1
|
Salvucci M, Zakaria Z, Carberry S, Tivnan A, Seifert V, Kögel D, Murphy BM, Prehn JHM. System-based approaches as prognostic tools for glioblastoma. BMC Cancer 2019; 19:1092. [PMID: 31718568 PMCID: PMC6852738 DOI: 10.1186/s12885-019-6280-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The evasion of apoptosis is a hallmark of cancer. Understanding this process holistically and overcoming apoptosis resistance is a goal of many research teams in order to develop better treatment options for cancer patients. Efforts are also ongoing to personalize the treatment of patients. Strategies to confirm the therapeutic efficacy of current treatments or indeed to identify potential novel additional options would be extremely beneficial to both clinicians and patients. In the past few years, system medicine approaches have been developed that model the biochemical pathways of apoptosis. These systems tools incorporate and analyse the complex biological networks involved. For their successful integration into clinical practice, it is mandatory to integrate systems approaches with routine clinical and histopathological practice to deliver personalized care for patients. RESULTS We review here the development of system medicine approaches that model apoptosis for the treatment of cancer with a specific emphasis on the aggressive brain cancer, glioblastoma. CONCLUSIONS We discuss the current understanding in the field and present new approaches that highlight the potential of system medicine approaches to influence how glioblastoma is diagnosed and treated in the future.
Collapse
Affiliation(s)
- Manuela Salvucci
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Zaitun Zakaria
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Steven Carberry
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Amanda Tivnan
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Volker Seifert
- Department of Neurosurgery, Frankfurt University Hospital, Frankfurt am Main, Germany
| | - Donat Kögel
- Department of Neurosurgery, Frankfurt University Hospital, Frankfurt am Main, Germany
| | - Brona M. Murphy
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Jochen H. M. Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| |
Collapse
|
2
|
Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements. Nat Commun 2017; 8:623. [PMID: 28931805 PMCID: PMC5606996 DOI: 10.1038/s41467-017-00353-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/23/2017] [Indexed: 01/05/2023] Open
Abstract
The immense and growing repositories of transcriptional data may contain critical insights for developing new therapies. Current approaches to mining these data largely rely on binary classifications of disease vs. control, and are not able to incorporate measures of disease severity. We report an analytical approach to integrate ordinal clinical information with transcriptomics. We apply this method to public data for a large cohort of Huntington’s disease patients and controls, identifying and prioritizing phenotype-associated genes. We verify the role of a high-ranked gene in dysregulation of sphingolipid metabolism in the disease and demonstrate that inhibiting the enzyme, sphingosine-1-phosphate lyase 1 (SPL), has neuroprotective effects in Huntington’s disease models. Finally, we show that one consequence of inhibiting SPL is intracellular inhibition of histone deacetylases, thus linking our observations in sphingolipid metabolism to a well-characterized Huntington’s disease pathway. Our approach is easily applied to any data with ordinal clinical measurements, and may deepen our understanding of disease processes. Identifying gene subsets affecting disease phenotypes from transcriptome data is challenge. Here, the authors develop a method that combines transcriptional data with disease ordinal clinical measurements to discover a sphingolipid metabolism regulator involving in Huntington’s disease progression.
Collapse
|
3
|
Zeng T, Zhang W, Yu X, Liu X, Li M, Chen L. Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals. Brief Bioinform 2015; 17:576-92. [DOI: 10.1093/bib/bbv078] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Indexed: 12/21/2022] Open
|
4
|
Kim TH, Monsefi N, Song JH, von Kriegsheim A, Vandamme D, Pertz O, Kholodenko BN, Kolch W, Cho KH. Network-based identification of feedback modules that control RhoA activity and cell migration. J Mol Cell Biol 2015; 7:242-52. [DOI: 10.1093/jmcb/mjv017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/25/2014] [Indexed: 01/19/2023] Open
|
5
|
Jenkinson C, Earl J, Ghaneh P, Halloran C, Carrato A, Greenhalf W, Neoptolemos J, Costello E. Biomarkers for early diagnosis of pancreatic cancer. Expert Rev Gastroenterol Hepatol 2015; 9:305-15. [PMID: 25373768 DOI: 10.1586/17474124.2015.965145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pancreatic ductal adenocarcinoma is an aggressive malignancy with a 5-year survival rate of approximately 5%. The lack of established strategies for early detection contributes to this poor prognosis. Although several novel candidate biomarkers have been proposed for earlier diagnosis, none have been adopted into routine clinical use. In this review, the authors examine the challenges associated with finding new pancreatic cancer diagnostic biomarkers and explore why translation of biomarker research for patient benefit has thus far failed. The authors also review recent progress and highlight advances in the understanding of the biology of pancreatic cancer that may lead to improvements in biomarker detection and implementation.
Collapse
Affiliation(s)
- Claire Jenkinson
- Department of Molecular and Clinical Cancer Medicine, National Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Daulby Street, Liverpool L69 3GA, UK
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Okser S, Pahikkala T, Aittokallio T. Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min 2013; 6:5. [PMID: 23448398 PMCID: PMC3606427 DOI: 10.1186/1756-0381-6-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/11/2013] [Indexed: 12/31/2022] Open
Abstract
A central challenge in systems biology and medical genetics is to understand how interactions among genetic loci contribute to complex phenotypic traits and human diseases. While most studies have so far relied on statistical modeling and association testing procedures, machine learning and predictive modeling approaches are increasingly being applied to mining genotype-phenotype relationships, also among those associations that do not necessarily meet statistical significance at the level of individual variants, yet still contributing to the combined predictive power at the level of variant panels. Network-based analysis of genetic variants and their interaction partners is another emerging trend by which to explore how sub-network level features contribute to complex disease processes and related phenotypes. In this review, we describe the basic concepts and algorithms behind machine learning-based genetic feature selection approaches, their potential benefits and limitations in genome-wide setting, and how physical or genetic interaction networks could be used as a priori information for providing improved predictive power and mechanistic insights into the disease networks. These developments are geared toward explaining a part of the missing heritability, and when combined with individual genomic profiling, such systems medicine approaches may also provide a principled means for tailoring personalized treatment strategies in the future.
Collapse
|
7
|
Translational research in infectious disease: current paradigms and challenges ahead. Transl Res 2012; 159:430-53. [PMID: 22633095 PMCID: PMC3361696 DOI: 10.1016/j.trsl.2011.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/23/2011] [Accepted: 12/24/2012] [Indexed: 12/25/2022]
Abstract
In recent years, the biomedical community has witnessed a rapid scientific and technologic evolution after the development and refinement of high-throughput methodologies. Concurrently and consequentially, the scientific perspective has changed from the reductionist approach of meticulously analyzing the fine details of a single component of biology to the "holistic" approach of broadmindedly examining the globally interacting elements of biological systems. The emergence of this new way of thinking has brought about a scientific revolution in which genomics, proteomics, metabolomics, and other "omics" have become the predominant tools by which large amounts of data are amassed, analyzed, and applied to complex questions of biology that were previously unsolvable. This enormous transformation of basic science research and the ensuing plethora of promising data, especially in the realm of human health and disease, have unfortunately not been followed by a parallel increase in the clinical application of this information. On the contrary, the number of new potential drugs in development has been decreasing steadily, suggesting the existence of roadblocks that prevent the translation of promising research into medically relevant therapeutic or diagnostic application. In this article, we will review, in a noninclusive fashion, several recent scientific advancements in the field of translational research, with a specific focus on how they relate to infectious disease. We will also present a current picture of the limitations and challenges that exist for translational research, as well as ways that have been proposed by the National Institutes of Health to improve the state of this field.
Collapse
Key Words
- 2-de, 2-dimensional electrophoresis
- 2-d dige, 2-dimensional differential in-gel electrophoresis
- cf, cystic fibrosis
- ctsa, clinical and translational science awards program
- ebv, epstein-barr virus
- fda, u.s. food and drug administration
- gwas, genome-wide association studies
- hcv, hepatitis c virus
- hmp, human microbiome project
- hplc, high-pressure liquid chromatography
- lc, liquid chromatography
- lsb, laboratory of systems biology
- mab, monoclonal antibody
- mrm/srm, multiple reaction monitoring/selective reaction monitoring
- ms, mass spectrometry
- ms/ms, tandem mass spectrometry
- ncats, national center for advancing translational sciences
- ncrr, national center of research resources
- niaid, national institute of allergy and infectious disease
- nih, national institutes of health
- nme, new molecular entity
- nmr, nuclear magnetic resonance
- pbmc, peripheral blood mononuclear cell
- pcr, polymerase chain reaction
- prr, pathogen recognition receptor
- qqq, triple quadrupole mass spectrometry
- sars-cov, coronavirus associated with severe acute respiratory syndrome
- snp, single nucleotide polymorphism
- tb, tuberculosis
- uti, urinary tract infection
- yfv, yellow fever virus
Collapse
|
8
|
Corander J, Aittokallio T, Ripatti S, Kaski S. The rocky road to personalized medicine: computational and statistical challenges. Per Med 2012; 9:109-114. [DOI: 10.2217/pme.12.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jukka Corander
- Department of Mathematics & Statistics, University of Helsinki, PO Box 68, 00014 Helsinki, Finland and Department of Mathematics, Åbo Akademi University, 20500 Åbo, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland and Department of Mathematics, University of Turku, 20014 Turku, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland and Public Health Genomics Unit, National Institute for Health & Welfare, Helsinki, Finland and Wellcome Trust Sanger Institute, Hinxton, UK
| | - Samuel Kaski
- Helsinki Institute for Information Technology, Aalto University, 00076 Aalto, Finland and Helsinki Institute for Information Technology, University of Helsinki, Finland
| |
Collapse
|