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Roodakker KR, Alhuseinalkhudhur A, Al-Jaff M, Georganaki M, Zetterling M, Berntsson SG, Danfors T, Strand R, Edqvist PH, Dimberg A, Larsson EM, Smits A. Region-by-region analysis of PET, MRI, and histology in en bloc-resected oligodendrogliomas reveals intra-tumoral heterogeneity. Eur J Nucl Med Mol Imaging 2018; 46:569-579. [PMID: 30109401 PMCID: PMC6351509 DOI: 10.1007/s00259-018-4107-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 06/04/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
Abstract
Purpose Oligodendrogliomas are heterogeneous tumors in terms of imaging appearance, and a deeper understanding of the histopathological tumor characteristics in correlation to imaging parameters is needed. We used PET-to-MRI-to-histology co-registration with the aim of studying intra-tumoral 11C-methionine (MET) uptake in relation to tumor perfusion and the protein expression of histological cell markers in corresponding areas. Methods Consecutive histological sections of four tumors covering the entire en bloc-removed tumor were immunostained with antibodies against IDH1-mutated protein (tumor cells), Ki67 (proliferating cells), and CD34 (blood vessels). Software was developed for anatomical landmarks-based co-registration of subsequent histological images, which were overlaid on corresponding MET PET scans and MRI perfusion maps. Regions of interest (ROIs) on PET were selected throughout the entire tumor volume, covering hot spot areas, areas adjacent to hot spots, and tumor borders with infiltrating zone. Tumor-to-normal tissue (T/N) ratios of MET uptake and mean relative cerebral blood volume (rCBV) were measured in the ROIs and protein expression of histological cell markers was quantified in corresponding regions. Statistical correlations were calculated between MET uptake, rCBV, and quantified protein expression. Results A total of 84 ROIs were selected in four oligodendrogliomas. A significant correlation (p < 0.05) between MET uptake and tumor cell density was demonstrated in all tumors separately. In two tumors, MET correlated with the density of proliferating cells and vessel cell density. There were no significant correlations between MET uptake and rCBV, and between rCBV and histological cell markers. Conclusions The MET uptake in hot spots, outside hotspots, and in infiltrating tumor edges unanimously reflects tumor cell density. The correlation between MET uptake and vessel density and density of proliferating cells is less stringent in infiltrating tumor edges and is probably more susceptible to artifacts caused by larger blood vessels surrounding the tumor. Although based on a limited number of samples, this study provides histological proof for MET as an indicator of tumor cell density and for the lack of statistically significant correlations between rCBV and histological cell markers in oligodendrogliomas. Electronic supplementary material The online version of this article (10.1007/s00259-018-4107-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenney Roy Roodakker
- Department of Neuroscience, Neurology, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden.
| | - Ali Alhuseinalkhudhur
- Department of Neuroscience, Neurology, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden
- Department of Surgical Sciences, Radiology, Uppsala University, Uppsala, Sweden
| | - Mohammed Al-Jaff
- Department of Information Technology, Division of Visual Information and Interaction, Uppsala University, Uppsala, Sweden
| | - Maria Georganaki
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Zetterling
- Department of Neuroscience, Section of Neurosurgery, Uppsala University, Uppsala, Sweden
| | - Shala G Berntsson
- Department of Neuroscience, Neurology, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden
| | - Torsten Danfors
- Department of Surgical Sciences, Radiology, Uppsala University, Uppsala, Sweden
| | - Robin Strand
- Department of Surgical Sciences, Radiology, Uppsala University, Uppsala, Sweden
- Department of Information Technology, Division of Visual Information and Interaction, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Elna-Marie Larsson
- Department of Surgical Sciences, Radiology, Uppsala University, Uppsala, Sweden
- Department of Radiology, Uppsala University Hospital, Uppsala, Sweden
| | - Anja Smits
- Department of Neuroscience, Neurology, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden
- Institute of Neuroscience and Physiology, Department of Clinical Neuroscience, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Al-Jaff M, Sandström E, Grabherr M. microTaboo: a general and practical solution to the k-disjoint problem. BMC Bioinformatics 2017; 18:228. [PMID: 28464826 PMCID: PMC5414201 DOI: 10.1186/s12859-017-1644-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 04/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem. Examples include finding sequences unique to a pathogen for probe-based infection diagnostics; reducing off-target hits for re-sequencing or genome editing; detecting sequence (e.g. phage or viral) insertions; and multiple substitution mutations. Since both sensitivity and specificity are critical, an exhaustive, yet efficient solution is desirable. RESULTS We present microTaboo, a method that allows for efficient and extensive sequence mining of unique (k-disjoint) sequences of up to 100 nucleotides in length. On a number of simulated and real data sets ranging from microbe- to mammalian-size genomes, we show that microTaboo is able to efficiently find all sub-sequences of a specified length W that do not occur within a threshold of k mismatches in any other sub-sequence. We exemplify that microTaboo has many practical applications, including point substitution detection, sequence insertion detection, padlock probe target search, and candidate CRISPR target mining. CONCLUSIONS microTaboo implements a solution to the k-disjoint problem in an alignment- and assembly free manner. microTaboo is available for Windows, Mac OS X, and Linux, running Java 7 and higher, under the GNU GPLv3 license, at: https://MohammedAlJaff.github.io/microTaboo.
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Affiliation(s)
- Mohammed Al-Jaff
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden
| | - Eric Sandström
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden
| | - Manfred Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden. .,Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123, Uppsala, Sweden.
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