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Nuankaew S, Boonyuen N, Thumanu K, Pornputtapong N. Development of a machine learning model for systematics of Aspergillus section Nigri using synchrotron radiation-based fourier transform infrared spectroscopy. Heliyon 2024; 10:e26812. [PMID: 38439823 PMCID: PMC10909729 DOI: 10.1016/j.heliyon.2024.e26812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Aspergillus section Nigri (black aspergilli) fungi are economically important food spoilage agents. Some species in this section also produce harmful mycotoxins in food. However, it is remarkably difficult to identify this fungal group at the species level using morphological and chemical characteristics. The molecular approach for classification is preferable; however, it is time-consuming, making it inappropriate for rapid testing of large numbers of samples. To address this, we explored synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIR) as a rapid method for obtaining data suitable for species classification. SR-FTIR data were obtained from the mycelia/conidia of 22 black aspergilli species. The Convolutional Neural Network (CNN) approach, a supervised deep learning algorithm, was used with SR-FTIR data to classify black aspergilli at the species level. A subset of the data was used to train the CNN model, and the model classification performance was evaluated using the validation data subsets. The model demonstrated a 95.97% accuracy in species classification on the testing (blind) data subset. The technique presented herein could be an alternative method for identifying problematic black aspergilli in the food industry.
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Affiliation(s)
- Salilaporn Nuankaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (SLRI), Nakhon Ratchasima, 30000, Thailand
| | - Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in DNA Barcoding of Thai Medicinal Plants, Chulalongkorn University, Bangkok, 10330, Thailand
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Koehler A, Scroferneker ML, de Souza NMP, de Moraes PC, Pereira BAS, de Souza Cavalcante R, Mendes RP, Corbellini VA. Rapid Classification of Serum from Patients with Paracoccidioidomycosis Using Infrared Spectroscopy, Univariate Statistics, and Linear Discriminant Analysis (LDA). J Fungi (Basel) 2024; 10:147. [PMID: 38392819 PMCID: PMC10890592 DOI: 10.3390/jof10020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/18/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis that is diagnosed by visualizing the fungus in clinical samples or by other methods, like serological techniques. However, all PCM diagnostic methods have limitations. The aim of this study was to develop a diagnostic tool for PCM based on Fourier transform infrared (FTIR) spectroscopy. A total of 224 serum samples were included: 132 from PCM patients and 92 constituting the control group (50 from healthy blood donors and 42 from patients with other systemic mycoses). Samples were analyzed by attenuated total reflection (ATR) and a t-test was performed to find differences in the spectra of the two groups. The wavenumbers that had p < 0.05 had their diagnostic potential evaluated using receiver operating characteristic (ROC) curves. The spectral region with the lowest p value was used for variable selection through principal component analysis (PCA). The selected variables were used in a linear discriminant analysis (LDA). In univariate analysis, the ROC curves with the best performance were obtained in the region 1551-1095 cm-1. The wavenumber that had the highest AUC value was 1264 cm-1, achieving a sensitivity of 97.73%, specificity of 76.01%, and accuracy of 94.22%. The total separation of groups was obtained in the PCA performed with a spectral range of 1551-1095 cm-1. LDA performed with the eight wavenumbers with the greatest weight from the group discrimination in the PCA obtained 100% accuracy. The methodology proposed here is simple, fast, and highly accurate, proving its potential to be applied in the diagnosis of PCM. The proposed method is more accurate than the currently known diagnostic methods, which is particularly relevant for a neglected tropical mycosis such as paracoccidioidomycosis.
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Affiliation(s)
- Alessandra Koehler
- Postgraduate Program of Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre 90035-003, Brazil
| | - Maria Lúcia Scroferneker
- Postgraduate Program of Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre 90035-003, Brazil
- Department of Microbiology, Immunology and Parasitology, ICBS, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre 90050-170, Brazil
| | | | - Paulo Cezar de Moraes
- Postgraduate Program of Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre 90035-003, Brazil
| | | | - Ricardo de Souza Cavalcante
- Tropical Diseases Area, School of Medicine, Universidade Estadual Paulista-UNESP, Botucatu 18618-687, Brazil
| | - Rinaldo Pôncio Mendes
- Tropical Diseases Area, School of Medicine, Universidade Estadual Paulista-UNESP, Botucatu 18618-687, Brazil
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and Education, Postgraduate Program in Health Promotion, Postgraduate Program in Environmental Technology, Universidade de Santa Cruz do Sul-UNISC, Santa Cruz do Sul 96815-900, Brazil
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Biricioiu MR, Sarbu M, Ica R, Vukelić Ž, Kalanj-Bognar S, Zamfir AD. Advances in Mass Spectrometry of Gangliosides Expressed in Brain Cancers. Int J Mol Sci 2024; 25:1335. [PMID: 38279335 PMCID: PMC10816113 DOI: 10.3390/ijms25021335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Gangliosides are highly abundant in the human brain where they are involved in major biological events. In brain cancers, alterations of ganglioside pattern occur, some of which being correlated with neoplastic transformation, while others with tumor proliferation. Of all techniques, mass spectrometry (MS) has proven to be one of the most effective in gangliosidomics, due to its ability to characterize heterogeneous mixtures and discover species with biomarker value. This review highlights the most significant achievements of MS in the analysis of gangliosides in human brain cancers. The first part presents the latest state of MS development in the discovery of ganglioside markers in primary brain tumors, with a particular emphasis on the ion mobility separation (IMS) MS and its contribution to the elucidation of the gangliosidome associated with aggressive tumors. The second part is focused on MS of gangliosides in brain metastases, highlighting the ability of matrix-assisted laser desorption/ionization (MALDI)-MS, microfluidics-MS and tandem MS to decipher and structurally characterize species involved in the metastatic process. In the end, several conclusions and perspectives are presented, among which the need for development of reliable software and a user-friendly structural database as a search platform in brain tumor diagnostics.
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Affiliation(s)
- Maria Roxana Biricioiu
- National Institute for Research and Development in Electrochemistry and Condensed Matter, 300224 Timisoara, Romania; (M.R.B.); (M.S.); (R.I.)
- Faculty of Physics, West University of Timisoara, 300223 Timisoara, Romania
| | - Mirela Sarbu
- National Institute for Research and Development in Electrochemistry and Condensed Matter, 300224 Timisoara, Romania; (M.R.B.); (M.S.); (R.I.)
| | - Raluca Ica
- National Institute for Research and Development in Electrochemistry and Condensed Matter, 300224 Timisoara, Romania; (M.R.B.); (M.S.); (R.I.)
| | - Željka Vukelić
- Department of Chemistry and Biochemistry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Svjetlana Kalanj-Bognar
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Alina D. Zamfir
- National Institute for Research and Development in Electrochemistry and Condensed Matter, 300224 Timisoara, Romania; (M.R.B.); (M.S.); (R.I.)
- Department of Technical and Natural Sciences, “Aurel Vlaicu” University of Arad, 310330 Arad, Romania
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Di Santo R, Niccolini B, Romanò S, Vaccaro M, Di Giacinto F, De Spirito M, Ciasca G. Advancements in Mid-Infrared spectroscopy of extracellular vesicles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123346. [PMID: 37774583 DOI: 10.1016/j.saa.2023.123346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/02/2023] [Indexed: 10/01/2023]
Abstract
Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.
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Affiliation(s)
- Riccardo Di Santo
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy.
| | - Benedetta Niccolini
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sabrina Romanò
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Vaccaro
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Flavio Di Giacinto
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Gabriele Ciasca
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
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Soares Martins T, Ferreira M, Magalhães S, Leandro K, Almeida LPD, Vogelgsang J, Breitling B, Hansen N, Esselmann H, Wiltfang J, da Cruz E Silva OAB, Nunes A, Henriques AG. FTIR Spectroscopy and Blood-Derived Extracellular Vesicles Duo in Alzheimer's Disease. J Alzheimers Dis 2024; 98:1157-1167. [PMID: 38489187 DOI: 10.3233/jad-231239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Background Alzheimer's disease (AD) diagnosis is difficult, and new accurate tools based on peripheral biofluids are urgently needed. Extracellular vesicles (EVs) emerged as a valuable source of biomarker profiles for AD, since their cargo is disease-specific and these can be easily isolated from easily accessible biofluids, as blood. Fourier Transform Infrared (FTIR) spectroscopy can be employed to analyze EVs and obtain the spectroscopic profiles from different regions of the spectra, simultaneously characterizing carbohydrates, nucleic acids, proteins, and lipids. Objective The aim of this study was to identify blood-derived EVs (bdEVs) spectroscopic signatures with AD discriminatory potential. Methods Herein, FTIR spectra of bdEVs from two biofluids (serum and plasma) and distinct sets of Controls and AD cases were acquired, and EVs' spectra analyzed. Results Analysis of bdEVs second derivative peaks area revealed differences between Controls and AD cases in distinct spectra regions, assigned to carbohydrates and nucleic acids, amides, and lipids. Conclusions EVs' spectroscopic profiles presented AD discriminatory value, supporting the use of bdEVs combined with FTIR as a screening or complementary tool for AD diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Maria Ferreira
- Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Sandra Magalhães
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Faculty of Medicine, UnIC@RISE - Cardiovascular Research and Development Center, University of Porto, Porto, Portugal
| | - Kevin Leandro
- Faculty of Pharmacy, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Luís P de Almeida
- Faculty of Pharmacy, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany
- Translational Neuroscience Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Benedict Breitling
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany
| | - Niels Hansen
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany
| | - Hermann Esselmann
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany
| | - Jens Wiltfang
- Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
| | - Odete A B da Cruz E Silva
- Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Alexandra Nunes
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Department of Medical Sciences, Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
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das Chagas E Silva de Carvalho LF, de Lima Morais TM, Nogueira MS. Providing potential solutions by using FT-IR spectroscopy for biofluid analysis: Clinical impact of optical screening and diagnostic tests. Photodiagnosis Photodyn Ther 2023; 44:103753. [PMID: 37597683 DOI: 10.1016/j.pdpdt.2023.103753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Currently, the potential of FT-IR spectroscopy for rapid diagnosis of many pathologies has been demonstrated by numerous research studies including those targeting COVID-19 detection. However, the number of clinicians aware of this potential and who are willing to use spectroscopy in their clinics and hospitals is still negligible. In addition, lack of awareness creates a huge gap between clinicians and researchers involved in clinical translation of current FT-IR technology hence hindering initiatives to bring basic and applied research together for the direct benefit of patients. METHODS Knowledge and medical training on FT-IR on the side of clinicians should be one of the first steps to be able to integrate it into the list of complementary exams which may be requested by health professionals. Countless FT-IR applications could have a life-changing impact on patients' lives, especially screening and diagnostic tests involving biofluids such as blood, saliva and urine which are routinely non-invasively or minimally-invasively. RESULTS Blood may be the most difficult to obtain by the invasive method of collection, but much can be evaluated in its components, and areas such as hematology, infectiology, oncology and endocrinology can be directly benefited. Urine with a relatively simple collection method can provide pertinent information from the entire urinary system, including the actual condition of the kidneys. Saliva collection can be simpler for the patient and can provide information on diseases affecting the mouth and digestive system and can be used to diagnose diseases such as oral cancer in its early-stages. An unavoidable second step is the active involvement of industries to design robust and portable instruments for specific purposes, as the medical community requires user-friendly instruments of advanced computational algorithms. A third step resides in the legal situation involving the global use of the technique as a new diagnostic modality. CONCLUSIONS It is important to note that decentralized funds for variety of technologies hinders the training of clinical and medical professionals for the use of newly arising technologies and affect the engagement of these professionals with technology developers. As a result of decentralized funding, research efforts are spread out over a range of technologies which take a long time to get validated and translated to the clinic. Partnership over similar groups of technologies and efforts to test the same technologies while overcoming barriers posed to technology validation in different areas around the globe may benefit the clinical/medical, research and industry community globally.
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Affiliation(s)
| | | | - Marcelo Saito Nogueira
- Tyndall National Institute, Lee Maltings, Dyke Parade, Cork T12 R5CP, Ireland; Department of Physics, University College Cork, College Road, Cork T12 K8AF, Ireland.
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Andrews LJ, Davies P, Herbert C, Kurian KM. Pre-diagnostic blood biomarkers for adult glioma. Front Oncol 2023; 13:1163289. [PMID: 37265788 PMCID: PMC10229864 DOI: 10.3389/fonc.2023.1163289] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Glioma is one of the most common malignant primary brain tumours in adults, of which, glioblastoma is the most prevalent and malignant entity. Glioma is often diagnosed at a later stage of disease progression, which means it is associated with significant mortality and morbidity. Therefore, there is a need for earlier diagnosis of these tumours, which would require sensitive and specific biomarkers. These biomarkers could better predict glioma onset to improve diagnosis and therapeutic options for patients. While liquid biopsies could provide a cheap and non-invasive test to improve the earlier detection of glioma, there is little known on pre-diagnostic biomarkers which predate disease detection. In this review, we examine the evidence in the literature for pre-diagnostic biomarkers in glioma, including metabolomics and proteomics. We also consider the limitations of these approaches and future research directions of pre-diagnostic biomarkers for glioma.
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Affiliation(s)
- Lily J. Andrews
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
| | - Philippa Davies
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
| | - Christopher Herbert
- Bristol Haematology and Oncology Centre, University Hospitals Bristol National Health Service (NHS) Foundation Trust, Bristol, United Kingdom
| | - Kathreena M. Kurian
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
- Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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Charlton CE, Poon MTC, Brennan PM, Fleuriot JD. Development of prediction models for one-year brain tumour survival using machine learning: a comparison of accuracy and interpretability. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 233:107482. [PMID: 36947980 DOI: 10.1016/j.cmpb.2023.107482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/15/2022] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND OBJECTIVE Prediction of survival in patients diagnosed with a brain tumour is challenging because of heterogeneous tumour behaviours and treatment response. Advances in machine learning have led to the development of clinical prognostic models, but due to the lack of model interpretability, integration into clinical practice is almost non-existent. In this retrospective study, we compare five classification models with varying degrees of interpretability for the prediction of brain tumour survival greater than one year following diagnosis. METHODS 1028 patients aged ≥16 years with a brain tumour diagnosis between April 2012 and April 2020 were included in our study. Three intrinsically interpretable 'glass box' classifiers (Bayesian Rule Lists [BRL], Explainable Boosting Machine [EBM], and Logistic Regression [LR]), and two 'black box' classifiers (Random Forest [RF] and Support Vector Machine [SVM]) were trained on electronic patients records for the prediction of one-year survival. All models were evaluated using balanced accuracy (BAC), F1-score, sensitivity, specificity, and receiver operating characteristics. Black box model interpretability and misclassified predictions were quantified using SHapley Additive exPlanations (SHAP) values and model feature importance was evaluated by clinical experts. RESULTS The RF model achieved the highest BAC of 78.9%, closely followed by SVM (77.7%), LR (77.5%) and EBM (77.1%). Across all models, age, diagnosis (tumour type), functional features, and first treatment were top contributors to the prediction of one year survival. We used EBM and SHAP to explain model misclassifications and investigated the role of feature interactions in prognosis. CONCLUSION Interpretable models are a natural choice for the domain of predictive medicine. Intrinsically interpretable models, such as EBMs, may provide an advantage over traditional clinical assessment of brain tumour prognosis by weighting potential risk factors and their interactions that may be unknown to clinicians. An agreement between model predictions and clinical knowledge is essential for establishing trust in the models decision making process, as well as trust that the model will make accurate predictions when applied to new data.
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Affiliation(s)
- Colleen E Charlton
- Artificial Intelligence and its Applications Institute, School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK.
| | - Michael T C Poon
- Cancer Research UK Brain Tumour Centre of Excellence, CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK; Department of Clinical Neuroscience, Royal Infirmary of Edinburgh, 51 Little France Crescent EH16 4SA, UK.; Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Paul M Brennan
- Cancer Research UK Brain Tumour Centre of Excellence, CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK; Department of Clinical Neuroscience, Royal Infirmary of Edinburgh, 51 Little France Crescent EH16 4SA, UK.; Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Jacques D Fleuriot
- Artificial Intelligence and its Applications Institute, School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
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Connal S, Cameron JM, Sala A, Brennan PM, Palmer DS, Palmer JD, Perlow H, Baker MJ. Liquid biopsies: the future of cancer early detection. J Transl Med 2023; 21:118. [PMID: 36774504 PMCID: PMC9922467 DOI: 10.1186/s12967-023-03960-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/01/2023] [Indexed: 02/13/2023] Open
Abstract
Cancer is a worldwide pandemic. The burden it imposes grows steadily on a global scale causing emotional, physical, and financial strains on individuals, families, and health care systems. Despite being the second leading cause of death worldwide, many cancers do not have screening programs and many people with a high risk of developing cancer fail to follow the advised medical screening regime due to the nature of the available screening tests and other challenges with compliance. Moreover, many liquid biopsy strategies being developed for early detection of cancer lack the sensitivity required to detect early-stage cancers. Early detection is key for improved quality of life, survival, and to reduce the financial burden of cancer treatments which are greater at later stage detection. This review examines the current liquid biopsy market, focusing in particular on the strengths and drawbacks of techniques in achieving early cancer detection. We explore the clinical utility of liquid biopsy technologies for the earlier detection of solid cancers, with a focus on how a combination of various spectroscopic and -omic methodologies may pave the way for more efficient cancer diagnostics.
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Affiliation(s)
- Siobhan Connal
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK
| | - James M. Cameron
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK
| | - Alexandra Sala
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK
| | - Paul M. Brennan
- grid.4305.20000 0004 1936 7988Translational Neurosurgery, Centre for Clinical Brain Sciences, 49 Little France Crescent, University of Edinburgh, Edinburgh, EH16 4BS UK
| | - David S. Palmer
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK
| | - Joshua D. Palmer
- grid.412332.50000 0001 1545 0811Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210 USA
| | - Haley Perlow
- grid.412332.50000 0001 1545 0811Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210 USA
| | - Matthew J. Baker
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK ,grid.7943.90000 0001 2167 3843School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE UK
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Discovering Glioma Tissue through Its Biomarkers' Detection in Blood by Raman Spectroscopy and Machine Learning. Pharmaceutics 2023; 15:pharmaceutics15010203. [PMID: 36678833 PMCID: PMC9862809 DOI: 10.3390/pharmaceutics15010203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
The most commonly occurring malignant brain tumors are gliomas, and among them is glioblastoma multiforme. The main idea of the paper is to estimate dependency between glioma tissue and blood serum biomarkers using Raman spectroscopy. We used the most common model of human glioma when continuous cell lines, such as U87, derived from primary human tumor cells, are transplanted intracranially into the mouse brain. We studied the separability of the experimental and control groups by machine learning methods and discovered the most informative Raman spectral bands. During the glioblastoma development, an increase in the contribution of lactate, tryptophan, fatty acids, and lipids in dried blood serum Raman spectra were observed. This overlaps with analogous results of glioma tissues from direct Raman spectroscopy studies. A non-linear relationship between specific Raman spectral lines and tumor size was discovered. Therefore, the analysis of blood serum can track the change in the state of brain tissues during the glioma development.
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11
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Sala A, Cameron JM, Jenkins CA, Barr H, Christie L, Conn JJA, Evans TRJ, Harris DA, Palmer DS, Rinaldi C, Theakstone AG, Baker MJ. Liquid Biopsy for Pancreatic Cancer Detection Using Infrared Spectroscopy. Cancers (Basel) 2022; 14:3048. [PMID: 35804820 PMCID: PMC9264892 DOI: 10.3390/cancers14133048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
Pancreatic cancer claims over 460,000 victims per year. The carbohydrate antigen (CA) 19-9 test is the blood test used for pancreatic cancer's detection; however, its levels can be raised in symptomatic patients with other non-malignant diseases, or with other tumors in the surrounding area. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy has demonstrated exceptional potential in cancer diagnostics, and its clinical implementation could represent a significant step towards early detection. This proof-of-concept study, investigating the use of ATR-FTIR spectroscopy on dried blood serum, focused on the discrimination of both cancer versus healthy control samples, and cancer versus symptomatic non-malignant control samples, as a novel liquid biopsy approach for pancreatic cancer diagnosis. Machine learning algorithms were applied, achieving results of up to 92% sensitivity and 88% specificity when discriminating between cancers (n = 100) and healthy controls (n = 100). An area under the curve (AUC) of 0.95 was obtained through receiver operating characteristic (ROC) analysis. Balanced sensitivity and specificity over 75%, with an AUC of 0.83, were achieved with cancers (n = 35) versus symptomatic controls (n = 35). Herein, we present these results as demonstration that our liquid biopsy approach could become a simple, minimally invasive, and reliable diagnostic test for pancreatic cancer detection.
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Affiliation(s)
- Alexandra Sala
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK; (A.S.); (L.C.); (D.S.P.)
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
| | - James M. Cameron
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
| | - Cerys A. Jenkins
- Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK;
| | - Hugh Barr
- Gloucestershire Hospitals NHS Foundation Trust, Gloucester GL1 2EL, UK;
| | - Loren Christie
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK; (A.S.); (L.C.); (D.S.P.)
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
| | - Justin J. A. Conn
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
| | | | - Dean A. Harris
- Singleton Hospital, Swansea Bay University Local Health Board, Swansea SA2 8QA, UK;
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK; (A.S.); (L.C.); (D.S.P.)
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
| | - Christopher Rinaldi
- Department of Pure and Applied Chemistry, University of Strathclyde, The Technology and Innovation Centre, Glasgow G1 1RD, UK; (C.R.); (A.G.T.)
| | - Ashton G. Theakstone
- Department of Pure and Applied Chemistry, University of Strathclyde, The Technology and Innovation Centre, Glasgow G1 1RD, UK; (C.R.); (A.G.T.)
| | - Matthew J. Baker
- Dxcover Limited, Royal College Building, Glasgow G1 1XW, UK; (J.M.C.); (J.J.A.C.)
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12
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Cameron JM, Brennan PM, Antoniou G, Butler HJ, Christie L, Conn JJA, Curran T, Gray E, Hegarty MG, Jenkinson MD, Orringer D, Palmer DS, Sala A, Smith BR, Baker MJ. Clinical validation of a spectroscopic liquid biopsy for earlier detection of brain cancer. Neurooncol Adv 2022; 4:vdac024. [PMID: 35316978 PMCID: PMC8934542 DOI: 10.1093/noajnl/vdac024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Diagnostic delays impact the quality of life and survival of patients with brain tumors. Earlier and expeditious diagnoses in these patients are crucial to reducing the morbidities and mortalities associated with brain tumors. A simple, rapid blood test that can be administered easily in a primary care setting to efficiently identify symptomatic patients who are most likely to have a brain tumor would enable quicker referral to brain imaging for those who need it most.
Methods
Blood serum samples from 603 patients were prospectively collected and analyzed. Patients either had non-specific symptoms that could be indicative of a brain tumor on presentation to the Emergency Department, or a new brain tumor diagnosis and referral to the neurosurgical unit, NHS Lothian, Scotland. Patient blood serum samples were analyzed using the Dxcover®Brain Cancer liquid biopsy. This technology utilizes infrared spectroscopy combined with a diagnostic algorithm to predict the presence of intracranial disease.
Results
Our liquid biopsy approach reported an area under the receiver operating characteristic curve of 0.8. The sensitivity-tuned model achieves a 96% sensitivity with 45% specificity (NPV 99.3%) and identified 100% of glioblastoma multiforme patients. When tuned for a higher specificity, the model yields sensitivity of 47% with 90% specificity (PPV 28.4%).
Conclusions
This simple, non-invasive blood test facilitates the triage and radiographic diagnosis of brain tumor patients, while providing reassurance to healthy patients. Minimizing time to diagnosis would facilitate identification of brain tumor patients at an earlier stage, enabling more effective, less morbid surgical and adjuvant care.
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Affiliation(s)
- James M Cameron
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Georgios Antoniou
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Holly J Butler
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Loren Christie
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Justin J A Conn
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Tom Curran
- Children’s Mercy Research Institute at the Children’s Mercy Hospital, Kansas City, KS, USA
| | - Ewan Gray
- Independent Health Economics Consultant, Edinburgh, UK
| | - Mark G Hegarty
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Michael D Jenkinson
- Institute of Translational Medicine, University of Liverpool & The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool, L9 7LJ, UK
| | - Daniel Orringer
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY 10018, USA
| | - David S Palmer
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Alexandra Sala
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G11XL, UK
| | - Benjamin R Smith
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Matthew J Baker
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
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Huber M, Kepesidis KV, Voronina L, Fleischmann F, Fill E, Hermann J, Koch I, Milger-Kneidinger K, Kolben T, Schulz GB, Jokisch F, Behr J, Harbeck N, Reiser M, Stief C, Krausz F, Zigman M. Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer. eLife 2021; 10:68758. [PMID: 34696827 PMCID: PMC8547961 DOI: 10.7554/elife.68758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/13/2021] [Indexed: 01/11/2023] Open
Abstract
Recent omics analyses of human biofluids provide opportunities to probe selected species of biomolecules for disease diagnostics. Fourier-transform infrared (FTIR) spectroscopy investigates the full repertoire of molecular species within a sample at once. Here, we present a multi-institutional study in which we analysed infrared fingerprints of plasma and serum samples from 1639 individuals with different solid tumours and carefully matched symptomatic and non-symptomatic reference individuals. Focusing on breast, bladder, prostate, and lung cancer, we find that infrared molecular fingerprinting is capable of detecting cancer: training a support vector machine algorithm allowed us to obtain binary classification performance in the range of 0.78-0.89 (area under the receiver operating characteristic curve [AUC]), with a clear correlation between AUC and tumour load. Intriguingly, we find that the spectral signatures differ between different cancer types. This study lays the foundation for high-throughput onco-IR-phenotyping of four common cancers, providing a cost-effective, complementary analytical tool for disease recognition.
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Affiliation(s)
- Marinus Huber
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Kosmas V Kepesidis
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Liudmila Voronina
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Frank Fleischmann
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Ernst Fill
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Jacqueline Hermann
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Member of the German Center for Lung Research, DZL, Asklepios Fachkliniken München-Gauting, Munich, Germany
| | - Katrin Milger-Kneidinger
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Internal Medicine V, Munich, Germany
| | - Thomas Kolben
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Obstetrics and Gynecology, Breast Center and Comprehensive Cancer Center (CCLMU), Munich, Germany
| | - Gerald B Schulz
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Friedrich Jokisch
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Jürgen Behr
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Internal Medicine V, Munich, Germany
| | - Nadia Harbeck
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Obstetrics and Gynecology, Breast Center and Comprehensive Cancer Center (CCLMU), Munich, Germany
| | - Maximilian Reiser
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Clinical Radiology, Munich, Germany
| | - Christian Stief
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Ferenc Krausz
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Mihaela Zigman
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
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14
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Theakstone AG, Brennan PM, Jenkinson MD, Mills SJ, Syed K, Rinaldi C, Xu Y, Goodacre R, Butler HJ, Palmer DS, Smith BR, Baker MJ. Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours. Cancers (Basel) 2021; 13:cancers13153851. [PMID: 34359751 PMCID: PMC8345395 DOI: 10.3390/cancers13153851] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.
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Affiliation(s)
- Ashton G. Theakstone
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK;
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
- Department of Pharmacology & Therapeutics, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha J. Mills
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Holly J. Butler
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - David S. Palmer
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK
| | - Benjamin R. Smith
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - Matthew J. Baker
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
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15
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Soares Martins T, Magalhães S, Rosa IM, Vogelgsang J, Wiltfang J, Delgadillo I, Catita J, da Cruz E Silva OAB, Nunes A, Henriques AG. Potential of FTIR Spectroscopy Applied to Exosomes for Alzheimer's Disease Discrimination: A Pilot Study. J Alzheimers Dis 2021; 74:391-405. [PMID: 32039849 DOI: 10.3233/jad-191034] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) diagnosis is based on psychological and imaging tests but can also include monitoring cerebrospinal fluid (CSF) biomarkers. However, CSF based-neurochemical approaches are expensive and invasive, limiting their use to well-equipped settings. In contrast, blood-based biomarkers are minimally invasive, cost-effective, and a widely accessible alternative. Blood-derived exosomes have recently emerged as a reliable AD biomarker source, carrying disease-specific cargo. Fourier-transformed infrared (FTIR) spectroscopy meets the criteria for an ideal diagnostic methodology since it is rapid, easy to implement, and has high reproducibility. This metabolome-based technique is useful for diagnosing a broad range of diseases, although to our knowledge, no reports for FTIR spectroscopy applied to exosomes in AD exist. In this ground-breaking pilot study, FTIR spectra of serum and serum-derived exosomes from two independent cohorts were acquired and analyzed using multivariate analysis. The regional UA-cohort includes 9 individuals, clinically diagnosed with AD, mean age of 78.7 years old; and the UMG-cohort comprises 12 individuals, clinically diagnosed with AD (based on molecular and/or imaging data), mean age of 73.2 years old. Unsupervised principal component analysis of FTIR spectra of serum-derived exosomes revealed higher discriminatory value for AD cases when compared to serum as a whole. Consistently, the partial least-squares analysis revealed that serum-derived exosomes present higher correlations than serum. In addition, the second derivative peak area calculation also revealed significant differences among Controls and AD cases. The results obtained suggest that this methodology can discriminate cases from Controls and thus be potential useful to assist in AD clinical diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sandra Magalhães
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,CICECO -Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ilka Martins Rosa
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Jens Wiltfang
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
| | | | - José Catita
- CEBIMED-Faculty of Health Sciences; University Fernando Pessoa, Porto, Portugal.,Paralab SA, Gondomar, Portugal
| | - Odete A B da Cruz E Silva
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,The Discovery CTR, University of Aveiro Campus, Aveiro, Portugal
| | - Alexandra Nunes
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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Brennan PM, Butler HJ, Christie L, Hegarty MG, Jenkinson MD, Keerie C, Norrie J, O'Brien R, Palmer DS, Smith BR, Baker MJ. Early diagnosis of brain tumours using a novel spectroscopic liquid biopsy. Brain Commun 2021; 3:fcab056. [PMID: 33997782 PMCID: PMC8111062 DOI: 10.1093/braincomms/fcab056] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/05/2022] Open
Abstract
Early diagnosis of brain tumours is challenging and a major unmet need. Patients with brain tumours most often present with non-specific symptoms more commonly associated with less serious diagnoses, making it difficult to determine which patients to prioritize for brain imaging. Delays in diagnosis affect timely access to treatment, with potential impacts on quality of life and survival. A test to help identify which patients with non-specific symptoms are most likely to have a brain tumour at an earlier stage would dramatically impact on patients by prioritizing demand on diagnostic imaging facilities. This clinical feasibility study of brain tumour early diagnosis was aimed at determining the accuracy of our novel spectroscopic liquid biopsy test for the triage of patients with non-specific symptoms that might be indicative of a brain tumour, for brain imaging. Patients with a suspected brain tumour based on assessment of their symptoms in primary care can be referred for open access CT scanning. Blood samples were prospectively obtained from 385 of such patients, or patients with a new brain tumour diagnosis. Samples were analysed using our spectroscopic liquid biopsy test to predict presence of disease, blinded to the brain imaging findings. The results were compared to the patient’s index brain imaging delivered as per standard care. Our test predicted the presence of glioblastoma, the most common and aggressive brain tumour, with 91% sensitivity, and all brain tumours with 81% sensitivity, and 80% specificity. Negative predictive value was 95% and positive predictive value 45%. The reported levels of diagnostic accuracy presented here have the potential to improve current symptom-based referral guidelines, and streamline assessment and diagnosis of symptomatic patients with a suspected brain tumour.
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Affiliation(s)
- Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Holly J Butler
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK
| | - Loren Christie
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK
| | - Mark G Hegarty
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK
| | - Michael D Jenkinson
- Institute of Translational Medicine, University of Liverpool & The Walton Centre NHS Foundation Trust, Liverpool L9 7LJ, UK
| | - Catriona Keerie
- Edinburgh Clinical Trials Unit, Usher Institute-University of Edinburgh, Edinburgh EH16 4UX, UK
| | - John Norrie
- Edinburgh Clinical Trials Unit, Usher Institute-University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Rachel O'Brien
- Emergency Medicine Research Group (EMERGE), Royal Infirmiry of Edinburgh, Edinburgh EH16 4SA, UK
| | - David S Palmer
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK.,Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow G11XL, UK
| | - Benjamin R Smith
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK
| | - Matthew J Baker
- ClinSpec Diagnostics Limited, Royal College Building, Glasgow G1 1XW, UK
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17
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Early economic evaluation to guide the development of a spectroscopic liquid biopsy for the detection of brain cancer. Int J Technol Assess Health Care 2021; 37:e41. [PMID: 33622443 DOI: 10.1017/s0266462321000143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVES An early economic evaluation to inform the translation into clinical practice of a spectroscopic liquid biopsy for the detection of brain cancer. Two specific aims are (1) to update an existing economic model with results from a prospective study of diagnostic accuracy and (2) to explore the potential of brain tumor-type predictions to affect patient outcomes and healthcare costs. METHODS A cost-effectiveness analysis from a UK NHS perspective of the use of spectroscopic liquid biopsy in primary and secondary care settings, as well as a cost-consequence analysis of the addition of tumor-type predictions was conducted. Decision tree models were constructed to represent simplified diagnostic pathways. Test diagnostic accuracy parameters were based on a prospective validation study. Four price points (GBP 50-200, EUR 57-228) for the test were considered. RESULTS In both settings, the use of liquid biopsy produced QALY gains. In primary care, at test costs below GBP 100 (EUR 114), testing was cost saving. At GBP 100 (EUR 114) per test, the ICER was GBP 13,279 (EUR 15,145), whereas at GBP 200 (EUR 228), the ICER was GBP 78,300 (EUR 89,301). In secondary care, the ICER ranged from GBP 11,360 (EUR 12,956) to GBP 43,870 (EUR 50,034) across the range of test costs. CONCLUSIONS The results demonstrate the potential for the technology to be cost-effective in both primary and secondary care settings. Additional studies of test use in routine primary care practice are needed to resolve the remaining issues of uncertainty-prevalence in this patient population and referral behavior.
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Abstract
State of the art of quantitative Vibrational Spectroscopic analysis of human blood serum is reviewed. Technical considerations for infrared absorption and Raman analysis are discussed. Quantitative analyses of Endogenous and Exogenous constituents are presented. The potential for clinical translation of spectroscopic serology is argued.
Analysis of bodily fluids using vibrational spectroscopy has attracted increasing attention in recent years. In particular, infrared spectroscopic screening of blood products, particularly blood serum, for disease diagnostics has been advanced considerably, attracting commercial interests. However, analyses requiring quantification of endogenous constituents or exogenous agents in blood are less well advanced. Recent advances towards this end are reviewed, focussing on infrared and Raman spectroscopic analyses of human blood serum. The importance of spectroscopic analysis in the native aqueous environment is highlighted, and the relative merits of infrared absorption versus Raman spectroscopy are considered, in this context. It is argued that Raman spectroscopic analysis is more suitable to quantitative analysis in liquid samples, and superior performance for quantification of high and low molecular weight components, is demonstrated. Applications for quantitation of viral loads, and therapeutic drug monitoring are also discussed.
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19
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Grant R, Dowswell T, Tomlinson E, Brennan PM, Walter FM, Ben-Shlomo Y, Hunt DW, Bulbeck H, Kernohan A, Robinson T, Lawrie TA. Interventions to reduce the time to diagnosis of brain tumours. Cochrane Database Syst Rev 2020; 9:CD013564. [PMID: 32901926 PMCID: PMC8082957 DOI: 10.1002/14651858.cd013564.pub2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Brain tumours are recognised as one of the most difficult cancers to diagnose because presenting symptoms, such as headache, cognitive symptoms, and seizures, may be more commonly attributable to other, more benign conditions. Interventions to reduce the time to diagnosis of brain tumours include national awareness initiatives, expedited pathways, and protocols to diagnose brain tumours, based on a person's presenting symptoms and signs; and interventions to reduce waiting times for brain imaging pathways. If such interventions reduce the time to diagnosis, it may make it less likely that people experience clinical deterioration, and different treatment options may be available. OBJECTIVES To systematically evaluate evidence on the effectiveness of interventions that may influence: symptomatic participants to present early (shortening the patient interval), thresholds for primary care referral (shortening the primary care interval), and time to imaging diagnosis (shortening the secondary care interval and diagnostic interval). To produce a brief economic commentary, summarising the economic evaluations relevant to these interventions. SEARCH METHODS For evidence on effectiveness, we searched CENTRAL, MEDLINE, and Embase from January 2000 to January 2020; Clinicaltrials.gov to May 2020, and conference proceedings from 2014 to 2018. For economic evidence, we searched the UK National Health Services Economic Evaluation Database from 2000 to December 2014. SELECTION CRITERIA We planned to include studies evaluating any active intervention that may influence the diagnostic pathway, e.g. clinical guidelines, direct access imaging, public health campaigns, educational initiatives, and other interventions that might lead to early identification of primary brain tumours. We planned to include randomised and non-randomised comparative studies. Included studies would include people of any age, with a presentation that might suggest a brain tumour. DATA COLLECTION AND ANALYSIS Two review authors independently assessed titles identified by the search strategy, and the full texts of potentially eligible studies. We resolved discrepancies through discussion or, if required, by consulting another review author. MAIN RESULTS We did not identify any studies for inclusion in this review. We excluded 115 studies. The main reason for exclusion of potentially eligible intervention studies was their study design, due to a lack of control groups. We found no economic evidence to inform a brief economic commentary on this topic. AUTHORS' CONCLUSIONS In this version of the review, we did not identify any studies that met the review inclusion criteria for either effectiveness or cost-effectiveness. Therefore, there is no evidence from good quality studies on the best strategies to reduce the time to diagnosis of brain tumours, despite the prioritisation of research on early diagnosis by the James Lind Alliance in 2015. This review highlights the need for research in this area.
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Affiliation(s)
- Robin Grant
- Edinburgh Centre for Neuro-Oncology (ECNO), Western General Hospital, Edinburgh, UK
| | - Therese Dowswell
- C/o Cochrane Pregnancy and Childbirth Group, Department of Women's and Children's Health, The University of Liverpool, Liverpool, UK
| | - Eve Tomlinson
- Cochrane Gynaecological, Neuro-oncology and Orphan Cancers, 1st Floor Education Centre, Royal United Hospital, Bath, UK
| | - Paul M Brennan
- Translational Neurosurgery Department, Western General Hospital, Edinburgh, UK
| | - Fiona M Walter
- Public Health & Primary Care, University of Cambridge, Cambridge, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - David William Hunt
- Foundation School/Dept of Clinical and Experimental Medicine, Royal Surrey County Hospital/University of Surrey, Guildford, UK
| | | | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tomos Robinson
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
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Sala A, Spalding KE, Ashton KM, Board R, Butler HJ, Dawson TP, Harris DA, Hughes CS, Jenkins CA, Jenkinson MD, Palmer DS, Smith BR, Thornton CA, Baker MJ. Rapid analysis of disease state in liquid human serum combining infrared spectroscopy and "digital drying". JOURNAL OF BIOPHOTONICS 2020; 13:e202000118. [PMID: 32506784 DOI: 10.1002/jbio.202000118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
In recent years, the diagnosis of brain tumors has been investigated with attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy on dried human serum samples to eliminate spectral interferences of the water component, with promising results. This research evaluates ATR-FTIR on both liquid and air-dried samples to investigate "digital drying" as an alternative approach for the analysis of spectra obtained from liquid samples. Digital drying approaches, consisting of water subtraction and least-squares method, have demonstrated a greater random forest (RF) classification performance than the air-dried spectra approach when discriminating cancer vs control samples, reaching sensitivity values higher than 93.0% and specificity values higher than 83.0%. Moreover, quantum cascade laser infrared (QCL-IR) based spectroscopic imaging is utilized on liquid samples to assess the implications of a deep-penetration light source on disease classification. The RF classification of QCL-IR data has provided sensitivity and specificity amounting to 85.1% and 75.3% respectively.
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Affiliation(s)
- Alexandra Sala
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Katie E Spalding
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Katherine M Ashton
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - Ruth Board
- Rosemere Cancer Centre, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - Holly J Butler
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Timothy P Dawson
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - Dean A Harris
- Swansea Bay University Local Health Board, Singleton Hospital, Swansea, UK
| | - Caryn S Hughes
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Cerys A Jenkins
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - Michael D Jenkinson
- University of Liverpool & The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - David S Palmer
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Benjamin R Smith
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Catherine A Thornton
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
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21
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Stratifying Brain Tumour Histological Sub-Types: The Application of ATR-FTIR Serum Spectroscopy in Secondary Care. Cancers (Basel) 2020; 12:cancers12071710. [PMID: 32605100 PMCID: PMC7408619 DOI: 10.3390/cancers12071710] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
Patients living with brain tumours have the highest average years of life lost of any cancer, ultimately reducing average life expectancy by 20 years. Diagnosis depends on brain imaging and most often confirmatory tissue biopsy for histology. The majority of patients experience non-specific symptoms, such as headache, and may be reviewed in primary care on multiple occasions before diagnosis is made. Sixty-two per cent of patients are diagnosed on brain imaging performed when they deteriorate and present to the emergency department. Histological diagnosis from invasive surgical biopsy is necessary prior to definitive treatment, because imaging techniques alone have difficulty in distinguishing between several types of brain cancer. However, surgery itself does not necessarily control tumour growth, and risks morbidity for the patient. Due to their similar features on brain scans, glioblastoma, primary central nervous system lymphoma and brain metastases have been known to cause radiological confusion. Non-invasive tests that support stratification of tumour subtype would enhance early personalisation of treatment selection and reduce the delay and risks associated with surgery for many patients. Techniques involving vibrational spectroscopy, such as attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, have previously demonstrated analytical capabilities for cancer diagnostics. In this study, infrared spectra from 641 blood serum samples obtained from brain cancer and control patients have been collected. Firstly, we highlight the capability of ATR-FTIR to distinguish between healthy controls and brain cancer at sensitivities and specificities above 90%, before defining subtle differences in protein secondary structures between patient groups through Amide I deconvolution. We successfully differentiate several types of brain lesions (glioblastoma, meningioma, primary central nervous system lymphoma and metastasis) with balanced accuracies >80%. A reliable blood serum test capable of stratifying brain tumours in secondary care could potentially avoid surgery and speed up the time to definitive therapy, which would be of great value for both neurologists and patients.
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22
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Cao J, Shi X, Gurav DD, Huang L, Su H, Li K, Niu J, Zhang M, Wang Q, Jiang M, Qian K. Metabolic Fingerprinting on Synthetic Alloys for Medulloblastoma Diagnosis and Radiotherapy Evaluation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000906. [PMID: 32342553 DOI: 10.1002/adma.202000906] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/17/2020] [Indexed: 05/25/2023]
Abstract
Diagnostics is the key in screening and treatment of cancer. As an emerging tool in precision medicine, metabolic analysis detects end products of pathways, and thus is more distal than proteomic/genetic analysis. However, metabolic analysis is far from ideal in clinical diagnosis due to the sample complexity and metabolite abundance in patient specimens. A further challenge is real-time and accurate tracking of treatment effect, e.g., radiotherapy. Here, Pd-Au synthetic alloys are reported for mass-spectrometry-based metabolic fingerprinting and analysis, toward medulloblastoma diagnosis and radiotherapy evaluation. A core-shell structure is designed using magnetic core particles to support Pd-Au alloys on the surface. Optimized synthetic alloys enhance the laser desorption/ionization efficacy and achieve direct detection of 100 nL of biofluids in seconds. Medulloblastoma patients are differentiated from healthy controls with average diagnostic sensitivity of 94.0%, specificity of 85.7%, and accuracy of 89.9%, by machine learning of metabolic fingerprinting. Furthermore, the radiotherapy process of patients is monitored and a preliminary panel of serum metabolite biomarkers is identified with gradual changes. This work will lead to the application-driven development of novel materials with tailored structural design and establishment of new protocols for precision medicine in near future.
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Affiliation(s)
- Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Xuejiao Shi
- Department of Oncology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, P. R. China
| | - Deepanjali D Gurav
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Lin Huang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Haiyang Su
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Keke Li
- Department of Oncology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, P. R. China
| | - Jingyang Niu
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Mengji Zhang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Qian Wang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Mawei Jiang
- Department of Oncology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
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23
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Biofluid diagnostics by FTIR spectroscopy: A platform technology for cancer detection. Cancer Lett 2020; 477:122-130. [DOI: 10.1016/j.canlet.2020.02.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 12/19/2022]
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24
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Cameron JM, Butler HJ, Smith BR, Hegarty MG, Jenkinson MD, Syed K, Brennan PM, Ashton K, Dawson T, Palmer DS, Baker MJ. Developing infrared spectroscopic detection for stratifying brain tumour patients: glioblastoma multiforme vs. lymphoma. Analyst 2020; 144:6736-6750. [PMID: 31612875 DOI: 10.1039/c9an01731c] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over a third of brain tumour patients visit their general practitioner more than five times prior to diagnosis in the UK, leading to 62% of patients being diagnosed as emergency presentations. Unfortunately, symptoms are non-specific to brain tumours, and the majority of these patients complain of headaches on multiple occasions before being referred to a neurologist. As there are currently no methods in place for the early detection of brain cancer, the affected patients' average life expectancy is reduced by 20 years. These statistics indicate that the current pathway is ineffective, and there is a vast need for a rapid diagnostic test. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is sensitive to the hallmarks of cancer, as it analyses the full range of macromolecular classes. The combination of serum spectroscopy and advanced data analysis has previously been shown to rapidly and objectively distinguish brain tumour severity. Recently, a novel high-throughput ATR accessory has been developed, which could be cost-effective to the National Health Service in the UK, and valuable for clinical translation. In this study, 765 blood serum samples have been collected from healthy controls and patients diagnosed with various types of brain cancer, contributing to one of the largest spectroscopic studies to date. Three robust machine learning techniques - random forest, partial least squares-discriminant analysis and support vector machine - have all provided promising results. The novel high-throughput technology has been validated by separating brain cancer and non-cancer with balanced accuracies of 90% which is comparable to the traditional fixed diamond crystal methodology. Furthermore, the differentiation of brain tumour type could be useful for neurologists, as some are difficult to distinguish through medical imaging alone. For example, the highly aggressive glioblastoma multiforme and primary cerebral lymphoma can appear similar on magnetic resonance imaging (MRI) scans, thus are often misdiagnosed. Here, we report the ability of infrared spectroscopy to distinguish between glioblastoma and lymphoma patients, at a sensitivity and specificity of 90.1% and 86.3%, respectively. A reliable serum diagnostic test could avoid the need for surgery and speed up time to definitive chemotherapy and radiotherapy.
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Affiliation(s)
- James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George St, Glasgow, G1 1RD, UK.
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25
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Lovergne L, Lovergne J, Bouzy P, Untereiner V, Offroy M, Garnotel R, Thiéfin G, Baker MJ, Sockalingum GD. Investigating pre-analytical requirements for serum and plasma based infrared spectro-diagnostic. JOURNAL OF BIOPHOTONICS 2019; 12:e201900177. [PMID: 31276294 DOI: 10.1002/jbio.201900177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 06/09/2023]
Abstract
Infrared spectroscopy is a rapid, easy-to-operate, label-free and therefore cost-effective technique. Many studies performed on biofluids (eg, serum, plasma, urine, sputum, bile and cerebrospinal fluid) have demonstrated its promising application as a clinical diagnostic tool. Given all these characteristics, infrared spectroscopy appears to be an ideal candidate to be implemented into the clinics. However, before considering its translation, a clear effort is needed to standardise protocols for biofluid spectroscopic analysis. To reach this goal, careful investigations to identify and track errors that can occur during the pre-analytical phase is a crucial step. Here, we report for the first time, results of investigations into pre-analytical factors that can affect the quality of the spectral data acquired on serum and plasma, such as the impact of long-term freezing time storage of samples as well as the month-to-month reproducibility of the spectroscopic analysis. The spectral data discrimination has revealed to be majorly impacted by a residual water content variation in serum and plasma dried samples.
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Affiliation(s)
- Lila Lovergne
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
- WESTChem, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Jean Lovergne
- WESTChem, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Pascaline Bouzy
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), Reims, France
| | - Marc Offroy
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
| | - Roselyne Garnotel
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
- CHU de Reims, Hôpital Maison Blanche, Laboratoire de Biochimie-Pharmacologie-Toxicologie, Reims, France
| | - Gérard Thiéfin
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
- CHU de Reims, Hôpital Robert Debré, Service d'hépato- Gastroentérologie, Reims, France
| | - Matthew J Baker
- WESTChem, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Ganesh D Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT EA7506, UFR de Pharmacie, Reims, France
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26
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Butler HJ, Brennan PM, Cameron JM, Finlayson D, Hegarty MG, Jenkinson MD, Palmer DS, Smith BR, Baker MJ. Development of high-throughput ATR-FTIR technology for rapid triage of brain cancer. Nat Commun 2019; 10:4501. [PMID: 31594931 PMCID: PMC6783469 DOI: 10.1038/s41467-019-12527-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022] Open
Abstract
Non-specific symptoms, as well as the lack of a cost-effective test to triage patients in primary care, has resulted in increased time-to-diagnosis and a poor prognosis for brain cancer patients. A rapid, cost-effective, triage test could significantly improve this patient pathway. A blood test using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy for the detection of brain cancer, alongside machine learning technology, is advancing towards clinical translation. However, whilst the methodology is simple and does not require extensive sample preparation, the throughput of such an approach is limited. Here we describe the development of instrumentation for the analysis of serum that is able to differentiate cancer and control patients at a sensitivity and specificity of 93.2% and 92.8%. Furthermore, preliminary data from the first prospective clinical validation study of its kind are presented, demonstrating how this innovative technology can triage patients and allow rapid access to imaging.
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Affiliation(s)
- Holly J Butler
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK. .,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
| | - Paul M Brennan
- Translational Neurosurgery, Department of Clinical Neurosciences, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Duncan Finlayson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Mark G Hegarty
- ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Michael D Jenkinson
- Institute of Translational Medicine, University of Liverpool & The Walton Centre NHS Foundation Trust, Lower Lane, Fazakerley, Liverpool, L9 7LJ, UK
| | - David S Palmer
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Benjamin R Smith
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK. .,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
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27
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Abstract
Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.
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Affiliation(s)
- Duncan Finlayson
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Christopher Rinaldi
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Matthew J Baker
- WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K.,ClinSpec Diagnostics Ltd. , Technology and Innovation Centre, 99 George Street , Glasgow G11RD , U.K
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28
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Ozawa M, Brennan PM, Zienius K, Kurian KM, Hollingworth W, Weller D, Grant R, Hamilton W, Ben-Shlomo Y. The usefulness of symptoms alone or combined for general practitioners in considering the diagnosis of a brain tumour: a case-control study using the clinical practice research database (CPRD) (2000-2014). BMJ Open 2019; 9:e029686. [PMID: 31471440 PMCID: PMC6720478 DOI: 10.1136/bmjopen-2019-029686] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To evaluate the utility of different symptoms, alone or combined, presented to primary care for an adult brain tumour diagnosis. DESIGN AND SETTING Matched case-control study, using the data from Clinical Practice Research Datalink (2000-2014) from primary care consultations in the UK. METHOD All presentations within 6 months of the index diagnosis date (cases) or equivalent (controls) were coded into 32 symptom groups. Sensitivity, specificity, positive predictive values (PPVs) and positive likelihood ratios were calculated for symptoms and combinations of symptoms with headache and cognitive features. Diagnostic odds ratios were calculated using conditional logistic regression, adjusted for age group, sex and Charlson comorbidity. Stratified analyses were performed for age group, sex and whether the tumour was of primary or secondary origin. RESULTS We included 8,184 cases and 28,110 controls. Seizure had the highest PPV of 1.6% (95% CI 1.4% to 1.7%) followed by weakness 1.5% (1.3 to 1.7) and confusion 1.4% (1.3 to 1.5). Combining headache with other symptoms increased the PPV. For example, headache plus combined cognitive symptoms PPV 7.2% (6.0 to 8.6); plus weakness 4.4% (3.2 to 6.2), compared with headache alone PPV 0.1%. The diagnostic ORs were generally larger for patients <70 years; this was most marked for confusion, seizure and visual symptoms. CONCLUSION We found seizure, weakness and confusion had relatively higher predictive values than many other symptoms. Headache on its own was a weak predictor but this was enhanced when combined with other symptoms especially in younger patients. Clinicians need to actively search for other neurological symptoms such as cognitive problems.
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Affiliation(s)
- Mio Ozawa
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Paul M Brennan
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, UK
| | - Karolis Zienius
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, UK
| | | | | | - David Weller
- General Practice, University of Edinburgh, Edinburgh, UK
| | - Robin Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Willie Hamilton
- Primary Care Diagnostics, University of Exeter Medical School, Exeter, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, University of Bristol, Bristol, UK
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29
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Missed opportunities for diagnosing brain tumours in primary care: a qualitative study of patient experiences. Br J Gen Pract 2019; 69:e224-e235. [PMID: 30858332 PMCID: PMC6428480 DOI: 10.3399/bjgp19x701861] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Background Brain tumours are uncommon, and have extremely poor outcomes. Patients and GPs may find it difficult to recognise early symptoms because they are often non-specific and more likely due to other conditions. Aim To explore patients’ experiences of symptom appraisal, help seeking, and routes to diagnosis. Design and setting Qualitative study set in the East and North West of England. Method In-depth interviews with adult patients recently diagnosed with a primary brain tumour and their family members were analysed thematically, using the Model of Pathways to Treatment as a conceptual framework. Results Interviews were carried out with 39 patients. Few participants (n = 7; 18%) presented as an emergency without having had a previous GP consultation; most had had one (n = 15; 38%), two (n = 9; 23%), or more (n = 8; 21%) GP consultations. Participants experienced multiple subtle ‘changes’ rather than ‘symptoms’, often noticed by others rather than the patient, which frequently led to loss of interest or less ability to engage with daily living activities. The most common changes were in cognition (speaking, writing, comprehension, memory, concentration, and multitasking), sleep, and other ‘head feelings’ such as dizziness. Not all patients experienced a seizure, and few seizures were experienced ‘out of the blue’. Quality of communication in GP consultations played a key role in patients’ subsequent symptom appraisal and the timing of their decision to re-consult. Conclusion Multiple subtle changes and frequent GP visits often precede brain tumour diagnosis, giving possible diagnostic opportunities for GPs. Refined community symptom awareness and GP guidance could enable more direct pathways to diagnosis, and potentially improve patient experiences and outcomes.
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Butler HJ, Smith BR, Fritzsch R, Radhakrishnan P, Palmer DS, Baker MJ. Optimised spectral pre-processing for discrimination of biofluids via ATR-FTIR spectroscopy. Analyst 2019; 143:6121-6134. [PMID: 30484797 DOI: 10.1039/c8an01384e] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pre-processing is an essential step in the analysis of spectral data. Mid-IR spectroscopy of biological samples is often subject to instrumental and sample specific variances which may often conceal valuable biological information. Whilst pre-processing can effectively reduce this unwanted variance, the plethora of possible processing steps has resulted in a lack of consensus in the field, often meaning that analysis outputs are not comparable. As pre-processing is specific to the sample under investigation, here we present a systematic approach for defining the optimum pre-processing protocol for biofluid ATR-FTIR spectroscopy. Using a trial-and-error based approach and a clinically relevant dataset describing control and brain cancer patients, the effects of pre-processing permutations on subsequent classification algorithms were observed, by assessing key diagnostic performance parameters, including sensitivity and specificity. It was found that optimum diagnostic performance correlated with the use of minimal binning and baseline correction, with derivative functions improving diagnostic performance most significantly. If smoothing is required, a Sovitzky-Golay approach was the preferred option in this investigation. Heavy binning appeared to reduce classification most significantly, alongside wavelet noise reduction (filter length ≥6), resulting in the lowest diagnostic performances of all pre-processing permutations tested.
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Affiliation(s)
- Holly J Butler
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
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