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Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024; 383:eabn3263. [PMID: 38422184 DOI: 10.1126/science.abn3263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
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Affiliation(s)
- Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tobias A Schmid
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Julie E Elie
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Amanda Kowalczyk
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ruby Redlich
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Varvara A Shvareva
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ashley Rakuljic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Maria B Ji
- Department of Psychology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ninad S Bhat
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Andrew Z Wang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Siddharth Annaldasula
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tianyu Lu
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Byung Kook Lim
- Neurobiology section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nathan L Clark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael M Yartsev
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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2
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de Oliveira KG, Bång-Rudenstam A, Beyer S, Boukredine A, Talbot H, Governa V, Johansson MC, Månsson AS, Forsberg-Nilsson K, Bengzon J, Malmström J, Welinder C, Belting M. Decoding of the surfaceome and endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche. Acta Neuropathol Commun 2024; 12:35. [PMID: 38414005 PMCID: PMC10898066 DOI: 10.1186/s40478-024-01740-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Immunotherapies with antibody-drug-conjugates (ADC) and CAR-T cells, targeted at tumor surface antigens (surfaceome), currently revolutionize clinical oncology. However, target identification warrants a better understanding of the surfaceome and how it is modulated by the tumor microenvironment. Here, we decode the surfaceome and endocytome and its remodeling by hypoxic stress in glioblastoma (GBM), the most common and aggressive brain tumor in adults. We employed a comprehensive approach for global and dynamic profiling of the surfaceome and endocytosed (endocytome) proteins and their regulation by hypoxia in patient-derived GBM cultures. We found a heterogeneous surface-endocytome profile and a divergent response to hypoxia across GBM cultures. We provide a quantitative ranking of more than 600 surface resident and endocytosed proteins, and their regulation by hypoxia, serving as a resource to the cancer research community. As proof-of-concept, the established target antigen CD44 was identified as a commonly and abundantly expressed surface protein with high endocytic activity. Among hypoxia induced proteins, we reveal CXADR, CD47, CD81, BSG, and FXYD6 as potential targets of the stressed GBM niche. We could validate these findings by immunofluorescence analyses in patient tumors and by increased expression in the hypoxic core of GBM spheroids. Selected candidates were finally confronted by treatment studies, showing their high capacity for internalization and ADC delivery. Importantly, we highlight the limited correlation between transcriptomics and proteomics, emphasizing the critical role of membrane protein enrichment strategies and quantitative mass spectrometry. Our findings provide a comprehensive understanding of the surface-endocytome and its remodeling by hypoxia in GBM as a resource for exploration of targets for immunotherapeutic approaches in GBM.
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Affiliation(s)
- Kelin Gonçalves de Oliveira
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Anna Bång-Rudenstam
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Sarah Beyer
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Axel Boukredine
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Hugo Talbot
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Valeria Governa
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Maria C Johansson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Ann-Sofie Månsson
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Johan Bengzon
- Department of Clinical Sciences, Section of Neurosurgery, Lund University, Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Lund, Section of Oncology, Lund University, Barngatan 4, 221 85, Lund, Sweden.
- Department of Hematology, Oncology and Radiophysics, Skåne University Hospital, Lund, Sweden.
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3
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Ilkhanizadeh S, Gracias A, Åslund AK, Bäck M, Simon R, Kavanagh E, Migliori B, Neofytou C, Nelander S, Westermark B, Uhrbom L, Forsberg-Nilsson K, Konradsson P, Teixeira AI, Uhlén P, Joseph B, Hermanson O, Nilsson KPR. Live Detection of Neural Progenitors and Glioblastoma Cells by an Oligothiophene Derivative. ACS Appl Bio Mater 2023; 6:3790-3797. [PMID: 37647213 PMCID: PMC10521023 DOI: 10.1021/acsabm.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
There is an urgent need for simple and non-invasive identification of live neural stem/progenitor cells (NSPCs) in the developing and adult brain as well as in disease, such as in brain tumors, due to the potential clinical importance in prognosis, diagnosis, and treatment of diseases of the nervous system. Here, we report a luminescent conjugated oligothiophene (LCO), named p-HTMI, for non-invasive and non-amplified real-time detection of live human patient-derived glioblastoma (GBM) stem cell-like cells and NSPCs. While p-HTMI stained only a small fraction of other cell types investigated, the mere addition of p-HTMI to the cell culture resulted in efficient detection of NSPCs or GBM cells from rodents and humans within minutes. p-HTMI is functionalized with a methylated imidazole moiety resembling the side chain of histidine/histamine, and non-methylated analogues were not functional. Cell sorting experiments of human GBM cells demonstrated that p-HTMI labeled the same cell population as CD271, a proposed marker for stem cell-like cells and rapidly migrating cells in glioblastoma. Our results suggest that the LCO p-HTMI is a versatile tool for immediate and selective detection of neural and glioma stem and progenitor cells.
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Affiliation(s)
| | - Aileen Gracias
- Department
of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Andreas K.O. Åslund
- IFM,
Department of Chemistry, Linköping
University, Linköping 581 83, Sweden
| | - Marcus Bäck
- IFM,
Department of Chemistry, Linköping
University, Linköping 581 83, Sweden
| | - Rozalyn Simon
- IFM,
Department of Chemistry, Linköping
University, Linköping 581 83, Sweden
| | - Edel Kavanagh
- Institute
of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bianca Migliori
- Department
of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Christina Neofytou
- Department
of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Sven Nelander
- Department
of Immunology, Genetics and Pathology, and Science for Life Laboratory,
Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Bengt Westermark
- Department
of Immunology, Genetics and Pathology, and Science for Life Laboratory,
Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Lene Uhrbom
- Department
of Immunology, Genetics and Pathology, and Science for Life Laboratory,
Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Karin Forsberg-Nilsson
- Department
of Immunology, Genetics and Pathology, and Science for Life Laboratory,
Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Peter Konradsson
- IFM,
Department of Chemistry, Linköping
University, Linköping 581 83, Sweden
| | - Ana I. Teixeira
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Per Uhlén
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bertrand Joseph
- Institute
of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Ola Hermanson
- Department
of Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - K. Peter R. Nilsson
- IFM,
Department of Chemistry, Linköping
University, Linköping 581 83, Sweden
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4
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Roy A, Sakthikumar S, Kozyrev SV, Nordin J, Pensch R, Mäkeläinen S, Pettersson M, Karlsson EK, Lindblad-Toh K, Forsberg-Nilsson K. Using evolutionary constraint to define novel candidate driver genes in medulloblastoma. Proc Natl Acad Sci U S A 2023; 120:e2300984120. [PMID: 37549291 PMCID: PMC10438395 DOI: 10.1073/pnas.2300984120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.
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Affiliation(s)
- Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Raphaela Pensch
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Suvi Mäkeläinen
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA02142
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA01605
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA01605
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, NottinghamNG72RD, United Kingdom
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5
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Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023. [PMID: 37104599 DOI: 0.1126/science.abn3943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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Affiliation(s)
- Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Irene M Kaplow
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Michael X Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Joel C Armstrong
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ana M Breit
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cornelia Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Daniel B Goodman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Kathleen C Keough
- Fauna Bio, Inc., Emeryville, CA 94608, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Bogdan Kirilenko
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Amanda Kowalczyk
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Colleen Lawless
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Abigail L Lind
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jennifer R S Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Lucas R Moreira
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ruby W Redlich
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Louise Ryan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Alejandro Valenzuela
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Franziska Wagner
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ashley R Brown
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Jenna Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Sergey V Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Kathleen M Morrill
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Austin Osmanski
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Nicole S Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - BaDoi N Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel E Schäffer
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Aryn P Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - James R Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Steven Gazal
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC 20008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Tomas Marques-Bonet
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Martin Nweeia
- Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada
- Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA
- Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Arcadi Navarro
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
- CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine S Pollard
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Irina Ruf
- Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA
| | - Andreas R Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
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6
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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7
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Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Hiller M, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Integrating gene annotation with orthology inference at scale. Science 2023; 380:eabn3107. [PMID: 37104600 DOI: 10.1126/science.abn3107] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.
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Affiliation(s)
- Bogdan M Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Moritz Blumer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Ariadna E Morales
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Alexis-Walid Ahmed
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Dimitrios-Georgios Kontopoulos
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Leon Hilgers
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
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8
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023; 380:eabn2937. [PMID: 37104612 PMCID: PMC10259825 DOI: 10.1126/science.abn2937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/09/2023] [Indexed: 04/29/2023]
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xue Li
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Diane P. Genereux
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Chao Wang
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - James Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Quan Sun
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jessica Johnson
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Elinor K. Karlsson
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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9
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Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Ryder OA, Shapiro B, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. The contribution of historical processes to contemporary extinction risk in placental mammals. Science 2023; 380:eabn5856. [PMID: 37104572 PMCID: PMC10184782 DOI: 10.1126/science.abn5856] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.
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Affiliation(s)
- Aryn P Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | | | | | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Aitor Serres-Armero
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 30008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | | | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 32, Sweden
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies, Barcelona 08010, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Violeta Munoz Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kathleen Foley
- College of Law, University of Iowa, Iowa City, IA 52242, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
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10
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Andrews G, Fan K, Pratt HE, Phalke N, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science 2023; 380:eabn7930. [PMID: 37104580 DOI: 10.1126/science.abn7930] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). We identified 439,461 cCREs and 2,024,062 TFBSs under evolutionary constraint. Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. Our annotations illuminate the regulatory functions of the human genome.
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Affiliation(s)
- Gregory Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nishigandha Phalke
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132 Uppsala, Sweden
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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11
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Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Springer MS, Murphy WJ, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. A genomic timescale for placental mammal evolution. Science 2023; 380:eabl8189. [PMID: 37104581 DOI: 10.1126/science.abl8189] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Victor C Mason
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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12
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Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 2023; 380:eabn2253. [PMID: 37104592 DOI: 10.1126/science.abn2253] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.
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Affiliation(s)
- James R Xue
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ava Mackay-Smith
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Michael X Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jared F Akers
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Mark Noble
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Terence D Capellini
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kristen J Brennand
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Ryan Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences Tufts University School of Medicine, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
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13
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. bioRxiv 2023:2023.03.10.531987. [PMID: 36945512 PMCID: PMC10028973 DOI: 10.1101/2023.03.10.531987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Steven Gazal
- Keck School of Medicine, University of Southern California; Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine; Pittsburgh, PA 15261, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Xue Li
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - James R. Xue
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Fauna Bio Incorporated; Emeryville, CA 94608, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland; Brisbane, Queensland, Australia
| | - Jessica Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | | | - Benedict Paten
- Genomics Institute, University of California Santa Cruz; Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine; New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin; Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
- Biodiscovery Institute, University of Nottingham; Nottingham, UK
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
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14
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Ilkhanizadeh S, Gracias A, Åslund AKO, Bäck M, Simon R, Neofytou C, Rraklli V, Migliori B, Kavanagh E, Nelander S, Westermark B, Uhrbom L, Forsberg-Nilsson K, Teixeira AI, Konradsson P, Uhlén P, Holmberg J, Joseph B, Nilsson KPR, Hermanson O. STEM-19. LIVE DETECTION OF NEURAL STEM AND GLIOBLASTOMA CELLS BY A LUMINESCENT CONJUGATED OLIGOTHIOPHENE DERIVATIVE. Neuro Oncol 2022. [PMCID: PMC9660628 DOI: 10.1093/neuonc/noac209.136] [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] Open
Abstract
Abstract
Glioblastoma (GBM) is an aggressive nervous system tumor with a mean survival time of 12-14 months. Cells with neural stem cell-like properties can be derived from GBM tumors. These cells seem to escape conventional irradiation treatment, chemotherapy, and surgery, and may play a crucial role for relapse. It is therefore urgent to develop novel approaches for reliable detection of neural stem cell-like cells in GBM. Here we report a luminescent conjugated oligothiophene (LCO), named GlioStem (p-HTMI), for non-invasive and non-amplified real-time detection of live human patient-derived GBM cells and embryonic neural stem/progenitor cells (NSPCs). Within a maximum of 10 minutes after administration of the molecule in vitro, in the existing media, fluorescence emission was observed without any modulation of the cells or additional vehicle, resulting in efficient detection of cytoplasmic luminescent signal in NSPCs or GBM cells from rodents and humans, detectable at Alexa488/GFP wavelength. GlioStem is functionalized with a methylated imidazole moiety resembling the side chain of histidine/histamine, and non-methylated analogues were not functional. In vitro, GlioStem was shown to identify fetal cortical NSPCs from rat (FGF2-expanded), embryonic stem cell-derived NSPCs from mouse (FGF2/EGF-expanded), and FGF2-exposed C6 glioma cell cultures from rat, but not any other cell types investigated. Cell sorting experiments of patient-derived, FGF2/EGF-expanded GBM cells demonstrated that GlioStem in addition to NSPC-markers like Nestin and Sox2 labeled the same population (overlap > 90%) of cells as CD271, a proposed marker for stem cell-like cells and rapidly migrating cells in glioblastoma. Our results suggest that the LCO GlioStem is a versatile tool for immediate and selective detection of subpopulations of neural stem and glioma cells.
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Affiliation(s)
| | - Aileen Gracias
- Department of Neuroscience, Karolinska Institutet , Stockholm , Sweden
| | | | - Marcus Bäck
- IFM, Department of Chemistry , Linköping , Sweden
| | | | | | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet , Stockholm , Sweden
| | - Bianca Migliori
- Department of Neuroscience, Karolinska Institutet , Stockholm , Sweden
| | - Edel Kavanagh
- Institute of Environmental Medicine, Karolinska Institutet , Stockholm , Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala , Sweden
| | - Bengt Westermark
- Uppsala University, Dept. Immunology, Genetics and Pathology , Uppsala , Sweden
| | | | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala , Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm , Sweden
| | | | - Per Uhlén
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm , Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet , Stockholm , Sweden
| | - Bertrand Joseph
- Institute of Environmental Medicine, Karolinska Institutet , Stockholm , Sweden
| | | | - Ola Hermanson
- Department of Neuroscience, Karolinska Institutet , Stockholm , Sweden
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15
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Governa V, Talbot H, Gonçalves de Oliveira K, Cerezo-Magaña M, Bång-Rudenstam A, Forsberg-Nilsson K, Malmström J, Bengzon J, Welinder C, Belting M. P12.02.A Landscape of surfaceome and endocytome in human glioma is divergent and depends on cellular spatial organization. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.267] [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: 11/13/2022] Open
Abstract
Abstract
Background
Cell-surface proteins have a key role in drug development, and tumor cell-surface proteins integrated with the plasma membrane (tumor surfaceome, TS) have attracted considerable attention as targets for immunotherapies in cancer. Checkpoint inhibitor blocking antibodies, antibody drug conjugates (ADCs), and CAR-T cells are all directed at the TS. However, a remaining challenge is the lack of strategies to comprehensively map potential TS target antigens for the design of more rational, individualized treatments. Of particular relevance, ADC and other intracellular drug delivery strategies rely on targets that functionally engage in endocytic internalization.
Material and Methods
With the aim to address these challenges and to provide insight into the complexity of the TS, we have developed a versatile technology for TS mapping (TS-MAP). As proof-of-concept, we focused on primary brain tumors that remain among the most aggressive forms of cancer, and for which attempts to conquer the most common variant, glioblastoma (GBM) have failed so far. TS-MAP is compatible with primary 3D cultures and intact patient glioma tumors with preserved tissue architecture, and specifically identifies proteins capable of endocytosis as tractable targets for ADCs and other modalities requiring toxic payload internalization. Moreover, we have curated a TS classifier (SURFME) for categorization of bona fide membrane proteins.
Results
We show how cellular spatial organization (2D vs. 3D) fundamentally transforms the surfaceome and endocytome in glioma with general implications for target screening approaches. The TS-MAP platform was further applied to profile the surfaceome and endocytome landscape in a cohort of freshly resected patient gliomas. We found a highly diverse TS repertoire between patient tumors, not directly associated with grade and histology, which highlights the need for individualized approaches.
Conclusions
The TS-MAP platform and SURFME classifier should be widely applicable to a variety of brain tumors. Our findings in GBM provide new layers of understanding fundamental to the future development of immunotherapy strategies, as well as new procedures for proteomics-based target identification aimed at a better understanding of how to harness the TS for personalized immunotherapy. Our results reflect the oncogenetic multiclonality and transcriptional diversity of gliomas, which warrants future studies that elucidate how the oncogenetic profile and spatial organization synergize to shape the full complexity of the tumor microenvironment.
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16
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Cerezo-Magaña M, Christianson HC, van Kuppevelt TH, Forsberg-Nilsson K, Belting M. Hypoxic Induction of Exosome Uptake through Proteoglycan-Dependent Endocytosis Fuels the Lipid Droplet Phenotype in Glioma. Mol Cancer Res 2020; 19:528-540. [PMID: 33288734 DOI: 10.1158/1541-7786.mcr-20-0560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/13/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
As an adaptive response to hypoxic stress, aggressive tumors rewire their metabolic phenotype into increased malignant behavior through extracellular lipid scavenging and storage in lipid droplets (LD). However, the underlying mechanisms and potential lipid source retrieved in the hypoxic tumor microenvironment remain poorly understood. Here, we show that exosome-like extracellular vesicles (EV), known as influential messengers in the tumor microenvironment, may also serve anabolic functions by transforming hypoxic, patient-derived human glioblastoma cell lines into the LD+ phenotype. EVs were internalized via a hypoxia-sensitive, endocytic mechanism that fueled LD formation through direct lipid transfer, and independently of fatty acid synthase activity. EVs can enter cells through multiple and yet ill-defined pathways. On a mechanistic level, we found that hypoxia-mediated EV uptake depends on increased heparan sulfate proteoglycan (HSPG) endocytosis that preferentially followed the lipid raft pathway. The functional relevance of HSPG was evidenced by the reversal of EV-mediated LD loading by targeting of HSPG receptor function. IMPLICATIONS: Together, our data extend the multifaceted role of EVs in cancer biology by showing their LD-inducing capacity in hypoxic glioma cells. Moreover, these findings highlight a potential function for HSPG-mediated endocytosis as a salvage pathway for EV retrieval during tumor stress conditions.
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Affiliation(s)
- Myriam Cerezo-Magaña
- Department of Clinical Sciences, Section of Oncology, Lund University, Lund, Sweden
| | | | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Belting
- Department of Clinical Sciences, Section of Oncology, Lund University, Lund, Sweden. .,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Skåne University Hospital, Lund, Sweden
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17
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Sakthikumar S, Roy A, Haseeb L, Pettersson ME, Sundström E, Marinescu VD, Lindblad-Toh K, Forsberg-Nilsson K. Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biol 2020; 21:127. [PMID: 32513296 PMCID: PMC7281935 DOI: 10.1186/s13059-020-02035-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 10/28/2019] [Accepted: 04/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions. RESULTS We validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites. CONCLUSIONS These results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.
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Affiliation(s)
- Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Lulu Haseeb
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Elisabeth Sundström
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.
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18
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Xiong A, Spyrou A, Forsberg-Nilsson K. Involvement of Heparan Sulfate and Heparanase in Neural Development and Pathogenesis of Brain Tumors. Adv Exp Med Biol 2020; 1221:365-403. [PMID: 32274718 DOI: 10.1007/978-3-030-34521-1_14] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Brain tumors are aggressive and devastating diseases. The most common type of brain tumor, glioblastoma (GBM), is incurable and has one of the worst five-year survival rates of all human cancers. GBMs are invasive and infiltrate healthy brain tissue, which is one main reason they remain fatal despite resection, since cells that have already migrated away lead to rapid regrowth of the tumor. Curative therapy for medulloblastoma (MB), the most common pediatric brain tumor, has improved, but the outcome is still poor for many patients, and treatment causes long-term complications. Recent advances in the classification of pediatric brain tumors reveal distinct subgroups, allowing more targeted therapy for the most aggressive forms, and sparing children with less malignant tumors the side-effects of massive treatment. Heparan sulfate proteoglycans (HSPGs), main components of the neurogenic niche, interact specifically with a large number of physiologically important molecules and vital roles for HS biosynthesis and degradation in neural stem cell differentiation have been presented. HSPGs are composed of a core protein with attached highly charged, sulfated disaccharide chains. The major enzyme that degrades HS is heparanase (HPSE), an important regulator of extracellular matrix (ECM) remodeling which has been suggested to promote the growth and invasion of other types of tumors. This is of clinical interest because GBM are highly invasive and children with metastatic MB at the time of diagnosis exhibit a worse outcome. Here we review the involvement of HS and HPSE in development of the nervous system and some of its most malignant brain tumors, glioblastoma and medulloblastoma.
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Affiliation(s)
- Anqi Xiong
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Insitutet, Stockholm, Sweden
| | - Argyris Spyrou
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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19
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Čančer M, Drews LF, Bengtsson J, Bolin S, Rosén G, Westermark B, Nelander S, Forsberg-Nilsson K, Uhrbom L, Weishaupt H, Swartling FJ. BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells. Cell Death Dis 2019; 10:881. [PMID: 31754113 PMCID: PMC6872649 DOI: 10.1038/s41419-019-2120-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 07/18/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common primary malignant brain tumor in adults. Patients usually undergo surgery followed by aggressive radio- and chemotherapy with the alkylating agent temozolomide (TMZ). Still, median survival is only 12–15 months after diagnosis. Many human cancers including GBMs demonstrate addiction to MYC transcription factor signaling and can become susceptible to inhibition of MYC downstream genes. JQ1 is an effective inhibitor of BET Bromodomains, a class of epigenetic readers regulating expression of downstream MYC targets. Here, we show that BET inhibition decreases viability of patient-derived GBM cell lines. We propose a distinct expression signature of MYCN-elevated GBM cells that correlates with significant sensitivity to BET inhibition. In tumors showing JQ1 sensitivity, we found enrichment of pathways regulating cell cycle, DNA damage response and repair. As DNA repair leads to acquired chemoresistance to TMZ, JQ1 treatment in combination with TMZ synergistically inhibited proliferation of MYCN-elevated cells. Bioinformatic analyses further showed that the expression of MYCN correlates with Aurora Kinase A levels and Aurora Kinase inhibitors indeed showed synergistic efficacy in combination with BET inhibition. Collectively, our data suggest that BET inhibitors could potentiate the efficacy of either TMZ or Aurora Kinase inhibitors in GBM treatment.
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Affiliation(s)
- Matko Čančer
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lisa F Drews
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Bengtsson
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Bolin
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriela Rosén
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Holger Weishaupt
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science For Life Laboratory, Uppsala University, Uppsala, Sweden.
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20
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Jimenez-Pascual A, Hale J, Bayik D, Silver D, Roversi G, Alban T, McIntyre T, Colombo G, Taraboletti G, Holmberg K, Forsberg-Nilsson K, Lathia J, Siebzehnrubl F. STEM-07. THE ATYPICAL METALLOPROTEINASE ADAMDEC1 MAINTAINS A NOVEL FGF MEDIATED SIGNALLING NETWORK IN GLIOBLASTOMA CANCER STEM CELLS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.981] [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: 11/12/2022] Open
Abstract
Abstract
Glioblastomas (GBM) are lethal brain tumors where poor outcome is attributed to cellular heterogeneity, therapeutic resistance, and a highly infiltrative nature. These characteristics are preferentially linked to GBM cancer stem cells (CSCs), but how CSCs maintain their stemness is incompletely understood and the subject of intense investigation. CSCs rely both on cell intrinsic programs and microenvironmental interactions to regulate their maintenance. Recent work has demonstrated that CSCs can modulate their surrounding microenvironment by metalloproteinase expression, allowing direct modification of the extracellular matrix that provides structural tissue integrity, and instructive signalling via engagement of key cell surface receptors and sequestration of essential growth factors. Here, we identify a novel growth factor signalling loop that induces and maintains CSCs via an atypical metalloproteinase, a disintegrin and metalloproteinase domain-like protein decysin 1 (ADAMDEC1), secreted by CSCs. ADAMDEC1 solubilizes fibroblast growth factor-2 (FGF2) in the tumor microenvironment. We find that CSCs exclusively express FGF receptor 1 (FGFR1), which upon binding of FGF2 induces upregulation of Zinc finger E-box-binding homeobox 1 (ZEB1). ZEB1 is a regulator of stemness and tumor initiation, and therefore ADAMDEC1-FGF2-FGFR1 signalling promotes malignancy in GBM. We further show that ERK phosphorylation drives ZEB1, which regulates ADAMDEC1 expression, creating a positive feedback loop via repression of microRNA-203. Genetic or pharmacological targeting of components of this axis attenuates self-renewal and tumor growth. These findings reveal a new signalling axis for CSC maintenance and highlight ADAMDEC1 and FGFR1 as potential therapeutic targets in GBM. In addition, these findings provide a new paradigm for GBM growth through which key growth factors embedded within the extracellular matrix can be selectively accessed by CSC for their maintenance.
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Affiliation(s)
| | | | - Defne Bayik
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | | | - Gustavo Roversi
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Tyler Alban
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | | | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Milan, Italy
| | | | | | | | - Justin Lathia
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
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21
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Jimenez-Pascual A, Hale J, Kordowski A, Pugh J, Rao S, Silver D, Alban T, Watson D, Chen R, McIntyre T, Colombo G, Taraboletti G, Holmberg K, Forsberg-Nilsson K, Lathia J, Siebzehnrubl F. The metalloproteinase ADAMDEC1 maintains a novel growth factor signalling loop in glioblastoma cancer stem cells. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz167.003] [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: 11/14/2022] Open
Abstract
Abstract
Glioblastomas (GBM) are lethal brain tumours where poor outcome is attributed to cellular heterogeneity, therapeutic resistance, and a highly infiltrative nature. These characteristics are preferentially linked to GBM cancer stem cells (GSCs), but how GSCs maintain their stemness is incompletely understood and the subject of intense investigation. Here, we identify a novel growth factor signalling loop that induces and maintains GSCs. This loop consists of an atypical metalloproteinase, a disintegrin and metalloproteinase domain-like protein decysin 1 (ADAMDEC1), secreted by GSCs. ADAMDEC1 solubilizes fibroblast growth factor-2 (FGF2) in the tumour microenvironment. We find that GSCs exclusively express FGF receptor 1 (FGFR1), which upon binding of FGF2 induces upregulation of Zinc finger E-box-binding homeobox 1 (ZEB1). ZEB1 is a regulator of stemness and tumour initiation, and therefore ADAMDEC1-FGF2-FGFR1 signalling promotes malignancy in GBM. We further show that ZEB1 regulates ADAMDEC1 expression, creating a positive feedback loop. Genetic or pharmacological targeting of components of this axis attenuates self-renewal and tumour growth. These findings reveal a new signalling axis for GSC maintenance and highlight ADAMDEC1 and FGFR1 as potential therapeutic targets in GBM.
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Affiliation(s)
| | - James Hale
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Anja Kordowski
- Cardiff University School of Biosciences, Cardiff, United Kingdom
| | - Jamie Pugh
- Cardiff University School of Biosciences, Cardiff, United Kingdom
| | - Shilpa Rao
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Daniel Silver
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Tyler Alban
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Defne Watson
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Rui Chen
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
| | - Thomas McIntyre
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, United States of America
| | - Giorgio Colombo
- University of Pavia and Institute of Molecular Recognition Chemistry (ICRM-CNR), Milano, Italy
| | | | - Karl Holmberg
- Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Justin Lathia
- Lerner Research Institute, Cleveland Clinic, Cleveland, United States of America
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, United States of America
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22
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Barash U, Spyrou A, Liu P, Vlodavsky E, Zhu C, Luo J, Su D, Ilan N, Forsberg-Nilsson K, Vlodavsky I, Yang X. Heparanase promotes glioma progression via enhancing CD24 expression. Int J Cancer 2019; 145:1596-1608. [PMID: 31032901 DOI: 10.1002/ijc.32375] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 02/05/2023]
Abstract
Heparanase is an endo-β-d-glucuronidase that cleaves heparan sulfate (HS) side chains of heparan sulfate proteoglycans. Compelling evidence tie heparanase levels with all steps of tumor formation including tumor initiation, growth, metastasis and chemo-resistance, likely involving augmentation of signaling pathways and gene transcription. In order to reveal the molecular mechanism(s) underlying the protumorigenic properties of heparanase, we established an inducible (Tet-on) system in U87 human glioma cells and applied gene array methodology in order to identify genes associated with heparanase induction. We found that CD24, a mucin-like cell adhesion protein, is consistently upregulated by heparanase and by heparanase splice variant devoid of enzymatic activity, whereas heparanase gene silencing was associated with decreased CD24 expression. This finding was further substantiated by a similar pattern of heparanase and CD24 immunostaining in glioma patients (Pearson's correlation; R = 0.66, p = 0.00001). Noteworthy, overexpression of CD24 stimulated glioma cell migration, invasion, colony formation in soft agar and tumor growth in mice suggesting that CD24 functions promote tumor growth. Likewise, anti-CD24 neutralizing monoclonal antibody attenuated glioma tumor growth, and a similar inhibition was observed in mice treated with a neutralizing mAb directed against L1 cell adhesion molecule (L1CAM), a ligand for CD24. Importantly, significant shorter patient survival was found in heparanase-high/CD24-high tumors vs. heparanase-high/CD24-low tumors for both high-grade and low-grade glioma (p = 0.02). Our results thus uncover a novel heparanase-CD24-L1CAM axis that plays a significant role in glioma tumorigenesis.
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Affiliation(s)
- Uri Barash
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Haifa, Israel
| | - Argyris Spyrou
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pei Liu
- Shantou University Medical College, Shantou, China
| | | | - Chenchen Zhu
- Shantou University Medical College, Shantou, China
| | - Juanjuan Luo
- Shantou University Medical College, Shantou, China
| | - Dongsheng Su
- Shantou University Medical College, Shantou, China
| | - Neta Ilan
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Haifa, Israel
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Haifa, Israel
| | - Xiaojun Yang
- Shantou University Medical College, Shantou, China
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23
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Kaffes I, Szulzewsky F, Chen Z, Herting CJ, Gabanic B, Velázquez Vega JE, Shelton J, Switchenko JM, Ross JL, McSwain LF, Huse JT, Westermark B, Nelander S, Forsberg-Nilsson K, Uhrbom L, Maturi NP, Cimino PJ, Holland EC, Kettenmann H, Brennan CW, Brat DJ, Hambardzumyan D. Human Mesenchymal glioblastomas are characterized by an increased immune cell presence compared to Proneural and Classical tumors. Oncoimmunology 2019; 8:e1655360. [PMID: 31646100 PMCID: PMC6791439 DOI: 10.1080/2162402x.2019.1655360] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 04/03/2019] [Revised: 07/15/2019] [Accepted: 08/09/2019] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive malignant primary brain tumor in adults, with a median survival of 14.6 months. Recent efforts have focused on identifying clinically relevant subgroups to improve our understanding of pathogenetic mechanisms and patient stratification. Concurrently, the role of immune cells in the tumor microenvironment has received increasing attention, especially T cells and tumor-associated macrophages (TAM). The latter are a mixed population of activated brain-resident microglia and infiltrating monocytes/monocyte-derived macrophages, both of which express ionized calcium-binding adapter molecule 1 (IBA1). This study investigated differences in immune cell subpopulations among distinct transcriptional subtypes of GBM. Human GBM samples were molecularly characterized and assigned to Proneural, Mesenchymal or Classical subtypes as defined by NanoString nCounter Technology. Subsequently, we performed and analyzed automated immunohistochemical stainings for TAM as well as specific T cell populations. The Mesenchymal subtype of GBM showed the highest presence of TAM, CD8+, CD3+ and FOXP3+ T cells, as compared to Proneural and Classical subtypes. High expression levels of the TAM-related gene AIF1, which encodes the TAM-specific protein IBA1, correlated with a worse prognosis in Proneural GBM, but conferred a survival benefit in Mesenchymal tumors. We used our data to construct a mathematical model that could reliably identify Mesenchymal GBM with high sensitivity using a combination of the aforementioned cell-specific IHC markers. In conclusion, we demonstrated that molecularly distinct GBM subtypes are characterized by profound differences in the composition of their immune microenvironment, which could potentially help to identify tumors amenable to immunotherapy.
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Affiliation(s)
- Ioannis Kaffes
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA.,Department of Cellular Neurosciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Frank Szulzewsky
- Department of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Zhihong Chen
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA.,Discovery and Developmental Therapeutics Program, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Cameron J Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Ben Gabanic
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Jennifer Shelton
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jeffrey M Switchenko
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - James L Ross
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Leon F McSwain
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Naga Prathyusha Maturi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Patrick J Cimino
- Department of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eric C Holland
- Department of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helmut Kettenmann
- Department of Cellular Neurosciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Cameron W Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Daniel J Brat
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Dolores Hambardzumyan
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA.,Discovery and Developmental Therapeutics Program, Winship Cancer Institute, Emory University, Atlanta, GA, USA
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24
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Jimenez-Pascual A, Hale JS, Kordowski A, Pugh J, Silver DJ, Bayik D, Roversi G, Alban TJ, Rao S, Chen R, McIntyre TM, Colombo G, Taraboletti G, Holmberg KO, Forsberg-Nilsson K, Lathia JD, Siebzehnrubl FA. ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells. Cancer Discov 2019; 9:1574-1589. [PMID: 31434712 DOI: 10.1158/2159-8290.cd-18-1308] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 07/02/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023]
Abstract
Glioblastomas (GBM) are lethal brain tumors where poor outcome is attributed to cellular heterogeneity, therapeutic resistance, and a highly infiltrative nature. These characteristics are preferentially linked to GBM cancer stem cells (GSC), but how GSCs maintain their stemness is incompletely understood and the subject of intense investigation. Here, we identify a novel signaling loop that induces and maintains GSCs consisting of an atypical metalloproteinase, ADAMDEC1, secreted by GSCs. ADAMDEC1 rapidly solubilizes FGF2 to stimulate FGFR1 expressed on GSCs. FGFR1 signaling induces upregulation of ZEB1 via ERK1/2 that regulates ADAMDEC1 expression through miR-203, creating a positive feedback loop. Genetic or pharmacologic targeting of components of this axis attenuates self-renewal and tumor growth. These findings reveal a new signaling axis for GSC maintenance and highlight ADAMDEC1 and FGFR1 as potential therapeutic targets in GBM. SIGNIFICANCE: Cancer stem cells (CSC) drive tumor growth in many cancers including GBM. We identified a novel sheddase, ADAMDEC1, which initiates an FGF autocrine loop to promote stemness in CSCs. This loop can be targeted to reduce GBM growth.This article is highlighted in the In This Issue feature, p. 1469.
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Affiliation(s)
- Ana Jimenez-Pascual
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - James S Hale
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio. .,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Anja Kordowski
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - Jamie Pugh
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - Daniel J Silver
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Defne Bayik
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Gustavo Roversi
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Tyler J Alban
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Shilpa Rao
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Rui Chen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Thomas M McIntyre
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia and Institute of Molecular Recognition Chemistry (ICRM-CNR), Milano, Italy
| | | | - Karl O Holmberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Justin D Lathia
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio. .,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Florian A Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom.
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25
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Munksgaard Thorén M, Chmielarska Masoumi K, Krona C, Huang X, Kundu S, Schmidt L, Forsberg-Nilsson K, Floyd Keep M, Englund E, Nelander S, Holmqvist B, Lundgren-Åkerlund E. Integrin α10, a Novel Therapeutic Target in Glioblastoma, Regulates Cell Migration, Proliferation, and Survival. Cancers (Basel) 2019; 11:cancers11040587. [PMID: 31027305 PMCID: PMC6521287 DOI: 10.3390/cancers11040587] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 03/22/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/28/2022] Open
Abstract
New, effective treatment strategies for glioblastomas (GBMs), the most malignant and invasive brain tumors in adults, are highly needed. In this study, we investigated the potential of integrin α10β1 as a therapeutic target in GBMs. Expression levels and the role of integrin α10β1 were studied in patient-derived GBM tissues and cell lines. The effect of an antibody–drug conjugate (ADC), an integrin α10 antibody conjugated to saporin, on GBM cells and in a xenograft mouse model was studied. We found that integrin α10β1 was strongly expressed in both GBM tissues and cells, whereas morphologically unaffected brain tissues showed only minor expression. Partial or no overlap was seen with integrins α3, α6, and α7, known to be expressed in GBM. Further analysis of a subpopulation of GBM cells selected for high integrin α10 expression demonstrated increased proliferation and sphere formation. Additionally, siRNA-mediated knockdown of integrin α10 in GBM cells led to decreased migration and increased cell death. Furthermore, the ADC reduced viability and sphere formation of GBM cells and induced cell death both in vitro and in vivo. Our results demonstrate that integrin α10β1 has a functional role in GBM cells and is a novel, potential therapeutic target for the treatment of GBM.
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Affiliation(s)
| | | | - Cecilia Krona
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
| | - Xiaoli Huang
- Xintela AB, Medicon Village, SE-223 81 Lund, Sweden.
| | - Soumi Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
| | | | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
| | - Marcus Floyd Keep
- Department of Neurosurgery, Sanford Brain and Spine Institute, Fargo, ND 58103, USA; Department of Surgery, School of Medicine, University of North Dakota, Fargo, ND 58102, USA.
| | - Elisabet Englund
- Neuropathology Lab, Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden.
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
| | - Bo Holmqvist
- ImaGene-iT AB, Medicon Village, SE-223 81 Lund, Sweden.
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26
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Karademir B, Sari G, Jannuzzi AT, Musunuri S, Wicher G, Grune T, Mi J, Hacioglu-Bay H, Forsberg-Nilsson K, Bergquist J, Jung T. Proteomic approach for understanding milder neurotoxicity of Carfilzomib against Bortezomib. Sci Rep 2018; 8:16318. [PMID: 30397214 PMCID: PMC6218500 DOI: 10.1038/s41598-018-34507-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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] [Received: 05/15/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022] Open
Abstract
The proteasomal system is responsible for the turnover of damaged proteins. Because of its important functions in oncogenesis, inhibiting the proteasomal system is a promising therapeutic approach for cancer treatment. Bortezomib (BTZ) is the first proteasome inhibitor approved by FDA for clinical applications. However neuropathic side effects are dose limiting for BTZ as many other chemotherapeutic agents. Therefore second-generation proteasome inhibitors have been developed including carfilzomib (CFZ). Aim of the present work was investigating the mechanisms of peripheral neuropathy triggered by the proteasome inhibitor BTZ and comparing the pathways affected by BTZ and CFZ, respectively. Neural stem cells, isolated from the cortex of E14 mouse embryos, were treated with BTZ and CFZ and mass spectrometry was used to compare the global protein pool of treated cells. BTZ was shown to cause more severe cytoskeletal damage, which is crucial in neural cell integrity. Excessive protein carbonylation and actin filament destabilization were also detected following BTZ treatment that was lower following CFZ treatment. Our data on cytoskeletal proteins, chaperone system, and protein oxidation may explain the milder neurotoxic effects of CFZ in clinical applications.
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Affiliation(s)
- Betul Karademir
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey.
| | - Gulce Sari
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey.,Department of Genetics and Bioengineering, Faculty of Engineering, Okan University, Istanbul, Turkey
| | - Ayse Tarbin Jannuzzi
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey
| | - Sravani Musunuri
- Department of Chemistry - BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Grzegorz Wicher
- Department of Immunology, Genetics and Pathology, Neuro-Oncology, Uppsala University, Uppsala, Sweden
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany.,German Center for Diabetes Research (DZD), 85764, Muenchen-Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), 10117, Berlin, Germany
| | - Jia Mi
- Department of Chemistry - BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden.,Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai, China
| | | | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Neuro-Oncology, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry - BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Tobias Jung
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany.,German Center for Diabetes Research (DZD), 85764, Muenchen-Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), 10117, Berlin, Germany
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27
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Čančer M, Drews L, Rosén G, Westermark B, Nelander S, Forsberg-Nilsson K, Uhrbom L, Weishaupt H, Swartling F. EXTH-65. BET INHIBITION IN COMBINATION WITH TEMOZOLOMIDE TARGETS MYCN-POSITIVE GLIOBLASTOMA CELLS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.412] [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: 11/12/2022] Open
Affiliation(s)
| | - Lisa Drews
- Max Planck Institute for Biology of Ageing, Cologne, Germany
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28
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Sakthikumar S, Elvers I, Kim J, Arendt ML, Thomas R, Turner-Maier J, Swofford R, Johnson J, Schumacher SE, Alföldi J, Axelsson E, Couto CG, Kisseberth WC, Pettersson ME, Getz G, Meadows JRS, Modiano JF, Breen M, Kierczak M, Forsberg-Nilsson K, Marinescu VD, Lindblad-Toh K. SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma. Cancer Res 2018; 78:3421-3431. [PMID: 29724721 DOI: 10.1158/0008-5472.can-17-3558] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 11/20/2017] [Revised: 03/15/2018] [Accepted: 04/30/2018] [Indexed: 11/16/2022]
Abstract
Osteosarcoma is a debilitating bone cancer that affects humans, especially children and adolescents. A homologous form of osteosarcoma spontaneously occurs in dogs, and its differential incidence observed across breeds allows for the investigation of tumor mutations in the context of multiple genetic backgrounds. Using whole-exome sequencing and dogs from three susceptible breeds (22 golden retrievers, 21 Rottweilers, and 23 greyhounds), we found that osteosarcoma tumors show a high frequency of somatic copy-number alterations (SCNA), affecting key oncogenes and tumor-suppressor genes. The across-breed results are similar to what has been observed for human osteosarcoma, but the disease frequency and somatic mutation counts vary in the three breeds. For all breeds, three mutational signatures (one of which has not been previously reported) and 11 significantly mutated genes were identified. TP53 was the most frequently altered gene (83% of dogs have either mutations or SCNA in TP53), recapitulating observations in human osteosarcoma. The second most frequently mutated gene, histone methyltransferase SETD2, has known roles in multiple cancers, but has not previously been strongly implicated in osteosarcoma. This study points to the likely importance of histone modifications in osteosarcoma and highlights the strong genetic similarities between human and dog osteosarcoma, suggesting that canine osteosarcoma may serve as an excellent model for developing treatment strategies in both species.Significance: Canine osteosarcoma genomics identify SETD2 as a possible oncogenic driver of osteosarcoma, and findings establish the canine model as a useful comparative model for the corresponding human disease. Cancer Res; 78(13); 3421-31. ©2018 AACR.
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Affiliation(s)
- Sharadha Sakthikumar
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute, Cambridge, Massachusetts
| | - Ingegerd Elvers
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute, Cambridge, Massachusetts
| | - Jaegil Kim
- Broad Institute, Cambridge, Massachusetts
| | - Maja L Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg D, Denmark
| | - Rachael Thomas
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina
| | | | | | | | | | | | - Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - C Guillermo Couto
- Department of Veterinary Clinical Sciences and Veterinary Medical Center, the Ohio State University, Columbus, Ohio
- Couto Veterinary Consultants, Hilliard, Ohio
| | - William C Kisseberth
- Department of Veterinary Clinical Sciences and Veterinary Medical Center, the Ohio State University, Columbus, Ohio
| | - Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gad Getz
- Broad Institute, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jaime F Modiano
- Animal Cancer Care and Research Program, College of Veterinary Medicine, St. Paul, Minnesota
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, St. Paul, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota
- Institute for Engineering and Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Matthew Breen
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina
| | - Marcin Kierczak
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Voichita D Marinescu
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Broad Institute, Cambridge, Massachusetts
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29
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Pinheiro T, Otrocka M, Seashore-Ludlow B, Rraklli V, Holmberg J, Forsberg-Nilsson K, Simon A, Kirkham M. Reprint of: A chemical screen identifies trifluoperazine as an inhibitor of glioblastoma growth. Biochem Biophys Res Commun 2018; 499:136-142. [PMID: 29580626 DOI: 10.1016/j.bbrc.2018.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 12/27/2022]
Abstract
Glioblastoma (GBM) is regarded as the most common malignant brain tumor but treatment options are limited. Thus, there is an unmet clinical need for compounds and corresponding targets that could inhibit GBM growth. We screened a library of 80 dopaminergic ligands with the aim of identifying compounds capable of inhibiting GBM cell line proliferation and survival. Out of 45 active compounds, 8 were further validated. We found that the dopamine receptor D2 antagonist trifluoperazine 2HCl inhibits growth and proliferation of GBM cells in a dose dependent manner. Trifluoperazine's inhibition of GBM cells is cell line dependent and correlates with variations in dopamine receptor expression profile. We conclude that components of the dopamine receptor signaling pathways are potential targets for pharmacological interventions of GBM growth.
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Affiliation(s)
- Tiago Pinheiro
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Karolinska Institutet, Stockholm, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Karolinska Institutet, Stockholm, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Kirkham
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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30
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Schmidt L, Baskaran S, Johansson P, Padhan N, Matuszewski D, Green LC, Elfineh L, Wee S, Häggblad M, Martens U, Westermark B, Forsberg-Nilsson K, Uhrbom L, Claesson-Welsh L, Andäng M, Sintorn IM, Lundgren B, Lönnstedt I, Krona C, Nelander S. Case-specific potentiation of glioblastoma drugs by pterostilbene. Oncotarget 2018; 7:73200-73215. [PMID: 27689322 PMCID: PMC5341973 DOI: 10.18632/oncotarget.12298] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 03/12/2016] [Accepted: 09/16/2016] [Indexed: 12/24/2022] Open
Abstract
Glioblastoma multiforme (GBM, astrocytoma grade IV) is the most common malignant primary brain tumor in adults. Addressing the shortage of effective treatment options for this cancer, we explored repurposing of existing drugs into combinations with potent activity against GBM cells. We report that the phytoalexin pterostilbene is a potentiator of two drugs with previously reported anti-GBM activity, the EGFR inhibitor gefitinib and the antidepressant sertraline. Combinations of either of these two compounds with pterostilbene suppress cell growth, viability, sphere formation and inhibit migration in tumor GBM cell (GC) cultures. The potentiating effect of pterostilbene was observed to a varying degree across a panel of 41 patient-derived GCs, and correlated in a case specific manner with the presence of missense mutation of EGFR and PIK3CA and a focal deletion of the chromosomal region 1p32. We identify pterostilbene-induced cell cycle arrest, synergistic inhibition of MAPK activity and induction of Thioredoxin interacting protein (TXNIP) as possible mechanisms behind pterostilbene's effect. Our results highlight a nontoxic stilbenoid compound as a modulator of anticancer drug response, and indicate that pterostilbene might be used to modulate two anticancer compounds in well-defined sets of GBM patients.
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Affiliation(s)
| | | | | | | | - Damian Matuszewski
- Centre for Image Analysis, Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Lydia C Green
- Sahlgrenska Cancer Center, Institute of Medicine, Gothenburg, Sweden
| | | | - Shimei Wee
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Maria Häggblad
- Cell Screening Facility, Science for Life Laboratory Stockholm, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Ulf Martens
- Cell Screening Facility, Science for Life Laboratory Stockholm, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | | | - Lene Uhrbom
- Life Laboratory, Uppsala University, Uppsala Sweden
| | | | - Michael Andäng
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Ida-Maria Sintorn
- Centre for Image Analysis, Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Bo Lundgren
- Cell Screening Facility, Science for Life Laboratory Stockholm, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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Pinheiro T, Otrocka M, Seashore-Ludlow B, Rraklli V, Holmberg J, Forsberg-Nilsson K, Simon A, Kirkham M. A chemical screen identifies trifluoperazine as an inhibitor of glioblastoma growth. Biochem Biophys Res Commun 2017; 494:477-483. [PMID: 29066348 DOI: 10.1016/j.bbrc.2017.10.106] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022]
Abstract
Glioblastoma (GBM) is regarded as the most common malignant brain tumor but treatment options are limited. Thus, there is an unmet clinical need for compounds and corresponding targets that could inhibit GBM growth. We screened a library of 80 dopaminergic ligands with the aim of identifying compounds capable of inhibiting GBM cell line proliferation and survival. Out of 45 active compounds, 8 were further validated. We found that the dopamine receptor D2 antagonist trifluoperazine 2HCl inhibits growth and proliferation of GBM cells in a dose dependent manner. Trifluoperazine's inhibition of GBM cells is cell line dependent and correlates with variations in dopamine receptor expression profile. We conclude that components of the dopamine receptor signaling pathways are potential targets for pharmacological interventions of GBM growth.
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Affiliation(s)
- Tiago Pinheiro
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Karolinska Institutet, Stockholm, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Karolinska Institutet, Stockholm, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Kirkham
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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32
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Wicher G, Wallenquist U, Lei Y, Enoksson M, Li X, Fuchs B, Abu Hamdeh S, Marklund N, Hillered L, Nilsson G, Forsberg-Nilsson K. Interleukin-33 Promotes Recruitment of Microglia/Macrophages in Response to Traumatic Brain Injury. J Neurotrauma 2017; 34:3173-3182. [PMID: 28490277 DOI: 10.1089/neu.2016.4900] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Traumatic brain injury (TBI) is a devastating condition, often leading to life-long consequences for patients. Even though modern neurointensive care has improved functional and cognitive outcomes, efficient pharmacological therapies are still lacking. Targeting peripherally derived, or resident inflammatory, cells that are rapid responders to brain injury is promising, but complex, given that the contribution of inflammation to exacerbation versus improved recovery varies with time post-injury. The injury-induced inflammatory response is triggered by release of alarmins, and in the present study we asked whether interleukin-33 (IL-33), an injury-associated nuclear alarmin, is involved in TBI. Here, we used samples from human TBI microdialysate, tissue sections from human TBI, and mouse models of central nervous system injury and found that expression of IL-33 in the brain was elevated from nondetectable levels, reaching a maximum after 72 h in both human samples and mouse models. Astrocytes and oligodendrocytes were the main producers of IL-33. Post-TBI, brains of mice deficient in the IL-33 receptor, ST2, contained fewer microglia/macrophages in the injured region than wild-type mice and had an altered cytokine/chemokine profile in response to injury. These observations indicate that IL-33 plays a role in neuroinflammation with microglia/macrophages being cellular targets for this interleukin post-TBI.
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Affiliation(s)
- Grzegorz Wicher
- 1 Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala, Sweden
| | - Ulrika Wallenquist
- 1 Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala, Sweden
| | - Ying Lei
- 2 Department of Medicine, Immunology and Allergy Unit, Karolinska Institutet and Karolinska University Hospital , Stockholm, Sweden
| | - Mattias Enoksson
- 2 Department of Medicine, Immunology and Allergy Unit, Karolinska Institutet and Karolinska University Hospital , Stockholm, Sweden
| | - Xiaofei Li
- 1 Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala, Sweden
| | - Barbara Fuchs
- 2 Department of Medicine, Immunology and Allergy Unit, Karolinska Institutet and Karolinska University Hospital , Stockholm, Sweden
| | - Sami Abu Hamdeh
- 3 Department of Neuroscience, Neurosurgery, Uppsala University , Uppsala, Sweden
| | - Niklas Marklund
- 3 Department of Neuroscience, Neurosurgery, Uppsala University , Uppsala, Sweden
| | - Lars Hillered
- 3 Department of Neuroscience, Neurosurgery, Uppsala University , Uppsala, Sweden
| | - Gunnar Nilsson
- 2 Department of Medicine, Immunology and Allergy Unit, Karolinska Institutet and Karolinska University Hospital , Stockholm, Sweden
| | - Karin Forsberg-Nilsson
- 1 Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala, Sweden
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33
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Spyrou A, Kundu S, Haseeb L, Yu D, Olofsson T, Dredge K, Hammond E, Barash U, Vlodavsky I, Forsberg-Nilsson K. Inhibition of Heparanase in Pediatric Brain Tumor Cells Attenuates their Proliferation, Invasive Capacity, and In Vivo Tumor Growth. Mol Cancer Ther 2017; 16:1705-1716. [PMID: 28716813 DOI: 10.1158/1535-7163.mct-16-0900] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/30/2017] [Accepted: 05/22/2017] [Indexed: 11/16/2022]
Abstract
Curative therapy for medulloblastoma and other pediatric embryonal brain tumors has improved, but the outcome still remains poor and current treatment causes long-term complications. Malignant brain tumors infiltrate the healthy brain tissue and, thus despite resection, cells that have already migrated cause rapid tumor regrowth. Heparan sulfate proteoglycans (HSPG), major components of the extracellular matrix (ECM), modulate the activities of a variety of proteins. The major enzyme that degrades HS, heparanase (HPSE), is an important regulator of the ECM. Here, we report that the levels of HPSE in pediatric brain tumors are higher than in healthy brain tissue and that treatment of pediatric brain tumor cells with HPSE stimulated their growth. In addition, the latent, 65 kDa form of HPSE (that requires intracellular enzymatic processing for activation) enhanced cell viability and rapidly activated the ERK and AKT signaling pathways, before enzymatically active HPSE was detected. The HPSE inhibitor PG545 efficiently killed pediatric brain tumor cells, but not normal human astrocytes, and this compound also reduced tumor cell invasion in vitro and potently reduced the size of flank tumors in vivo Our findings indicate that HPSE in malignant brain tumors affects both the tumor cells themselves and their ECM. In conclusion, HPSE plays a substantial role in childhood brain tumors, by contributing to tumor aggressiveness and thereby represents a potential therapeutic target. Mol Cancer Ther; 16(8); 1705-16. ©2017 AACR.
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Affiliation(s)
- Argyris Spyrou
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Soumi Kundu
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lulu Haseeb
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Di Yu
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tommie Olofsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Keith Dredge
- Zucero Therapeutics Pty Ltd., Darra, Brisbane, Queensland, Australia
| | - Edward Hammond
- Zucero Therapeutics Pty Ltd., Darra, Brisbane, Queensland, Australia
| | - Uri Barash
- Cancer and Vascular Biology Research Center, Bruce Rappaport Faculty of Medicine, Haifa, Israel
| | - Israel Vlodavsky
- Cancer and Vascular Biology Research Center, Bruce Rappaport Faculty of Medicine, Haifa, Israel
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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34
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Xiong A, Kundu S, Forsberg M, Xiong Y, Bergström T, Paavilainen T, Kjellén L, Li JP, Forsberg-Nilsson K. Heparanase confers a growth advantage to differentiating murine embryonic stem cells, and enhances oligodendrocyte formation. Matrix Biol 2016; 62:92-104. [PMID: 27890389 DOI: 10.1016/j.matbio.2016.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 01/23/2023]
Abstract
Heparan sulfate proteoglycans (HSPGs), ubiquitous components of mammalian cells, play important roles in development and homeostasis. These molecules are located primarily on the cell surface and in the pericellular matrix, where they interact with a multitude of macromolecules, including many growth factors. Manipulation of the enzymes involved in biosynthesis and modification of HSPG structures alters the properties of stem cells. Here, we focus on the involvement of heparanase (HPSE), the sole endo-glucuronidase capable of cleaving of HS, in differentiation of embryonic stem cells into the cells of the neural lineage. Embryonic stem (ES) cells overexpressing HPSE (Hpse-Tg) proliferated more rapidly than WT ES cells in culture and formed larger teratomas in vivo. In addition, differentiating Hpse-Tg ES cells also had a higher growth rate, and overexpression of HPSE in NSPCs enhanced Erk and Akt phosphorylation. Employing a two-step, monolayer differentiation, we observed an increase in HPSE as wild-type (WT) ES cells differentiated into neural stem and progenitor cells followed by down-regulation of HPSE as these NSPCs differentiated into mature cells of the neural lineage. Furthermore, NSPCs overexpressing HPSE gave rise to more oligodendrocytes than WT cultures, with a concomitant reduction in the number of neurons. Our present findings emphasize the importance of HS, in neural differentiation and suggest that by regulating the availability of growth factors and, or other macromolecules, HPSE promotes differentiation into oligodendrocytes.
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Affiliation(s)
- Anqi Xiong
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Soumi Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Maud Forsberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Yuyuan Xiong
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Tobias Bergström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Tanja Paavilainen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Lena Kjellén
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Jin-Ping Li
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
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35
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Kundu S, Xiong A, Spyrou A, Wicher G, Marinescu VD, Edqvist PHD, Zhang L, Essand M, Dimberg A, Smits A, Ilan N, Vlodavsky I, Li JP, Forsberg-Nilsson K. Heparanase Promotes Glioma Progression and Is Inversely Correlated with Patient Survival. Mol Cancer Res 2016; 14:1243-1253. [PMID: 27565180 DOI: 10.1158/1541-7786.mcr-16-0223] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/08/2016] [Accepted: 08/12/2016] [Indexed: 11/16/2022]
Abstract
Malignant glioma continues to be fatal, despite improved insight into its underlying molecular mechanisms. The most malignant form, glioblastoma (GBM), is characterized by aberrant activation of receptor tyrosine kinases (RTK) and infiltrative growth. Heparan sulfate proteoglycans (HSPG), integral components of the extracellular matrix of brain tumors, can regulate activation of many RTK pathways. This prompted us to investigate heparanase (HPSE), which cleaves HSPGs, for its role in glioma. This hypothesis was evaluated using tissue microarrays, GBM cells derived from patients, murine in vitro and in vivo models of glioma, and public databases. Downregulation of HPSE attenuated glioma cell proliferation, whereas addition of HPSE stimulated growth and activated ERK and AKT signaling. Using HPSE transgenic and knockout mice, it was demonstrated that tumor development in vivo was positively correlated to HPSE levels in the brain. HPSE also modified the tumor microenvironment, influencing reactive astrocytes, microglia/monocytes, and tumor angiogenesis. Furthermore, inhibition of HPSE reduces tumor cell numbers, both in vitro and in vivo HPSE was highly expressed in human glioma and GBM cell lines, compared with normal brain tissue. Indeed, a correlation was observed between high levels of HPSE and shorter survival of patients with high-grade glioma. In conclusion, these data provide proof-of-concept for anti-HPSE treatment of malignant glioma, as well as novel insights for the development of HPSE as a therapeutic target. IMPLICATIONS This study aims to target both the malignant brain tumor cells per se and their microenvironment by changing the level of an enzyme, HPSE, that breaks down modified sugar chains on cell surfaces and in the extracellular space. Mol Cancer Res; 14(12); 1243-53. ©2016 AACR.
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Affiliation(s)
- Soumi Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anqi Xiong
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Argyris Spyrou
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Grzegorz Wicher
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik D Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lei Zhang
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja Smits
- Department of Neuroscience, Neurology, Uppsala University, Uppsala, Sweden
| | - Neta Ilan
- Cancer and Vascular Biology Research Center, The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Israel Vlodavsky
- Cancer and Vascular Biology Research Center, The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Jin-Ping Li
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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36
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Roy A, Coum A, Marinescu VD, Põlajeva J, Smits A, Nelander S, Uhrbom L, Westermark B, Forsberg-Nilsson K, Pontén F, Tchougounova E. Glioma-derived plasminogen activator inhibitor-1 (PAI-1) regulates the recruitment of LRP1 positive mast cells. Oncotarget 2016; 6:23647-61. [PMID: 26164207 PMCID: PMC4695142 DOI: 10.18632/oncotarget.4640] [Citation(s) in RCA: 26] [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: 04/28/2015] [Accepted: 06/12/2015] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GBM) is a high-grade glioma with a complex microenvironment, including various inflammatory cells and mast cells (MCs) as one of them. Previously we had identified glioma grade-dependent MC recruitment. In the present study we investigated the role of plasminogen activator inhibitor 1 (PAI-1) in MC recruitment. PAI-1, a primary regulator in the fibrinolytic cascade is capable of forming a complex with fibrinolytic system proteins together with low-density lipoprotein receptor-related protein 1 (LRP1). We found that neutralizing PAI-1 attenuated infiltration of MCs. To address the potential implication of LRP1 in this process, we used a LRP1 antagonist, receptor-associated protein (RAP), and demonstrated the attenuation of MC migration. Moreover, a positive correlation between the number of MCs and the level of PAI-1 in a large cohort of human glioma samples was observed. Our study demonstrated the expression of LRP1 in human MC line LAD2 and in MCs in human high-grade glioma. The activation of potential PAI-1/LRP1 axis with purified PAI-1 promoted increased phosphorylation of STAT3 and subsequently exocytosis in MCs. These findings indicate the influence of the PAI-1/LRP1 axis on the recruitment of MCs in glioma. The connection between high-grade glioma and MC infiltration could contribute to patient tailored therapy and improve patient stratification in future therapeutic trials.
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Affiliation(s)
- Ananya Roy
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Antoine Coum
- Department of Engineering, Nanoscience Centre, Cambridge University, Cambridge, UK
| | - Voichita D Marinescu
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Anja Smits
- Department of Neuroscience, Neurology, Uppsala University, Uppsala, Sweden.,Present address: Danish Epilepsy Center, Dianalund, Denmark
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Elena Tchougounova
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Wee B, Pietras A, Ozawa T, Bazzoli E, Podlaha O, Antczak C, Westermark B, Nelander S, Uhrbom L, Forsberg-Nilsson K, Djaballah H, Michor F, Holland EC. ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells. Sci Rep 2016; 6:25956. [PMID: 27456282 PMCID: PMC4960591 DOI: 10.1038/srep25956] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023] Open
Abstract
Glioma cells with stem cell traits are thought to be responsible for tumor maintenance and therapeutic failure. Such cells can be enriched based on their inherent drug efflux capability mediated by the ABC transporter ABCG2 using the side population assay, and their characteristics include increased self-renewal, high stem cell marker expression and high tumorigenic capacity in vivo. Here, we show that ABCG2 can actively drive expression of stem cell markers and self-renewal in glioma cells. Stem cell markers and self-renewal was enriched in cells with high ABCG2 activity, and could be specifically inhibited by pharmacological and genetic ABCG2 inhibition. Importantly, despite regulating these key characteristics of stem-like tumor cells, ABCG2 activity did not affect radiation resistance or tumorigenicity in vivo. ABCG2 effects were Notch-independent and mediated by diverse mechanisms including the transcription factor Mef. Our data demonstrate that characteristics of tumor stem cells are separable, and highlight ABCG2 as a potential driver of glioma stemness.
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Affiliation(s)
- Boyoung Wee
- Cancer Biology and Genetics Program, New York, NY 10021, USA.,Brain Tumor Center, New York, NY 10021, USA
| | - Alexander Pietras
- Human Biology Division, Solid Tumor and Translational Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98104, USA.,Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE-22363 Lund, Sweden
| | - Tatsuya Ozawa
- Human Biology Division, Solid Tumor and Translational Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98104, USA
| | - Elena Bazzoli
- Centro San Giovanni di Dio - Fatebenefratelli, IRCCS, 25123 Bs, Italy
| | - Ondrej Podlaha
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Christophe Antczak
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Eric C Holland
- Human Biology Division, Solid Tumor and Translational Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98104, USA
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38
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Arvidsson PI, Sandberg K, Forsberg-Nilsson K. Open for collaboration: an academic platform for drug discovery and development at SciLifeLab. Drug Discov Today 2016; 21:1690-1698. [PMID: 27373760 DOI: 10.1016/j.drudis.2016.06.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 05/19/2016] [Accepted: 06/27/2016] [Indexed: 02/03/2023]
Abstract
The Science for Life Laboratory Drug Discovery and Development (SciLifeLab DDD) platform reaches out to Swedish academia with an industry-standard infrastructure for academic drug discovery, supported by earmarked funds from the Swedish government. In this review, we describe the build-up and operation of the platform, and reflect on our first two years of operation, with the ambition to share learnings and best practice with academic drug discovery centers globally. We also discuss how the Swedish Teacher Exemption Law, an internationally unique aspect of the innovation system, has shaped the operation. Furthermore, we address how this investment in infrastructure and expertise can be utilized to facilitate international collaboration between academia and industry in the best interest of those ultimately benefiting the most from translational pharmaceutical research - the patients.
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Affiliation(s)
- Per I Arvidsson
- Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Kristian Sandberg
- Science for Life Laboratory, Drug Discovery & Development Platform & Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, Uppsala, Sweden; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
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39
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Truvé K, Dickinson P, Xiong A, York D, Jayashankar K, Pielberg G, Koltookian M, Murén E, Fuxelius HH, Weishaupt H, Swartling FJ, Andersson G, Hedhammar Å, Bongcam-Rudloff E, Forsberg-Nilsson K, Bannasch D, Lindblad-Toh K. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus. PLoS Genet 2016; 12:e1006000. [PMID: 27171399 PMCID: PMC4865040 DOI: 10.1371/journal.pgen.1006000] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 03/30/2016] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10-8). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.
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Affiliation(s)
- Katarina Truvé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- * E-mail: (KT); (KLT)
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Anqi Xiong
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel York
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Kartika Jayashankar
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Gerli Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michele Koltookian
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Eva Murén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hans-Henrik Fuxelius
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Holger Weishaupt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik J. Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Danika Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- * E-mail: (KT); (KLT)
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Xie Y, Bergström T, Jiang Y, Johansson P, Marinescu VD, Lindberg N, Segerman A, Wicher G, Niklasson M, Baskaran S, Sreedharan S, Everlien I, Kastemar M, Hermansson A, Elfineh L, Libard S, Holland EC, Hesselager G, Alafuzoff I, Westermark B, Nelander S, Forsberg-Nilsson K, Uhrbom L. The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes. EBioMedicine 2015; 2:1351-63. [PMID: 26629530 PMCID: PMC4634360 DOI: 10.1016/j.ebiom.2015.08.026] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/14/2015] [Accepted: 08/14/2015] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most frequent and malignant form of primary brain tumor. GBM is essentially incurable and its resistance to therapy is attributed to a subpopulation of cells called glioma stem cells (GSCs). To meet the present shortage of relevant GBM cell (GC) lines we developed a library of annotated and validated cell lines derived from surgical samples of GBM patients, maintained under conditions to preserve GSC characteristics. This collection, which we call the Human Glioblastoma Cell Culture (HGCC) resource, consists of a biobank of 48 GC lines and an associated database containing high-resolution molecular data. We demonstrate that the HGCC lines are tumorigenic, harbor genomic lesions characteristic of GBMs, and represent all four transcriptional subtypes. The HGCC panel provides an open resource for in vitro and in vivo modeling of a large part of GBM diversity useful to both basic and translational GBM research. The HGCC resource contains 48 annotated human GBM cell lines and an interactive database The GBM cell lines are propagated in stem cell conditions and display GSC characteristics The HGCC resource provides cell lines of all molecular (TCGA) subtypes All data connected with the HGCC cell lines can be accessed at hgcc.se
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Affiliation(s)
- Yuan Xie
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Tobias Bergström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Yiwen Jiang
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Patrik Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Voichita Dana Marinescu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Nanna Lindberg
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., PO Box 19024, Seattle, WA 98109, United States
| | - Anna Segerman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Grzegorz Wicher
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Mia Niklasson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Sathishkumar Baskaran
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Smitha Sreedharan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Isabelle Everlien
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Marianne Kastemar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Annika Hermansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Lioudmila Elfineh
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Sylwia Libard
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Eric Charles Holland
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., PO Box 19024, Seattle, WA 98109, United States
| | - Göran Hesselager
- Department of Neuroscience, Uppsala University, Uppsala University Hospital, SE-751 85 Uppsala, Sweden
| | - Irina Alafuzoff
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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Wee S, Niklasson M, Marinescu VD, Segerman A, Schmidt L, Hermansson A, Dirks P, Forsberg-Nilsson K, Westermark B, Uhrbom L, Linnarsson S, Nelander S, Andäng M. Selective calcium sensitivity in immature glioma cancer stem cells. PLoS One 2014; 9:e115698. [PMID: 25531110 PMCID: PMC4274094 DOI: 10.1371/journal.pone.0115698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022] Open
Abstract
Tumor-initiating cells are a subpopulation in aggressive cancers that exhibit traits shared with stem cells, including the ability to self-renew and differentiate, commonly referred to as stemness. In addition, such cells are resistant to chemo- and radiation therapy posing a therapeutic challenge. To uncover stemness-associated functions in glioma-initiating cells (GICs), transcriptome profiles were compared to neural stem cells (NSCs) and gene ontology analysis identified an enrichment of Ca2+ signaling genes in NSCs and the more stem-like (NSC-proximal) GICs. Functional analysis in a set of different GIC lines regarding sensitivity to disturbed homeostasis using A23187 and Thapsigargin, revealed that NSC-proximal GICs were more sensitive, corroborating the transcriptome data. Furthermore, Ca2+ drug sensitivity was reduced in GICs after differentiation, with most potent effect in the NSC-proximal GIC, supporting a stemness-associated Ca2+ sensitivity. NSCs and the NSC-proximal GIC line expressed a larger number of ion channels permeable to potassium, sodium and Ca2+. Conversely, a higher number of and higher expression levels of Ca2+ binding genes that may buffer Ca2+, were expressed in NSC-distal GICs. In particular, expression of the AMPA glutamate receptor subunit GRIA1, was found to associate with Ca2+ sensitive NSC-proximal GICs, and decreased as GICs differentiated along with reduced Ca2+ drug sensitivity. The correlation between high expression of Ca2+ channels (such as GRIA1) and sensitivity to Ca2+ drugs was confirmed in an additional nine novel GIC lines. Calcium drug sensitivity also correlated with expression of the NSC markers nestin (NES) and FABP7 (BLBP, brain lipid-binding protein) in this extended analysis. In summary, NSC-associated NES+/FABP7+/GRIA1+ GICs were selectively sensitive to disturbances in Ca2+ homeostasis, providing a potential target mechanism for eradication of an immature population of malignant cells.
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Affiliation(s)
- Shimei Wee
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Maria Niklasson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Voichita Dana Marinescu
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Anna Segerman
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Linnéa Schmidt
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Annika Hermansson
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Peter Dirks
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Michael Andäng
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
- * E-mail:
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42
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Xiong A, Kundu S, Forsberg-Nilsson K. Heparan sulfate in the regulation of neural differentiation and glioma development. FEBS J 2014; 281:4993-5008. [DOI: 10.1111/febs.13097] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/17/2014] [Accepted: 10/02/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Anqi Xiong
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory; Rudbeck Laboratory; Uppsala University; Uppsala Sweden
| | - Soumi Kundu
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory; Rudbeck Laboratory; Uppsala University; Uppsala Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, and Science for Life Laboratory; Rudbeck Laboratory; Uppsala University; Uppsala Sweden
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Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 2014; 345:1074-1079. [PMID: 25170157 DOI: 10.1126/science.1253714] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Carl-Johan Rubin
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Federica Di Palma
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.,Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK
| | - Frank W Albert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Alvaro Martinez Barrio
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerli Pielberg
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nima Rafati
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jason Turner-Maier
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Shady Younis
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Production, Ain Shams University, Shoubra El-Kheima, Cairo, Egypt
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Hinxton, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joel M Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Hinxton, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard Bolet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | | | - Hernán A Burbano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Campos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Jean L Chang
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Veronique Duranthon
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna Italy
| | - Hervé Garreau
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | - David Heiman
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rose G Mage
- Laboratory of Immunology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Ze Peng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | | | - Claire Rogel-Gaillard
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F- 78350, Jouy-en-Josas, France
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Hinxton, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados, (IESA-CSIC) Campo Santo de los Mártires 7, Córdoba Spain
| | - Anqi Xiong
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarah Young
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jeffrey M Good
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Eric S Lander
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n. 4169-007 Porto, Portugal
| | - Kerstin Lindblad-Toh
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leif Andersson
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, USA
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Bergström T, Holmqvist K, Tararuk T, Johansson S, Forsberg-Nilsson K. Developmentally regulated collagen/integrin interactions confer adhesive properties to early postnatal neural stem cells. Biochim Biophys Acta Gen Subj 2014; 1840:2526-32. [PMID: 24462579 DOI: 10.1016/j.bbagen.2014.01.021] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND It is becoming increasingly apparent that the extracellular matrix acts as an important regulator of the neural stem niche. Previously we found that neural stem and progenitor cells (NSPCs) derived from the early postnatal subventricular zone of mice adhere to a collagen/hyaluronan hydrogel, whereas NSPCs from the adult and embryonic brain do not. METHODS To examine the specific adhesive properties of young stem cells in more detail, NSPCs isolated from embryonic, postnatal day 6 (P6), and adult mouse brains were cultured on collagen I. RESULTS Early postnatal NSPCs formed paxillin-positive focal adhesions on collagen I, and these adhesions could be prevented by an antibody that blocked integrin β1. Furthermore, we found the corresponding integrin alpha subunits α2 and α11 levels to be highest at the postnatal stage. Gene ontology analysis of differentially expressed genes showed higher expression of transcripts involved in vasculature development and morphogenesis in P6 stem cells, compared to adult. CONCLUSIONS The ability to interact with the extracellular matrix differs between postnatal and adult NSPCs. GENERAL SIGNIFICANCE Our observations that the specific adhesive properties of early postnatal NSPCs, which are lost in the adult brain, can be ascribed to the integrin subunits expressed by the former furthering our understanding of the developing neurogenic niche. This article is part of a Special Issue entitled Matrix-mediated cell behaviour and properties.
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Affiliation(s)
- Tobias Bergström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala Sweden
| | - Karin Holmqvist
- Merck Sharp & Dohme (Sweden) AB, Rotebergsvägen 3, Box 7125, SE-192 07 Sollentuna, Sweden
| | - Tatsiana Tararuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala Sweden
| | - Staffan Johansson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala Sweden
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45
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Wicher G, Husic E, Nilsson G, Forsberg-Nilsson K. Developmental expression of IL-33 in the mouse brain. Neurosci Lett 2013; 555:171-6. [PMID: 24076135 DOI: 10.1016/j.neulet.2013.09.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 12/31/2022]
Abstract
IL-33 has important functions in inflammatory and autoimmune diseases. In the brain, models of experimental encephalomyelitis are accompanied by up-regulation of IL-33 expression, and the cytokine is seen as an amplifier of the innate immune response. Little is known, however, about IL-33 the normal brain in adult life, or during development. We have analyzed the expression of IL-33 in the mouse brain during embryonic and postnatal development. Here we report that IL-33 expression was first detected in the CNS during late embryogenesis. From postnatal day 2 (P2) until P9 the expression increased and was strongest in the cerebellum, pons and thalamus, as well as in olfactory bulbs. Expression of IL-33 then became weaker and declined until P23, and it was not present in the adult brain. Both astrocytes and oligodendrocyte precursors expressed IL-33. The vast majority of IL-33 positive cells in the brain displayed nuclear staining, and this was found to be the case also in vitro, using mixed glial cultures. Our data suggest that IL-33 expression is under tight regulation in the normal brain. Its detection during the first three weeks of postnatal life coincides with important parts of the CNS developmental programs, such as general growth and myelination. This opens the possibility that IL-33 plays a role also in the absence of an inflammatory response.
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Affiliation(s)
- Grzegorz Wicher
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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Savary K, Caglayan D, Caja L, Tzavlaki K, Bin Nayeem S, Bergström T, Jiang Y, Uhrbom L, Forsberg-Nilsson K, Westermark B, Heldin CH, Ferletta M, Moustakas A. Snail depletes the tumorigenic potential of glioblastoma. Oncogene 2013; 32:5409-20. [PMID: 23524585 PMCID: PMC3898470 DOI: 10.1038/onc.2013.67] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [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: 05/21/2012] [Revised: 12/02/2012] [Accepted: 01/05/2013] [Indexed: 12/26/2022]
Abstract
Glioblastoma multiforme (GBM) is an aggressive brain malignancy characterized by high heterogeneity and invasiveness. It is increasingly accepted that the refractory feature of GBM to current therapies stems from the existence of few tumorigenic cells that sustain tumor growth and spreading, the so-called glioma-initiating cells (GICs). Previous studies showed that cytokines of the bone morphogenetic protein (BMP) family induce differentiation of the GICs, and thus act as tumor suppressors. Molecular pathways that explain this behavior of BMP cytokines remain largely elusive. Here, we show that BMP signaling induces Smad-dependent expression of the transcriptional regulator Snail in a rapid and sustained manner. Consistent with its already established promigratory function in other cell types, we report that Snail silencing decreases GBM cell migration. Consequently, overexpression of Snail increases GBM invasiveness in a mouse xenograft model. Surprisingly, we found that Snail depletes the GBM capacity to form gliomaspheres in vitro and to grow tumors in vivo, both of which are important features shared by GICs. Thus Snail, acting downstream of BMP signaling, dissociates the invasive capacity of GBM cells from their tumorigenic potential.
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Affiliation(s)
- K Savary
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Biomedical Center, Uppsala University, Uppsala, Sweden
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47
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Yu D, Jin C, Ramachandran M, Xu J, Nilsson B, Korsgren O, Le Blanc K, Uhrbom L, Forsberg-Nilsson K, Westermark B, Adamson R, Maitland N, Fan X, Essand M. Adenovirus serotype 5 vectors with Tat-PTD modified hexon and serotype 35 fiber show greatly enhanced transduction capacity of primary cell cultures. PLoS One 2013; 8:e54952. [PMID: 23372800 PMCID: PMC3555985 DOI: 10.1371/journal.pone.0054952] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [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: 08/01/2012] [Accepted: 12/18/2012] [Indexed: 12/14/2022] Open
Abstract
Recombinant adenovirus serotype 5 (Ad5) vectors represent one of the most efficient gene delivery vectors in life sciences. However, Ad5 is dependent on expression of the coxsackievirus-adenovirus-receptor (CAR) on the surface of target cell for efficient transduction, which limits it’s utility for certain cell types. Herein we present a new vector, Ad5PTDf35, which is an Ad5 vector having serotype 35 fiber-specificity and Tat-PTD hexon-modification. This vector shows dramatically increased transduction capacity of primary human cell cultures including T cells, monocytes, macrophages, dendritic cells, pancreatic islets and exocrine cells, mesenchymal stem cells and tumor initiating cells. Biodistribution in mice following systemic administration (tail-vein injection) show significantly reduced uptake in the liver and spleen of Ad5PTDf35 compared to unmodified Ad5. Therefore, replication-competent viruses with these modifications may be further developed as oncolytic agents for cancer therapy. User-friendly backbone plasmids containing these modifications were developed for compatibility to the AdEasy-system to facilitate the development of surface-modified adenoviruses for gene delivery to difficult-to-transduce cells in basic, pre-clinical and clinical research.
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Affiliation(s)
- Di Yu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Chuan Jin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mohanraj Ramachandran
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jing Xu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Berith Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olle Korsgren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Katarina Le Blanc
- Division of Clinical Immunology, Karolinska University Hospital, Huddinge, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rachel Adamson
- Department of Biology, YCR Cancer Research Unit, University of York, Heslington, United Kingdom
| | - Norman Maitland
- Department of Biology, YCR Cancer Research Unit, University of York, Heslington, United Kingdom
| | - Xiaolong Fan
- Rausing Laboratory, Lund University, Lund, Sweden
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Edqvist PHD, Niklasson M, Vidal-Sanz M, Hallböök F, Forsberg-Nilsson K. Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation. PLoS One 2012; 7:e42488. [PMID: 22880002 PMCID: PMC3411765 DOI: 10.1371/journal.pone.0042488] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 07/09/2012] [Indexed: 01/24/2023] Open
Abstract
Platelet-derived growth factor (PDGF) plays an important role in development of the central nervous system, including the retina. Excessive PDGF signaling is associated with proliferative retinal disorders. We reported previously that transgenic mice in which PDGF-B was over-expressed under control of the nestin enhancer, nes/tk-PdgfB-lacZ, exhibited enhanced apoptosis in the developing corpus striatum. These animals display enlarged lateral ventricles after birth as well as behavioral aberrations as adults. Here, we report that in contrast to the relatively mild central nervous system phenotype, development of the retina is severely disturbed in nes/tk-PdgfB-lacZ mice. In transgenic retinas all nuclear layers were disorganized and photoreceptor segments failed to develop properly. Since astrocyte precursor cells did not populate the retina, retinal vascular progenitors could not form a network of vessels. With time, randomly distributed vessels resembling capillaries formed, but there were no large trunk vessels and the intraocular pressure was reduced. In addition, we observed a delayed regression of the hyaloid vasculature. The prolonged presence of this structure may contribute to the other abnormalities observed in the retina, including the defective lamination.
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Affiliation(s)
- Per-Henrik D. Edqvist
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mia Niklasson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Finn Hallböök
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Wallenquist U, Holmqvist K, Hånell A, Marklund N, Hillered L, Forsberg-Nilsson K. Ibuprofen attenuates the inflammatory response and allows formation of migratory neuroblasts from grafted stem cells after traumatic brain injury. Restor Neurol Neurosci 2012; 30:9-19. [PMID: 22377906 DOI: 10.3233/rnn-2011-0606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE There is hope for neural stem and progenitor cells (NSPC) to enhance regeneration when transplanted to the injured brain after traumatic brain injury (TBI). So far, the therapeutic effects of NSPC transplantation have been hampered mainly by the notable death of the transplanted cells. Neuroinflammation may lead to additional cell death after TBI and we hypothesized that survival of grafted NSPC could be enhanced by anti-inflammatory treatment. METHODS Mice that were subjected to controlled cortical impact TBI and grafted with NSPC, were treated with the non-steroidal anti-inflammatory drug ibuprofen. RESULTS Ibuprofen was found to down-regulate the TBI-induced inflammatory response. In addition, migrating neuroblasts from transplanted cells were observed near the contusion and in the ipsilateral hippocampus in ibuprofen-treated animals only, suggesting that the anti-inflammatory treatment had beneficial effects on graft survival and/or differentiation. However, Morris Water Maze performance or TBI-induced tissue loss was not influenced by ibuprofen treatment. CONCLUSIONS Our data suggests that anti-inflammatory strategies may be a complement to enhance the outcome for the cell transplants following TBI.
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Affiliation(s)
- U Wallenquist
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
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Abstract
Neural stem cells are the origins of neurons and glia and generate all the differentiated neural cells of the mammalian central nervous system via the formation of intermediate precursors. Although less frequent, neural stem cells persevere in the postnatal brain where they generate neurons and glia. Adult neurogenesis occurs throughout life in a few limited brain regions. Regulation of neural stem cell number during central nervous system development and in adult life is associated with rigorous control. Failure in this regulation may lead to e.g. brain malformation, impaired learning and memory, or tumor development. Signaling pathways that are perturbed in glioma are the same that are important for neural stem cell self-renewal, differentiation, survival, and migration. The heterogeneity of human gliomas has impeded efficient treatment, but detailed molecular characterization together with novel stem cell-like glioma cell models that reflect the original tumor gives opportunities for research into new therapies. The observation that neural stem cells can be isolated and expanded in vitro has opened new avenues for medical research, with the hope that they could be used to compensate the loss of cells that features in several severe neurological diseases. Multipotent neural stem cells can be isolated from the embryonic and adult brain and maintained in culture in a defined medium. In addition, neural stem cells can be derived from embryonic stem cells and induced pluripotent stem cells by in vitro differentiation, thus adding to available models to study stem cells in health and disease.
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Affiliation(s)
- Tobias Bergström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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