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Vo T, Balderson B, Jones K, Ni G, Crawford J, Millar A, Tolson E, Singleton M, Kojic M, Robertson T, Walters S, Mulay O, Bhuva DD, Davis MJ, Wainwright BJ, Nguyen Q, Genovesi LA. Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition. Genome Med 2023; 15:29. [PMID: 37127652 PMCID: PMC10150495 DOI: 10.1186/s13073-023-01185-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/20/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classified into four major subgroups based on gene expression and genomic features. Single-cell transcriptome studies have defined the cellular states underlying each MB subgroup; however, the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined. METHODS Here, we used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of MB and show that cells specific to a transcriptional state or spatial location are pivotal for CDK4/6 inhibitor, Palbociclib, treatment response. We integrated spatial gene expression with histological annotation and single-cell gene expression data from MB, developing an analysis strategy to spatially map cell type responses within the hybrid system of human and mouse cells and their interface within an intact brain tumour section. RESULTS We distinguish neoplastic and non-neoplastic cells within tumours and from the surrounding cerebellar tissue, further refining pathological annotation. We identify a regional response to Palbociclib, with reduced proliferation and induced neuronal differentiation in both treated tumours. Additionally, we resolve at a cellular resolution a distinct tumour interface where the tumour contacts neighbouring mouse brain tissue consisting of abundant astrocytes and microglia and continues to proliferate despite Palbociclib treatment. CONCLUSIONS Our data highlight the power of using spatial transcriptomics to characterise the response of a tumour to a targeted therapy and provide further insights into the molecular and cellular basis underlying the response and resistance to CDK4/6 inhibitors in SHH MB.
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Affiliation(s)
- Tuan Vo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Brad Balderson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Kahli Jones
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Guiyan Ni
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Amanda Millar
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Elissa Tolson
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Matthew Singleton
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Marija Kojic
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Thomas Robertson
- Department of Pathology, Royal Brisbane and Women's Hospital, University of Queensland, Brisbane, QLD, 4029, Australia
| | - Shaun Walters
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Onkar Mulay
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dharmesh D Bhuva
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Faculty of Medicine, South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Melissa J Davis
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Faculty of Medicine, South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Brandon J Wainwright
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Laura A Genovesi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
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Vo T, Balderson B, Jones K, Crawford J, Millar A, Tolson E, Ruitenberg M, Robertson T, Bhuva D, Davis M, Wainwright B, Nguyen Q, Genovesi L. MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition. Neuro Oncol 2022. [PMCID: PMC9165004 DOI: 10.1093/neuonc/noac079.381] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Medulloblastoma (MB) is a malignant tumour of the cerebellum which can be classified into four major subgroups on the basis of gene expression and genomic features. Single cell transcriptome studies have defined the cellular states underlying each MB subgroup, however the spatial organisation of these diverse cell states and how this impacts response to therapy remains to be determined. Here, we used spatially resolved transcriptomics to define the cellular diversity within a sonic hedgehog (SHH) patient-derived model of MB and identify how cells specific to a transcriptional state or spatial location are pivotal in responses to treatment with the CDK4/6 inhibitor, Palbociclib. We distinguish neoplastic and non-neoplastic cells within tumours and from the surrounding cerebellar tissue, further refining pathological annotation. We identify a regional response to Palbociclib, with reduced proliferation and induced neuronal differentiation in the majority of the tumours. Additionally, we resolve in cellular resolution a distinct tumour “interface” where the tumour contacts neighbouring mouse brain consisting of abundant astrocytes and microglia and continues to proliferate despite Palbociclib treatment. Our data highlight the power of this approach to characterise the response of a tumour to targeted therapy and provide further insights into the molecular and cellular basis underlying the response and resistance to CDK4/6 inhibitors in SHH MB
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Affiliation(s)
- Tuan Vo
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Brad Balderson
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Kahli Jones
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Amanda Millar
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Elissa Tolson
- The University of Queensland Diamantina Institute, The University of Queensland , Woolloongabba, QLD , Australia
| | - Marc Ruitenberg
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia , QLD , Australia
| | - Thomas Robertson
- Department of Pathology, Royal Brisbane and Women’s Hospital, University of Queensland , Brisbane, QLD , Australia
| | - Dharmesh Bhuva
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC , Australia
| | - Melissa Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC , Australia
| | - Brandon Wainwright
- The University of Queensland Diamantina Institute, The University of Queensland , Woolloongabba, QLD , Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
| | - Laura Genovesi
- The University of Queensland Diamantina Institute, The University of Queensland , Woolloongabba, QLD , Australia
- Institute for Molecular Bioscience, St Lucia , QLD , Australia
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Genovesi L, Millar A, Tolson E, Singleton M, Hassall E, Kojic M, Brighi C, Girald E, Andradas C, Kuchibhotla M, Endersby R, Gottardo N, Bernard A, Adolphe C, Olson J, Davis M, Wainwright B. MOMC-5. Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma. Neurooncol Adv 2021. [PMCID: PMC8255431 DOI: 10.1093/noajnl/vdab070.015] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality and morbidity. Existing treatment protocols are aggressive in nature resulting in significant neurological, intellectual and physical disabilities for the children undergoing treatment. Clearly, there is an urgent need for improved, targeted therapies that minimize these harmful side effects. Methods We identified candidate drugs for MB using a network-based systems-pharmacogenomics approach: based on results from a functional genomics screen, we identified a network of interactions implicated in human MB growth regulation. We then integrated drugs and their known mechanisms of action, along with gene expression data from a large collection of medulloblastoma patients to identify drugs with potential to treat MB. Results Our analyses identified drugs targeting CDK4, CDK6, and AURKA as strong candidates for MB; all of these genes are well validated as drug targets in other tumour types. We also identified non-WNT MB as a novel indication for drugs targeting TUBB, CAD, SNRPA, SLC1A5, PTPRS, P4HB and CHEK2. Based upon these analyses we subsequently demonstrated that one of these drugs, the new microtubule stabilizing agent, ixabepilone, blocked tumour growth in vivo in mice bearing Sonic Hedgehog and Group 3 patient-derived xenograft tumours, providing the first demonstration of its efficacy in MB. Conclusions Our findings confirm that this data-driven systems pharmacogenomics strategy is a powerful approach for the discovery and validation of novel therapeutic candidates relevant to MB treatment, and along with data validating ixabepilone in PDX models of the two most aggressive subtypes of medulloblastoma, we present the network analysis framework as a resource for the field.
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Affiliation(s)
- Laura Genovesi
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Amanda Millar
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Elissa Tolson
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Matthew Singleton
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Emily Hassall
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Marija Kojic
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Caterina Brighi
- Australian Institute for Bioengineering and Nanotechnology, St Lucia, QLD, Australia
| | - Emily Girald
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | | | | | | | | | - Anne Bernard
- QFAB Bioinformatics, Institute for Molecular Bioscience, St Lucia, QLD, Australia
| | - Christelle Adolphe
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - James Olson
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Melissa Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, USA
| | - Brandon Wainwright
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, USA
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Genovesi LA, Millar A, Tolson E, Singleton M, Hassall E, Kojic M, Brighi C, Girard E, Andradas C, Kuchibhotla M, Bhuva DD, Endersby R, Gottardo NG, Bernard A, Adolphe C, Olson JM, Taylor MD, Davis MJ, Wainwright BJ. Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma. Genome Med 2021; 13:103. [PMID: 34154646 PMCID: PMC8215804 DOI: 10.1186/s13073-021-00920-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/04/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality and morbidity. Existing treatment protocols are aggressive in nature resulting in significant neurological, intellectual and physical disabilities for the children undergoing treatment. Thus, there is an urgent need for improved, targeted therapies that minimize these harmful side effects. METHODS We identified candidate drugs for MB using a network-based systems-pharmacogenomics approach: based on results from a functional genomics screen, we identified a network of interactions implicated in human MB growth regulation. We then integrated drugs and their known mechanisms of action, along with gene expression data from a large collection of medulloblastoma patients to identify drugs with potential to treat MB. RESULTS Our analyses identified drugs targeting CDK4, CDK6 and AURKA as strong candidates for MB; all of these genes are well validated as drug targets in other tumour types. We also identified non-WNT MB as a novel indication for drugs targeting TUBB, CAD, SNRPA, SLC1A5, PTPRS, P4HB and CHEK2. Based upon these analyses, we subsequently demonstrated that one of these drugs, the new microtubule stabilizing agent, ixabepilone, blocked tumour growth in vivo in mice bearing patient-derived xenograft tumours of the Sonic Hedgehog and Group 3 subtype, providing the first demonstration of its efficacy in MB. CONCLUSIONS Our findings confirm that this data-driven systems pharmacogenomics strategy is a powerful approach for the discovery and validation of novel therapeutic candidates relevant to MB treatment, and along with data validating ixabepilone in PDX models of the two most aggressive subtypes of medulloblastoma, we present the network analysis framework as a resource for the field.
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Affiliation(s)
- Laura A Genovesi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Amanda Millar
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Elissa Tolson
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Matthew Singleton
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Emily Hassall
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Marija Kojic
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Caterina Brighi
- ARC Centre of Excellence for Convergent Bio-Nano Science and Technology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Emily Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Clara Andradas
- Brain Tumour Research Program, Telethon Kids Cancer Centre, Telethon Kids Institute, Nedlands, WA, 6009, Australia
| | - Mani Kuchibhotla
- Brain Tumour Research Program, Telethon Kids Cancer Centre, Telethon Kids Institute, Nedlands, WA, 6009, Australia
| | - Dharmesh D Bhuva
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Raelene Endersby
- Brain Tumour Research Program, Telethon Kids Cancer Centre, Telethon Kids Institute, Nedlands, WA, 6009, Australia
| | - Nicholas G Gottardo
- Brain Tumour Research Program, Telethon Kids Cancer Centre, Telethon Kids Institute, Nedlands, WA, 6009, Australia
| | - Anne Bernard
- QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christelle Adolphe
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Michael D Taylor
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, MSG 1X8, Canada
- Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, MSG 1X8, Canada
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
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Starobova H, Monteleone M, Adolphe C, Batoon L, Sandrock CJ, Tay B, Deuis JR, Smith AV, Mueller A, Nadar EI, Lawrence GP, Mayor A, Tolson E, Levesque JP, Pettit AR, Wainwright BJ, Schroder K, Vetter I. Vincristine-induced peripheral neuropathy is driven by canonical NLRP3 activation and IL-1β release. J Exp Med 2021; 218:e20201452. [PMID: 33656514 PMCID: PMC7933984 DOI: 10.1084/jem.20201452] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/09/2020] [Accepted: 01/19/2021] [Indexed: 12/29/2022] Open
Abstract
Vincristine is an important component of many regimens used for pediatric and adult malignancies, but it causes a dose-limiting sensorimotor neuropathy for which there is no effective treatment. This study aimed to delineate the neuro-inflammatory mechanisms contributing to the development of mechanical allodynia and gait disturbances in a murine model of vincristine-induced neuropathy, as well as to identify novel treatment approaches. Here, we show that vincristine-induced peripheral neuropathy is driven by activation of the NLRP3 inflammasome and subsequent release of interleukin-1β from macrophages, with mechanical allodynia and gait disturbances significantly reduced in knockout mice lacking NLRP3 signaling pathway components, or after treatment with the NLRP3 inhibitor MCC950. Moreover, treatment with the IL-1 receptor antagonist anakinra prevented the development of vincristine-induced neuropathy without adversely affecting chemotherapy efficacy or tumor progression in patient-derived medulloblastoma xenograph models. These results detail the neuro-inflammatory mechanisms leading to vincristine-induced peripheral neuropathy and suggest that repurposing anakinra may be an effective co-treatment strategy to prevent vincristine-induced peripheral neuropathy.
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Affiliation(s)
- Hana Starobova
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mercedes Monteleone
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Christelle Adolphe
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Lena Batoon
- Mater Research Institute and Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Cheyenne J. Sandrock
- Mater Research Institute and Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Bryan Tay
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jennifer R. Deuis
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alexandra V. Smith
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alexander Mueller
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Evelyn Israel Nadar
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Grace Pamo Lawrence
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Amanda Mayor
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Elissa Tolson
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jean-Pierre Levesque
- Mater Research Institute and Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Allison R. Pettit
- Mater Research Institute and Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Brandon J. Wainwright
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Kate Schroder
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
- The School of Pharmacy, The University of Queensland, Woolloongabba, Queensland, Australia
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