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Hiatt JB, Doebley AL, Arnold HU, Adil M, Sandborg H, Persse TW, Ko M, Wu F, Quintanal Villalonga A, Santana-Davila R, Eaton K, Dive C, Rudin CM, Thomas A, Houghton AM, Ha G, MacPherson D. Molecular phenotyping of small cell lung cancer using targeted cfDNA profiling of transcriptional regulatory regions. Sci Adv 2024; 10:eadk2082. [PMID: 38598634 PMCID: PMC11006233 DOI: 10.1126/sciadv.adk2082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
We report an approach for cancer phenotyping based on targeted sequencing of cell-free DNA (cfDNA) for small cell lung cancer (SCLC). In SCLC, differential activation of transcription factors (TFs), such as ASCL1, NEUROD1, POU2F3, and REST defines molecular subtypes. We designed a targeted capture panel that identifies chromatin organization signatures at 1535 TF binding sites and 13,240 gene transcription start sites and detects exonic mutations in 842 genes. Sequencing of cfDNA from SCLC patient-derived xenograft models captured TF activity and gene expression and revealed individual highly informative loci. Prediction models of ASCL1 and NEUROD1 activity using informative loci achieved areas under the receiver operating characteristic curve (AUCs) from 0.84 to 0.88 in patients with SCLC. As non-SCLC (NSCLC) often transforms to SCLC following targeted therapy, we applied our framework to distinguish NSCLC from SCLC and achieved an AUC of 0.99. Our approach shows promising utility for SCLC subtyping and transformation monitoring, with potential applicability to diverse tumor types.
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Affiliation(s)
- Joseph B. Hiatt
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Veterans Affairs Puget Sound Healthcare System - Seattle Branch, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Henry U. Arnold
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mohamed Adil
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Holly Sandborg
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas W. Persse
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Feinan Wu
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alvaro Quintanal Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rafael Santana-Davila
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Keith Eaton
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Charles M. Rudin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Graduate Program in Pharmacology, Weill Cornell Medical College; New York, NY, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - A. McGarry Houghton
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David MacPherson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Bristol JA, Nelson SE, Ohashi M, Casco A, Hayes M, Ranheim EA, Pawelski AS, Singh DR, Hodson DJ, Johannsen EC, Kenney SC. Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice. PLoS Pathog 2024; 20:e1012132. [PMID: 38620028 PMCID: PMC11045125 DOI: 10.1371/journal.ppat.1012132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/25/2024] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
Epstein-Barr virus (EBV) is an important cause of human lymphomas, including Burkitt lymphoma (BL). EBV+ BLs are driven by Myc translocation and have stringent forms of viral latency that do not express either of the two major EBV oncoproteins, EBNA2 (which mimics Notch signaling) and LMP1 (which activates NF-κB signaling). Suppression of Myc-induced apoptosis, often through mutation of the TP53 (p53) gene or inhibition of pro-apoptotic BCL2L11 (BIM) gene expression, is required for development of Myc-driven BLs. EBV+ BLs contain fewer cellular mutations in apoptotic pathways compared to EBV-negative BLs, suggesting that latent EBV infection inhibits Myc-induced apoptosis. Here we use an EBNA2-deleted EBV virus (ΔEBNA2 EBV) to create the first in vivo model for EBV+ BL-like lymphomas derived from primary human B cells. We show that cord blood B cells infected with both ΔEBNA2 EBV and a Myc-expressing vector proliferate indefinitely on a CD40L/IL21 expressing feeder layer in vitro and cause rapid onset EBV+ BL-like tumors in NSG mice. These LMP1/EBNA2-negative Myc-driven lymphomas have wild type p53 and very low BIM, and express numerous germinal center B cell proteins (including TCF3, BACH2, Myb, CD10, CCDN3, and GCSAM) in the absence of BCL6 expression. Myc-induced activation of Myb mediates expression of many of these BL-associated proteins. We demonstrate that Myc blocks LMP1 expression both by inhibiting expression of cellular factors (STAT3 and Src) that activate LMP1 transcription and by increasing expression of proteins (DNMT3B and UHRF1) known to enhance DNA methylation of the LMP1 promoters in human BLs. These results show that latent EBV infection collaborates with Myc over-expression to induce BL-like human B-cell lymphomas in mice. As NF-κB signaling retards the growth of EBV-negative BLs, Myc-mediated repression of LMP1 may be essential for latent EBV infection and Myc translocation to collaboratively induce human BLs.
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Affiliation(s)
- Jillian A. Bristol
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Scott E. Nelson
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Makoto Ohashi
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Alejandro Casco
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Mitchell Hayes
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Erik A. Ranheim
- Department of Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Abigail S. Pawelski
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Deo R. Singh
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Daniel J. Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Eric C. Johannsen
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shannon C. Kenney
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Buddenkotte T, Rundo L, Woitek R, Escudero Sanchez L, Beer L, Crispin-Ortuzar M, Etmann C, Mukherjee S, Bura V, McCague C, Sahin H, Pintican R, Zerunian M, Allajbeu I, Singh N, Sahdev A, Havrilesky L, Cohn DE, Bateman NW, Conrads TP, Darcy KM, Maxwell GL, Freymann JB, Öktem O, Brenton JD, Sala E, Schönlieb CB. Deep learning-based segmentation of multisite disease in ovarian cancer. Eur Radiol Exp 2023; 7:77. [PMID: 38057616 PMCID: PMC10700248 DOI: 10.1186/s41747-023-00388-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/21/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE To determine if pelvic/ovarian and omental lesions of ovarian cancer can be reliably segmented on computed tomography (CT) using fully automated deep learning-based methods. METHODS A deep learning model for the two most common disease sites of high-grade serous ovarian cancer lesions (pelvis/ovaries and omentum) was developed and compared against the well-established "no-new-Net" framework and unrevised trainee radiologist segmentations. A total of 451 CT scans collected from four different institutions were used for training (n = 276), evaluation (n = 104) and testing (n = 71) of the methods. The performance was evaluated using the Dice similarity coefficient (DSC) and compared using a Wilcoxon test. RESULTS Our model outperformed no-new-Net for the pelvic/ovarian lesions in cross-validation, on the evaluation and test set by a significant margin (p values being 4 × 10-7, 3 × 10-4, 4 × 10-2, respectively), and for the omental lesions on the evaluation set (p = 1 × 10-3). Our model did not perform significantly differently in segmenting pelvic/ovarian lesions (p = 0.371) compared to a trainee radiologist. On an independent test set, the model achieved a DSC performance of 71 ± 20 (mean ± standard deviation) for pelvic/ovarian and 61 ± 24 for omental lesions. CONCLUSION Automated ovarian cancer segmentation on CT scans using deep neural networks is feasible and achieves performance close to a trainee-level radiologist for pelvic/ovarian lesions. RELEVANCE STATEMENT Automated segmentation of ovarian cancer may be used by clinicians for CT-based volumetric assessments and researchers for building complex analysis pipelines. KEY POINTS • The first automated approach for pelvic/ovarian and omental ovarian cancer lesion segmentation on CT images has been presented. • Automated segmentation of ovarian cancer lesions can be comparable with manual segmentation of trainee radiologists. • Careful hyperparameter tuning can provide models significantly outperforming strong state-of-the-art baselines.
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Affiliation(s)
- Thomas Buddenkotte
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department for Diagnostic and Interventional Radiology and Nuclear Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- jung diagnostics GmbH, Hamburg, Germany
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Information and Electrical Engineering and Applied Mathematics, University of Salerno, Fisciano, Italy
| | - Ramona Woitek
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, Danube Private University, Krems, Austria
| | - Lorena Escudero Sanchez
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Lucian Beer
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Mireia Crispin-Ortuzar
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Christian Etmann
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Subhadip Mukherjee
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Vlad Bura
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Radiology and Medical Imaging, County Clinical Emergency Hospital, Cluj-Napoca-Napoca, Romania
| | - Cathal McCague
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Hilal Sahin
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Radiology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Roxana Pintican
- Department of Radiology and Medical Imaging, County Clinical Emergency Hospital, Cluj-Napoca-Napoca, Romania
- Department of Radiology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca-Napoca, Romania
| | - Marta Zerunian
- Department of Medical-Surgical and Translational Medicine-Radiology Unit, Sapienza University of Rome, Sant'Andrea Hospital, Rome, Italy
| | - Iris Allajbeu
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Naveena Singh
- Department of Clinical Pathology, Barts Health NHS Trust, London, UK
| | - Anju Sahdev
- Department of Radiology, Barts Health NHS Trust, London, UK
| | | | - David E Cohn
- Departmant of Obstetrics and Gynecology, Division of Gynecologic Oncology, Ohio State University Comprehensive Cancer Center, Ohio State University College of Medicine, Columbus, OH, USA
| | - Nicholas W Bateman
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
| | - Thomas P Conrads
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
- Inova Center for Personalized Health, Inova Schar Cancer Institute, Falls Church, VA, USA
| | - Kathleen M Darcy
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
| | - G Larry Maxwell
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - John B Freymann
- Cancer Imaging Informatics Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ozan Öktem
- Department of Mathematics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James D Brenton
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
- Dipartimento Di Scienze Radiologiche Ed Ematologiche, Universita Cattolica del Sacro Cuore, Rome, Italy.
- Dipartimento Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - Carola-Bibiane Schönlieb
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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Lewis D, McHugh DJ, Li KL, Zhu X, Mcbain C, Lloyd SK, Jackson A, Pathmanaban ON, King AT, Coope DJ. Detection of early changes in the post-radiosurgery vestibular schwannoma microenvironment using multinuclear MRI. Sci Rep 2021; 11:15712. [PMID: 34344960 PMCID: PMC8333359 DOI: 10.1038/s41598-021-95022-6] [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: 03/01/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Stereotactic radiosurgery (SRS) is an established, effective therapy against vestibular schwannoma (VS). The mechanisms of tumour response are, however, unknown and in this study we sought to evaluate changes in the irradiated VS tumour microenvironment through a multinuclear MRI approach. Five patients with growing sporadic VS underwent a multi-timepoint comprehensive MRI protocol, which included diffusion tensor imaging (DTI), dynamic contrast-enhanced (DCE) MRI and a spiral 23Na-MRI acquisition for total sodium concentration (TSC) quantification. Post-treatment voxelwise changes in TSC, DTI metrics and DCE-MRI derived microvascular biomarkers (Ktrans, ve and vp) were evaluated and compared against pre-treatment values. Changes in tumour TSC and microvascular parameters were observable as early as 2 weeks post-treatment, preceding changes in structural imaging. At 6 months post-treatment there were significant voxelwise increases in tumour TSC (p < 0.001) and mean diffusivity (p < 0.001, repeated-measures ANOVA) with marked decreases in tumour microvascular parameters (p < 0.001, repeated-measures ANOVA). This study presents the first in vivo evaluation of alterations in the VS tumour microenvironment following SRS, demonstrating that changes in tumour sodium homeostasis and microvascular parameters can be imaged as early as 2 weeks following treatment. Future studies should seek to investigate these clinically relevant MRI metrics as early biomarkers of SRS response.
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Affiliation(s)
- Daniel Lewis
- Dept. of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Stott Lane, Salford, Greater Manchester, M6 8HD, UK.
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK.
- Division of Informatics, Imaging and Data Sciences, Wolfson Molecular Imaging Centre (WMIC), University of Manchester, Manchester, UK.
| | - Damien J McHugh
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ka-Loh Li
- Division of Informatics, Imaging and Data Sciences, Wolfson Molecular Imaging Centre (WMIC), University of Manchester, Manchester, UK
| | - Xiaoping Zhu
- Division of Informatics, Imaging and Data Sciences, Wolfson Molecular Imaging Centre (WMIC), University of Manchester, Manchester, UK
| | - Catherine Mcbain
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK
- Department of Clinical Oncology, Christie NHS Foundation Trust, Manchester, UK
| | - Simon K Lloyd
- Department of Otolaryngology, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Department of Otolaryngology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Alan Jackson
- Division of Informatics, Imaging and Data Sciences, Wolfson Molecular Imaging Centre (WMIC), University of Manchester, Manchester, UK
| | - Omar N Pathmanaban
- Dept. of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Stott Lane, Salford, Greater Manchester, M6 8HD, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology & Regenerative Medicine, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Andrew T King
- Dept. of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Stott Lane, Salford, Greater Manchester, M6 8HD, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, UK
| | - David J Coope
- Dept. of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Stott Lane, Salford, Greater Manchester, M6 8HD, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
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5
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Maiter A, Riemer F, Allinson K, Zaccagna F, Crispin-Ortuzar M, Gehrung M, McLean MA, Priest AN, Grist J, Matys T, Graves MJ, Gallagher FA. Investigating the relationship between diffusion kurtosis tensor imaging (DKTI) and histology within the normal human brain. Sci Rep 2021; 11:8857. [PMID: 33893338 PMCID: PMC8065051 DOI: 10.1038/s41598-021-87857-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/07/2020] [Accepted: 03/26/2021] [Indexed: 01/13/2023] Open
Abstract
Measurements of water diffusion with MRI have been used as a biomarker of tissue microstructure and heterogeneity. In this study, diffusion kurtosis tensor imaging (DKTI) of the brain was undertaken in 10 healthy volunteers at a clinical field strength of 3 T. Diffusion and kurtosis metrics were measured in regions-of-interest on the resulting maps and compared with quantitative analysis of normal post-mortem tissue histology from separate age-matched donors. White matter regions showed low diffusion (0.60 ± 0.04 × 10-3 mm2/s) and high kurtosis (1.17 ± 0.06), consistent with a structured heterogeneous environment comprising parallel neuronal fibres. Grey matter showed intermediate diffusion (0.80 ± 0.02 × 10-3 mm2/s) and kurtosis (0.82 ± 0.05) values. An important finding is that the subcortical regions investigated (thalamus, caudate and putamen) showed similar diffusion and kurtosis properties to white matter. Histological staining of the subcortical nuclei demonstrated that the predominant grey matter was permeated by small white matter bundles, which could account for the similar kurtosis to white matter. Quantitative histological analysis demonstrated higher mean tissue kurtosis and vector standard deviation values for white matter (1.08 and 0.81) compared to the subcortical regions (0.34 and 0.59). Mean diffusion on DKTI was positively correlated with tissue kurtosis (r = 0.82, p < 0.05) and negatively correlated with vector standard deviation (r = -0.69, p < 0.05). This study demonstrates how DKTI can be used to study regional structural variations in the cerebral tissue microenvironment and could be used to probe microstructural changes within diseased tissue in the future.
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Affiliation(s)
- Ahmed Maiter
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
| | - Frank Riemer
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
- MMIV, Department of Radiology, Haukeland University Hospital, Bergen, Norway
| | - Kieren Allinson
- Department of Pathology, Addenbrooke's Hospital NHS Foundation Trust, Cambridge, UK
| | - Fulvio Zaccagna
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
| | | | - Marcel Gehrung
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Mary A McLean
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Andrew N Priest
- Department of Radiology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - James Grist
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
| | - Tomasz Matys
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
| | - Martin J Graves
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
- Department of Radiology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ferdia A Gallagher
- Department of Radiology, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK.
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6
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Henderson F, Jones E, Denbigh J, Christie L, Chapman R, Hoyes E, Claude E, Williams KJ, Roncaroli F, McMahon A. 3D DESI-MS lipid imaging in a xenograft model of glioblastoma: a proof of principle. Sci Rep 2020; 10:16512. [PMID: 33020565 PMCID: PMC7536442 DOI: 10.1038/s41598-020-73518-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 07/06/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Desorption electrospray ionisation mass spectrometry (DESI-MS) can image hundreds of molecules in a 2D tissue section, making it an ideal tool for mapping tumour heterogeneity. Tumour lipid metabolism has gained increasing attention over the past decade; and here, lipid heterogeneity has been visualised in a glioblastoma xenograft tumour using 3D DESI-MS imaging. The use of an automatic slide loader automates 3D imaging for high sample-throughput. Glioblastomas are highly aggressive primary brain tumours, which display heterogeneous characteristics and are resistant to chemotherapy and radiotherapy. It is therefore important to understand biochemical contributions to their heterogeneity, which may be contributing to treatment resistance. Adjacent sections to those used for DESI-MS imaging were used for H&E staining and immunofluorescence to identify different histological regions, and areas of hypoxia. Comparing DESI-MS imaging with biological staining allowed association of different lipid species with hypoxic and viable tissue within the tumour, and hence mapping of molecularly different tumour regions in 3D space. This work highlights that lipids are playing an important role in the heterogeneity of this xenograft tumour model, and DESI-MS imaging can be used for lipid 3D imaging in an automated fashion to reveal heterogeneity, which is not apparent in H&E stains alone.
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Affiliation(s)
- Fiona Henderson
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Manchester, M13 9PT, UK
| | | | | | - Lidan Christie
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
| | | | - Emmy Hoyes
- Waters Corporation, Wilmslow, SK9 4AX, UK
| | | | - Kaye J Williams
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Manchester, M13 9PT, UK
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester and Manchester Centre for Clinical Neuroscience, Salford, UK
| | - Adam McMahon
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK.
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