobilized CD34+ derived monocytes. Gene expression and proteomics studies of the in vitro generated erythroid islands detected the expression of erythroblast macrophage protein (EMP), intercellular adhesion molecule 4 (ICAM-4), CD163 and DNASE2. 78% of the erythroblasts in contact with macrophages reached the pre reticulocyte orthochromatic stage of differentiation within 14 days of culture. The addition of conditioned medium from cultures of CD146+ marrow fibroblasts resulted in a 700-fold increase in total cell number and a 90-fold increase in erythroid cell number. This novel CD34+ cell derived erythroid island may serve as a platform to explore the molecular basis of red cell maturation and production under normal, stress and pathological conditions.
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11
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Huang J, Woods P, Normolle D, Goff JP, Benos PV, Stehle CJ, Steinman RA. Downregulation of estrogen receptor and modulation of growth of breast cancer cell lines mediated by paracrine stromal cell signals. Breast Cancer Res Treat 2016; 161:229-243. [PMID: 27853906 DOI: 10.1007/s10549-016-4052-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE Breast cancers have a poorer prognosis if estrogen receptor expression was lost during recurrence. It is unclear whether this conversion is cell autonomous or whether it can be promoted by the microenvironment during cancer dormancy. We explored the ability of marrow-derived stromal cell lines to arrest co-cultured breast cancer cells and suppress estrogen receptor alpha (ER) expression during arrest, facilitating the emergence of estrogen-independent breast cancer clones. METHODS Cancer cell growth, ER protein, microRNA, and mRNA levels were measured in breast cancer cell lines exposed to conditioned medium from marrow stromal lines in the presence and absence of estrogen and of signaling pathway modulators. RESULTS We demonstrate that paracrine signaling from the stromal cell line HS5 downregulated ER in T47D and MCF7 breast cancer cells. This occurred at the mRNA level and also through decreased ER protein stability. Additionally, conditioned medium (CM) from HS5 arrested the breast cancer cells in G0/G1 in part through interleukin-1 (IL1) and inhibited cancer cell growth despite the activation of proliferative pathways (Erk and AKT) by the CM. Similar findings were observed for CM from the hFOB 1.19 osteoblastic cell line but not from two other fibroblastic marrow lines, HS27A and KM101. HS5-CM inhibition of MCF7 proliferation could not be restored by exogenous ER, but was restored by the IL1-antagonist IL1RA. In the presence of IL1RA, HS5-CM activation of AKT and Erk enabled the outgrowth of breast cancer cells with suppressed ER that were fulvestrant-resistant and estrogen-independent. CONCLUSIONS We conclude that marrow-derived stromal cells can destabilize estrogen receptor protein to convert the ER status of growth-arrested ER+ breast cancer cell lines. The balance between stromal pro- and anti-proliferative signals controlled the switch from a dormant phenotype to estrogen-independent cancer cell growth.
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Affiliation(s)
- J Huang
- Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Suite 2.26f Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - P Woods
- Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Suite 2.26f Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - D Normolle
- Department of Biostatistics, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, USA
| | - J P Goff
- Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Suite 2.26f Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - P V Benos
- Department of Computational Biology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, USA
| | - C J Stehle
- Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Suite 2.26f Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - R A Steinman
- Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Suite 2.26f Hillman Cancer Center, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, USA.
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12
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Brechbuhl HM, Finlay-Schultz J, Yamamoto TM, Gillen AE, Cittelly DM, Tan AC, Sams SB, Pillai MM, Elias AD, Robinson WA, Sartorius CA, Kabos P. Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen. Clin Cancer Res 2016; 23:1710-1721. [PMID: 27702820 DOI: 10.1158/1078-0432.ccr-15-2851] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 01/02/2023]
Abstract
Purpose: Antiendocrine therapy remains the most effective treatment for estrogen receptor-positive (ER+) breast cancer, but development of resistance is a major clinical complication. Effective targeting of mechanisms that control the loss of ER dependency in breast cancer remains elusive. We analyzed breast cancer-associated fibroblasts (CAF), the largest component of the tumor microenvironment, as a factor contributing to ER expression levels and antiendocrine resistance.Experimental Design: Tissues from patients with ER+ breast cancer were analyzed for the presence of CD146-positive (CD146pos) and CD146-negative (CD146neg) fibroblasts. ER-dependent proliferation and tamoxifen sensitivity were evaluated in ER+ tumor cells cocultured with CD146pos or CD146neg fibroblasts. RNA sequencing was used to develop a high-confidence gene signature that predicts for disease recurrence in tamoxifen-treated patients with ER+ breast cancer.Results: We demonstrate that ER+ breast cancers contain two CAF subtypes defined by CD146 expression. CD146neg CAFs suppress ER expression in ER+ breast cancer cells, decrease tumor cell sensitivity to estrogen, and increase tumor cell resistance to tamoxifen therapy. Conversely, the presence of CD146pos CAFs maintains ER expression in ER+ breast cancer cells and sustains estrogen-dependent proliferation and sensitivity to tamoxifen. Conditioned media from CD146pos CAFs with tamoxifen-resistant breast cancer cells are sufficient to restore tamoxifen sensitivity. Gene expression profiles of patient breast tumors with predominantly CD146neg CAFs correlate with inferior clinical response to tamoxifen and worse patient outcomes.Conclusions: Our data suggest that CAF composition contributes to treatment response and patient outcomes in ER+ breast cancer and should be considered a target for drug development. Clin Cancer Res; 23(7); 1710-21. ©2016 AACR.
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Affiliation(s)
- Heather M Brechbuhl
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado.
| | | | - Tomomi M Yamamoto
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado
| | - Austin E Gillen
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado
| | - Diana M Cittelly
- Department of Pathology, University of Colorado Denver, Aurora, Colorado
| | - Aik-Choon Tan
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado
| | - Sharon B Sams
- Department of Pathology, University of Colorado Denver, Aurora, Colorado
| | - Manoj M Pillai
- Section of Hematology, Division of Hematology, Yale Cancer Center and Yale University School of Medicine, New Haven, Connecticut
| | - Anthony D Elias
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado
| | - William A Robinson
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado
| | - Carol A Sartorius
- Department of Pathology, University of Colorado Denver, Aurora, Colorado
| | - Peter Kabos
- Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, Colorado.
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13
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Cavnar SP, Xiao A, Gibbons AE, Rickelmann AD, Neely T, Luker KE, Takayama S, Luker GD. Imaging Sensitivity of Quiescent Cancer Cells to Metabolic Perturbations in Bone Marrow Spheroids. Tomography 2016; 2:146-157. [PMID: 27478871 PMCID: PMC4963031 DOI: 10.18383/j.tom.2016.00157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Malignant cells from breast cancer and other common cancers such as prostate and melanoma may persist in bone marrow as quiescent, non-dividing cells that remain viable for years or even decades before resuming proliferation to cause recurrent disease. This phenomenon, referred to clinically as tumor dormancy, poses tremendous challenges to curing patients with breast cancer. Quiescent tumor cells resist chemotherapy drugs that predominantly target proliferating cells, limiting success of neo-adjuvant and adjuvant therapies. We recently developed a 3D spheroid model of quiescent breast cancer cells in bone marrow for mechanistic and drug testing studies. We combined this model with optical imaging methods for label-free detection of cells preferentially utilizing glycolysis versus oxidative metabolism to investigate the metabolic state of co-culture spheroids with different bone marrow stromal and breast cancer cells. Through imaging and biochemical assays, we identified different metabolic states of bone marrow stromal cells that control metabolic status and flexibilities of co-cultured breast cancer cells. We tested metabolic stresses and targeted inhibition of specific metabolic pathways to identify approaches to preferentially eliminate quiescent breast cancer cells from bone marrow environments. These studies establish an integrated imaging approach to analyze metabolism in complex tissue environments to identify new metabolically-targeted cancer therapies.
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Affiliation(s)
- Stephen P. Cavnar
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Annie Xiao
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anne E. Gibbons
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Andrew D. Rickelmann
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Taylor Neely
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kathryn E. Luker
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
| | - Shuichi Takayama
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan College of Engineering, Ann Arbor, Michigan
- Department of Macromolecular Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan; and
| | - Gary D. Luker
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
- Department of Radiology, Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Macromolecular Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan; and
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
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14
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery. F1000Res 2016; 5:291. [PMID: 27158451 DOI: 10.12688/f1000research.8182.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/24/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical informatics, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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15
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research. F1000Res 2016; 5:291. [PMID: 27158452 PMCID: PMC4856112 DOI: 10.12688/f1000research.8182.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 12/19/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at
http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical Informatics Division, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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16
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Zhou R, Kuang Y, Zhou J, Du X, Li J, Shi J, Haburcak R, Xu B. Nanonets Collect Cancer Secretome from Pericellular Space. PLoS One 2016; 11:e0154126. [PMID: 27100780 PMCID: PMC4839576 DOI: 10.1371/journal.pone.0154126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/09/2016] [Indexed: 01/08/2023] Open
Abstract
Identifying novel cancer biomarkers is important for early cancer detection as it can reduce mortality rates. The cancer secretome, the collection of all macromolecules secreted by a tumor cell, alters its composition compared to normal tissue, and this change plays an important role in the observation of cancer progression. The collection and accurate analysis of cancer secretomes could lead to the discovery of novel biomarkers, thus improving outcomes of cancer treatment. We unexpectedly discovered that enzyme-instructed self-assembly (EISA) of a D-peptide hydrogelator results in nanonets/hydrogel around cancer cells that overexpress ectophosphatases. Here we show that these nanonets are able to rapidly collect proteins in the pericellular space (i.e., near the surface) of cancer cells. Because the secretory substances are at their highest concentration near the cell surface, the use of pericellular nanonets to collect the cancer secretome maximizes the yield and quality of samples, reduces pre-analytical variations, and allows the dynamic profiling of secretome samples. Thus, this new approach has great potential in identifying the heterotypic signaling in tumor microenvironments thereby improving the understanding of tumor microenvironments and accelerating the discovery of potential biomarkers in cancer biology. Data are available via ProteomeXchange with identifier PXD003924.
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Affiliation(s)
- Rong Zhou
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yi Kuang
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jie Zhou
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Xuewen Du
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jie Li
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Richard Haburcak
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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17
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Abstract
Genetically-encoded fluorescence resonance energy transfer (FRET) reporters are powerful tools to analyze cell signaling and function at single cell resolution in standard two-dimensional cell cultures, but these reporters rarely have been applied to three-dimensional environments. FRET interactions between donor and acceptor molecules typically are determined by changes in relative fluorescence intensities, but wavelength-dependent differences in absorption of light complicate this analysis method in three-dimensional settings. Here we report fluorescence lifetime imaging microscopy (FLIM) with phasor analysis, a method that displays fluorescence lifetimes on a pixel-wise basis in real time, to quantify apoptosis in breast cancer cells stably expressing a genetically encoded FRET reporter. This microscopic imaging technology allowed us to identify treatment-induced apoptosis in single breast cancer cells in environments ranging from two-dimensional cell culture, spheroids with cancer and bone marrow stromal cells, and living mice with orthotopic human breast cancer xenografts. Using this imaging strategy, we showed that combined metabolic therapy targeting glycolysis and glutamine pathways significantly reduced overall breast cancer metabolism and induced apoptosis. We also determined that distinct subpopulations of bone marrow stromal cells control resistance of breast cancer cells to chemotherapy, suggesting heterogeneity of treatment responses of malignant cells in different bone marrow niches. Overall, this study establishes FLIM with phasor analysis as an imaging tool for apoptosis in cell-based assays and living mice, enabling real-time, cellular-level assessment of treatment efficacy and heterogeneity.
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Affiliation(s)
| | | | | | - Gary D. Luker
- Microbiology and Immunology, University of Michigan, Ann Arbor, MI
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18
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Zheng B, Ohuchida K, Chijiiwa Y, Zhao M, Mizuuchi Y, Cui L, Horioka K, Ohtsuka T, Mizumoto K, Oda Y, Hashizume M, Nakamura M, Tanaka M. CD146 attenuation in cancer-associated fibroblasts promotes pancreatic cancer progression. Mol Carcinog 2015; 55:1560-1572. [DOI: 10.1002/mc.22409] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/10/2015] [Accepted: 08/31/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Biao Zheng
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Kenoki Ohuchida
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
- Advanced Medical Initiatives; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Yoshiro Chijiiwa
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Ming Zhao
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Yusuke Mizuuchi
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
- Department of Anatomic Pathology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Lin Cui
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Kohei Horioka
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Takao Ohtsuka
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Kazuhiro Mizumoto
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
- Kyushu University Hospital Cancer Center; Fukuoka Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Makoto Hashizume
- Advanced Medical Initiatives; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| | - Masao Tanaka
- Department of Surgery and Oncology; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
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19
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Li X, Li D, Pang X, Yang G, Deeg HJ, Guan F. Quantitative analysis of glycans, related genes, and proteins in two human bone marrow stromal cell lines using an integrated strategy. Exp Hematol 2015; 43:760-9.e7. [PMID: 25936519 DOI: 10.1016/j.exphem.2015.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022]
Abstract
Altered expression of glycans is associated with cell-cell signal transduction and regulation of cell functions in the bone marrow micro-environment. Studies of this micro-environment often use two human bone marrow stromal cell lines, HS5 and HS27a, co-cultured with myeloid cells. We hypothesized that differential protein glycosylation between these two cell lines may contribute to functional differences in in vitro co-culture models. In this study, we applied an integrated strategy using genomic, proteomic, and functional glycomic techniques for global expression profiling of N-glycans and their related genes and enzymes in HS5 cells versus HS27a cells. HS5 cells had significantly enhanced levels of bisecting N-glycans (catalyzed by MGAT3 [β-1,4-mannosyl-glycoprotein 4-β-N-acetylglucosaminyltransferase]), whereas HS27a cells had enhanced levels of Galβ1,4GlcNAc (catalyzed by β4GalT1 [β4-galactosyltransferase I]). This integrated strategy provides useful information regarding the functional roles of glycans and their related glycogenes and glycosyltransferases in the bone marrow microenvironment, and a basis for future studies of crosstalk among stromal cells and myeloma cells in co-culture.
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Affiliation(s)
- Xiang Li
- Wuxi Medical School, Jiangnan University, Wuxi, China
| | - Dongliang Li
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xingchen Pang
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ganglong Yang
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center and Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Feng Guan
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
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20
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Iwata M, Torok-Storb B, Wayner EA, Carter WG. CDCP1 identifies a CD146 negative subset of marrow fibroblasts involved with cytokine production. PLoS One 2014; 9:e109304. [PMID: 25275584 PMCID: PMC4183599 DOI: 10.1371/journal.pone.0109304] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/10/2014] [Indexed: 01/15/2023] Open
Abstract
In vitro expanded bone marrow stromal cells contain at least two populations of fibroblasts, a CD146/MCAM positive population, previously reported to be critical for establishing the stem cell niche and a CD146-negative population that expresses CUB domain-containing protein 1 (CDCP1)/CD318. Immunohistochemistry of marrow biopsies shows that clusters of CDCP1+ cells are present in discrete areas distinct from areas of fibroblasts expressing CD146. Using a stromal cell line, HS5, which approximates primary CDCP1+ stromal cells, we show that binding of an activating antibody against CDCP1 results in tyrosine-phosphorylation of CDCP1, paralleled by phosphorylation of Src Family Kinases (SFKs) Protein Kinase C delta (PKC-δ). When CDCP1 expression is knocked-down by siRNA, the expression and secretion of myelopoietic cytokines is increased. These data suggest CDCP1 expression can be used to identify a subset of marrow fibroblasts functionally distinct from CD146+ fibroblasts. Furthermore the CDCP1 protein may contribute to the defining function of these cells by regulating cytokine expression.
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Affiliation(s)
- Mineo Iwata
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Beverly Torok-Storb
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elizabeth A. Wayner
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - William G. Carter
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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