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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
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Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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3
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Papathomas TG, Sun N, Chortis V, Taylor AE, Arlt W, Richter S, Eisenhofer G, Ruiz-Babot G, Guasti L, Walch AK. Novel methods in adrenal research: a metabolomics approach. Histochem Cell Biol 2019; 151:201-216. [PMID: 30725173 DOI: 10.1007/s00418-019-01772-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Metabolic alterations have implications in a spectrum of tissue functions and disease. Aided by novel molecular biological and computational tools, our understanding of physiological and pathological processes underpinning endocrine and endocrine-related disease has significantly expanded over the last decade. Herein, we focus on novel metabolomics-related methodologies in adrenal research: in situ metabolomics by mass spectrometry imaging, steroid metabolomics by gas and liquid chromatography-mass spectrometry, energy pathway metabologenomics by liquid chromatography-mass spectrometry-based metabolomics of Krebs cycle intermediates, and cellular reprogramming to generate functional steroidogenic cells and hence to modulate the steroid metabolome. All four techniques to assess and/or modulate the metabolome in biological systems provide tremendous opportunities to manage neoplastic and non-neoplastic disease of the adrenal glands in the era of precision medicine. In this context, we discuss emerging clinical applications and/or promising metabolic-driven research towards diagnostic, prognostic, predictive and therapeutic biomarkers in tumours arising from the adrenal gland and extra-adrenal paraganglia as well as modern approaches to delineate and reprogram adrenal metabolism.
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Affiliation(s)
- Thomas G Papathomas
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Vasileios Chortis
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Angela E Taylor
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Susan Richter
- Faculty of Medicine Carl Gustav Carus, School of Medicine, Technische Universität Dresden, Dresden, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Graeme Eisenhofer
- Faculty of Medicine Carl Gustav Carus, School of Medicine, Technische Universität Dresden, Dresden, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Internal Medicine III, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Gerard Ruiz-Babot
- Department of Internal Medicine III, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, USA
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leonardo Guasti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Axel Karl Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
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Galanis E, Nassiri F, Coy S, Nejad R, Zadeh G, Santagata S. Integrating Genomics Into Neuro-Oncology Clinical Trials and Practice. Am Soc Clin Oncol Educ Book 2018; 38:148-157. [PMID: 30231374 DOI: 10.1200/edbk_200989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Important advances in our understanding of the molecular biology of brain tumors have resulted in a rapid evolution in the taxonomy of central nervous system (CNS) tumors, which culminated in the revised 2016 World Health Organization classification of CNS tumors that incorporates an integrated molecular/histologic diagnostic approach. Our expanding understanding of brain tumor genomics and molecular evolution during the disease course has started to impact clinical management. Furthermore, incorporation of genomic information in ongoing and planned neuro-oncology clinical trials is expected to lead to improved outcomes and result in personalized treatment options for patients with CNS malignancies.
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Affiliation(s)
- Evanthia Galanis
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Farhad Nassiri
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Shannon Coy
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Romina Nejad
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Gelareh Zadeh
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Sandro Santagata
- From the Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN; Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; MacFeeters Hamilton Centre for Neuro-Oncology Research, University of Toronto, Toronto, ON, Canada; Ludwig Center at Harvard, Department of Pathology, Boston Children's Hospital, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
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Rae Buchberger A, DeLaney K, Johnson J, Li L. Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights. Anal Chem 2018; 90:240-265. [PMID: 29155564 PMCID: PMC5959842 DOI: 10.1021/acs.analchem.7b04733] [Citation(s) in RCA: 561] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amanda Rae Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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