1
|
Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
Collapse
Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
2
|
Chou H, Godbeer L, Ball ML. Establishing breath as a biomarker platform-take home messages from the Breath Biopsy Conference 2023. J Breath Res 2024; 18:030401. [PMID: 38631337 DOI: 10.1088/1752-7163/ad3fdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
The annual Breath Biopsy Conference hosted by Owlstone Medical gathers together the leading experts, early career researchers, and physicians working with breath as a biomarker platform for clinical purposes. The current topics in breath research are discussed and presented, and an overarching topical theme is identified and discussed as part of an expert panel to close the conference. The profiling of normal breath composition and the establishment of standards for analyzing breath compared to background signal were two important topics that were major focuses of this conference, as well as important innovative progress that has been made since last year, including the development of a non-invasive breath test for lung cancer and liver disease. This meeting report offers an overview of the key take-home messages from the various presentations, posters, and discussions from the conference.
Collapse
Affiliation(s)
- Hsuan Chou
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GJ, United Kingdom
| | - Lucy Godbeer
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GJ, United Kingdom
| | - Madeleine L Ball
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GJ, United Kingdom
| |
Collapse
|
3
|
The Effect of Tedlar Bags on the Composition of Exhaled Human Breath Samples. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5665921. [PMID: 36212946 PMCID: PMC9546690 DOI: 10.1155/2022/5665921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
Abstract
The PVF Tedlar is widely used for gas collection in clinical diagnostics and environmental research. However, sample collection is frequently associated with the degradation, adsorption, or transformation of sensitive chemicals. Here, we explore to what extent the Tedlar bag collection effects the composition of expired breath samples. Collected breath samples were analyzed using the EESI-MS technique after the storage time of 30 min, 1 h, 2 h, 3 h, 4 h, 5 h, and 6 h, respectively. Our results demonstrated the gradual MS signal decay after 3 h storage. The decay rate of 3 h is about 45% and 6 h is about 88%. Therefore, the Tedlar bag is suggested as a reliable breath holder on the time scale of <3 h.
Collapse
|
4
|
Wieczorek M, Weston A, Ledenko M, Thomas JN, Carter R, Patel T. A deep learning approach for detecting liver cirrhosis from volatolomic analysis of exhaled breath. Front Med (Lausanne) 2022; 9:992703. [PMID: 36250077 PMCID: PMC9556819 DOI: 10.3389/fmed.2022.992703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Liver disease such as cirrhosis is known to cause changes in the composition of volatile organic compounds (VOC) present in patient breath samples. Previous studies have demonstrated the diagnosis of liver cirrhosis from these breath samples, but studies are limited to a handful of discrete, well-characterized compounds. We utilized VOC profiles from breath samples from 46 individuals, 35 with cirrhosis and 11 healthy controls. A deep-neural network was optimized to discriminate between healthy controls and individuals with cirrhosis. A 1D convolutional neural network (CNN) was accurate in predicting which patients had cirrhosis with an AUC of 0.90 (95% CI: 0.75, 0.99). Shapley Additive Explanations characterized the presence of discrete, observable peaks which were implicated in prediction, and the top peaks (based on the average SHAP profiles on the test dataset) were noted. CNNs demonstrate the ability to predict the presence of cirrhosis based on a full volatolomics profile of patient breath samples. SHAP values indicate the presence of discrete, detectable peaks in the VOC signal.
Collapse
Affiliation(s)
- Mikolaj Wieczorek
- Digital Innovation Lab, Mayo Clinic, Jacksonville, FL, United States
| | - Alexander Weston
- Digital Innovation Lab, Mayo Clinic, Jacksonville, FL, United States
| | - Matthew Ledenko
- Department of Transplant, Mayo Clinic, Jacksonville, FL, United States
| | | | - Rickey Carter
- Digital Innovation Lab, Mayo Clinic, Jacksonville, FL, United States
| | - Tushar Patel
- Department of Transplant, Mayo Clinic, Jacksonville, FL, United States
- *Correspondence: Tushar Patel,
| |
Collapse
|
5
|
Lawson J, Nakhleh M, Smolinska A. Reproducibility and reporting, the routes to progress in breath research - highlights from the Breath Biopsy Conference 2021. J Breath Res 2022; 16. [PMID: 35405666 DOI: 10.1088/1752-7163/ac661d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/11/2022]
Abstract
With the continued presence of COVID-19 worldwide, it has been a challenge for the breath research community to progress with clinical studies and travel restrictions have also limited the opportunities to meet up, share ideas and celebrate the latest advances. The Breath Biopsy Conference 2021 provided a much-needed opportunityoffered the chance to catch up with the latest breath research and to share the researchprogress that researchers in the community have been able to progress make in these difficult times. Limited opportunities for clinical research have provided opportunitiesled many in the field to look more closely at different methods for breath collection and have contributed to the growing calls for consistent standards in how results are reported, shared and even how breath studies themselves are carried out. As such, standardization was a key theme for this year's event and featured prominently in the keynotes, discussions and throughout many of the presentation sessions. With over 900 registrants, almost 400 live attendees and 16 speakers, the Breath Biopsy Conference continues to bring together breath research leaders from around the world. This article provides an overview of the highlights from this event.
Collapse
Affiliation(s)
- Jonathan Lawson
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire, CB4 0GJ, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Morad Nakhleh
- Owlstone Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GD, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Agnieszka Smolinska
- Toxicology Department, Maastricht University, Universiteitssingel, Maastricht, Maastricht, 6229 ER, NETHERLANDS
| |
Collapse
|
6
|
Schmidt AJ, Salman D, Pleil J, Thomas CLP, Davis CE. IABR Symposium 2021 meeting report: breath standardization, sampling, and testing in a time of COVID-19. J Breath Res 2021; 16. [PMID: 34663766 DOI: 10.1088/1752-7163/ac3096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022]
Abstract
Due to COVID-19 travel disruptions, the International Association of Breath Research hosted the planned 2021 Breath Summit virtually as a symposium with oral and poster presentations. The event was comprised of a week-long social media asynchronous online event for sharing research abstracts, posters and discussions. Subsequently, there were two days of real-time webinar platform interactions each featuring three technical presentations, open forum questions, answers, and commentary. The symposium was well attended and well received. It allowed the breath community to share new research and to reconnect with colleagues and friends. This report presents an overview of the topics presented and various salient discussion points.
Collapse
Affiliation(s)
- Alexander J Schmidt
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, CA, United States of America.,UC Davis Lung Center, One Shields Avenue, Davis, CA 95616, United States of America
| | - Dahlia Salman
- Centre of Analytical Science, Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Joachim Pleil
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - C L Paul Thomas
- Centre of Analytical Science, Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Cristina E Davis
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, CA, United States of America.,UC Davis Lung Center, One Shields Avenue, Davis, CA 95616, United States of America.,VA Northern California Health Care System, 10535, Hospital Way, Mather, CA 95655, United States of America
| |
Collapse
|
7
|
Lawson J, Beauchamp J. Pursuing breath research in unprecedented circumstances-report from the Breath Biopsy Conference 2020. J Breath Res 2021; 15. [PMID: 34107459 DOI: 10.1088/1752-7163/ac09d3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/09/2021] [Indexed: 12/17/2022]
Abstract
The global outbreak of Sars-CoV-2 commencing early in 2020 had a dramatic impact on breath research, imposing abrupt restrictions but also presenting unforeseen opportunities. Taking place against the background of the COVID-19 pandemic, the 2020 Breath Biopsy Conference provided the breath research community with a platform to showcase and discuss the latest findings, including COVID-19 related research. As with most conferences under the present circumstance, it differed from its predecessor meetings by shifting to a virtual format, but retained its broad scope and interactive nature. The conference centred on four key themes, featuring applications of volatile organic compounds, breath biomarkers for liver disease, study design and data analytics, and, notably this year, breath-based endeavours to detect COVID-19 infection. This meeting report summarizes the events of the conference and spotlights selected contributions.
Collapse
Affiliation(s)
- Jonathan Lawson
- Owlstone Medical Ltd, 183 Cambridge Science Park, Milton Road, Cambridge, CB4 0GJ, United Kingdom
| | - Jonathan Beauchamp
- Fraunhofer Institute for Process Engineering and Packaging IVV, Freising, Germany
| |
Collapse
|