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Yapp C, Nirmal AJ, Zhou F, Maliga Z, Tefft JB, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK. Multiplexed 3D Analysis of Immune States and Niches in Human Tissue. bioRxiv 2024:2023.11.10.566670. [PMID: 38014052 PMCID: PMC10680601 DOI: 10.1101/2023.11.10.566670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Tissue homeostasis and the emergence of disease are controlled by changes in the proportions of resident and recruited cells, their organization into cellular neighbourhoods, and their interactions with acellular tissue components. Highly multiplexed tissue profiling (spatial omics)1 makes it possible to study this microenvironment in situ, usually in 4-5 micron thick sections (the standard histopathology format)2. Microscopy-based tissue profiling is commonly performed at a resolution sufficient to determine cell types but not to detect subtle morphological features associated with cytoskeletal reorganisation, juxtracrine signalling, or membrane trafficking3. Here we describe a high-resolution 3D imaging approach able to characterize a wide variety of organelles and structures at sub-micron scale while simultaneously quantifying millimetre-scale spatial features. This approach combines cyclic immunofluorescence (CyCIF) imaging4 of over 50 markers with confocal microscopy of archival human tissue thick enough (30-40 microns) to fully encompass two or more layers of intact cells. 3D imaging of entire cell volumes substantially improves the accuracy of cell phenotyping and allows cell proximity to be scored using plasma membrane apposition, not just nuclear position. In pre-invasive melanoma in situ5, precise phenotyping shows that adjacent melanocytic cells are plastic in state and participate in tightly localised niches of interferon signalling near sites of initial invasion into the underlying dermis. In this and metastatic melanoma, mature and precursor T cells engage in an unexpectedly diverse array of juxtracrine and membrane-membrane interactions as well as looser "neighbourhood" associations6 whose morphologies reveal functional states. These data provide new insight into the transitions occurring during early tumour formation and immunoediting and demonstrate the potential for phenotyping of tissues at a level of detail previously restricted to cultured cells and organoids.
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Affiliation(s)
- Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Felix Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
| | - Paula Montero Llopis
- Microscopy Resources on the North Quad (MicRoN), Harvard Medical School, Boston, MA 02115, USA
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Ludwig Centre at Harvard, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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2
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Nirmal AJ, Yapp C, Santagata S, Sorger PK. Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images. bioRxiv 2023:2023.11.15.567196. [PMID: 38014110 PMCID: PMC10680730 DOI: 10.1101/2023.11.15.567196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Highly multiplexed tissue imaging and in situ spatial profiling aim to extract single-cell data from specimens containing closely packed cells of diverse morphology. This is challenging due to the difficulty of accurately assigning boundaries between cells (segmentation) and then generating per-cell staining intensities. Existing methods use gating to convert per-cell intensity data to positive and negative scores; this is a common approach in flow cytometry, but one that is problematic in imaging. In contrast, human experts identify cells in crowded environments using morphological, neighborhood, and intensity information. Here we describe a computational approach (Cell Spotter or CSPOT) that uses supervised machine learning in combination with classical segmentation to perform automated cell type calling. CSPOT is robust to artifacts that commonly afflict tissue imaging and can replace conventional gating. The end-to-end Python implementation of CSPOT can be integrated into cloud-based image processing pipelines to substantially improve the speed, accuracy, and reproducibility of single-cell spatial data.
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Affiliation(s)
- Ajit J. Nirmal
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clarence Yapp
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sandro Santagata
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K. Sorger
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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3
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Coy S, Cheng B, Lee JS, Rashid R, Browning L, Xu Y, Chakrabarty SS, Yapp C, Chan S, Tefft JB, Scott E, Spektor A, Ligon KL, Baker GJ, Pellman D, Sorger PK, Santagata S. 2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer. bioRxiv 2023:2023.11.07.566063. [PMID: 37986801 PMCID: PMC10659270 DOI: 10.1101/2023.11.07.566063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Nuclear atypia, including altered nuclear size, contour, and chromatin organization, is ubiquitous in cancer cells. Atypical primary nuclei and micronuclei can rupture during interphase; however, the frequency, causes, and consequences of nuclear rupture are unknown in most cancers. We demonstrate that nuclear envelope rupture is surprisingly common in many human cancers, particularly glioblastoma. Using highly-multiplexed 2D and super-resolution 3D-imaging of glioblastoma tissues and patient-derived xenografts and cells, we link primary nuclear rupture with reduced lamin A/C and micronuclear rupture with reduced lamin B1. Moreover, ruptured glioblastoma cells activate cGAS-STING-signaling involved in innate immunity. We observe that local patterning of cell states influences tumor spatial organization and is linked to both lamin expression and rupture frequency, with neural-progenitor-cell-like states exhibiting the lowest lamin A/C levels and greatest susceptibility to primary nuclear rupture. Our study reveals that nuclear instability is a core feature of cancer, and links nuclear integrity, cell state, and immune signaling.
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Affiliation(s)
- Shannon Coy
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Cheng
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jong Suk Lee
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rumana Rashid
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lindsay Browning
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yilin Xu
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sankha S. Chakrabarty
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sabrina Chan
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Juliann B. Tefft
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emily Scott
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alexander Spektor
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana Farber Cancer Institute, Boston, MA, USA
| | - Keith L. Ligon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory J. Baker
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter K. Sorger
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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4
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Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Xie Y, Sokolov A, Tyson DR. Addressing persistent challenges in digital image analysis of cancerous tissues. bioRxiv 2023:2023.07.21.548450. [PMID: 37547011 PMCID: PMC10401923 DOI: 10.1101/2023.07.21.548450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The National Cancer Institute (NCI) supports many research programs and consortia, many of which use imaging as a major modality for characterizing cancerous tissue. A trans-consortia Image Analysis Working Group (IAWG) was established in 2019 with a mission to disseminate imaging-related work and foster collaborations. In 2022, the IAWG held a virtual hackathon focused on addressing challenges of analyzing high dimensional datasets from fixed cancerous tissues. Standard image processing techniques have automated feature extraction, but the next generation of imaging data requires more advanced methods to fully utilize the available information. In this perspective, we discuss current limitations of the automated analysis of multiplexed tissue images, the first steps toward deeper understanding of these limitations, what possible solutions have been developed, any new or refined approaches that were developed during the Image Analysis Hackathon 2022, and where further effort is required. The outstanding problems addressed in the hackathon fell into three main themes: 1) challenges to cell type classification and assessment, 2) translation and visual representation of spatial aspects of high dimensional data, and 3) scaling digital image analyses to large (multi-TB) datasets. We describe the rationale for each specific challenge and the progress made toward addressing it during the hackathon. We also suggest areas that would benefit from more focus and offer insight into broader challenges that the community will need to address as new technologies are developed and integrated into the broad range of image-based modalities and analytical resources already in use within the cancer research community.
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5
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Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. Nat Cancer 2023; 4:1036-1052. [PMID: 37349501 PMCID: PMC10368530 DOI: 10.1038/s43018-023-00576-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [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: 09/07/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Precision medicine is critically dependent on better methods for diagnosing and staging disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E)-stained tissue (not genomics) remains the primary diagnostic method in cancer. Recently developed highly multiplexed tissue imaging methods promise to enhance research studies and clinical practice with precise, spatially resolved single-cell data. Here, we describe the 'Orion' platform for collecting H&E and high-plex immunofluorescence images from the same cells in a whole-slide format suitable for diagnosis. Using a retrospective cohort of 74 colorectal cancer resections, we show that immunofluorescence and H&E images provide human experts and machine learning algorithms with complementary information that can be used to generate interpretable, multiplexed image-based models predictive of progression-free survival. Combining models of immune infiltration and tumor-intrinsic features achieves a 10- to 20-fold discrimination between rapid and slow (or no) progression, demonstrating the ability of multimodal tissue imaging to generate high-performance biomarkers.
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Affiliation(s)
- Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | | | | | - Shannon Coy
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Juliann B Tefft
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | | | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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6
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Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell 2023; 186:363-381.e19. [PMID: 36669472 PMCID: PMC10019067 DOI: 10.1016/j.cell.2022.12.028] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [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: 04/01/2021] [Revised: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/20/2023]
Abstract
Advanced solid cancers are complex assemblies of tumor, immune, and stromal cells characterized by high intratumoral variation. We use highly multiplexed tissue imaging, 3D reconstruction, spatial statistics, and machine learning to identify cell types and states underlying morphological features of known diagnostic and prognostic significance in colorectal cancer. Quantitation of these features in high-plex marker space reveals recurrent transitions from one tumor morphology to the next, some of which are coincident with long-range gradients in the expression of oncogenes and epigenetic regulators. At the tumor invasive margin, where tumor, normal, and immune cells compete, T cell suppression involves multiple cell types and 3D imaging shows that seemingly localized 2D features such as tertiary lymphoid structures are commonly interconnected and have graded molecular properties. Thus, while cancer genetics emphasizes the importance of discrete changes in tumor state, whole-specimen imaging reveals large-scale morphological and molecular gradients analogous to those in developing tissues.
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Affiliation(s)
- Jia-Ren Lin
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shu Wang
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Shannon Coy
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yu-An Chen
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Madison Tyler
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maulik K Nariya
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Cody N Heiser
- Program in Chemical & Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sandro Santagata
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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7
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Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Commun Biol 2022; 5:1066. [PMID: 36207580 PMCID: PMC9546880 DOI: 10.1038/s42003-022-03975-9] [Citation(s) in RCA: 6] [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: 08/05/2021] [Accepted: 09/12/2022] [Indexed: 02/01/2023] Open
Abstract
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
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Affiliation(s)
- Sean M. Gross
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Mark A. Dane
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Rebecca L. Smith
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kaylyn L. Devlin
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Ian C. McLean
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Daniel S. Derrick
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Caitlin E. Mills
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Kartik Subramanian
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Alexandra B. London
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Denis Torre
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John Erol Evangelista
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel J. B. Clarke
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Zhuorui Xie
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Cemal Erdem
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Nicholas Lyons
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ted Natoli
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sarah Pessa
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Xiaodong Lu
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James Mullahoo
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan Li
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Miriam Adam
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Brook Wassie
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Moqing Liu
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - David F. Kilburn
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Tiera A. Liby
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Elmar Bucher
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Crystal Sanchez-Aguila
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kenneth Daily
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Larsson Omberg
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Yunguan Wang
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Connor Jacobson
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Clarence Yapp
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Mirra Chung
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Dusica Vidovic
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Stephan Schurer
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Albert Lee
- grid.94365.3d0000 0001 2297 5165Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Ajay Pillai
- grid.94365.3d0000 0001 2297 5165Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Aravind Subramanian
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Malvina Papanastasiou
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ernest Fraenkel
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Heidi S. Feiler
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Gordon B. Mills
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Division of Oncological Sciences, OHSU, Portland, OR USA
| | - Jake D. Jaffe
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Avi Ma’ayan
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Marc R. Birtwistle
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Peter K. Sorger
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - James E. Korkola
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Joe W. Gray
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Laura M. Heiser
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
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8
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Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics 2022; 38:4613-4621. [PMID: 35972352 PMCID: PMC9525007 DOI: 10.1093/bioinformatics/btac544] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 06/07/2021] [Revised: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Stitching microscope images into a mosaic is an essential step in the analysis and visualization of large biological specimens, particularly human and animal tissues. Recent approaches to highly multiplexed imaging generate high-plex data from sequential rounds of lower-plex imaging. These multiplexed imaging methods promise to yield precise molecular single-cell data and information on cellular neighborhoods and tissue architecture. However, attaining mosaic images with single-cell accuracy requires robust image stitching and image registration capabilities that are not met by existing methods. RESULTS We describe the development and testing of ASHLAR, a Python tool for coordinated stitching and registration of 103 or more individual multiplexed images to generate accurate whole-slide mosaics. ASHLAR reads image formats from most commercial microscopes and slide scanners, and we show that it performs better than existing open-source and commercial software. ASHLAR outputs standard OME-TIFF images that are ready for analysis by other open-source tools and recently developed image analysis pipelines. AVAILABILITY AND IMPLEMENTATION ASHLAR is written in Python and is available under the MIT license at https://github.com/labsyspharm/ashlar. The newly published data underlying this article are available in Sage Synapse at https://dx.doi.org/10.7303/syn25826362; the availability of other previously published data re-analyzed in this article is described in Supplementary Table S4. An informational website with user guides and test data is available at https://labsyspharm.github.io/ashlar/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremy L Muhlich
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-An Chen
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clarence Yapp
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas Russell
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sandro Santagata
- Human Tumor Atlas Network, Harvard Medical School, Boston, MA 02115, USA,Harvard Ludwig Cancer Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
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9
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Wu HJ, Temko D, Maliga Z, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ, Michor F. Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell Genom 2022; 2:100165. [PMID: 36419822 PMCID: PMC9681138 DOI: 10.1016/j.xgen.2022.100165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Intra-tumor heterogeneity (ITH) of human tumors is important for tumor progression, treatment response, and drug resistance. However, the spatial distribution of ITH remains incompletely understood. Here, we present spatial analysis of ITH in lung adenocarcinomas from 147 patients using multi-region mass spectrometry of >5,000 regions, single-cell copy number sequencing of ~2,000 single cells, and cyclic immunofluorescence of >10 million cells. We identified two distinct spatial patterns among tumors, termed clustered and random geographic diversification (GD). These patterns were observed in the same samples using both proteomic and genomic data. The random proteomic GD pattern, which is characterized by decreased cell adhesion and lower levels of tumor-interacting endothelial cells, was significantly associated with increased risk of recurrence or death in two independent patient cohorts. Our study presents comprehensive spatial mapping of ITH in lung adenocarcinoma and provides insights into the mechanisms and clinical consequences of GD.
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Affiliation(s)
- Hua-Jun Wu
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and Institute, Beijing, China,These authors contributed equally
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,These authors contributed equally
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA,These authors contributed equally
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jamie Dean
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Charlotte Lee
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Boston, MA 02215, USA
| | - Qiong Xu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Connor A. Jacobson
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA,Ludwig Center at Harvard, Boston, MA 02215, USA
| | - Erin H. Seeley
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Nicholas Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert J. Downey
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Correspondence: (R.J.D.), (F.M.)
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA,Ludwig Center at Harvard, Boston, MA 02215, USA,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Lead contact,Correspondence: (R.J.D.), (F.M.)
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10
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Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 2022; 377:eabo1984. [PMID: 35926050 PMCID: PMC9528698 DOI: 10.1126/science.abo1984] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medicine I, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Nikolay Shvetsov
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Emily R Nadelmann
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilian University of Munich, 81377 Munich, Germany
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Christoph Lippert
- Digital Health-Machine Learning group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, 14482 Potsdam, Germany.,Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiac Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Rasheda A Chowdhury
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Henrik Fox
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jan Gummert
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Ruoyan Li
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Barbara McDonough
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Farnoush Shahriaran
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Fabian J Theis
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Young-Ae Lee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), 85748 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
| | | | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
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11
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Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer Discov 2022; 12:1518-1541. [PMID: 35404441 PMCID: PMC9167783 DOI: 10.1158/2159-8290.cd-21-1357] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [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: 10/13/2021] [Revised: 02/05/2022] [Accepted: 04/01/2022] [Indexed: 11/16/2022]
Abstract
Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially resolved microregion transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanoma in situ, and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor-stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1-PDL1-mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can coexist within a few millimeters of each other in a single specimen. SIGNIFICANCE The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classic histopathology, spatial profiling of proteins and mRNA reveals recurrent morphologic and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell-cell contact. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Ajit J. Nirmal
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Tuulia Vallius
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Brian Quattrochi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alyce A. Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Connor A. Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Roxanne J. Pelletier
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Raquel Arias-Camison
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
| | - Christine G. Lian
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - George F. Murphy
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
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12
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Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311-315. [PMID: 34824477 PMCID: PMC8916956 DOI: 10.1038/s41592-021-01308-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [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] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023]
Abstract
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.
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Affiliation(s)
- Denis Schapiro
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | - Artem Sokolov
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Yu-An Chen
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jeremy L Muhlich
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Joshua Hess
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Allison L Creason
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Ajit J Nirmal
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory J Baker
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Maulik K Nariya
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zoltan Maliga
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Connor A Jacobson
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Matthew W Hodgman
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Juha Ruokonen
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel Persson
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Courtney Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Shamilene Sivagnanam
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Jeremy Goecks
- Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Robert J Coffey
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Sandro Santagata
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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13
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Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods 2022; 19:262-267. [PMID: 35277708 PMCID: PMC9009186 DOI: 10.1038/s41592-022-01415-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.
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Affiliation(s)
- Denis Schapiro
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Yu-An Chen
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR, USA
| | - Yubin Xie
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Muhlich
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Raquel Arias-Camison
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sarah Arena
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | | | | | - Madison Tyler
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Erik A Burlingame
- Oregon Health and Science University, Portland, OR, USA
- Indica Labs, Albuquerque, NM, USA
| | - Young H Chang
- Oregon Health and Science University, Portland, OR, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Julia L Drewes
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter Bankhead
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Joseph T Roland
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John M Herndon
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Michael Angelo
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Garry Nolan
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Jason R Swedlow
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Nikolaus Schultz
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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14
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Guerriero JL, Baker GJ, Lin JR, Chen YA, Pastorello R, Vallius T, Davis J, Yapp C, Church SE, Miller E, Färkkilä A, Vinayak S, Telli ML, Fulci G, D'Andrea A, Shapiro GI, Tolaney SM, Santagata S, Sorger PK, Mittendorf EA. Abstract P2-07-13: High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-07-13] [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
Background: TOPACIO was a phase I/II study evaluating the PARP inhibitor (PARPi) niraparib in combination with the anti-PD-1 antibody pembrolizumab in patients with locally advanced and metastatic triple-negative breast cancer (TNBC, n=55) and ovarian cancer irrespective of BRCA mutation status. In the efficacy-evaluable population (n=47) the objective response rate (ORR) was 21% and disease control rate (DCR) 49%. Although activity was greater in patients with BRCA mutations (7/15, ORR=47% and 12/15, DCR=80%), durable clinical benefit was seen in patients with wild-type BRCA tumors (3/27, ORR=11% and 9/27, DCR=33%). In a limited cohort of 20 patients with durable clinical benefit, there were 8 BRCA wildtype patients, four of whom had mutations in genes associated with the homologous recombination repair and other DNA damage repair pathways. Pre-treatment tissues were collected and evaluated for tumor PD-L1 status. Patients with PD-L1 positive tumors (28/47, 60%) had a higher response rate (9/28, ORR=32%) than those with PD-L1 negative tumors (1/13, ORR=8%; 6 tumors had unknown PD-L1 status). It remains unstudied whether the tumor’s gene expression profile or immune status in baseline biospecimens is predictive of treatment response. In this study we conducted exploratory biomarker analyses to test the hypothesis that gene expression patterns and immune status are associated with treatment response. Methods: Transcriptional profiling of baseline samples was performed using the BC360 (n=41) and PanCancer IO360 (n=42) panels (Nanostring) and multigene signatures were used to measure tumor and immune activities as well as relative immune cell abundance. Transcriptional analysis was paired with high-dimensional, single-cell cyclic immunofluorescence (CyCIF) of samples that had adequate tissue for analysis (n=19) to characterize the composition and topology of the immune microenvironment at single-cell resolution. Results: Nanostring transcriptional analysis revealed that PAM50 genes stratified tumor samples into 4 subgroups with distinct histology as determined by CyCIF. Each subgroup was capable of responding to niraparib plus pembrolizumab. Multiple genes involved in WNT signaling (WNT5B, TANKS1, TANKS2, PARP4, and NET02) were associated with favorable clinical responses. Low neuropilin and tolloid-like protein 2 (NETO2) gene expression was strongly correlated with favorable progression free survival (PFS; R=-0.61, p=0.0008, Spearman’s correlation), suggesting it may be a predictive biomarker of therapeutic response. Nanostring gene expression signatures for tumor inflammation, apoptosis, and inflammatory chemokines also distinguished responders from non-responders (p<0.05). CyCIF analysis performed on whole tissue sections accounting for 2.97 million single cells revealed 43 distinct cell-states comprising the tumor microenvironment. PD1+CD4+ T cells were significantly correlated with extended PFS (R=0.65, p=0.006, Spearman’s correlation). However, PD1+CD4+ T cells were less abundant in patients who continue to respond to the therapy (2.7-fold reduced, p=0.004), suggesting two groups of responders. Conclusion: WNT signaling, NETO2 and PD1+CD4 T cells are candidate biomarkers for predicting response to niraparib plus pembrolizumab. Further studies are underway to characterize the biological underpinnings of these correlative findings.
Citation Format: Jennifer L Guerriero, Gregory J Baker, Jia-Ren Lin, Yu-An Chen, Ricardo Pastorello, Tuulia Vallius, Janae Davis, Clarence Yapp, Sarah E Church, Eric Miller, Anniina Färkkilä, Shaveta Vinayak, Melinda L Telli, Giulia Fulci, Alan D'Andrea, Geoffrey I Shapiro, Sara M Tolaney, Sandro Santagata, Peter K Sorger, Elizabeth A Mittendorf. High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-07-13.
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Affiliation(s)
- Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| | - Gregory J Baker
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | | | - Tuulia Vallius
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Janae Davis
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | | | | | - Anniina Färkkilä
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Shaveta Vinayak
- University of Washington, Seattle Cancer Care Alliance, Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Alan D'Andrea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
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15
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Inde Z, Croker BA, Yapp C, Joshi GN, Spetz J, Fraser C, Qin X, Xu L, Deskin B, Ghelfi E, Webb G, Carlin AF, Zhu YP, Leibel SL, Garretson AF, Clark AE, Duran JM, Pretorius V, Crotty-Alexander LE, Li C, Lee JC, Sodhi C, Hackam DJ, Sun X, Hata AN, Kobzik L, Miller J, Park JA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. Sci Adv 2021; 7:eabf8609. [PMID: 34407940 PMCID: PMC8373124 DOI: 10.1126/sciadv.abf8609] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Novel coronavirus disease 2019 (COVID-19) severity is highly variable, with pediatric patients typically experiencing less severe infection than adults and especially the elderly. The basis for this difference is unclear. We find that mRNA and protein expression of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, increases with advancing age in distal lung epithelial cells. However, in humans, ACE2 expression exhibits high levels of intra- and interindividual heterogeneity. Further, cells infected with SARS-CoV-2 experience endoplasmic reticulum stress, triggering an unfolded protein response and caspase-mediated apoptosis, a natural host defense system that halts virion production. Apoptosis of infected cells can be selectively induced by treatment with apoptosis-modulating BH3 mimetic drugs. Notably, epithelial cells within young lungs and airways are more primed to undergo apoptosis than those in adults, which may naturally hinder virion production and support milder COVID-19 severity.
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Affiliation(s)
- Zintis Inde
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Ben A Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarence Yapp
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Gaurav N Joshi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Integrated Cellular Imaging Core, Emory University, Atlanta, GA, USA
| | - Johan Spetz
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Cameron Fraser
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Xingping Qin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Le Xu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian Deskin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabrielle Webb
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Aaron F Garretson
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jason M Duran
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Victor Pretorius
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | | | - Chendi Li
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Chhinder Sodhi
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - David J Hackam
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Aaron N Hata
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lester Kobzik
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeffrey Miller
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jin-Ah Park
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Douglas Brownfield
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Kristopher A Sarosiek
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
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16
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Inde Z, Yapp C, Joshi GN, Spetz J, Fraser C, Deskin B, Ghelfi E, Sodhi C, Hackam DJ, Kobzik L, Croker BA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity. bioRxiv 2020:2020.09.13.276923. [PMID: 32935109 PMCID: PMC7491524 DOI: 10.1101/2020.09.13.276923] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Angiotensin-converting enzyme 2 (ACE2) maintains cardiovascular and renal homeostasis but also serves as the entry receptor for the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), the causal agent of novel coronavirus disease 2019 (COVID-19). COVID-19 disease severity is typically lower in pediatric patients than adults (particularly the elderly), but higher rates of hospitalizations requiring intensive care are observed in infants than in older children - the reasons for these differences are unknown. ACE2 is expressed in several adult tissues and cells, including alveolar type 2 cells of the distal lung epithelium, but expression at other ages is largely unexplored. Here we show that ACE2 transcripts are expressed in the lung and trachea shortly after birth, downregulated during childhood, and again expressed at high levels in late adulthood. Notably, the repertoire of cells expressing ACE2 protein in the mouse lung and airways shifts during key phases of lung maturation. In particular, podoplanin-positive cells, which are likely alveolar type I cells responsible for gas exchange, express ACE2 only in advanced age. Similar patterns of expression were evident in analysis of human lung tissue from over 100 donors, along with extreme inter- and intra-individual heterogeneity in ACE2 protein expression in epithelial cells. Furthermore, we find that apoptosis, which is a natural host defense system against viral infection, is dynamically regulated during lung maturation, resulting in periods of heightened apoptotic priming and dependence on pro-survival BCL-2 family proteins including MCL-1. Infection of human lung cells with SARS-CoV-2 triggers an unfolded protein stress response and upregulation of the endogenous MCL-1 inhibitor Noxa; in young individuals, MCL-1 inhibition is sufficient to trigger apoptosis in lung epithelial cells and may thus limit virion production and inflammatory signaling. Overall, we identify strong and distinct correlates of COVID-19 disease severity across lifespan and advance our understanding of the regulation of ACE2 and cell death programs in the mammalian lung. Furthermore, our work provides the framework for translation of apoptosis modulating drugs as novel treatments for COVID-19.
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Affiliation(s)
- Zintis Inde
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Clarence Yapp
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA
| | - Gaurav N. Joshi
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
- Integrated Cellular Imaging Core, Emory University, Atlanta, GA
| | - Johan Spetz
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Cameron Fraser
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
| | - Brian Deskin
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
| | - Chhinder Sodhi
- Department of Surgery, Johns Hopkins University, Baltimore, MD
| | - David J. Hackam
- Department of Surgery, Johns Hopkins University, Baltimore, MD
| | - Lester Kobzik
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
| | - Ben A. Croker
- Division of Allergy, Immunology and Rheumatology, University of California, San Diego, CA
| | - Douglas Brownfield
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University, Baltimore, MD
| | - Kristopher A. Sarosiek
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA
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17
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Melms JC, Yapp C, Mills CE, Sorger P, Izar B. Abstract 2168: A growth rate corrected metric for cytotoxic co-culture systems. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2168] [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
Tumor/T-cell co-cultures in combination with large-scale genome-editing tools emerged as powerful tools for discovery of drivers of resistance to immunotherapies. Traditionally, chromium or lactate-dehydrogenase release and/or target cell viability counts before and after co-culture treatment are used as surrogate endpoint assays to estimate the selection pressure applied. These assays cannot dissect growth arrest, cell death, cell viability and target cell outgrowth, all of which occur as a consequence of released cytokines and direct tumor/T-cell interactions, hence, significantly impact the interpretation of small- and large-scale screens in co-culture models. These biases are particularly relevant when comparing cell lines or genotypes with different growth kinetics. Here, we use a dual reporter system and adopt pharmaco-mathematical principles to dissect these biases to create a growth-rate corrected co-culture metric (GRC), which normalizes T-cell mediated antiproliferative and cytotoxic effects in tumor target cells. We illustrate the value of this metric by comparing fast and slow-growing tumor cells in autologous patient-derived melanoma/T-cell co-culture pairs. At tumor-T-cell ratios resulting in a half maximal relative reduction of target cell counts compared to controls, the fast-proliferating cell line had not changed in absolute cell counts since baseline while the slow-growing cell line showed a 50% reduction. This indicates that in one instance (fast growing cell line) growth-retardation occurred due to a balance of immune editing and target cell proliferation, while in the other (slow-growing cell line) T-cell mediated killing resulted in net loss of tumor cells. Using GRC, these differences can be readily distinguished, and comparable selection conditions can be selected. This has important implications for large-scale screens with perturbations within cancer cells: drop-outs from a screen in the fast-growing cell line would not only contain perturbations that increase specific sensitivity to T-cell mediated cytotoxicity, but also perturbations causing a general loss in proliferation/survival fitness. In addition, some of the discrepancy in recently published screens may be explained by differences in models with varying proliferation rates and therefore selection conditions. In summary, the GRC metric enhances the interpretation of co-culture experiments and could contribute to improved selection of targets from large-scale screens investigating resistance to T-cell mediated toxicity for drug development.
Citation Format: Johannes Christian Melms, Clarence Yapp, Caitlin Elizabeth Mills, Peter Sorger, Benjamin Izar. A growth rate corrected metric for cytotoxic co-culture systems [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 2168.
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Affiliation(s)
| | | | | | | | - Benjamin Izar
- 1Columbia University Medical Center, New York City, NY
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18
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Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun 2020; 11:2543. [PMID: 32424117 PMCID: PMC7235235 DOI: 10.1038/s41467-020-16344-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Anniina Färkkilä
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.,Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Doga C Gulhan
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Connor A Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Huy Nguyen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Bose Kochupurakkal
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yinghui Zhou
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Julie R Graham
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Bruce J Dezube
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Pamela Munster
- Helen Diller Family Comprehensive Cancer Center, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Sandro Santagata
- Brigham and Women's Hospital, Laboratory for Systems Pharmacology, 75 Francis Street, Boston, MA, 02115, USA
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ana Lako
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dipanjan Chowdhury
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Ursula A Matulonis
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | | | - Alan D D'Andrea
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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19
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Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun 2020; 11:1459. [PMID: 32193378 PMCID: PMC7081234 DOI: 10.1038/s41467-020-15315-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [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: 09/27/2019] [Accepted: 02/26/2020] [Indexed: 11/09/2022] Open
Abstract
Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed immunogenomic profiling and highly multiplexed single-cell imaging on tumor samples from patients enrolled in a Phase I/II trial of niraparib and pembrolizumab in ovarian cancer (NCT02657889). We identify two determinants of response; mutational signature 3 reflecting defective homologous recombination DNA repair, and positive immune score as a surrogate of interferon-primed exhausted CD8 + T-cells in the tumor microenvironment. Presence of one or both features associates with an improved outcome while concurrent absence yields no responses. Single-cell spatial analysis reveals prominent interactions of exhausted CD8 + T-cells and PD-L1 + macrophages and PD-L1 + tumor cells as mechanistic determinants of response. Furthermore, spatial analysis of two extreme responders shows differential clustering of exhausted CD8 + T-cells with PD-L1 + macrophages in the first, and exhausted CD8 + T-cells with cancer cells harboring genomic PD-L1 and PD-L2 amplification in the second.
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Affiliation(s)
- Anniina Färkkilä
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.,Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Doga C Gulhan
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Connor A Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Huy Nguyen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Bose Kochupurakkal
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yu-An Chen
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | - Yinghui Zhou
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Julie R Graham
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Bruce J Dezube
- TESARO: A GSK company, 1000 Winter Street, Waltham, MA, 02451, USA
| | - Pamela Munster
- Helen Diller Family Comprehensive Cancer Center, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Sandro Santagata
- Brigham and Women's Hospital, Laboratory for Systems Pharmacology, 75 Francis Street, Boston, MA, 02115, USA
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Ana Lako
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dipanjan Chowdhury
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Ursula A Matulonis
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, 200 Longwood Avenue, MA, 02115, USA
| | | | - Alan D D'Andrea
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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20
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Rao SR, Howarth A, Kratschmer P, Snaith AE, Yapp C, Ebner D, Hamdy FC, Edwards CM. Transcriptomic and Functional Screens Reveal MicroRNAs That Modulate Prostate Cancer Metastasis. Front Oncol 2020; 10:292. [PMID: 32231998 PMCID: PMC7082744 DOI: 10.3389/fonc.2020.00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/28/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Identifying new mechanisms that underlie the complex process of metastasis is vital to combat this fatal step in prostate cancer (PCa) progression. Small non-coding RNAs are emerging as important regulators of tumor cell biology. Here we take an integrative approach to elucidate the contribution of microRNAs to metastatic progression, combining transcriptomic analysis with functional screens for migration and morphology. We developed high-content microscopy, high-throughput functional screens for migration and morphology in PCa cells using a microRNA library. RNA-Seq analysis of paired epithelial and mesenchymal PCa cells identified differential expression of 200 microRNAs. Data integration identified two microRNAs that inhibited migration, induced an epithelial-like morphology and were increased in epithelial PCa cells. An overrepresentation of the AAGUGC seed sequence was detected in all three datasets. Analysis of published datasets of patients with PCa identified microRNAs of clinical relevance. The integration of high-throughput functional and expression analyses identifies microRNAs with clinical significance that modulate metastatic behavior in PCa.
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Affiliation(s)
- Srinivasa R Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Alison Howarth
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Patrick Kratschmer
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Ann E Snaith
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Clarence Yapp
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Daniel Ebner
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Claire M Edwards
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom.,Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
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21
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Melms JC, Vallabhaneni S, Mills CE, Yapp C, Chen JY, Morelli E, Waszyk P, Kumar S, Deming D, Moret N, Rodriguez S, Subramanian K, Rogava M, Cartwright ANR, Luoma A, Mei S, Brinker TJ, Miller DM, Spektor A, Schadendorf D, Riggi N, Wucherpfennig KW, Sorger PK, Izar B. Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity. Cancer Res 2020; 80:798-810. [PMID: 31882401 PMCID: PMC7029677 DOI: 10.1158/0008-5472.can-19-2330] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/27/2019] [Revised: 10/30/2019] [Accepted: 12/20/2019] [Indexed: 01/09/2023]
Abstract
Patients with melanoma resistant to RAF/MEK inhibitors (RMi) are frequently resistant to other therapies, such as immune checkpoint inhibitors (ICI), and individuals succumb to their disease. New drugs that control tumor growth and favorably modulate the immune environment are therefore needed. We report that the small-molecule CX-6258 has potent activity against both RMi-sensitive (RMS) and -resistant (RMR) melanoma cell lines. Haspin kinase (HASPIN) was identified as a target of CX-6258. HASPIN inhibition resulted in reduced proliferation, frequent formation of micronuclei, recruitment of cGAS, and activation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. In murine models, CX-6258 induced a potent cGAS-dependent type-I IFN response in tumor cells, increased IFNγ-producing CD8+ T cells, and reduced Treg frequency in vivo. HASPIN was more strongly expressed in malignant compared with healthy tissue and its inhibition by CX-6258 had minimal toxicity in ex vivo-expanded human tumor-infiltrating lymphocytes (TIL), proliferating TILs, and in vitro differentiated neurons, suggesting a potential therapeutic index for anticancer therapy. Furthermore, the activity of CX-6258 was validated in several Ewing sarcoma and multiple myeloma cell lines. Thus, HASPIN inhibition may overcome drug resistance in melanoma, modulate the immune environment, and target a vulnerability in different cancer lineages. SIGNIFICANCE: HASPIN inhibition by CX-6258 is a novel and potent strategy for RAF/MEK inhibitor-resistant melanoma and potentially other tumor types. HASPIN inhibition has direct antitumor activity and induces a favorable immune microenvironment.
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Affiliation(s)
- Johannes C Melms
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Columbia University Medical Center, Division of Hematology and Oncology, New York, New York
- Columbia Center for Translational Immunology, New York, New York
| | - Sreeram Vallabhaneni
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Caitlin E Mills
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Clarence Yapp
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Jia-Yun Chen
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Eugenio Morelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patricia Waszyk
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Sushil Kumar
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Derrick Deming
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nienke Moret
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Steven Rodriguez
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Kartik Subramanian
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Meri Rogava
- Columbia University Medical Center, Division of Hematology and Oncology, New York, New York
- Columbia Center for Translational Immunology, New York, New York
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Adam N R Cartwright
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shaolin Mei
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Titus J Brinker
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - David M Miller
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Alexander Spektor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
| | - Nicolo Riggi
- Experimental Pathology Service, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center for Cancer Research at Harvard, Boston, Massachusetts
| | - Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Columbia University Medical Center, Division of Hematology and Oncology, New York, New York
- Columbia Center for Translational Immunology, New York, New York
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Ludwig Center for Cancer Research at Harvard, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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22
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Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data 2019; 6:323. [PMID: 31848351 PMCID: PMC6917801 DOI: 10.1038/s41597-019-0332-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
In this data descriptor, we document a dataset of multiplexed immunofluorescence images and derived single-cell measurements of immune lineage and other markers in formaldehyde-fixed and paraffin-embedded (FFPE) human tonsil and lung cancer tissue. We used tissue cyclic immunofluorescence (t-CyCIF) to generate fluorescence images which we artifact corrected using the BaSiC tool, stitched and registered using the ASHLAR algorithm, and segmented using ilastik software and MATLAB. We extracted single-cell features from these images using HistoCAT software. The resulting dataset can be visualized using image browsers and analyzed using high-dimensional, single-cell methods. This dataset is a valuable resource for biological discovery of the immune system in normal and diseased states as well as for the development of multiplexed image analysis and viewing tools.
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Affiliation(s)
- Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Giorgio Gaglia
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Yu-An Chen
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Jia-Ren Lin
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Ziming Du
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Zoltan Maliga
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Denis Schapiro
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Clarence Yapp
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Jeremy Muhlich
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Artem Sokolov
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | - Peter Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States.
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States.
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, United States.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States.
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, United States.
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23
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Xu C, Theisen E, Maloney R, Peng J, Santiago I, Yapp C, Werkhoven Z, Rumbaut E, Shum B, Tarnogorska D, Borycz J, Tan L, Courgeon M, Griffin T, Levin R, Meinertzhagen IA, de Bivort B, Drugowitsch J, Pecot MY. Control of Synaptic Specificity by Establishing a Relative Preference for Synaptic Partners. Neuron 2019; 103:865-877.e7. [PMID: 31300277 PMCID: PMC6728174 DOI: 10.1016/j.neuron.2019.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 08/24/2018] [Revised: 04/19/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
The ability of neurons to identify correct synaptic partners is fundamental to the proper assembly and function of neural circuits. Relative to other steps in circuit formation such as axon guidance, our knowledge of how synaptic partner selection is regulated is severely limited. Drosophila Dpr and DIP immunoglobulin superfamily (IgSF) cell-surface proteins bind heterophilically and are expressed in a complementary manner between synaptic partners in the visual system. Here, we show that in the lamina, DIP mis-expression is sufficient to promote synapse formation with Dpr-expressing neurons and that disrupting DIP function results in ectopic synapse formation. These findings indicate that DIP proteins promote synapses to form between specific cell types and that in their absence, neurons synapse with alternative partners. We propose that neurons have the capacity to synapse with a broad range of cell types and that synaptic specificity is achieved by establishing a preference for specific partners.
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Affiliation(s)
- Chundi Xu
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA.
| | - Emma Theisen
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Ryan Maloney
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Jing Peng
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Ivan Santiago
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary Werkhoven
- Center for Brain Science and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elijah Rumbaut
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Bryan Shum
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Dorota Tarnogorska
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jolanta Borycz
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Liming Tan
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maximilien Courgeon
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Tessa Griffin
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Raina Levin
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Ian A Meinertzhagen
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Benjamin de Bivort
- Center for Brain Science and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jan Drugowitsch
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA
| | - Matthew Y Pecot
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA 02115, USA.
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24
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Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P. Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Nat Biotechnol 2019; 37:1080-1090. [PMID: 31427819 PMCID: PMC6728175 DOI: 10.1038/s41587-019-0207-y] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [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: 01/11/2019] [Accepted: 06/27/2019] [Indexed: 01/13/2023]
Abstract
Spatial mapping of proteins in tissues is hindered by limitations in multiplexing, sensitivity and throughput. Here we report immunostaining with signal amplification by exchange reaction (Immuno-SABER), which achieves highly multiplexed signal amplification via DNA-barcoded antibodies and orthogonal DNA concatemers generated by primer exchange reaction (PER). SABER offers independently programmable signal amplification without in situ enzymatic reactions, and intrinsic scalability to rapidly amplify and visualize a large number of targets when combined with fast exchange cycles of fluorescent imager strands. We demonstrate 5- to 180-fold signal amplification in diverse samples (cultured cells, cryosections, formalin-fixed paraffin-embedded sections and whole-mount tissues), as well as simultaneous signal amplification for ten different proteins using standard equipment and workflows. We also combined SABER with expansion microscopy to enable rapid, multiplexed super-resolution tissue imaging. Immuno-SABER presents an effective and accessible platform for multiplexed and amplified imaging of proteins with high sensitivity and throughput.
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Affiliation(s)
- Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Jocelyn Y Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Allen Zhu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Koray Kirli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marcelo Cicconet
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Brian J Beliveau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sylvain W Lapan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Siyuan Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Millicent Lin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - German Pihan
- Pathology Department, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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25
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Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLife 2018; 7:e31657. [PMID: 29993362 PMCID: PMC6075866 DOI: 10.7554/elife.31657] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [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] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 06/29/2018] [Indexed: 12/20/2022] Open
Abstract
The architecture of normal and diseased tissues strongly influences the development and progression of disease as well as responsiveness and resistance to therapy. We describe a tissue-based cyclic immunofluorescence (t-CyCIF) method for highly multiplexed immuno-fluorescence imaging of formalin-fixed, paraffin-embedded (FFPE) specimens mounted on glass slides, the most widely used specimens for histopathological diagnosis of cancer and other diseases. t-CyCIF generates up to 60-plex images using an iterative process (a cycle) in which conventional low-plex fluorescence images are repeatedly collected from the same sample and then assembled into a high-dimensional representation. t-CyCIF requires no specialized instruments or reagents and is compatible with super-resolution imaging; we demonstrate its application to quantifying signal transduction cascades, tumor antigens and immune markers in diverse tissues and tumors. The simplicity and adaptability of t-CyCIF makes it an effective method for pre-clinical and clinical research and a natural complement to single-cell genomics.
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Affiliation(s)
- Jia-Ren Lin
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Ludwig Center for Cancer Research at HarvardHarvard Medical SchoolBostonUnited States
| | - Benjamin Izar
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Ludwig Center for Cancer Research at HarvardHarvard Medical SchoolBostonUnited States
- Department of Medical OncologyDana-Farber Cancer InstituteBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shu Wang
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Harvard Graduate Program in BiophysicsHarvard UniversityCambridgeUnited States
| | - Clarence Yapp
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
| | - Shaolin Mei
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Department of Medical OncologyDana-Farber Cancer InstituteBostonUnited States
| | - Parin M Shah
- Department of Medical OncologyDana-Farber Cancer InstituteBostonUnited States
| | - Sandro Santagata
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Ludwig Center for Cancer Research at HarvardHarvard Medical SchoolBostonUnited States
- Department of PathologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Department of Oncologic PathologyDana-Farber Cancer InstituteBostonUnited States
| | - Peter K Sorger
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
- Ludwig Center for Cancer Research at HarvardHarvard Medical SchoolBostonUnited States
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26
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Iordachescu A, Amin HD, Rankin SM, Williams RL, Yapp C, Bannerman A, Pacureanu A, Addison O, Hulley PA, Grover LM. An In Vitro Model for the Development of Mature Bone Containing an Osteocyte Network. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Alexandra Iordachescu
- School of Chemical Engineering; University of Birmingham; Edgbaston Birmingham B15 2TT UK
- Botnar Research Centre (NDORMS); University of Oxford; Old Road Headington Oxford OX3 7LD UK
| | - Harsh D. Amin
- Inflammation, Development and Repair; National Heart & Lung Institute; Faculty of Medicine; Imperial College London; London SW7 2AZ UK
- Centre for Blast Injury Studies; Department of Bioengineering; Imperial College London; London SW7 2AZ UK
| | - Sara M. Rankin
- Inflammation, Development and Repair; National Heart & Lung Institute; Faculty of Medicine; Imperial College London; London SW7 2AZ UK
- Centre for Blast Injury Studies; Department of Bioengineering; Imperial College London; London SW7 2AZ UK
| | - Richard L. Williams
- School of Chemical Engineering; University of Birmingham; Edgbaston Birmingham B15 2TT UK
| | - Clarence Yapp
- Botnar Research Centre (NDORMS); University of Oxford; Old Road Headington Oxford OX3 7LD UK
- Department of Cell Biology; Harvard Medical School; 240 Longwood Ave Boston MA 02115 USA
| | - Alistair Bannerman
- School of Chemical Engineering; University of Birmingham; Edgbaston Birmingham B15 2TT UK
| | - Alexandra Pacureanu
- European Synchrotron Radiation Facility; Beamline Groups Unit; 71 avenue des Martyrs 38000 Grenoble France
| | - Owen Addison
- School of Dentistry; University of Birmingham; 5 Mill Pool Way Edgbaston Birmingham B5 7EG UK
| | - Philippa A. Hulley
- Botnar Research Centre (NDORMS); University of Oxford; Old Road Headington Oxford OX3 7LD UK
| | - Liam M. Grover
- School of Chemical Engineering; University of Birmingham; Edgbaston Birmingham B15 2TT UK
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27
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017; 56:15555-15559. [PMID: 28976073 PMCID: PMC5725665 DOI: 10.1002/anie.201706788] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/07/2017] [Indexed: 12/13/2022]
Abstract
Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell-permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure-activity relationships, leading to the development of a small molecule with around 75-fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.
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Affiliation(s)
- Philip A. Gerken
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Yijia Zhang
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Shane A. Chandler
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Fengling Li
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Justin L. P. Benesch
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Masoud Vedadi
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Martin D. Smith
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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28
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philip A. Gerken
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Jamie R. Wolstenhulme
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Yijia Zhang
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Shane A. Chandler
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Fengling Li
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Justin L. P. Benesch
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Masoud Vedadi
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Akane Kawamura
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Martin D. Smith
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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29
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Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UC, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S. Selective Targeting of Bromodomains of the Bromodomain-PHD Fingers Family Impairs Osteoclast Differentiation. ACS Chem Biol 2017; 12:2619-2630. [PMID: 28849908 PMCID: PMC5662925 DOI: 10.1021/acschembio.7b00481] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 01/16/2023]
Abstract
Histone acetyltransferases of the MYST family are recruited to chromatin by BRPF scaffolding proteins. We explored functional consequences and the therapeutic potential of inhibitors targeting acetyl-lysine dependent protein interaction domains (bromodomains) present in BRPF1-3 in bone maintenance. We report three potent and selective inhibitors: one (PFI-4) with high selectivity for the BRPF1B isoform and two pan-BRPF bromodomain inhibitors (OF-1, NI-57). The developed inhibitors displaced BRPF bromodomains from chromatin and did not inhibit cell growth and proliferation. Intriguingly, the inhibitors impaired RANKL-induced differentiation of primary murine bone marrow cells and human primary monocytes into bone resorbing osteoclasts by specifically repressing transcriptional programs required for osteoclastogenesis. The data suggest a key role of BRPF in regulating gene expression during osteoclastogenesis, and the excellent druggability of these bromodomains may lead to new treatment strategies for patients suffering from bone loss or osteolytic malignant bone lesions.
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Affiliation(s)
- Julia C. Meier
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Cynthia Tallant
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Oleg Fedorov
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Hanna Witwicka
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Sung-Yong Hwang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Ruud G. van Stiphout
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Catherine Rogers
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Clarence Yapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Brian S. Gerstenberger
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Vita Fedele
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Pavel Savitsky
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - David Heidenreich
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | | | - Dafydd R. Owen
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Paul V. Fish
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Niall M. Igoe
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Elliott D. Bayle
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Bernard Haendler
- Drug Discovery, Bayer Pharma
AG, Müllerstrasse
178, D-13353 Berlin, Germany
| | | | - Francesca Buffa
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Paul E. Brennan
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Susanne Müller
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Anne Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul R. Odgren
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Mark J. Birnbaum
- Department of Biology, Merrimack College, North Andover, Massachusetts, United States
| | - Stefan Knapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
- German Cancer Network (DKTK), Frankfurt site, 60438 Frankfurt am Main, Germany
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30
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Niederhuber MJ, Lambert TJ, Yapp C, Silver PA, Polka JK. Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix. Mol Biol Cell 2017; 28:2734-2745. [PMID: 28963440 PMCID: PMC5620380 DOI: 10.1091/mbc.e17-01-0069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 01/30/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 11/11/2022] Open
Abstract
Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for the organization of this lattice in beta-type carboxysomes of the freshwater cyanobacterium Synechococcus elongatus, CcmM, occurs in two isoforms thought to localize differentially within the carboxysome matrix. Here we use wide-field time-lapse and three-dimensional structured illumination microscopy (3D-SIM) to study the recruitment and localization of these two isoforms. We demonstrate that this superresolution technique is capable of distinguishing the localizations of the outer protein shell of the carboxysome and its internal cargo. We develop an automated analysis pipeline to analyze and quantify 3D-SIM images and generate a population-level description of the carboxysome shell protein, RuBisCO, and CcmM isoform localization. We find that both CcmM isoforms have similar spatial and temporal localization, prompting a revised model of the internal arrangement of the β-carboxysome.
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Affiliation(s)
- Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
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31
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Kawamura A, Münzel M, Kojima T, Yapp C, Bhushan B, Goto Y, Tumber A, Katoh T, King ONF, Passioura T, Walport LJ, Hatch SB, Madden S, Müller S, Brennan PE, Chowdhury R, Hopkinson RJ, Suga H, Schofield CJ. Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nat Commun 2017; 8:14773. [PMID: 28382930 PMCID: PMC5384220 DOI: 10.1038/ncomms14773] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/01/2017] [Indexed: 12/28/2022] Open
Abstract
The JmjC histone demethylases (KDMs) are linked to tumour cell proliferation and are current cancer targets; however, very few highly selective inhibitors for these are available. Here we report cyclic peptide inhibitors of the KDM4A-C with selectivity over other KDMs/2OG oxygenases, including closely related KDM4D/E isoforms. Crystal structures and biochemical analyses of one of the inhibitors (CP2) with KDM4A reveals that CP2 binds differently to, but competes with, histone substrates in the active site. Substitution of the active site binding arginine of CP2 to N-ɛ-trimethyl-lysine or methylated arginine results in cyclic peptide substrates, indicating that KDM4s may act on non-histone substrates. Targeted modifications to CP2 based on crystallographic and mass spectrometry analyses results in variants with greater proteolytic robustness. Peptide dosing in cells manifests KDM4A target stabilization. Although further development is required to optimize cellular activity, the results reveal the feasibility of highly selective non-metal chelating, substrate-competitive inhibitors of the JmjC KDMs.
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Affiliation(s)
- Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Münzel
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Tatsuya Kojima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Bhaskar Bhushan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Oliver N. F. King
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Stephanie B. Hatch
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Madden
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- JST, CREST, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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32
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Tumber A, Nuzzi A, Hookway ES, Hatch SB, Velupillai S, Johansson C, Kawamura A, Savitsky P, Yapp C, Szykowska A, Wu N, Bountra C, Strain-Damerell C, Burgess-Brown NA, Ruda GF, Fedorov O, Munro S, England KS, Nowak RP, Schofield CJ, La Thangue NB, Pawlyn C, Davies F, Morgan G, Athanasou N, Müller S, Oppermann U, Brennan PE. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol 2017; 24:371-380. [PMID: 28262558 PMCID: PMC5361737 DOI: 10.1016/j.chembiol.2017.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 10/31/2016] [Accepted: 02/01/2017] [Indexed: 12/16/2022]
Abstract
Methylation of lysine residues on histone tail is a dynamic epigenetic modification that plays a key role in chromatin structure and gene regulation. Members of the KDM5 (also known as JARID1) sub-family are 2-oxoglutarate (2-OG) and Fe2+-dependent oxygenases acting as histone 3 lysine 4 trimethyl (H3K4me3) demethylases, regulating proliferation, stem cell self-renewal, and differentiation. Here we present the characterization of KDOAM-25, an inhibitor of KDM5 enzymes. KDOAM-25 shows biochemical half maximal inhibitory concentration values of <100 nM for KDM5A-D in vitro, high selectivity toward other 2-OG oxygenases sub-families, and no off-target activity on a panel of 55 receptors and enzymes. In human cell assay systems, KDOAM-25 has a half maximal effective concentration of ∼50 μM and good selectivity toward other demethylases. KDM5B is overexpressed in multiple myeloma and negatively correlated with the overall survival. Multiple myeloma MM1S cells treated with KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation.
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Affiliation(s)
- Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Andrea Nuzzi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Edward S Hookway
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Stephanie B Hatch
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Catrine Johansson
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK; Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Pavel Savitsky
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Na Wu
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Gian Filippo Ruda
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Shonagh Munro
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Radoslaw P Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | | | | | - Charlotte Pawlyn
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Faith Davies
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Gareth Morgan
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Nick Athanasou
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK.
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
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Hatch SB, Yapp C, Montenegro RC, Savitsky P, Gamble V, Tumber A, Ruda GF, Bavetsias V, Fedorov O, Atrash B, Raynaud F, Lanigan R, Carmichael L, Tomlin K, Burke R, Westaway SM, Brown JA, Prinjha RK, Martinez ED, Oppermann U, Schofield CJ, Bountra C, Kawamura A, Blagg J, Brennan PE, Rossanese O, Müller S. Assessing histone demethylase inhibitors in cells: lessons learned. Epigenetics Chromatin 2017; 10:9. [PMID: 28265301 PMCID: PMC5333395 DOI: 10.1186/s13072-017-0116-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The first KDM inhibitors for KDM1 have entered clinical trials, and efforts are ongoing to develop potent, selective and cell-active 'probe' molecules for this target class. Robust cellular assays to assess the specific engagement of KDM inhibitors in cells as well as their cellular selectivity are a prerequisite for the development of high-quality inhibitors. Here we describe the use of a high-content cellular immunofluorescence assay as a method for demonstrating target engagement in cells. RESULTS A panel of assays for the Jumonji C subfamily of KDMs was developed to encompass all major branches of the JmjC phylogenetic tree. These assays compare compound activity against wild-type KDM proteins to a catalytically inactive version of the KDM, in which residues involved in the active-site iron coordination are mutated to inactivate the enzyme activity. These mutants are critical for assessing the specific effect of KDM inhibitors and for revealing indirect effects on histone methylation status. The reported assays make use of ectopically expressed demethylases, and we demonstrate their use to profile several recently identified classes of KDM inhibitors and their structurally matched inactive controls. The generated data correlate well with assay results assessing endogenous KDM inhibition and confirm the selectivity observed in biochemical assays with isolated enzymes. We find that both cellular permeability and competition with 2-oxoglutarate affect the translation of biochemical activity to cellular inhibition. CONCLUSIONS High-content-based immunofluorescence assays have been established for eight KDM members of the 2-oxoglutarate-dependent oxygenases covering all major branches of the JmjC-KDM phylogenetic tree. The usage of both full-length, wild-type and catalytically inactive mutant ectopically expressed protein, as well as structure-matched inactive control compounds, allowed for detection of nonspecific effects causing changes in histone methylation as a result of compound toxicity. The developed assays offer a histone lysine demethylase family-wide tool for assessing KDM inhibitors for cell activity and on-target efficacy. In addition, the presented data may inform further studies to assess the cell-based activity of histone lysine methylation inhibitors.
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Affiliation(s)
- Stephanie B. Hatch
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Raquel C. Montenegro
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Medical Faculty, Research and Drug Development Center, Federal University of Ceará, Rua Cel. Nunes de Melo n.1000—Rodolfo Teófilo, 60, Fortaleza, CE 430-270 Brazil
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Vicki Gamble
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Gian Filippo Ruda
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rachel Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susan M. Westaway
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Jack A. Brown
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Rab K. Prinjha
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Elisabeth D. Martinez
- Hamon Center for Therapeutic Oncology Research, and Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Udo Oppermann
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, OX3 7LD UK
| | | | - Chas Bountra
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Akane Kawamura
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Olivia Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
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Fusco DN, Pratt H, Kandilas S, Cheon SSY, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O'Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol 2017; 8:240. [PMID: 28265266 PMCID: PMC5316548 DOI: 10.3389/fmicb.2017.00240] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 10/31/2016] [Accepted: 02/03/2017] [Indexed: 01/07/2023] Open
Abstract
Flaviviral infections including dengue virus are an increasing clinical problem worldwide. Dengue infection triggers host production of the type 1 IFN, IFN alpha, one of the strongest and broadest acting antivirals known. However, dengue virus subverts host IFN signaling at early steps of IFN signal transduction. This subversion allows unbridled viral replication which subsequently triggers ongoing production of IFN which, again, is subverted. Identification of downstream IFN antiviral effectors will provide targets which could be activated to restore broad acting antiviral activity, stopping the signal to produce endogenous IFN at toxic levels. To this end, we performed a targeted functional genomic screen for IFN antiviral effector genes (IEGs), identifying 56 IEGs required for antiviral effects of IFN against fully infectious dengue virus. Dengue IEGs were enriched for genes encoding nuclear receptor interacting proteins, including HELZ2, MAP2K4, SLC27A2, HSP90AA1, and HSP90AB1. We focused on HELZ2 (Helicase With Zinc Finger 2), an IFN stimulated gene and IEG which encodes a promiscuous nuclear factor coactivator that exists in two isoforms. The two unique HELZ2 isoforms are both IFN responsive, contain ISRE elements, and gene products increase in the nucleus upon IFN stimulation. Chromatin immunoprecipitation-sequencing revealed that the HELZ2 complex interacts with triglyceride-regulator LMF1. Mass spectrometry revealed that HELZ2 knockdown cells are depleted of triglyceride subsets. We thus sought to determine whether HELZ2 interacts with a nuclear receptor known to regulate immune response and lipid metabolism, AHR, and identified HELZ2:AHR interactions via co-immunoprecipitation, found that AHR is a dengue IEG, and that an AHR ligand, FICZ, exhibits anti-dengue activity. Primary bone marrow derived macrophages from HELZ2 knockout mice, compared to wild type controls, exhibit enhanced dengue infectivity. Overall, these findings reveal that IFN antiviral response is mediated by HELZ2 transcriptional upregulation, enrichment of HELZ2 protein levels in the nucleus, and activation of a transcriptional program that appears to modulate intracellular lipid state. IEGs identified in this study may serve as both (1) potential targets for host directed antiviral design, downstream of the common flaviviral subversion point, as well as (2) possible biomarkers, whose variation, natural, or iatrogenic, could affect host response to viral infections.
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Affiliation(s)
- Dahlene N Fusco
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Laboratory for Systems Pharmacology, Harvard Medical SchoolBoston, MA, USA
| | - Henry Pratt
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Stephen Kandilas
- Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA; Department of Medicine, Athens University Medical SchoolAthens, Greece
| | | | - Wenyu Lin
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - D Alex Cronkite
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Megha Basavappa
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Kate L Jeffrey
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital Boston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital Boston, MA, USA
| | - Clarence Yapp
- Laboratory for Systems Pharmacology, Harvard Medical School Boston, MA, USA
| | - Xu Shi
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center Boston, MA, USA
| | - John F O'Sullivan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
| | - Robert E Gerszten
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical CenterBoston, MA, USA; Division of Cardiology, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Takuya Tomaru
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Satoshi Yoshino
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Tetsurou Satoh
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine Maebashi, Japan
| | - Raymond T Chung
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital Boston, MA, USA
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Dakin SG, Martinez FO, Yapp C, Wells G, Oppermann U, Dean BJF, Smith RDJ, Wheway K, Watkins B, Roche L, Carr AJ. Inflammation activation and resolution in human tendon disease. Sci Transl Med 2016; 7:311ra173. [PMID: 26511510 DOI: 10.1126/scitranslmed.aac4269] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Improved understanding of the role of inflammation in tendon disease is required to facilitate therapeutic target discovery. We studied supraspinatus tendons from patients experiencing pain before and after surgical subacromial decompression treatment. Tendons were classified as having early, intermediate, or advanced disease, and inflammation was characterized through activation of pathways mediated by interferon (IFN), nuclear factor κB (NF-κB), glucocorticoid receptor, and signal transducer and activator of transcription 6 (STAT-6). Inflammation signatures revealed expression of genes and proteins induced by IFN and NF-κB in early-stage disease and genes and proteins induced by STAT-6 and glucocorticoid receptor activation in advanced-stage disease. The proresolving proteins FPR2/ALX and ChemR23 were increased in early-stage disease compared to intermediate- to advanced-stage disease. Patients who were pain-free after treatment had tendons with increased expression of CD206 and ALOX15 mRNA compared to tendons from patients who continued to experience pain after treatment, suggesting that these genes and their pathways may moderate tendon pain. Stromal cells from diseased tendons cultured in vitro showed increased expression of NF-κB and IFN target genes after treatment with lipopolysaccharide or IFNγ compared to stromal cells derived from healthy tendons. We identified 15-epi lipoxin A4, a stable lipoxin isoform derived from aspirin treatment, as potentially beneficial in the resolution of tendon inflammation.
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Affiliation(s)
- Stephanie G Dakin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Fernando O Martinez
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington OX3 7DQ, UK
| | - Graham Wells
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK
| | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. Structural Genomics Consortium, University of Oxford, Old Road Campus, Headington OX3 7DQ, UK
| | - Benjamin J F Dean
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Richard D J Smith
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Kim Wheway
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Bridget Watkins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Lucy Roche
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Headington OX3 7LD, UK. NIHR Oxford Biomedical Research Unit, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
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Yapp C, Carr AJ, Price A, Oppermann U, Snelling SJB. H3K27me3 demethylases regulate in vitro chondrogenesis and chondrocyte activity in osteoarthritis. Arthritis Res Ther 2016; 18:158. [PMID: 27388528 PMCID: PMC4936015 DOI: 10.1186/s13075-016-1053-7] [Citation(s) in RCA: 24] [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: 02/05/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022] Open
Abstract
Background Epigenetic changes (i.e., chromatin modifications) occur during chondrogenesis and in osteoarthritis (OA). We investigated the effect of H3K27me3 demethylase inhibition on chondrogenesis and assessed its utility in cartilage tissue engineering and in understanding cartilage destruction in OA. Methods We used a high-content screen to assess the effect of epigenetic modifying compounds on collagen output during chondrogenesis of monolayer human mesenchymal stem cells (MSCs). The impact of GSK-J4 on gene expression, glycosaminoglycan output and collagen formation during differentiation of MSCs into cartilage discs was investigated. Expression of lysine (K)-specific demethylase 6A (UTX) and Jumonji domain-containing 3 (JMJD3), the HEK27Me3 demethylases targeted by GSK-J4, was measured in damaged and undamaged cartilage from patients with OA. The impact of GSK-J4 on ex vivo cartilage destruction and expression of OA-related genes in human articular chondrocytes (HACs) was assessed. H3K27Me3 demethylase regulation of transforming growth factor (TGF)-β-induced gene expression was measured in MSCs and HACs. Results Treatment of chondrogenic MSCs with the H3K27me3 demethylase inhibitor GSK-J4, which targets JMJD3 and UTX, inhibited collagen output; expression of chondrogenic genes, including SOX9 and COL2A1; and disrupted glycosaminoglycan and collagen synthesis. JMJD3 but not UTX expression was increased during chondrogenesis and in damaged OA cartilage, suggesting a predominant role of JMJD3 in chondrogenesis and OA. GSK-J4 prevented ex vivo cartilage destruction and expression of the OA-related genes MMP13 and PTGS2. TGF-β is a key regulator of chondrogenesis and articular cartilage homeostasis, and TGF-β-induced gene expression was inhibited by GSK-J4 treatment of both chondrogenic MSCs and HACs. Conclusions Overall, we show that H3K27me3 demethylases modulate chondrogenesis and that enhancing this activity may improve production of tissue-engineered cartilage. In contrast, targeted inhibition of H3K27me3 demethylases could provide a novel approach in OA therapeutics. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-1053-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clarence Yapp
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK
| | - Andrew Price
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK
| | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK.,Oxford Stem Cell Institute, Oxford, UK
| | - Sarah J B Snelling
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.
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Sutherell C, Tallant C, Monteiro O, Yapp C, Fuchs J, Fedorov O, Siejka P, Müller S, Knapp S, Brenton JD, Brennan PE, Ley SV. Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex. J Med Chem 2016; 59:5095-101. [PMID: 27119626 PMCID: PMC4920105 DOI: 10.1021/acs.jmedchem.5b01997] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 12/23/2015] [Indexed: 12/18/2022]
Abstract
Bromodomain containing proteins PB1, SMARCA4, and SMARCA2 are important components of SWI/SNF chromatin remodeling complexes. We identified bromodomain inhibitors that target these proteins and display unusual binding modes involving water displacement from the KAc binding site. The best compound binds the fifth bromodomain of PB1 with a KD of 124 nM, SMARCA2B and SMARCA4 with KD values of 262 and 417 nM, respectively, and displays excellent selectivity over bromodomains other than PB1, SMARCA2, and SMARCA4.
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Affiliation(s)
- Charlotte
L. Sutherell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
- Cancer
Research
UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, U.K.
| | - Cynthia Tallant
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Octovia
P. Monteiro
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Clarence Yapp
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Julian
E. Fuchs
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
| | - Oleg Fedorov
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Paulina Siejka
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Suzanne Müller
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Stefan Knapp
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
- Department
of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James D. Brenton
- Cancer
Research
UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, U.K.
| | - Paul E. Brennan
- The Structural Genomics
Consortium, University of Oxford, Old
Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Headington, Oxford OX3 7FZ, U.K.
| | - Steven V. Ley
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K.
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Yapp C, Rogers C, Savitsky P, Philpott M, Müller S. Frapid: achieving full automation of FRAP for chemical probe validation. Biomed Opt Express 2016; 7:422-441. [PMID: 26977352 PMCID: PMC4771461 DOI: 10.1364/boe.7.000422] [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] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 06/05/2023]
Abstract
Fluorescence Recovery After Photobleaching (FRAP) is an established method for validating chemical probes against the chromatin reading bromodomains, but so far requires constant human supervision. Here, we present Frapid, an automated open source code implementation of FRAP that fully handles cell identification through fuzzy logic analysis, drug dispensing with a custom-built fluid handler, image acquisition & analysis, and reporting. We successfully tested Frapid on 3 bromodomains as well as on spindlin1 (SPIN1), a methyl lysine binder, for the first time.
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Affiliation(s)
- Clarence Yapp
- Target Discovery Institute, NDMRB, University of Oxford, Oxford, OX3 7FZ, UK
- Botnar Research Centre, NDORMS, University of Oxford, Oxford, OX3 7LD, UK
| | - Catherine Rogers
- Target Discovery Institute, NDMRB, University of Oxford, Oxford, OX3 7FZ, UK
| | - Pavel Savitsky
- Structural Genomics Consortium, ORCRB, University of Oxford, Oxford, OX3 7DQ, UK
| | - Martin Philpott
- Botnar Research Centre, NDORMS, University of Oxford, Oxford, OX3 7LD, UK
| | - Susanne Müller
- Target Discovery Institute, NDMRB, University of Oxford, Oxford, OX3 7FZ, UK
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Smith RD, Carr A, Dakin SG, Snelling SJ, Yapp C, Hakimi O, Hakimi O. The response of tenocytes to commercial scaffolds used for rotator cuff repair. Eur Cell Mater 2016; 31:107-18. [PMID: 26815643 DOI: 10.22203/ecm.v031a08] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Surgical repairs of rotator cuff tears have high re-tear rates and many scaffolds have been developed to augment the repair. Understanding the interaction between patients' cells and scaffolds is important for improving scaffold performance and tendon healing. In this in vitro study, we investigated the response of patient-derived tenocytes to eight different scaffolds. Tested scaffolds included X-Repair, Poly-Tape, LARS Ligament, BioFiber (synthetic scaffolds), BioFiber-CM (biosynthetic scaffold), GraftJacket, Permacol, and Conexa (biological scaffolds). Cell attachment, proliferation, gene expression, and morphology were assessed. After one day, more cells attached to synthetic scaffolds with dense, fine and aligned fibres (X-Repair and Poly-Tape). Despite low initial cell attachment, the human dermal scaffold (GraftJacket) promoted the greatest proliferation of cells over 13 days. Expression of collagen types I and III were upregulated in cells grown on non-cross-linked porcine dermis (Conexa). Interestingly, the ratio of collagen I to collagen III mRNA was lower on all dermal scaffolds compared to synthetic and biosynthetic scaffolds. These findings demonstrate significant differences in the response of patient-derived tendon cells to scaffolds that are routinely used for rotator cuff surgery. Synthetic scaffolds promoted increased cell adhesion and a tendon-like cellular phenotype, while biological scaffolds promoted cell proliferation and expression of collagen genes. However, no single scaffold was superior. Our results may help understand the way that patients' cells interact with scaffolds and guide the development of new scaffolds in the future.
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Affiliation(s)
- R D Smith
- The Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Oxford, OX3 7LD,
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40
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Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, Olzscha H, Monteiro O, Martin S, Philpott M, Tumber A, Filippakopoulos P, Yapp C, Wells C, Che KH, Bannister A, Robson S, Kumar U, Parr N, Lee K, Lugo D, Jeffrey P, Taylor S, Vecellio ML, Bountra C, Brennan PE, O’Mahony A, Velichko S, Müller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S. Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy. Cancer Res 2015; 75:5106-5119. [PMID: 26552700 PMCID: PMC4948672 DOI: 10.1158/0008-5472.can-15-0236] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [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: 01/28/2015] [Accepted: 08/07/2015] [Indexed: 01/11/2023]
Abstract
The histone acetyltransferases CBP/p300 are involved in recurrent leukemia-associated chromosomal translocations and are key regulators of cell growth. Therefore, efforts to generate inhibitors of CBP/p300 are of clinical value. We developed a specific and potent acetyl-lysine competitive protein-protein interaction inhibitor, I-CBP112, that targets the CBP/p300 bromodomains. Exposure of human and mouse leukemic cell lines to I-CBP112 resulted in substantially impaired colony formation and induced cellular differentiation without significant cytotoxicity. I-CBP112 significantly reduced the leukemia-initiating potential of MLL-AF9(+) acute myeloid leukemia cells in a dose-dependent manner in vitro and in vivo. Interestingly, I-CBP112 increased the cytotoxic activity of BET bromodomain inhibitor JQ1 as well as doxorubicin. Collectively, we report the development and preclinical evaluation of a novel, potent inhibitor targeting CBP/p300 bromodomains that impairs aberrant self-renewal of leukemic cells. The synergistic effects of I-CBP112 and current standard therapy (doxorubicin) as well as emerging treatment strategies (BET inhibition) provide new opportunities for combinatorial treatment of leukemia and potentially other cancers.
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Affiliation(s)
- Sarah Picaud
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angeliki Thanasopoulou
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katharina Leonards
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Katherine Jones
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Julia Meier
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Heidi Olzscha
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Octovia Monteiro
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah Martin
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martin Philpott
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Ludwig Institute for Cancer Research (LICR), Roosevelt Drive, Oxford OX3 7DQ,
UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher Wells
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ka Hing Che
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Andrew Bannister
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Samuel Robson
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Umesh Kumar
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Nigel Parr
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Kevin Lee
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Dave Lugo
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Philip Jeffrey
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Simon Taylor
- Experimental Medicines Unit, GlaxoSmithKline, Medicines Research
Centre, Stevenage, UK
| | - Matteo L. Vecellio
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Chas Bountra
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alison O’Mahony
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Sharlene Velichko
- BioSeek Division of DiscoveRx Corporation, 310 Utah Street, Suite
100, South San Francisco, CA, 94080, USA
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Duncan Hay
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
| | - Danette L. Daniels
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin,
U.S.A 53711
| | - Nicholas B. La Thangue
- Laboratory of Cancer Biology, Department of Oncology, Medical
Sciences Division, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, University of
Cambridge, Cambridge CB2 1QN, UK
| | - Rab Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline,
Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Jürg Schwaller
- Laboratory of Childhood Leukemia, Department of Biomedicine,
University of Basel and Basel University Children’s Hospital, Hebelstrasse 20
CH - 4031 Basel, Switzerland
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford,
Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive,
Oxford OX3 7DQ, UK
- Nuffield Department of Clinical Medicine, University of Oxford,
Target Discovery Institute (TDI), Roosevelt Drive, Oxford OX3 7BN, UK
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41
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Thinnes CC, Tumber A, Yapp C, Scozzafava G, Yeh T, Chan MC, Tran TA, Hsu K, Tarhonskaya H, Walport LJ, Wilkins SE, Martinez ED, Müller S, Pugh CW, Ratcliffe PJ, Brennan PE, Kawamura A, Schofield CJ. Betti reaction enables efficient synthesis of 8-hydroxyquinoline inhibitors of 2-oxoglutarate oxygenases. Chem Commun (Camb) 2015; 51:15458-61. [PMID: 26345662 DOI: 10.1039/c5cc06095h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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] [Indexed: 02/11/2024]
Abstract
There is interest in developing potent, selective, and cell-permeable inhibitors of human ferrous iron and 2-oxoglutarate (2OG) oxygenases for use in functional and target validation studies. The 3-component Betti reaction enables efficient one-step C-7 functionalisation of modified 8-hydroxyquinolines (8HQs) to produce cell-active inhibitors of KDM4 histone demethylases and other 2OG oxygenases; the work exemplifies how a template-based metallo-enzyme inhibitor approach can be used to give biologically active compounds.
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Affiliation(s)
- C C Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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Kuzma-Kuzniarska M, Yapp C, Pearson-Jones TW, Jones AK, Hulley PA. 52 IN VITROAND EX VIVOASSESSMENT OF GAP JUNCTION FUNCTION IN TENDON USING FRAP. Br J Sports Med 2014. [DOI: 10.1136/bjsports-2014-094114.52] [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: 11/04/2022]
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43
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Dakin SG, Martinez FO, Wells G, Yapp C, Carr A. 23 Diversity Of Macrophage Signatures Across A Spectrum Of Supraspinatus Pathology: Abstract 23 Table 1. Br J Sports Med 2014. [DOI: 10.1136/bjsports-2014-094114.23] [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: 11/03/2022]
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Hay DA, Fedorov O, Martin S, Singleton DC, Tallant C, Wells C, Picaud S, Philpott M, Monteiro OP, Rogers CM, Conway SJ, Rooney TPC, Tumber A, Yapp C, Filippakopoulos P, Bunnage ME, Müller S, Knapp S, Schofield CJ, Brennan PE. Discovery and optimization of small-molecule ligands for the CBP/p300 bromodomains. J Am Chem Soc 2014; 136:9308-19. [PMID: 24946055 PMCID: PMC4183655 DOI: 10.1021/ja412434f] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [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] [Indexed: 12/14/2022]
Abstract
![]()
Small-molecule inhibitors that target
bromodomains outside
of the bromodomain and extra-terminal (BET) sub-family are lacking.
Here, we describe highly potent and selective ligands for the bromodomain
module of the human lysine acetyl transferase CBP/p300, developed
from a series of 5-isoxazolyl-benzimidazoles. Our starting
point was a fragment hit, which was optimized into a more potent and
selective lead using parallel synthesis employing Suzuki couplings,
benzimidazole-forming reactions, and reductive aminations.
The selectivity of the lead compound against other bromodomain
family members was investigated using a thermal stability assay, which
revealed some inhibition of the structurally related BET family members.
To address the BET selectivity issue, X-ray crystal structures of
the lead compound bound to the CREB binding protein (CBP) and the
first bromodomain of BRD4 (BRD4(1)) were used to guide the design
of more selective compounds. The crystal structures obtained revealed
two distinct binding modes. By varying the aryl substitution pattern
and developing conformationally constrained analogues, selectivity
for CBP over BRD4(1) was increased. The optimized compound is highly
potent (Kd = 21 nM) and selective, displaying
40-fold selectivity over BRD4(1). Cellular activity was demonstrated
using fluorescence recovery after photo-bleaching (FRAP) and a p53
reporter assay. The optimized compounds are cell-active and have nanomolar
affinity for CBP/p300; therefore, they should be useful in studies
investigating the biological roles of CBP and p300 and to validate
the CBP and p300 bromodomains as therapeutic targets.
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Affiliation(s)
- Duncan A Hay
- Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3TA, U.K
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45
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Hakimi O, Poulson R, Thakkar D, Yapp C, Carr A. Ascorbic acid is essential for significant collagen deposition by human tenocytes in vitro. ACTA ACUST UNITED AC 2014. [DOI: 10.5455/oams.030514.or.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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46
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Kuzma-Kuzniarska M, Yapp C, Pearson-Jones TW, Jones AK, Hulley PA. Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching. J Biomed Opt 2014; 19:15001. [PMID: 24390370 PMCID: PMC4019415 DOI: 10.1117/1.jbo.19.1.015001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 07/31/2013] [Revised: 11/11/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
Gap junction-mediated intercellular communication influences a variety of cellular activities. In tendons, gap junctions modulate collagen production, are involved in strain-induced cell death, and are involved in the response to mechanical stimulation. The aim of the present study was to investigate gap junction-mediated intercellular communication in healthy human tendon-derived cells using fluorescence recovery after photobleaching (FRAP). The FRAP is a noninvasive technique that allows quantitative measurement of gap junction function in living cells. It is based on diffusion-dependent redistribution of a gap junction-permeable fluorescent dye. Using FRAP, we showed that human tenocytes form functional gap junctions in monolayer and three-dimensional (3-D) collagen I culture. Fluorescently labeled tenocytes following photobleaching rapidly reacquired the fluorescent dye from neighboring cells, while HeLa cells, which do not communicate by gap junctions, remained bleached. Furthermore, both 18 β-glycyrrhetinic acid and carbenoxolone, standard inhibitors of gap junction activity, impaired fluorescence recovery in tendon cells. In both monolayer and 3-D cultures, intercellular communication in isolated cells was significantly decreased when compared with cells forming many cell-to-cell contacts. In this study, we used FRAP as a tool to quantify and experimentally manipulate the function of gap junctions in human tenocytes in both two-dimensional (2-D) and 3-D cultures.
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Affiliation(s)
- Maria Kuzma-Kuzniarska
- University of Oxford, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7LD, United Kingdom
| | - Clarence Yapp
- University of Oxford, Structural Genomics Consortium, Oxford OX3 7DQ, United Kingdom
| | - Thomas W. Pearson-Jones
- University of Oxford, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7LD, United Kingdom
| | - Andrew K. Jones
- Oxford Brookes University, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences Oxford OX3 0BP, United Kingdom
| | - Philippa A. Hulley
- University of Oxford, Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7LD, United Kingdom
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Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden BD, Filippakopoulos P, Müller S, Knapp S, Brennan PE. [1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains. J Med Chem 2013; 57:462-76. [PMID: 24313754 PMCID: PMC3906316 DOI: 10.1021/jm401568s] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [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] [Indexed: 12/24/2022]
Abstract
Bromodomains are gaining increasing interest as drug targets. Commercially sourced and de novo synthesized substituted [1,2,4]triazolo[4,3-a]phthalazines are potent inhibitors of both the BET bromodomains such as BRD4 as well as bromodomains outside the BET family such as BRD9, CECR2, and CREBBP. This new series of compounds is the first example of submicromolar inhibitors of bromodomains outside the BET subfamily. Representative compounds are active in cells exhibiting potent cellular inhibition activity in a FRAP model of CREBBP and chromatin association. The compounds described are valuable starting points for discovery of selective bromodomain inhibitors and inhibitors with mixed bromodomain pharmacology.
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Affiliation(s)
- Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
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Rotili D, Tomassi S, Conte M, Benedetti R, Tortorici M, Ciossani G, Valente S, Marrocco B, Labella D, Novellino E, Mattevi A, Altucci L, Tumber A, Yapp C, King ONF, Hopkinson RJ, Kawamura A, Schofield CJ, Mai A. Pan-histone demethylase inhibitors simultaneously targeting Jumonji C and lysine-specific demethylases display high anticancer activities. J Med Chem 2013; 57:42-55. [PMID: 24325601 DOI: 10.1021/jm4012802] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In prostate cancer, two different types of histone lysine demethylases (KDM), LSD1/KDM1 and JMJD2/KDM4, are coexpressed and colocalize with the androgen receptor. We designed and synthesized hybrid LSD1/JmjC or "pan-KDM" inhibitors 1-6 by coupling the skeleton of tranylcypromine 7, a known LSD1 inhibitor, with 4-carboxy-4'-carbomethoxy-2,2'-bipyridine 8 or 5-carboxy-8-hydroxyquinoline 9, two 2-oxoglutarate competitive templates developed for JmjC inhibition. Hybrid compounds 1-6 are able to simultaneously target both KDM families and have been validated as potential antitumor agents in cells. Among them, 2 and 3 increase H3K4 and H3K9 methylation levels in cells and cause growth arrest and substantial apoptosis in LNCaP prostate and HCT116 colon cancer cells. When tested in noncancer mesenchymal progenitor (MePR) cells, 2 and 3 induced little and no apoptosis, respectively, thus showing cancer-selective inhibiting action.
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Affiliation(s)
- Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome , P. le A. Moro 5, 00185 Rome, Italy
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Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JBL, King ONF, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer T, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller-Knapp S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A. 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation. Chem Sci 2013; 4:3110-3117. [PMID: 26682036 PMCID: PMC4678600 DOI: 10.1039/c3sc51122g] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, N-oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and γ-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.
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Affiliation(s)
- Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ka Hing Che
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | - Xuan Shirley Li
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Jan B. L. Kristensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Oliver N. F. King
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Kar Kheng Yeoh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Jacob T. Bush
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Clarisse Lejeune
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Nathan R. Rose
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Eleanor A. Bagg
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Wyatt W. Yue
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Lars Olsen
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | | | - Robert J. Klose
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Peter J. Ratcliffe
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK
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Adekanmbi I, Zargar Baboldashti N, Yapp C, Franklin S, Thompson MS. Corrigendum to ‘A novel in vitro loading system for high frequency loading of cultured tendon fascicles’ [Med. Eng. Phys. 35 (2013) 205–210]. Med Eng Phys 2013. [DOI: 10.1016/j.medengphy.2013.03.017] [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: 11/29/2022]
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