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Barbosa JMG, Filho NRA. The human volatilome meets cancer diagnostics: past, present, and future of noninvasive applications. Metabolomics 2024; 20:113. [PMID: 39375265 DOI: 10.1007/s11306-024-02180-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/22/2024] [Indexed: 10/09/2024]
Abstract
BACKGROUND Cancer is a significant public health problem, causing dozens of millions of deaths annually. New cancer screening programs are urgently needed for early cancer detection, as this approach can improve treatment outcomes and increase patient survival. The search for affordable, noninvasive, and highly accurate cancer detection methods revealed a valuable source of tumor-derived metabolites in the human metabolome through the exploration of volatile organic compounds (VOCs) in noninvasive biofluids. AIM OF REVIEW This review discusses volatilomics-based approaches for cancer detection using noninvasive biomatrices (breath, saliva, skin secretions, urine, feces, and earwax). We presented the historical background, the latest approaches, and the required stages for clinical validation of volatilomics-based methods, which are still lacking in terms of making noninvasive methods available and widespread to the population. Furthermore, insights into the usefulness and challenges of volatilomics in clinical implementation steps for each biofluid are highlighted. KEY SCIENTIFIC CONCEPTS OF REVIEW We outline the methodologies for using noninvasive biomatrices with up-and-coming clinical applications in cancer diagnostics. Several challenges and advantages associated with the use of each biomatrix are discussed, aiming at encouraging the scientific community to strengthen efforts toward the necessary steps to speed up the clinical translation of volatile-based cancer detection methods, as well as discussing in favor of (i) hybrid applications (i.e., using more than one biomatrix) to describe metabolite modulations that can be "cancer volatile fingerprints" and (ii) in multi-omics approaches integrating genomics, transcriptomics, and proteomics into the volatilomic data, which might be a breakthrough for diagnostic purposes, onco-pathway assessment, and biomarker validations.
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Affiliation(s)
- João Marcos G Barbosa
- Laboratório de Métodos de Extração E Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
| | - Nelson R Antoniosi Filho
- Laboratório de Métodos de Extração E Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
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Capuano R, Ciotti M, Catini A, Bernardini S, Di Natale C. Clinical applications of volatilomic assays. Crit Rev Clin Lab Sci 2024:1-20. [PMID: 39129534 DOI: 10.1080/10408363.2024.2387038] [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: 03/14/2024] [Revised: 04/23/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
The study of metabolomics is revealing immense potential for diagnosis, therapy monitoring, and understanding of pathogenesis processes. Volatilomics is a subcategory of metabolomics interested in the detection of molecules that are small enough to be released in the gas phase. Volatile compounds produced by cellular processes are released into the blood and lymph, and can reach the external environment through different pathways, such as the blood-air interface in the lung that are detected in breath, or the blood-water interface in the kidney that leads to volatile compounds detected in urine. Besides breath and urine, additional sources of volatile compounds such as saliva, blood, feces, and skin are available. Volatilomics traces its roots back over fifty years to the pioneering investigations in the 1970s. Despite extensive research, the field remains in its infancy, hindered by a lack of standardization despite ample experimental evidence. The proliferation of analytical instrumentations, sample preparations and methods of volatilome sampling still make it difficult to compare results from different studies and to establish a common standard approach to volatilomics. This review aims to provide an overview of volatilomics' diagnostic potential, focusing on two key technical aspects: sampling and analysis. Sampling poses a challenge due to the susceptibility of human samples to contamination and confounding factors from various sources like the environment and lifestyle. The discussion then delves into targeted and untargeted approaches in volatilomics. Some case studies are presented to exemplify the results obtained so far. Finally, the review concludes with a discussion on the necessary steps to fully integrate volatilomics into clinical practice.
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Affiliation(s)
- Rosamaria Capuano
- Department of Electronic Engineering, University of Rome Tor Vergata, Roma, Italy
- Interdepartmental Center for Volatilomics, "A. D'Amico", University of Rome Tor Vergata, Rome, Italy
| | - Marco Ciotti
- Department of Laboratory Medicine, University Hospital Tor Vergata, Rome, Italy
| | - Alexandro Catini
- Department of Electronic Engineering, University of Rome Tor Vergata, Roma, Italy
- Interdepartmental Center for Volatilomics, "A. D'Amico", University of Rome Tor Vergata, Rome, Italy
| | - Sergio Bernardini
- Interdepartmental Center for Volatilomics, "A. D'Amico", University of Rome Tor Vergata, Rome, Italy
- Department of Laboratory Medicine, University Hospital Tor Vergata, Rome, Italy
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Corrado Di Natale
- Department of Electronic Engineering, University of Rome Tor Vergata, Roma, Italy
- Interdepartmental Center for Volatilomics, "A. D'Amico", University of Rome Tor Vergata, Rome, Italy
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Kashyap B, Kullaa A. Salivary Metabolites Produced by Oral Microbes in Oral Diseases and Oral Squamous Cell Carcinoma: A Review. Metabolites 2024; 14:277. [PMID: 38786754 PMCID: PMC11122927 DOI: 10.3390/metabo14050277] [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: 03/06/2024] [Revised: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, salivary metabolome studies have provided new biological information and salivary biomarkers to diagnose different diseases at early stages. The saliva in the oral cavity is influenced by many factors that are reflected in the salivary metabolite profile. Oral microbes can alter the salivary metabolite profile and may express oral inflammation or oral diseases. The released microbial metabolites in the saliva represent the altered biochemical pathways in the oral cavity. This review highlights the oral microbial profile and microbial metabolites released in saliva and its use as a diagnostic biofluid for different oral diseases. The importance of salivary metabolites produced by oral microbes as risk factors for oral diseases and their possible relationship in oral carcinogenesis is discussed.
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Affiliation(s)
| | - Arja Kullaa
- Institute of Dentistry, University of Eastern Finland, 70211 Kuopio, Finland;
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Radaic A, Kamarajan P, Cho A, Wang S, Hung GC, Najarzadegan F, Wong DT, Ton-That H, Wang CY, Kapila YL. Biological biomarkers of oral cancer. Periodontol 2000 2023:10.1111/prd.12542. [PMID: 38073011 PMCID: PMC11163022 DOI: 10.1111/prd.12542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/09/2023] [Indexed: 06/12/2024]
Abstract
The oral squamous cell carcinoma (OSCC) 5 year survival rate of 41% has marginally improved in the last few years, with less than a 1% improvement per year from 2005 to 2017, with higher survival rates when detected at early stages. Based on histopathological grading of oral dysplasia, it is estimated that severe dysplasia has a malignant transformation rate of 7%-50%. Despite these numbers, oral dysplasia grading does not reliably predict its clinical behavior. Thus, more accurate markers predicting oral dysplasia progression to cancer would enable better targeting of these lesions for closer follow-up, especially in the early stages of the disease. In this context, molecular biomarkers derived from genetics, proteins, and metabolites play key roles in clinical oncology. These molecular signatures can help predict the likelihood of OSCC development and/or progression and have the potential to detect the disease at an early stage and, support treatment decision-making and predict treatment responsiveness. Also, identifying reliable biomarkers for OSCC detection that can be obtained non-invasively would enhance management of OSCC. This review will discuss biomarkers for OSCC that have emerged from different biological areas, including genomics, transcriptomics, proteomics, metabolomics, immunomics, and microbiomics.
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Affiliation(s)
- Allan Radaic
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pachiyappan Kamarajan
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Alex Cho
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Sandy Wang
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Guo-Chin Hung
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Fereshteh Najarzadegan
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - David T Wong
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Hung Ton-That
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Cun-Yu Wang
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Yvonne L Kapila
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, California, USA
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Vassilenko V, Moura PC, Raposo M. Diagnosis of Carcinogenic Pathologies through Breath Biomarkers: Present and Future Trends. Biomedicines 2023; 11:3029. [PMID: 38002028 PMCID: PMC10669878 DOI: 10.3390/biomedicines11113029] [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: 10/04/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The assessment of volatile breath biomarkers has been targeted with a lot of interest by the scientific and medical communities during the past decades due to their suitability for an accurate, painless, non-invasive, and rapid diagnosis of health states and pathological conditions. This paper reviews the most relevant bibliographic sources aiming to gather the most pertinent volatile organic compounds (VOCs) already identified as putative cancer biomarkers. Here, a total of 265 VOCs and the respective bibliographic sources are addressed regarding their scientifically proven suitability to diagnose a total of six carcinogenic diseases, namely lung, breast, gastric, colorectal, prostate, and squamous cell (oesophageal and laryngeal) cancers. In addition, future trends in the identification of five other forms of cancer, such as bladder, liver, ovarian, pancreatic, and thyroid cancer, through perspective volatile breath biomarkers are equally presented and discussed. All the results already achieved in the detection, identification, and quantification of endogenous metabolites produced by all kinds of normal and abnormal processes in the human body denote a promising and auspicious future for this alternative diagnostic tool, whose future passes by the development and employment of newer and more accurate collection and analysis techniques, and the certification for utilisation in real clinical scenarios.
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Affiliation(s)
- Valentina Vassilenko
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-UNL, 2829-516 Caparica, Portugal;
| | - Pedro Catalão Moura
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-UNL, 2829-516 Caparica, Portugal;
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Yang M, Su Y, Zheng H, Xu K, Yuan Q, Cai Y, Aihaiti Y, Xu P. Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks. BMC Musculoskelet Disord 2023; 24:799. [PMID: 37814309 PMCID: PMC10561475 DOI: 10.1186/s12891-023-06936-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023] Open
Abstract
OBJECTIVE This study aimed at constructing a network of competing endogenous RNA (ceRNA) in the synovial tissues of rheumatoid arthritis (RA). It seeks to discern potential biomarkers and explore the long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) axes that are intricately linked to the pathophysiological mechanisms underpinning RA, and providing a scientific basis for the pathogenesis and treatment of RA. METHODS Microarray data pertaining to RA synovial tissue, GSE103578, GSE128813, and GSE83147, were acquired from the Gene Expression Omnibus (GEO) database ( http://www.ncbi.nlm.nih.gov/geo ). Conducted to discern both differentially expressed lncRNAs (DELncRNAs) and differentially expressed genes (DEGs). A ceRNA network was obtained through key lncRNAs, key miRNAs, and key genes. Further investigations involved co-expression analyses to uncover the lncRNA-miRNA-mRNA axes contributing to the pathogenesis of RA. To delineate the immune-relevant facets of this axis, we conducted an assessment of key genes, emphasizing those with the most substantial immunological correlations, employing the GeneCards database. Finally, gene set enrichment analysis (GSEA) was executed on the identified key lncRNAs to elucidate their functional implications in RA. RESULTS The 2 key lncRNAs, 7 key miRNAs and 6 key genes related to the pathogenesis of RA were obtained, as well as 2 key lncRNA-miRNA-mRNA axes (KRTAP5-AS1-hsa-miR-30b-5p-PNN, XIST-hsa-miR-511-3p/hsa-miR-1277-5p-F2RL1). GSEA of two key lncRNAs obtained biological processes and signaling pathways related to RA synovial lesions. CONCLUSION The findings of this investigation hold promise in furnishing a foundational framework and guiding future research endeavors aimed at comprehending the etiology and therapeutic interventions for RA.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yani Su
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Haishi Zheng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Qiling Yuan
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yongsong Cai
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yirixiati Aihaiti
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China.
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Chuchueva N, Carta F, Nguyen HN, Luevano J, Lewis IA, Rios-Castillo I, Fanos V, King E, Swistushkin V, Reshetov I, Rusetsky Y, Shestakova K, Moskaleva N, Mariani C, Castillo-Carniglia A, Grapov D, Fahrmann J, La Frano MR, Puxeddu R, Appolonova SA, Brito A. Metabolomics of head and neck cancer in biofluids: an integrative systematic review. Metabolomics 2023; 19:77. [PMID: 37644353 DOI: 10.1007/s11306-023-02038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/27/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Head and neck cancer (HNC) is the fifth most common cancer globally. Diagnosis at early stages are critical to reduce mortality and improve functional and esthetic outcomes associated with HNC. Metabolomics is a promising approach for discovery of biomarkers and metabolic pathways for risk assessment and early detection of HNC. OBJECTIVES To summarize and consolidate the available evidence on metabolomics and HNC in plasma/serum, saliva, and urine. METHODS A systematic search of experimental research was executed using PubMed and Web of Science. Available data on areas under the curve was extracted. Metabolic pathway enrichment analysis were performed to identify metabolic pathways altered in HNC. Fifty-four studies were eligible for data extraction (33 performed in plasma/serum, 15 in saliva and 6 in urine). RESULTS Metabolites with high discriminatory performance for detection of HNC included single metabolites and combination panels of several lysoPCs, pyroglutamate, glutamic acid, glucose, tartronic acid, arachidonic acid, norvaline, linoleic acid, propionate, acetone, acetate, choline, glutamate and others. The glucose-alanine cycle and the urea cycle were the most altered pathways in HNC, among other pathways (i.e. gluconeogenesis, glycine and serine metabolism, alanine metabolism, etc.). Specific metabolites that can potentially serve as complementary less- or non-invasive biomarkers, as well as metabolic pathways integrating the data from the available studies, are presented. CONCLUSION The present work highlights utility of metabolite-based biomarkers for risk assessment, early detection, and prognostication of HNC, as well as facilitates incorporation of available metabolomics studies into multi-omics data integration and big data analytics for personalized health.
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Affiliation(s)
- Natalia Chuchueva
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Central State Medical Academy, Moscow, Russia
| | - Filippo Carta
- Unit of Otorhinolaryngology, Department of Surgery, Azienda Ospedaliero-Universitaria Di Cagliari, University of Cagliari, Cagliari, Italy
| | - Hoang N Nguyen
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Jennifer Luevano
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Isaiah A Lewis
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Vassilios Fanos
- Department of Pediatrics and Clinical Medicine, Section of Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, Azienda Ospedaliero-Universitaria Di Cagliari, Cagliari University, Cagliari, Italy
| | - Emma King
- Cancer Research Center, University of Southampton, Southampton, UK
- Department of Otolaryngology, Poole Hospital National Health Service Foundation Trust, Longfleet Road, Poole, UK
| | | | - Igor Reshetov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Yury Rusetsky
- Central State Medical Academy, Moscow, Russia
- Otorhinolaryngological Surgical Department With a Group of Head and Neck Diseases, National Medical Research Center of Children's Health, Moscow, Russia
| | - Ksenia Shestakova
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology. I.M. Sechenov First, Moscow State Medical University, Moscow, Russia
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia Moskaleva
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology. I.M. Sechenov First, Moscow State Medical University, Moscow, Russia
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Cinzia Mariani
- Unit of Otorhinolaryngology, Department of Surgery, Azienda Ospedaliero-Universitaria Di Cagliari, University of Cagliari, Cagliari, Italy
| | - Alvaro Castillo-Carniglia
- Society and Health Research Center, Facultad de Ciencias Sociales y Artes, Universidad Mayor, Santiago, Chile
- Millennium Nucleus for the Evaluation and Analysis of Drug Policies (nDP) and Millennium Nucleus on Sociomedicine (SocioMed), Santiago, Chile
| | | | | | - Michael R La Frano
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
- Cal Poly Metabolomics Service Center, California Polytechnic State University, San Luis Obispo, CA, USA
- Roy J.Carver Metabolomics Core Facility, University of Illinois, Urbana-Champaign, IL, USA
| | - Roberto Puxeddu
- King's College Hospital London, Dubai, United Arab Emirates
- Section of Otorhinolaryngology, Department of Surgery, University of Cagliari, Cagliari, Italy
| | - Svetlana A Appolonova
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology. I.M. Sechenov First, Moscow State Medical University, Moscow, Russia
- Russian Center of Forensic-Medical Expertise of Ministry of Health, Moscow, Russia
| | - Alex Brito
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology. I.M. Sechenov First, Moscow State Medical University, Moscow, Russia.
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
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Pan Q, Liu QY, Zheng J, Li YH, Xiang S, Sun XJ, He XS. Volatile and semi-volatile organic compounds in landfill gas: Composition characteristics and health risks. ENVIRONMENT INTERNATIONAL 2023; 174:107886. [PMID: 36989764 DOI: 10.1016/j.envint.2023.107886] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Gas emitted from landfills contains a large quantity of volatile organic compounds (VOCs) and semi-volatile organic compounds (SVOCs), some of which are carcinogenic, teratogenic, and mutagenic, thereby posing a serious threat to the health of landfill workers and nearby residents. However, the global hazards of VOCs and SVOCs in landfill gas to human health remain unclear. To quantify the global risk distributions of these pollutants, we collected the composition and concentration data of VOCs and SVOCs from 72 landfills in 20 countries from the core database of Web of Science and assessed their human health risks as well as analyzed their influencing factors. Organic compounds in landfill gas were found to primarily result from the biodegradation of natural organic waste or the emissions and volatilization of chemical products, with the concentration range of 1 × 10-1-1 × 106 μg/m3. The respiratory system, in particular, lung was the major target organ of VOCs and SVOCs, with additional adverse health impacts ranging from headache and allergies to lung cancer. Aromatic and halogenated compounds were the primary sources of health risk, while ethyl acetate and acetone from the biodegradation of natural organic waste also exceeded the acceptable levels for human health. Overall, VOCs and SVOCs affected residents within 1,000 m of landfills. Air temperature, relative humidity, air pressure, wind direction, and wind speed were the major factors that influenced the health risks of VOCs and SVOCs. Currently, landfill risk assessments of VOCs and SVOCs are primarily based on respiratory inhalation, with health risks due to other exposure routes remaining poorly elucidated. In addition, potential health risks due to the transport and transformation of landfill gas emitted into the atmosphere should be further studied.
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Affiliation(s)
- Qi Pan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541000, China
| | - Qing-Yu Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jing Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541000, China
| | - Yan-Hong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541000, China
| | - Song Xiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiao-Jie Sun
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541000, China
| | - Xiao-Song He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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da Costa BRB, da Silva RR, Bigão VLCP, Peria FM, De Martinis BS. Hybrid volatilomics in cancer diagnosis by HS-GC-FID fingerprinting. J Breath Res 2023; 17. [PMID: 36634358 DOI: 10.1088/1752-7163/acb284] [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: 09/28/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023]
Abstract
Assessing volatile organic compounds (VOCs) as cancer signatures is one of the most promising techniques toward developing non-invasive, simple, and affordable diagnosis. Here, we have evaluated the feasibility of employing static headspace extraction (HS) followed by gas chromatography with flame ionization detector (GC-FID) as a screening tool to discriminate between cancer patients (head and neck-HNC,n= 15; and gastrointestinal cancer-GIC,n= 19) and healthy controls (n= 37) on the basis of a non-target (fingerprinting) analysis of oral fluid and urine. We evaluated the discrimination considering a single bodily fluid and adopting the hybrid approach, in which the oral fluid and urinary VOCs profiles were combined through data fusion. We used supervised orthogonal partial least squares discriminant analysis for classification, and we assessed the prediction power of the models by analyzing the values of goodness of prediction (Q2Y), area under the curve (AUC), sensitivity, and specificity. The individual models HNC urine, HNC oral fluid, and GIC oral fluid successfully discriminated between healthy controls and positive samples (Q2Y = 0.560, 0.525, and 0.559; AUC = 0.814, 0.850, and 0.926; sensitivity = 84.8, 70.2, and 78.6%; and specificity = 82.3; 81.5; 87.5%, respectively), whereas GIC urine was not adequate (Q2Y = 0.292, AUC = 0.694, sensitivity = 66.1%, and specificity = 77.0%). Compared to the respective individual models, Q2Y for the hybrid models increased (0.623 for hybrid HNC and 0.562 for hybrid GIC). However, sensitivity was higher for HNC urine and GIC oral fluid than for hybrid HNC (75.6%) and hybrid GIC (69.8%), respectively. These results suggested that HS-GC-FID fingerprinting is suitable and holds great potential for cancer screening. Additionally, the hybrid approach tends to increase the predictive power if the individual models present suitable quality parameter values. Otherwise, it is more advantageous to use a single body fluid for analysis.
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Affiliation(s)
- Bruno Ruiz Brandão da Costa
- Department of Clinical, Toxicological and Food Sciences, School of Pharmaceutical, Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-903, Brazil
| | - Ricardo Roberto da Silva
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-903, Brazil
| | - Vítor Luiz Caleffo Piva Bigão
- Department of Clinical, Toxicological and Food Sciences, School of Pharmaceutical, Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-903, Brazil
| | - Fernanda Maris Peria
- Division of Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto CEP 14049-900, Brazil
| | - Bruno Spinosa De Martinis
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-901, Brazil
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Volatilomics: An Emerging and Promising Avenue for the Detection of Potential Prostate Cancer Biomarkers. Cancers (Basel) 2022; 14:cancers14163982. [PMID: 36010975 PMCID: PMC9406416 DOI: 10.3390/cancers14163982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary The lack of highly specific and sensitive biomarkers for the early detection of prostate cancer (PCa) is a major barrier to its management. Volatilomics emerged as a non-invasive, simple, inexpensive, and easy-to-use approach for cancer screening, characterization of disease progression, and follow-up of the treatment’s success. We provide a brief overview of the potential of volatile organic metabolites (VOMs) for the establishment of PCa biomarkers from non-invasive matrices. Endogenous VOMs have been investigated as potential biomarkers since changes in these VOMs can be characteristic of specific disease processes. Recent studies have shown that the conjugation of the prostate-specific antigen (PSA) screening with other methodologies, such as risk calculators, biomarkers, and imaging tests, can attenuate overdiagnosis and under-detection issues. This means that the combination of volatilomics with other methodologies could be extremely valuable for the differentiation of clinical phenotypes in a group of patients, providing more personalized treatments. Abstract Despite the spectacular advances in molecular medicine, including genomics, proteomics, transcriptomics, lipidomics, and personalized medicine, supported by the discovery of the human genome, prostate cancer (PCa) remains the most frequent malignant tumor and a leading cause of oncological death in men. New methods for prognostic, diagnostic, and therapy evaluation are mainly based on the combination of imaging techniques with other methodologies, such as gene or protein profiling, aimed at improving PCa management and surveillance. However, the lack of highly specific and sensitive biomarkers for its early detection is a major hurdle to this goal. Apart from classical biomarkers, the study of endogenous volatile organic metabolites (VOMs) biosynthesized by different metabolic pathways and found in several biofluids is emerging as an innovative, efficient, accessible, and non-invasive approach to establish the volatilomic biosignature of PCa patients, unravelling potential biomarkers. This review provides a brief overview of the challenges of PCa screening methods and emergent biomarkers. We also focus on the potential of volatilomics for the establishment of PCa biomarkers from non-invasive matrices.
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Xu N, Solari A, Goeman JJ. Closed testing with Globaltest, with application in metabolomics. Biometrics 2022. [PMID: 35567306 DOI: 10.1111/biom.13693] [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: 10/17/2021] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
The Globaltest is a powerful test for the global null hypothesis that there is no association between a group of features and a response of interest, which is popular in pathway testing in metabolomics. Evaluating multiple feature sets, however, requires multiple testing correction. In this paper, we propose a multiple testing method, based on closed testing, specifically designed for the Globaltest. The proposed method controls the family-wise error rate simultaneously over all possible feature sets, and therefore allows post hoc inference, i.e. the researcher may choose feature sets of interest after seeing the data without jeopardizing error control. To circumvent the exponential computation time of closed testing, we derive a novel shortcut that allows exact closed testing to be performed on the scale of metabolomics data. An R package ctgt is available on CRAN for the implementation of the shortcut procedure, with applications on several real metabolomics data examples. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ningning Xu
- Department of Biomedical Data Sciences, Leiden University Medical Center, The Netherlands
| | - Aldo Solari
- Department of Economics, Management and Statistics, University of Milano-Bicocca, Italy
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, The Netherlands
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Nijakowski K, Gruszczyński D, Kopała D, Surdacka A. Salivary Metabolomics for Oral Squamous Cell Carcinoma Diagnosis: A Systematic Review. Metabolites 2022; 12:metabo12040294. [PMID: 35448481 PMCID: PMC9029144 DOI: 10.3390/metabo12040294] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer in which the consumption of tobacco and alcohol is considered to be the main aetiological factor. Salivary metabolome profiling could identify novel biochemical pathways involved in the pathogenesis of various diseases. This systematic review was designed to answer the question “Are salivary metabolites reliable for the diagnosis of oral squamous cell carcinoma?”. Following the inclusion and exclusion criteria, nineteen studies were included (according to PRISMA statement guidelines). In all included studies, the diagnostic material was unstimulated whole saliva, whose metabolome changes were determined by different spectroscopic methods. At the metabolic level, OSCC patients differed significantly not only from healthy subjects but also from patients with oral leukoplakia, lichen planus or other oral potentially malignant disorders. Among the detected salivary metabolites, there were the indicators of the impaired metabolic pathways, such as choline metabolism, amino acid pathways, polyamine metabolism, urea cycle, creatine metabolism, glycolysis or glycerolipid metabolism. In conclusion, saliva contains many potential metabolites, which can be used reliably to early diagnose and monitor staging in patients with OSCC. However, further investigations are necessary to confirm these findings and to identify new salivary metabolic biomarkers.
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Affiliation(s)
- Kacper Nijakowski
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland;
- Correspondence:
| | - Dawid Gruszczyński
- Student’s Scientific Group, Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland; (D.G.); (D.K.)
| | - Dariusz Kopała
- Student’s Scientific Group, Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland; (D.G.); (D.K.)
| | - Anna Surdacka
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland;
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Cain CN, Sudol PE, Berrier KL, Synovec RE. Development of variance rank initiated-unsupervised sample indexing for gas chromatography-mass spectrometry analysis. Talanta 2021; 233:122495. [PMID: 34215113 DOI: 10.1016/j.talanta.2021.122495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 02/08/2023]
Abstract
Traditional non-targeted chemometric workflows for gas chromatography-mass spectrometry (GC-MS) data rely on using supervised methods, which requires a priori knowledge of sample class membership. Herein, we propose a simple, unsupervised chemometric workflow known as variance rank initiated-unsupervised sample indexing (VRI-USI). VRI-USI discovers analyte peaks exhibiting high relative variance across all samples, followed by k-means clustering on the individual peaks. Based upon how the samples cluster for a given peak, a sample index assignment is provided. Using a probabilistic argument, if the same sample index assignment appears for several discovered peaks, then this outcome strongly suggests that the samples are properly classified by that particular sample index assignment. Thus, relevant chemical differences between the samples have been discovered in an unsupervised fashion. The VRI-USI workflow is demonstrated on three, increasingly difficult datasets: simulations, yeast metabolomics, and human cancer metabolomics. For simulated GC-MS datasets, VRI-USI discovered 85-90% of analytes modeled to vary between sample classes. Nineteen out of 53 peaks in the peak table developed for the yeast metabolome dataset had the same sample index assignments, indicating that those indices are most likely due to class-distinguishing chemical differences. A t-test revealed that 22 out of 53 peaks were statistically significant (p < 0.05) when using those sample index assignments. Likewise, for the human cancer metabolomics study, VRI-USI discovered 25 analytes that were statistically different (p < 0.05) using the sample index assignments determined to highlight meaningful sample-based differences. For all datasets, the sample index assignments that were deduced from VRI-USI were the correct class-based difference when using prior knowledge. VRI-USI holds promise as an exploratory data analysis workflow for studies in which analysts do not readily have a priori class information or want to uncover the underlying nature of their dataset.
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Affiliation(s)
- Caitlin N Cain
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA, 98195, USA
| | - Paige E Sudol
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA, 98195, USA
| | - Kelsey L Berrier
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA, 98195, USA
| | - Robert E Synovec
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA, 98195, USA.
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Salivary Metabolomics for Diagnosis and Monitoring Diseases: Challenges and Possibilities. Metabolites 2021; 11:metabo11090587. [PMID: 34564402 PMCID: PMC8469343 DOI: 10.3390/metabo11090587] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/21/2022] Open
Abstract
Saliva is a useful biological fluid and a valuable source of biological information. Saliva contains many of the same components that can be found in blood or serum, but the components of interest tend to be at a lower concentration in saliva, and their analysis demands more sensitive techniques. Metabolomics is starting to emerge as a viable method for assessing the salivary metabolites which are generated by the biochemical processes in elucidating the pathways underlying different oral and systemic diseases. In oral diseases, salivary metabolomics has concentrated on periodontitis and oral cancer. Salivary metabolites of systemic diseases have been investigated mostly in the early diagnosis of different cancer, but also neurodegenerative diseases. This mini-review article aims to highlight the challenges and possibilities of salivary metabolomics from a clinical viewpoint. Furthermore, applications of the salivary metabolic profile in diagnosis and prognosis, monitoring the treatment success, and planning of personalized treatment of oral and systemic diseases are discussed.
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Evaluation of salivary VOC profile composition directed towards oral cancer and oral lesion assessment. Clin Oral Investig 2021; 25:4415-4430. [PMID: 33387033 DOI: 10.1007/s00784-020-03754-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Endogenous substances have been analyzed in biological samples in order to be related with metabolic dysfunctions and diseases. The study aimed to investigate profiles of volatile organic compounds (VOCs) from fresh and incubated saliva donated by healthy controls, individuals with oral tissue lesions and with oral cancer, in order to assess case-specific biomarkers of oxidative stress. MATERIALS AND METHODS VOCs were pre-concentrated using headspace-solid phase microextraction and analyzed using gas chromatography-mass spectrometry. Then, VOCs positively modulated by incubation process were subtracted, yielding profiles with selected features. Principal component analysis and hierarchical cluster analysis were used to inspect data distribution, while univariate statistics was applied to indicate potential markers of oral cancer. Machine learning algorithm was implemented, aiming multiclass prediction. RESULTS The removal of bacterial contribution to VOC profiles allowed the obtaining of more specific case-related patterns. Artificial neural network model included 9 most relevant compounds (1-octen-3-ol, hexanoic acid, E-2-octenal, heptanoic acid, octanoic acid, E-2-nonenal, nonanoic acid, 2,4-decadienal and 9-undecenoic acid). Model performance was assessed using 10-fold cross validation and receiver operating characteristic curves. Obtained overall accuracy was 90%. Oral cancer cases were predicted with 100% of sensitivity and specificity. CONCLUSIONS The selected VOCs were ascribed to lipid oxidation mechanism and presented potential to differentiate oral cancer from other inflammatory conditions. CLINICAL RELEVANCE These results highlight the importance of interpretation of saliva composition and the clinical value of salivary VOCs. Elucidated metabolic alterations have the potential to aid the early detection of oral cancer and the monitoring of oral lesions.
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Fuchsmann P, Tena Stern M, Münger LH, Pimentel G, Burton KJ, Vionnet N, Vergères G. Nutrivolatilomics of Urinary and Plasma Samples to Identify Candidate Biomarkers after Cheese, Milk, and Soy-Based Drink Intake in Healthy Humans. J Proteome Res 2020; 19:4019-4033. [DOI: 10.1021/acs.jproteome.0c00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | | | | | | | | | - Nathalie Vionnet
- Service of Endocrinology, Diabetes and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Guy Vergères
- Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland
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Pereira JAM, Porto-Figueira P, Taware R, Sukul P, Rapole S, Câmara JS. Unravelling the Potential of Salivary Volatile Metabolites in Oral Diseases. A Review. Molecules 2020; 25:E3098. [PMID: 32646009 PMCID: PMC7412334 DOI: 10.3390/molecules25133098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/24/2022] Open
Abstract
Fostered by the advances in the instrumental and analytical fields, in recent years the analysis of volatile organic compounds (VOCs) has emerged as a new frontier in medical diagnostics. VOCs analysis is a non-invasive, rapid and inexpensive strategy with promising potential in clinical diagnostic procedures. Since cellular metabolism is altered by diseases, the resulting metabolic effects on VOCs may serve as biomarkers for any given pathophysiologic condition. Human VOCs are released from biomatrices such as saliva, urine, skin emanations and exhaled breath and are derived from many metabolic pathways. In this review, the potential of VOCs present in saliva will be explored as a monitoring tool for several oral diseases, including gingivitis and periodontal disease, dental caries, and oral cancer. Moreover, the analytical state-of-the-art for salivary volatomics, e.g., the most common extraction techniques along with the current challenges and future perspectives will be addressed unequivocally.
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Affiliation(s)
- Jorge A. M. Pereira
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
| | - Priscilla Porto-Figueira
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind Road, SPPU Campus, Pune 411007, India; (R.T.); (S.R.)
| | - Pritam Sukul
- Department of Anaesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany;
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind Road, SPPU Campus, Pune 411007, India; (R.T.); (S.R.)
| | - José S. Câmara
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
- Faculdade de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
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Konings H, Stappers S, Geens M, De Winter BY, Lamote K, van Meerbeeck JP, Specenier P, Vanderveken OM, Ledeganck KJ. A Literature Review of the Potential Diagnostic Biomarkers of Head and Neck Neoplasms. Front Oncol 2020; 10:1020. [PMID: 32670885 PMCID: PMC7332560 DOI: 10.3389/fonc.2020.01020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Head and neck neoplasms have a poor prognosis because of their late diagnosis. Finding a biomarker to detect these tumors in an early phase could improve the prognosis and survival rate. This literature review provides an overview of biomarkers, covering the different -omics fields to diagnose head and neck neoplasms in the early phase. To date, not a single biomarker, nor a panel of biomarkers for the detection of head and neck tumors has been detected with clinical applicability. Limitations for the clinical implementation of the investigated biomarkers are mainly the heterogeneity of the study groups (e.g., small population in which the biomarker was tested, and/or only including high-risk populations) and a low sensitivity and/or specificity of the biomarkers under study. Further research on biomarkers to diagnose head and neck neoplasms in an early stage, is therefore needed.
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Affiliation(s)
- Heleen Konings
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sofie Stappers
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Margot Geens
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Benedicte Y De Winter
- Laboratorium of Experimental Medicine and Pediatrics and Member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Kevin Lamote
- Laboratorium of Experimental Medicine and Pediatrics and Member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Department of Pneumology, Antwerp University Hospital, Edegem, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Jan P van Meerbeeck
- Laboratorium of Experimental Medicine and Pediatrics and Member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Department of Pneumology, Antwerp University Hospital, Edegem, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Pol Specenier
- Department of Oncology, Antwerp University Hospital, Edegem, Belgium.,Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Olivier M Vanderveken
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Otorhinolaryngology-Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium.,Department of Translational Neurosciences, Antwerp University, Antwerp, Belgium
| | - Kristien J Ledeganck
- Laboratorium of Experimental Medicine and Pediatrics and Member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
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Taware R, Taunk K, Kumar TVS, Pereira JAM, Câmara JS, Nagarajaram HA, Kundu GC, Rapole S. Extracellular volatilomic alterations induced by hypoxia in breast cancer cells. Metabolomics 2020; 16:21. [PMID: 31980945 DOI: 10.1007/s11306-020-1635-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/03/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The metabolic shift induced by hypoxia in cancer cells has not been explored at volatilomic level so far. The volatile organic metabolites (VOMs) constitute an important part of the metabolome and their investigation could provide us crucial aspects of hypoxia driven metabolic reconfiguration in cancer cells. OBJECTIVE To identify the altered volatilomic response induced by hypoxia in metastatic/aggressive breast cancer (BC) cells. METHODS BC cells were cultured under normoxic and hypoxic conditions and VOMs were extracted using HS-SPME approach and profiled by standard GC-MS system. Univariate and multivariate statistical approaches (p < 0.05, Log2 FC ≥ 0.58/≤ - 0.58, PC1 > 0.13/< - 0.13) were applied to select the VOMs differentially altered after hypoxic treatment. Metabolic pathway analysis was also carried out in order to identify altered metabolic pathways induced by the hypoxia in the selected BC cells. RESULTS Overall, 20 VOMs were found to be significantly altered (p < 0.05, PC1 > 0.13/< - 0.13) upon hypoxic exposure to BC cells. Further, cell line specific volatilomic alterations were extracted by comparative metabolic analysis of aggressive (MDA-MB-231) vs. non-aggressive (MCF-7) cells incubated under hypoxia and normoxia. In this case, 15 and 12 VOMs each were found to be significantly altered in aggressive cells when exposed to hypoxic and normoxic condition respectively. Out of these, 9 VOMs were found to be uniquely associated with hypoxia, 6 were specific to normoxia and 6 were found common to both the conditions. Formic acid was identified as the most prominent molecule with higher abundance levels in aggressive as compared to non-aggressive cells in both conditions. Furthermore, metabolic pathway analyses revealed that fatty acid biosynthesis and nicotinate and nicotinamide metabolism were significantly altered in aggressive as compared to non-aggressive cells in normoxia and hypoxia respectively. CONCLUSIONS Higher formate overflow was observed in aggressive cells compared to non-aggressive cells incubated under both the conditions, reinforcing its correlation with aggressive and invasive cancer type. Moreover, under hypoxia, aggressive cells preferred to be bioenergetically more efficient whereas, under normoxia, fatty acid biosynthesis was favoured when compared to non-aggressive cells.
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Affiliation(s)
- Ravindra Taware
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Totakura V S Kumar
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science (NCCS), Ganeshkhind, Pune, 411007, India
| | - Jorge A M Pereira
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020105, Funchal, Portugal
| | - José S Câmara
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020105, Funchal, Portugal
- Faculdade de Ciências Exatas E da Engenharia, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
| | - H A Nagarajaram
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Gopal C Kundu
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science (NCCS), Ganeshkhind, Pune, 411007, India
- School of Biotechnology, KIIT Deemed to be University, Institute of Eminence, Bhubaneswar, 751024, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
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Nalbantoglu S, Karadag A. Introductory Chapter: Insight into the OMICS Technologies and Molecular Medicine. Mol Med 2019. [DOI: 10.5772/intechopen.86450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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