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Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 2020; 587:246-251. [PMID: 33177663 PMCID: PMC7673649 DOI: 10.1038/s41586-020-2871-y] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.
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Affiliation(s)
- Joel Armstrong
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Adam M Novak
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Alden Deran
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Duo Xie
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Diane Genereux
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Voichita Dana Marinescu
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessica Alföldi
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Robert S Harris
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David Haussler
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Elinor Karlsson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erich D Jarvis
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
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Jiang Y, Marinescu VD, Xie Y, Jarvius M, Maturi NP, Haglund C, Olofsson S, Lindberg N, Olofsson T, Leijonmarck C, Hesselager G, Alafuzoff I, Fryknäs M, Larsson R, Nelander S, Uhrbom L. Glioblastoma Cell Malignancy and Drug Sensitivity Are Affected by the Cell of Origin. Cell Rep 2017; 18:977-990. [PMID: 28122246 DOI: 10.1016/j.celrep.2017.01.003] [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] [Received: 10/16/2015] [Revised: 09/12/2016] [Accepted: 12/31/2016] [Indexed: 12/26/2022] Open
Abstract
The identity of the glioblastoma (GBM) cell of origin and its contributions to disease progression and treatment response remain largely unknown. We have analyzed how the phenotypic state of the initially transformed cell affects mouse GBM development and essential GBM cell (GC) properties. We find that GBM induced in neural stem-cell-like glial fibrillary acidic protein (GFAP)-expressing cells in the subventricular zone of adult mice shows accelerated tumor development and produces more malignant GCs (mGC1GFAP) that are less resistant to cancer drugs, compared with those originating from more differentiated nestin- (mGC2NES) or 2,'3'-cyclic nucleotide 3'-phosphodiesterase (mGC3CNP)-expressing cells. Transcriptome analysis of mouse GCs identified a 196 mouse cell origin (MCO) gene signature that was used to partition 61 patient-derived GC lines. Human GC lines that clustered with the mGC1GFAP cells were also significantly more self-renewing, tumorigenic, and sensitive to cancer drugs compared with those that clustered with mouse GCs of more differentiated origin.
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Affiliation(s)
- Yiwen Jiang
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Voichita Dana Marinescu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Yuan Xie
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Malin Jarvius
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 75185 Uppsala, Sweden
| | - Naga Prathyusha Maturi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Caroline Haglund
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 75185 Uppsala, Sweden
| | - Sara Olofsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Nanna Lindberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Tommie Olofsson
- Department of Forensic Medicine, The National Board of Forensic Medicine, Box 1024, 75140 Uppsala, Sweden
| | - Caroline Leijonmarck
- Department of Neuroscience, Uppsala University, Uppsala University Hospital, 75185 Uppsala, Sweden
| | - Göran Hesselager
- Department of Neuroscience, Uppsala University, Uppsala University Hospital, 75185 Uppsala, Sweden
| | - Irina Alafuzoff
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Mårten Fryknäs
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 75185 Uppsala, Sweden
| | - Rolf Larsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 75185 Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.
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Xie Y, Sundström A, Tan EJ, Marinescu VD, Maturi NP, Tirfing M, Blokzijl A, Jin C, Chen L, Essand M, Swartling F, Nelander S, Jiang Y, Uhrbom L. CBIO-25. HIGH EXPRESSION OF LGR5 MAINTAINS GLIOBLASTOMA STEM CELLS IN A PRONEURAL STATE AND PROMOTES SELF-RENEWAL AND INVASION. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jiang Y, Marinescu VD, Xie Y, Jarvius M, Maturi NP, Haglund C, Olofsson S, Lindberg N, Olofsson T, Leijonmarck C, Hesselager G, Alafuzoff I, Fryknäs M, Larsson R, Nelander S, Uhrbom L. Glioblastoma Cell Malignancy and Drug Sensitivity Are Affected by the Cell of Origin. Cell Rep 2017; 19:1080-1081. [PMID: 28467901 DOI: 10.1016/j.celrep.2017.04.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Darmanis S, Gallant CJ, Marinescu VD, Niklasson M, Segerman A, Flamourakis G, Fredriksson S, Assarsson E, Lundberg M, Nelander S, Westermark B, Landegren U. Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells. Cell Rep 2015; 14:380-9. [PMID: 26748716 PMCID: PMC4713867 DOI: 10.1016/j.celrep.2015.12.021] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022] Open
Abstract
Significant advances have been made in methods to analyze genomes and transcriptomes of single cells, but to fully define cell states, proteins must also be accessed as central actors defining a cell's phenotype. Methods currently used to analyze endogenous protein expression in single cells are limited in specificity, throughput, or multiplex capability. Here, we present an approach to simultaneously and specifically interrogate large sets of protein and RNA targets in lysates from individual cells, enabling investigations of cell functions and responses. We applied our method to investigate the effects of BMP4, an experimental therapeutic agent, on early-passage glioblastoma cell cultures. We uncovered significant heterogeneity in responses to treatment at levels of RNA and protein, with a subset of cells reacting in a distinct manner to BMP4. Moreover, we found overall poor correlation between protein and RNA at the level of single cells, with proteins more accurately defining responses to treatment.
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Affiliation(s)
- Spyros Darmanis
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden
| | - Caroline Julie Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden
| | - Voichita Dana Marinescu
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden
| | - Mia Niklasson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden
| | - Anna Segerman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden
| | - Georgios Flamourakis
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden
| | | | | | | | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
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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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7
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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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