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Martin FL, Morais CLM, Dickinson AW, Saba T, Bongers T, Singh MN, Bury D. Point-of-Care Disease Screening in Primary Care Using Saliva: A Biospectroscopy Approach for Lung Cancer and Prostate Cancer. J Pers Med 2023; 13:1533. [PMID: 38003848 PMCID: PMC10672293 DOI: 10.3390/jpm13111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Saliva is a largely unexplored liquid biopsy that can be readily obtained noninvasively. Not dissimilar to blood plasma or serum, it contains a vast array of bioconstituents that may be associated with the absence or presence of a disease condition. Given its ease of access, the use of saliva is potentially ideal in a point-of-care screening or diagnostic test. Herein, we developed a swab "dip" test in saliva obtained from consenting patients participating in a lung cancer-screening programme being undertaken in north-west England. A total of 998 saliva samples (31 designated as lung-cancer positive and 17 as prostate-cancer positive) were taken in the order in which they entered the clinic (i.e., there was no selection of participants) during the course of this prospective screening programme. Samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. In addition to unsupervised classification on resultant infrared (IR) spectra using principal component analysis (PCA), a range of feature selection/extraction algorithms were tested. Following preprocessing, the data were split between training (70% of samples, 22 lung-cancer positive versus 664 other) and test (30% of samples, 9 lung-cancer positive versus 284 other) sets. The training set was used for model construction and the test set was used for validation. The best model was the PCA-quadratic discriminant analysis (QDA) algorithm. This PCA-QDA model was built using 8 PCs (90.4% of explained variance) and resulted in 93% accuracy for training and 91% for testing, with clinical sensitivity at 100% and specificity at 91%. Additionally, for prostate cancer patients amongst the male cohort (n = 585), following preprocessing, the data were split between training (70% of samples, 12 prostate-cancer positive versus 399 other) and test (30% of samples, 5 prostate-cancer positive versus 171 other) sets. A PCA-QDA model, again the best model, was built using 5 PCs (84.2% of explained variance) and resulted in 97% accuracy for training and 93% for testing, with clinical sensitivity at 100% and specificity at 92%. These results point to a powerful new approach towards the capability to screen large cohorts of individuals in primary care settings for underlying malignant disease.
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Affiliation(s)
- Francis L. Martin
- Biocel UK Ltd., Hull HU10 6TS, UK;
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Camilo L. M. Morais
- Center for Education, Science and Technology of the Inhamuns Region, State University of Ceará, Tauá 63660-000, Brazil;
| | - Andrew W. Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Maneesh N. Singh
- Biocel UK Ltd., Hull HU10 6TS, UK;
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
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Martin FL, Dickinson AW, Saba T, Bongers T, Singh MN, Bury D. ATR-FTIR Spectroscopy with Chemometrics for Analysis of Saliva Samples Obtained in a Lung-Cancer-Screening Programme: Application of Swabs as a Paradigm for High Throughput in a Clinical Setting. J Pers Med 2023; 13:1039. [PMID: 37511652 PMCID: PMC10381591 DOI: 10.3390/jpm13071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
There is an increasing need for inexpensive and rapid screening tests in point-of-care clinical oncology settings. Herein, we develop a swab "dip" test in saliva obtained from consenting patients participating in a lung-cancer-screening programme being undertaken in North West England. In a pilot study, a total of 211 saliva samples (n = 170 benign, 41 designated cancer-positive) were randomly taken during the course of this prospective lung-cancer-screening programme. The samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. An exploratory analysis using principal component analysis (PCA,) with or without linear discriminant analysis (LDA), was then undertaken. Three pairwise comparisons were undertaken including: (1) benign vs. cancer following swab analysis; (2) benign vs. cancer following swab analysis with the subtraction of dry swab spectra; and (3) benign vs. cancer following swab analysis with the subtraction of wet swab spectra. Consistent and remarkably similar patterns of clustering for the benign control vs. cancer categories, irrespective of whether the swab plus saliva sample was analysed or whether there was a subtraction of wet or dry swab spectra, was observed. In each case, MANOVA demonstrated that this segregation of categories is highly significant. A k-NN (using three nearest neighbours) machine-learning algorithm also showed that the specificity (90%) and sensitivity (75%) are consistent for each pairwise comparison. In detailed analyses, the swab as a substrate did not alter the level of spectral discrimination between benign control vs. cancer saliva samples. These results demonstrate a novel swab "dip" test using saliva as a biofluid that is highly applicable to be rolled out into a larger lung-cancer-screening programme.
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Affiliation(s)
- Francis L Martin
- Biocel UK Ltd., Hull HU10 6TS, UK
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Andrew W Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Maneesh N Singh
- Biocel UK Ltd., Hull HU10 6TS, UK
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
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Cockell CS, McLean CM, Perera L, Aka S, Stevens A, Dickinson AW. Growth of Non-Halophilic Bacteria in the Sodium-Magnesium-Sulfate-Chloride Ion System: Unravelling the Complexities of Ion Interactions in Terrestrial and Extraterrestrial Aqueous Environments. Astrobiology 2020; 20:944-955. [PMID: 32434375 DOI: 10.1089/ast.2019.2092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Motivated by an interest in understanding the habitability of aqueous environments on Earth and in extraterrestrial settings, this study investigated the influence of ions in an artificial sodium-magnesium-sulfate-chloride ion system on the growth parameters (lag phase, growth rate, and final cell concentration) of bacteria. These four ions, in different combinations, are key components of many aqueous environments on Earth and elsewhere. We investigated non-halophilic bacteria deliberately to remove the bias of prior adaptations to high concentrations of selected ions so that we could compare the effects of different ions. We tested the hypothesis that water activity determined the growth parameters independent of the ion types. Neither water activity or ionic strength alone could predict growth. However, when ionic strengths were matched, many differences in growth parameters could be explained by the water activity. We suggest that species-specific effects (caused by differences in biochemical and physiological influences), the role of individual ions in cellular processes, and potentially the chaotropicity and kosmotropicity of solutions influenced the growth. Our data show that although extreme combinations of these ions allow for general predictions on the habitability of extraterrestrial aqueous environments, a complex interplay of ionic effects influences the growth and thus the adaptations required for given ion combinations. The data also show that an accurate quantification of the habitability of ocean worlds, such as Europa and Enceladus, can only be made when samples are obtained from these water bodies and the ion combinations are determined.
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Affiliation(s)
- Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Claire-Marie McLean
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Liam Perera
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Salomé Aka
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Stevens
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew W Dickinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
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Dickinson AW, Power A, Hansen MG, Brandt KK, Piliposian G, Appleby P, O'Neill PA, Jones RT, Sierocinski P, Koskella B, Vos M. Heavy metal pollution and co-selection for antibiotic resistance: A microbial palaeontology approach. Environ Int 2019; 132:105117. [PMID: 31473413 DOI: 10.1016/j.envint.2019.105117] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Frequent and persistent heavy metal pollution has profound effects on the composition and activity of microbial communities. Heavy metals select for metal resistance but can also co-select for resistance to antibiotics, which is a global health concern. We here document metal concentration, metal resistance and antibiotic resistance along a sediment archive from a pond in the North West of the United Kingdom covering over a century of anthropogenic pollution. We specifically focus on zinc, as it is a ubiquitous and toxic metal contaminant known to co-select for antibiotic resistance, to assess the impact of temporal variation in heavy metal pollution on microbial community diversity and to quantify the selection effects of differential heavy metal exposure on antibiotic resistance. Zinc concentration and bioavailability was found to vary over the core, likely reflecting increased industrialisation around the middle of the 20th century. Zinc concentration had a significant effect on bacterial community composition, as revealed by a positive correlation between the level of zinc tolerance in culturable bacteria and zinc concentration. The proportion of zinc resistant isolates was also positively correlated with resistance to three clinically relevant antibiotics (oxacillin, cefotaxime and trimethoprim). The abundance of the class 1 integron-integrase gene, intI1, marker for anthropogenic pollutants correlated with the prevalence of zinc- and cefotaxime resistance but not with oxacillin and trimethoprim resistance. Our microbial palaeontology approach reveals that metal-contaminated sediments from depths that pre-date the use of antibiotics were enriched in antibiotic resistant bacteria, demonstrating the pervasive effects of metal-antibiotic co-selection in the environment.
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Affiliation(s)
- A W Dickinson
- College of Life and Environmental Science, University of Exeter, Penryn, UK; UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| | - A Power
- Biocatalysis Centre, University of Exeter, Exeter, UK
| | - M G Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - K K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - G Piliposian
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - P Appleby
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - P A O'Neill
- Welcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, University of Exeter, Exeter, UK
| | - R T Jones
- School of Geography, College of Life and Environmental Sciences, University of Exeter, Amory Building, Rennes Drive, Exeter, UK
| | - P Sierocinski
- College of Life and Environmental Science, University of Exeter, Penryn, UK
| | - B Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - M Vos
- European Centre for Environment and Human Health, College of Medicine and Health, University of Exeter, Penryn, UK
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Cockell CS, Harrison JP, Stevens AH, Payler SJ, Hughes SS, Kobs Nawotniak SE, Brady AL, Elphic R, Haberle CW, Sehlke A, Beaton KH, Abercromby AF, Schwendner P, Wadsworth J, Landenmark H, Cane R, Dickinson AW, Nicholson N, Perera L, Lim DS. A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars. Astrobiology 2019; 19:284-299. [PMID: 30840501 PMCID: PMC6442273 DOI: 10.1089/ast.2018.1870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.
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Affiliation(s)
- Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Address correspondence to: Charles S. Cockell, School of Physics and Astronomy, University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
| | - Jesse P. Harrison
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Adam H. Stevens
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Samuel J. Payler
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Scott S. Hughes
- Department of Geosciences, Idaho State University, Pocatello, Idaho, USA
| | | | - Allyson L. Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton, Canada
| | - R.C. Elphic
- NASA Ames Research Center, Mountain View, California, USA
| | | | | | | | - Andrew F.J. Abercromby
- Biomedical Research & Environmental Sciences Division (SK), NASA Johnson Space Center, Houston, Texas, USA
| | - Petra Schwendner
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Jennifer Wadsworth
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Hanna Landenmark
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Rosie Cane
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Andrew W. Dickinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Natasha Nicholson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Liam Perera
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Darlene S.S. Lim
- NASA Ames Research Center, Mountain View, California, USA
- Bay Area Environmental Research Institute (BAERI), Moffett Field, California, USA
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Lane SM, Dickinson AW, Tregenza T, House CM. Sexual Selection on male cuticular hydrocarbons via male-male competition and female choice. J Evol Biol 2016; 29:1346-55. [PMID: 27037514 PMCID: PMC4999037 DOI: 10.1111/jeb.12875] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/31/2016] [Indexed: 01/25/2023]
Abstract
Traditional views of sexual selection assumed that male–male competition and female mate choice work in harmony, selecting upon the same traits in the same direction. However, we now know that this is not always the case and that these two mechanisms often impose conflicting selection on male sexual traits. Cuticular hydrocarbons (CHCs) have been shown to be linked to both social dominance and male attractiveness in several insect species. However, although several studies have estimated the strength and form of sexual selection imposed on male CHCs by female mate choice, none have established whether these chemical traits are also subject to sexual selection via male–male competition. Using a multivariate selection analysis, we estimate and compare sexual selection exerted by male–male competition and female mate choice on male CHC composition in the broad‐horned flour beetle Gnatocerus cornutus. We show that male–male competition exerts strong linear selection on both overall CHC abundance and body size in males, while female mate choice exerts a mixture of linear and nonlinear selection, targeting not just the overall amount of CHCs expressed but the relative abundance of specific hydrocarbons as well. We discuss the potential implications of this antagonistic selection with regard to male reproductive success.
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Affiliation(s)
- S M Lane
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK
| | - A W Dickinson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK
| | - T Tregenza
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK
| | - C M House
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK
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Abstract
A Monte-Carlo simulation is performed to evaluate the power of the Terpstra-Jonckheere test for monotonic trend as applied to binary data. The effects of the magnitude and shape of the underlying response and of varying the number of treatment levels for in vitro experiments in cytogenetics are examined. It is shown that choice of the number and spacing of the treatment levels can be critical factors in determining the power of the test. These findings indicate that selection of the proper experimental design is a very important step in the process of conducting a viable study.
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Erickson MM, Poklis A, Gantner GE, Dickinson AW, Hillman LS. Tissue mineral levels in victims of sudden infant death syndrome II. Essential minerals: copper, zinc, calcium, and magnesium. Pediatr Res 1983; 17:784-7. [PMID: 6634242 DOI: 10.1203/00006450-198310000-00003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Deficiencies of various vitamin and minerals per se have been suggested as possible causes of sudden infant death syndrome (SIDS). Further, a deficiency of essential minerals may lead to enhanced toxicity of toxic elements, in particular, lead and cadmium to explore the possibility of mineral deficiencies or interactions with the toxic metals, lead and cadmium, lung, liver, kidney, and rib specimens were obtained at autopsy from 66 SIDS infants and 23 infants who died suddenly from other cases. Tissue copper, zinc, calcium, and magnesium were measured by atomic absorption spectroscopy. No differences were found between SIDS and non-SIDS for any element in any tissue except for more magnesium in the liver (P less than 0.0001) and less copper in the lungs (P less than 0.02) in the SIDS group. Only sporadic interactions between toxic and essential elements could be found. We found no evidence of any essential mineral deficiencies per se or significant interactions of essential and toxic minerals that might potentiate the effects of toxic metals. The physiologic significance, if any, of the higher liver magnesium and lower lung copper found in SIDS is unclear.
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Abstract
Lung, liver, kidney, and rib specimens were obtained at autopsy from 66 sudden infant death syndrome (SIDS) infants and 23 infants who died suddenly from other causes between the ages of 4-26 wk. Tissue levels of lead and cadmium were measured by atomic absorption spectroscopy and are expressed as microgram/g dry weight. Because these metals are cumulative with age in storage tissues, the levels were corrected for age (adjusted to age 13 wk). The SIDS liver and rib specimens contained significantly more lead than non-SIDS tissues (liver, 1.095 microgram/g versus 0.761 microgram/g, P less than 0.05; rib, 1.754 microgram/g versus 1.041 microgram/g, P less than 0.01, respectively). There were no significant differences in cadmium concentration between the SIDS and non-SIDS tissues. All four tissues showed significant increases with age in both lead and cadmium concentrations in SIDS. The increase in lung lead concentration with age was significantly greater in SIDS than in non-SIDS cases, P less than 0.05. In non-SIDS only kidney cadmium showed an increase with age (P less than 0.0001). These data collectively suggest an increased exposure of the SIDS infant to lead either prenatally and/or postnatally. Any physiologic effects of the increased tissue lead levels are unknown. They may be only a marker of the known epidemiology of SIDS.
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