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López-López Á, López-Gonzálvez Á, Barbas C. Metabolomics for searching validated biomarkers in cancer studies: a decade in review. Expert Rev Mol Diagn 2024; 24:601-626. [PMID: 38904089 DOI: 10.1080/14737159.2024.2368603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
INTRODUCTION In the dynamic landscape of modern healthcare, the ability to anticipate and diagnose diseases, particularly in cases where early treatment significantly impacts outcomes, is paramount. Cancer, a complex and heterogeneous disease, underscores the critical importance of early diagnosis for patient survival. The integration of metabolomics information has emerged as a crucial tool, complementing the genotype-phenotype landscape and providing insights into active metabolic mechanisms and disease-induced dysregulated pathways. AREAS COVERED This review explores a decade of developments in the search for biomarkers validated within the realm of cancer studies. By critically assessing a diverse array of research articles, clinical trials, and studies, this review aims to present an overview of the methodologies employed and the progress achieved in identifying and validating biomarkers in metabolomics results for various cancer types. EXPERT OPINION Through an exploration of more than 800 studies, this review has allowed to establish a general idea about state-of-art in the search of biomarkers in metabolomics studies involving cancer which include certain level of results validation. The potential for metabolites as diagnostic markers to reach the clinic and make a real difference in patient health is substantial, but challenges remain to be explored.
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Affiliation(s)
- Ángeles López-López
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Ángeles López-Gonzálvez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
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Miller HA, Suliman S, Frieboes HB. Pulmonary Fibrosis Diagnosis and Disease Progression Detected Via Hair Metabolome Analysis. Lung 2024:10.1007/s00408-024-00712-3. [PMID: 38861171 DOI: 10.1007/s00408-024-00712-3] [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: 03/13/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Fibrotic interstitial lung disease is often identified late due to non-specific symptoms, inadequate access to specialist care, and clinical unawareness precluding proper and timely treatment. Biopsy histological analysis is definitive but rarely performed due to its invasiveness. Diagnosis typically relies on high-resolution computed tomography, while disease progression is evaluated via frequent pulmonary function testing. This study tested the hypothesis that pulmonary fibrosis diagnosis and progression could be non-invasively and accurately evaluated from the hair metabolome, with the longer-term goal to minimize patient discomfort. METHODS Hair specimens collected from pulmonary fibrosis patients (n = 56) and healthy subjects (n = 14) were processed for metabolite extraction using 2DLC/MS-MS, and data were analyzed via machine learning. Metabolomic data were used to train machine learning classification models tuned via a rigorous combination of cross validation, feature selection, and testing with a hold-out dataset to evaluate classifications of diseased vs. healthy subjects and stable vs. progressed disease. RESULTS Prediction of pulmonary fibrosis vs. healthy achieved AUROCTRAIN = 0.888 (0.794-0.982) and AUROCTEST = 0.908, while prediction of stable vs. progressed disease achieved AUROCTRAIN = 0.833 (0.784 - 0.882) and AUROCTEST = 0. 799. Top metabolites for diagnosis included ornithine, 4-(methylnitrosamino)-1-3-pyridyl-N-oxide-1-butanol, Thr-Phe, desthiobiotin, and proline. Top metabolites for progression included azelaic acid, Thr-Phe, Ala-Tyr, indoleacetyl glutamic acid, and cytidine. CONCLUSION This study provides novel evidence that pulmonary fibrosis diagnosis and progression may in principle be evaluated from the hair metabolome. Longer term, this approach may facilitate non-invasive and accurate detection and monitoring of fibrotic lung diseases.
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Affiliation(s)
- Hunter A Miller
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA
| | - Sally Suliman
- Division of Pulmonary Medicine, University of Louisville, Louisville, KY, USA
- University of Arizona Medical Center Phoenix, Phoenix, AZ, USA
| | - Hermann B Frieboes
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
- UofL Health - Brown Cancer Center, University of Louisville, Louisville, KY, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, KY, USA.
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Ren F, Fei Q, Qiu K, Zhang Y, Zhang H, Sun L. Liquid biopsy techniques and lung cancer: diagnosis, monitoring and evaluation. J Exp Clin Cancer Res 2024; 43:96. [PMID: 38561776 PMCID: PMC10985944 DOI: 10.1186/s13046-024-03026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer stands as the most prevalent form of cancer globally, posing a significant threat to human well-being. Due to the lack of effective and accurate early diagnostic methods, many patients are diagnosed with advanced lung cancer. Although surgical resection is still a potential means of eradicating lung cancer, patients with advanced lung cancer usually miss the best chance for surgical treatment, and even after surgical resection patients may still experience tumor recurrence. Additionally, chemotherapy, the mainstay of treatment for patients with advanced lung cancer, has the potential to be chemo-resistant, resulting in poor clinical outcomes. The emergence of liquid biopsies has garnered considerable attention owing to their noninvasive nature and the ability for continuous sampling. Technological advancements have propelled circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), tumor metabolites, tumor-educated platelets (TEPs), and tumor-associated antigens (TAA) to the forefront as key liquid biopsy biomarkers, demonstrating intriguing and encouraging results for early diagnosis and prognostic evaluation of lung cancer. This review provides an overview of molecular biomarkers and assays utilized in liquid biopsies for lung cancer, encompassing CTCs, ctDNA, non-coding RNA (ncRNA), EVs, tumor metabolites, TAAs and TEPs. Furthermore, we expound on the practical applications of liquid biopsies, including early diagnosis, treatment response monitoring, prognostic evaluation, and recurrence monitoring in the context of lung cancer.
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Affiliation(s)
- Fei Ren
- Department of Geriatrics, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Qian Fei
- Department of Oncology, Shengjing Hospital of China Medical University, Shen Yang, 110000, China
| | - Kun Qiu
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Yuanjie Zhang
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shen Yang, 110000, China.
| | - Lei Sun
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China.
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La Monica S, Vacondio F, Eltayeb K, Lodola A, Volta F, Viglioli M, Ferlenghi F, Galvani F, Galetti M, Bonelli M, Fumarola C, Cavazzoni A, Flammini L, Verzè M, Minari R, Petronini PG, Tiseo M, Mor M, Alfieri R. Targeting glucosylceramide synthase induces antiproliferative and proapoptotic effects in osimertinib-resistant NSCLC cell models. Sci Rep 2024; 14:6491. [PMID: 38499619 PMCID: PMC10948837 DOI: 10.1038/s41598-024-57028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
The EGFR tyrosine kinase inhibitor osimertinib has been approved for the first-line treatment of EGFR-mutated Non-Small Cell Lung Cancer (NSCLC) patients. Despite its efficacy, patients develop resistance. Mechanisms of resistance are heterogeneous and not fully understood, and their characterization is essential to find new strategies to overcome resistance. Ceramides are well-known regulators of apoptosis and are converted into glucosylceramides (GlcCer) by glucosylceramide synthase (GCS). A higher content of GlcCers was observed in lung pleural effusions from NSCLC patients and their role in osimertinib-resistance has not been documented. The aim of this study was to determine the therapeutic potential of inhibiting GCS in NSCLC EGFR-mutant models resistant to osimertinib in vitro and in vivo. Lipidomic analysis showed a significant increase in the intracellular levels of glycosylceramides, including GlcCers in osimertinib resistant clones compared to sensitive cells. In resistant cells, the GCS inhibitor PDMP caused cell cycle arrest, inhibition of 2D and 3D cell proliferation, colony formation and migration capability, and apoptosis induction. The intratumoral injection of PDMP completely suppressed the growth of OR xenograft models. This study demonstrated that dysregulation of ceramide metabolism is involved in osimertinib-resistance and targeting GCS may be a promising therapeutic strategy for patients progressed to osimertinib.
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Affiliation(s)
- Silvia La Monica
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Kamal Eltayeb
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Alessio Lodola
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Francesco Volta
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Martina Viglioli
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | | | - Francesca Galvani
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Maricla Galetti
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL-Italian Workers' Compensation Authority, 00078, Monte Porzio Catone, Rome, Italy
| | - Mara Bonelli
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Claudia Fumarola
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Andrea Cavazzoni
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Lisa Flammini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Michela Verzè
- Medical Oncology Unit, University Hospital of Parma, 43126, Parma, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, 43126, Parma, Italy
| | | | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy.
- Medical Oncology Unit, University Hospital of Parma, 43126, Parma, Italy.
| | - Marco Mor
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Roberta Alfieri
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
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Çalışkan M, Tazaki K. AI/ML advances in non-small cell lung cancer biomarker discovery. Front Oncol 2023; 13:1260374. [PMID: 38148837 PMCID: PMC10750392 DOI: 10.3389/fonc.2023.1260374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths among both men and women, representing approximately 25% of cancer fatalities each year. The treatment landscape for non-small cell lung cancer (NSCLC) is rapidly evolving due to the progress made in biomarker-driven targeted therapies. While advancements in targeted treatments have improved survival rates for NSCLC patients with actionable biomarkers, long-term survival remains low, with an overall 5-year relative survival rate below 20%. Artificial intelligence/machine learning (AI/ML) algorithms have shown promise in biomarker discovery, yet NSCLC-specific studies capturing the clinical challenges targeted and emerging patterns identified using AI/ML approaches are lacking. Here, we employed a text-mining approach and identified 215 studies that reported potential biomarkers of NSCLC using AI/ML algorithms. We catalogued these studies with respect to BEST (Biomarkers, EndpointS, and other Tools) biomarker sub-types and summarized emerging patterns and trends in AI/ML-driven NSCLC biomarker discovery. We anticipate that our comprehensive review will contribute to the current understanding of AI/ML advances in NSCLC biomarker research and provide an important catalogue that may facilitate clinical adoption of AI/ML-derived biomarkers.
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Affiliation(s)
- Minal Çalışkan
- Translational Science Department, Precision Medicine Function, Daiichi Sankyo, Inc., Basking Ridge, NJ, United States
| | - Koichi Tazaki
- Translational Science Department I, Precision Medicine Function, Daiichi Sankyo, Tokyo, Japan
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Corona G, Di Gregorio E, Buonadonna A, Lombardi D, Scalone S, Steffan A, Miolo G. Pharmacometabolomics of trabectedin in metastatic soft tissue sarcoma patients. Front Pharmacol 2023; 14:1212634. [PMID: 37637412 PMCID: PMC10450632 DOI: 10.3389/fphar.2023.1212634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
Objective: Trabectedin is an anti-cancer drug commonly used for the treatment of patients with metastatic soft tissue sarcoma (mSTS). Despite its recognized efficacy, significant variability in pharmacological response has been observed among mSTS patients. To address this issue, this pharmacometabolomics study aimed to identify pre-dose plasma metabolomics signatures that can explain individual variations in trabectedin pharmacokinetics and overall clinical response to treatment. Methods: In this study, 40 mSTS patients treated with trabectedin administered by 24 h-intravenous infusion at a dose of 1.5 mg/m2 were enrolled. The patients' baseline plasma metabolomics profiles, which included derivatives of amino acids and bile acids, were analyzed using multiple reaction monitoring LC-MS/MS together with their pharmacokinetics profile of trabectedin. Multivariate Partial least squares regression and univariate statistical analyses were utilized to identify correlations between baseline metabolite concentrations and trabectedin pharmacokinetics, while Partial Least Squares-Discriminant Analysis was employed to evaluate associations with clinical response. Results: The multiple regression model, derived from the correlation between the AUC of trabectedin and pre-dose metabolomics, exhibited the best performance by incorporating cystathionine, hemoglobin, taurocholic acid, citrulline, and the phenylalanine/tyrosine ratio. This model demonstrated a bias of 4.6% and a precision of 17.4% in predicting drug AUC, effectively accounting for up to 70% of the inter-individual pharmacokinetic variability. Through the use of Partial least squares-Discriminant Analysis, cystathionine and hemoglobin were identified as specific metabolic signatures that effectively distinguish patients with stable disease from those with progressive disease. Conclusions: The findings from this study provide compelling evidence to support the utilization of pre-dose metabolomics in uncovering the underlying causes of pharmacokinetic variability of trabectedin, as well as facilitating the identification of patients who are most likely to benefit from this treatment.
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Affiliation(s)
- Giuseppe Corona
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Emanuela Di Gregorio
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Angela Buonadonna
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Davide Lombardi
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Simona Scalone
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Gianmaria Miolo
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
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Wang W, Rong Z, Wang G, Hou Y, Yang F, Qiu M. Cancer metabolites: promising biomarkers for cancer liquid biopsy. Biomark Res 2023; 11:66. [PMID: 37391812 DOI: 10.1186/s40364-023-00507-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/27/2023] [Indexed: 07/02/2023] Open
Abstract
Cancer exerts a multitude of effects on metabolism, including the reprogramming of cellular metabolic pathways and alterations in metabolites that facilitate inappropriate proliferation of cancer cells and adaptation to the tumor microenvironment. There is a growing body of evidence suggesting that aberrant metabolites play pivotal roles in tumorigenesis and metastasis, and have the potential to serve as biomarkers for personalized cancer therapy. Importantly, high-throughput metabolomics detection techniques and machine learning approaches offer tremendous potential for clinical oncology by enabling the identification of cancer-specific metabolites. Emerging research indicates that circulating metabolites have great promise as noninvasive biomarkers for cancer detection. Therefore, this review summarizes reported abnormal cancer-related metabolites in the last decade and highlights the application of metabolomics in liquid biopsy, including detection specimens, technologies, methods, and challenges. The review provides insights into cancer metabolites as a promising tool for clinical applications.
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Affiliation(s)
- Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China
| | - Zhiwei Rong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Hou
- Department of Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- Clinical Research Center, Peking University, Beijing, 100191, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
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8
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Miller HA, Miller DM, van Berkel VH, Frieboes HB. Evaluation of Lung Cancer Patient Response to First-Line Chemotherapy by Integration of Tumor Core Biopsy Metabolomics with Multiscale Modeling. Ann Biomed Eng 2023; 51:820-832. [PMID: 36224485 PMCID: PMC10023290 DOI: 10.1007/s10439-022-03096-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022]
Abstract
The standard of care for intermediate (Stage II) and advanced (Stages III and IV) non-small cell lung cancer (NSCLC) involves chemotherapy with taxane/platinum derivatives, with or without radiation. Ideally, patients would be screened a priori to allow non-responders to be initially treated with second-line therapies. This evaluation is non-trivial, however, since tumors behave as complex multiscale systems. To address this need, this study employs a multiscale modeling approach to evaluate first-line chemotherapy response of individual patient tumors based on metabolomic analysis of tumor core biopsies obtained during routine clinical evaluation. Model parameters were calculated for a patient cohort as a function of these metabolomic profiles, previously obtained from high-resolution 2DLC-MS/MS analysis. Evaluation metrics were defined to classify patients as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD) following first-line chemotherapy. Response was simulated for each patient and compared to actual response. The results show that patient classifications were significantly separated from each other, and also when grouped as DC vs. PD and as CR/PR vs. SD/PD, by fraction of initial tumor radius metric at 6 days post simulated bolus drug injection. This study shows that patient first-line chemotherapy response can in principle be evaluated from multiscale modeling integrated with tumor tissue metabolomic data, offering a first step towards individualized lung cancer treatment prognosis.
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Affiliation(s)
- Hunter A Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Donald M Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Victor H van Berkel
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Cardiovascular and Thoracic Surgery, University of Louisville, Louisville, KY, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA.
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA.
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, KY, USA.
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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Mei L, Zhang Z, Li X, Yang Y, Qi R. Metabolomics profiling in prediction of chemo-immunotherapy efficiency in advanced non-small cell lung cancer. Front Oncol 2023; 12:1025046. [PMID: 36733356 PMCID: PMC9887290 DOI: 10.3389/fonc.2022.1025046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Background To explore potential metabolomics biomarker in predicting the efficiency of the chemo-immunotherapy in patients with advanced non-small cell lung cancer (NSCLC). Methods A total of 83 eligible patients were assigned to receive chemo-immunotherapy. Serum samples were prospectively collected before the treatment to perform metabolomics profiling analyses under the application of gas chromatography mass spectrometry (GC-MS). The key metabolites were identified using projection to latent structures discriminant analysis (PLS-DA). The key metabolites were used for predicting the chemo-immunotherapy efficiency in advanced NSCLC patients. Results Seven metabolites including pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate were identified as the key metabolites to the chemo-immunotherapy response. The receiver operating characteristic curves (AUC) were 0.79 (95% CI: 0.69-0.90), 0.60 (95% CI: 0.48-0.73), 0.69 (95% CI: 0.57-0.80), 0.63 (95% CI: 0.51-0.75), 0.60 (95% CI: 0.48-0.72), 0.56 (95% CI: 0.43-0.67), and 0.67 (95% CI: 0.55-0.80) for the key metabolites, respectively. A binary logistic regression was used to construct a combined biomarker model to improve the discriminating efficiency. The AUC was 0.86 (95% CI: 0.77-0.94) for the combined biomarker model. Pathway analyses showed that urea cycle, glucose-alanine cycle, glycine and serine metabolism, alanine metabolism, and glutamate metabolism were the key metabolic pathway to the chemo-immunotherapy response in patients with advanced NSCLC. Conclusion Metabolomics analyses of key metabolites and pathways revealed that GC-MS could be used to predict the efficiency of chemo-immunotherapy. Pyruvate, threonine, alanine, urea, oxalate, elaidic acid and glutamate played a central role in the metabolic of PD patients with advanced NSCLC.
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Affiliation(s)
- Lihong Mei
- Department of Dermatology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Zhihua Zhang
- Department of Echocardiography, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xushuo Li
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Ying Yang
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Ruixue Qi
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China,*Correspondence: Ruixue Qi,
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11
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Liao J, Li X, Gan Y, Han S, Rong P, Wang W, Li W, Zhou L. Artificial intelligence assists precision medicine in cancer treatment. Front Oncol 2023; 12:998222. [PMID: 36686757 PMCID: PMC9846804 DOI: 10.3389/fonc.2022.998222] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/22/2022] [Indexed: 01/06/2023] Open
Abstract
Cancer is a major medical problem worldwide. Due to its high heterogeneity, the use of the same drugs or surgical methods in patients with the same tumor may have different curative effects, leading to the need for more accurate treatment methods for tumors and personalized treatments for patients. The precise treatment of tumors is essential, which renders obtaining an in-depth understanding of the changes that tumors undergo urgent, including changes in their genes, proteins and cancer cell phenotypes, in order to develop targeted treatment strategies for patients. Artificial intelligence (AI) based on big data can extract the hidden patterns, important information, and corresponding knowledge behind the enormous amount of data. For example, the ML and deep learning of subsets of AI can be used to mine the deep-level information in genomics, transcriptomics, proteomics, radiomics, digital pathological images, and other data, which can make clinicians synthetically and comprehensively understand tumors. In addition, AI can find new biomarkers from data to assist tumor screening, detection, diagnosis, treatment and prognosis prediction, so as to providing the best treatment for individual patients and improving their clinical outcomes.
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Affiliation(s)
- Jinzhuang Liao
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaoying Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yu Gan
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuangze Han
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Wei Wang
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Li Zhou
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Pathology, The Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
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12
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Li J, Liu K, Ji Z, Wang Y, Yin T, Long T, Shen Y, Cheng L. Serum untargeted metabolomics reveal metabolic alteration of non-small cell lung cancer and refine disease detection. Cancer Sci 2022; 114:680-689. [PMID: 36310111 PMCID: PMC9899604 DOI: 10.1111/cas.15629] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 01/07/2023] Open
Abstract
This study was performed to characterize the metabolic alteration of non-small-cell lung cancer (NSCLC) and discover blood-based metabolic biomarkers relevant to lung cancer detection. An untargeted metabolomics-based approach was applied in a case-control study with 193 NSCLC patients and 243 healthy controls. Serum metabolomics were determined by using an ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. We screened differential metabolites based on univariate and multivariate analysis, followed by identification of the metabolites and related pathways. For NSCLC detection, machine learning was employed to develop and validate the model based on the altered serum metabolite features. The serum metabolic pattern of NSCLC was definitely different from the healthy condition. In total, 278 altered features were found in the serum of NSCLC patients comparing with healthy people. About one-fifth of the abundant differential features were identified successfully. The altered metabolites were enriched in metabolic pathways such as phenylalanine metabolism, linoleic acid metabolism, and biosynthesis of bile acids. We demonstrated a panel of 10 metabolic biomarkers which representing excellent discriminating capability for NSCLC discrimination, with a combined area under the curve (AUC) in the validation set of 0.95 (95% CI: 0.91-0.98). Moreover, this model showed a desirable performance for the detection of NSCLC at an early stage (AUC = 0.95, 95% CI: 0.92-0.97). Our study offers a perspective on NSCLC metabolic alteration. The finding of the biomarkers might shed light on the clinical detection of lung cancer, especially for those cancers in an early stage in Chinese population.
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Affiliation(s)
- Jiaoyuan Li
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Ke Liu
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zhi Ji
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yi Wang
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Tongxin Yin
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Tingting Long
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Ying Shen
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Liming Cheng
- Department of Laboratory MedicineTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
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13
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Developing machine learning algorithms for dynamic estimation of progression during active surveillance for prostate cancer. NPJ Digit Med 2022; 5:110. [PMID: 35933478 PMCID: PMC9357044 DOI: 10.1038/s41746-022-00659-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/14/2022] [Indexed: 11/15/2022] Open
Abstract
Active Surveillance (AS) for prostate cancer is a management option that continually monitors early disease and considers intervention if progression occurs. A robust method to incorporate “live” updates of progression risk during follow-up has hitherto been lacking. To address this, we developed a deep learning-based individualised longitudinal survival model using Dynamic-DeepHit-Lite (DDHL) that learns data-driven distribution of time-to-event outcomes. Further refining outputs, we used a reinforcement learning approach (Actor-Critic) for temporal predictive clustering (AC-TPC) to discover groups with similar time-to-event outcomes to support clinical utility. We applied these methods to data from 585 men on AS with longitudinal and comprehensive follow-up (median 4.4 years). Time-dependent C-indices and Brier scores were calculated and compared to Cox regression and landmarking methods. Both Cox and DDHL models including only baseline variables showed comparable C-indices but the DDHL model performance improved with additional follow-up data. With 3 years of data collection and 3 years follow-up the DDHL model had a C-index of 0.79 (±0.11) compared to 0.70 (±0.15) for landmarking Cox and 0.67 (±0.09) for baseline Cox only. Model calibration was good across all models tested. The AC-TPC method further discovered 4 distinct outcome-related temporal clusters with distinct progression trajectories. Those in the lowest risk cluster had negligible progression risk while those in the highest cluster had a 50% risk of progression by 5 years. In summary, we report a novel machine learning approach to inform personalised follow-up during active surveillance which improves predictive power with increasing data input over time.
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14
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Cang S, Liu R, Mu K, Tang Q, Cui H, Bi K, Zhang Y, Li Q. Assessment of Plasma Amino Acids, Purines, Tricarboxylic Acid Cycle Metabolites, and Lipids Levels in NSCLC Patients Based on LC-MS/MS Quantification. J Pharm Biomed Anal 2022; 221:114990. [DOI: 10.1016/j.jpba.2022.114990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/31/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022]
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15
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Miller HA, van Berkel VH, Frieboes HB. Lung cancer survival prediction and biomarker identification with an ensemble machine learning analysis of tumor core biopsy metabolomic data. Metabolomics 2022; 18:57. [PMID: 35857204 PMCID: PMC9737952 DOI: 10.1007/s11306-022-01918-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/30/2022] [Indexed: 12/14/2022]
Abstract
INTRODUCTION While prediction of short versus long term survival from lung cancer is clinically relevant in the context of patient management and therapy selection, it has proven difficult to identify reliable biomarkers of survival. Metabolomic markers from tumor core biopsies have been shown to reflect cancer metabolic dysregulation and hold prognostic value. OBJECTIVES Implement and validate a novel ensemble machine learning approach to evaluate survival based on metabolomic biomarkers from tumor core biopsies. METHODS Data were obtained from tumor core biopsies evaluated with high-resolution 2DLC-MS/MS. Unlike biofluid samples, analysis of tumor tissue is expected to accurately reflect the cancer metabolism and its impact on patient survival. A comprehensive suite of machine learning algorithms were trained as base learners and then combined into a stacked-ensemble meta-learner for predicting "short" versus "long" survival on an external validation cohort. An ensemble method of feature selection was employed to find a reliable set of biomarkers with potential clinical utility. RESULTS Overall survival (OS) is predicted in external validation cohort with AUROCTEST of 0.881 with support vector machine meta learner model, while progression-free survival (PFS) is predicted with AUROCTEST of 0.833 with boosted logistic regression meta learner model, outperforming a nomogram using covariate data (staging, age, sex, treatment vs. non-treatment) as predictors. Increased relative abundance of guanine, choline, and creatine corresponded with shorter OS, while increased leucine and tryptophan corresponded with shorter PFS. In patients that expired, N6,N6,N6-Trimethyl-L-lysine, L-pyrogluatmic acid, and benzoic acid were increased while cystine, methionine sulfoxide and histamine were decreased. In patients with progression, itaconic acid, pyruvate, and malonic acid were increased. CONCLUSION This study demonstrates the feasibility of an ensemble machine learning approach to accurately predict patient survival from tumor core biopsy metabolomic data.
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Affiliation(s)
- Hunter A Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
| | - Victor H van Berkel
- UofL Health-Brown Cancer Center, University of Louisville, Louisville, USA
- Department of Cardiovascular and Thoracic Surgery, University of Louisville, Louisville, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA.
- UofL Health-Brown Cancer Center, University of Louisville, Louisville, USA.
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, USA.
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16
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Anil Kumar C, Harish S, Ravi P, SVN M, Kumar BPP, Mohanavel V, Alyami NM, Priya SS, Asfaw AK. Lung Cancer Prediction from Text Datasets Using Machine Learning. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6254177. [PMID: 35872862 PMCID: PMC9303121 DOI: 10.1155/2022/6254177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022]
Abstract
Lung cancer is the major cause of cancer-related death in this generation, and it is expected to remain so for the foreseeable future. It is feasible to treat lung cancer if the symptoms of the disease are detected early. It is possible to construct a sustainable prototype model for the treatment of lung cancer using the current developments in computational intelligence without negatively impacting the environment. Because it will reduce the number of resources squandered as well as the amount of work necessary to complete manual tasks, it will save both time and money. To optimise the process of detection from the lung cancer dataset, a machine learning model based on support vector machines (SVMs) was used. Using an SVM classifier, lung cancer patients are classified based on their symptoms at the same time as the Python programming language is utilised to further the model implementation. The effectiveness of our SVM model was evaluated in terms of several different criteria. Several cancer datasets from the University of California, Irvine, library were utilised to evaluate the evaluated model. As a result of the favourable findings of this research, smart cities will be able to deliver better healthcare to their citizens. Patients with lung cancer can obtain real-time treatment in a cost-effective manner with the least amount of effort and latency from any location and at any time. The proposed model was compared with the existing SVM and SMOTE methods. The proposed method gets a 98.8% of accuracy rate when comparing the existing methods.
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Affiliation(s)
- C. Anil Kumar
- Department of Electronics and Communication Engineering, R. L. Jalappa Institute of Technology Doddaballapur, Bangalore, Karnataka 561203, India
| | - S. Harish
- Department of Electronics and Communication Engineering, R. L. Jalappa Institute of Technology Doddaballapur, Bangalore, Karnataka 561203, India
| | - Prabha Ravi
- Medical Electronics Engineering, Ramaiah Institute of Technology, Bangalore, Karnataka 560054, India
| | - Murthy SVN
- Department of Computer Science and Engineering, S J C Institute of Technology, Chikkaballapur, Karnataka 562101, India
| | - B. P. Pradeep Kumar
- Department of Electronics and Communication Engineering, HKBK College of Engineering, Bangalore, Karnataka 560045, India
| | - V. Mohanavel
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Chennai 600073, Tamil Nadu, India
- Department of Mechanical Engineering, Chandigarh University, Mohali, 140413 Punjab, India
| | - Nouf M. Alyami
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - S. Shanmuga Priya
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Amare Kebede Asfaw
- Department of Computer Science, Kombolcha Institute of Technology, Wollo University, Ethiopia
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17
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N. Mueller A, Morrisey S, A. Miller H, Hu X, Kumar R, T. Ngo P, Yan J, B. Frieboes H. Prediction of lung cancer immunotherapy response via machine learning analysis of immune cell lineage and surface markers. Cancer Biomark 2022; 34:681-692. [DOI: 10.3233/cbm-210529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: Although advances have been made in cancer immunotherapy, patient benefits remain elusive. For non-small cell lung cancer (NSCLC), monoclonal antibodies targeting programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) have shown survival benefit compared to chemotherapy. Personalization of treatment would be facilitated by a priori identification of patients likely to benefit. OBJECTIVE: This pilot study applied a suite of machine learning methods to analyze mass cytometry data of immune cell lineage and surface markers from blood samples of a small cohort (n= 13) treated with Pembrolizumab, Atezolizumab, Durvalumab, or Nivolumab as monotherapy. METHODS: Four different comparisons were evaluated between data collected at an initial visit (baseline), after 12-weeks of immunotherapy, and from healthy (control) samples: healthy vs patients at baseline, Responders vs Non-Responders at baseline, Healthy vs 12-week Responders, and Responders vs Non-Responders at 12-weeks. The algorithms Random Forest, Partial Least Squares Discriminant Analysis, Multi-Layer Perceptron, and Elastic Net were applied to find features differentiating between these groups and provide for the capability to predict outcomes. RESULTS: Particular combinations and proportions of immune cell lineage and surface markers were sufficient to accurately discriminate between the groups without overfitting the data. In particular, markers associated with the B-cell phenotype were identified as key features. CONCLUSIONS: This study illustrates a comprehensive machine learning analysis of circulating immune cell characteristics of NSCLC patients with the potential to predict response to immunotherapy. Upon further evaluation in a larger cohort, the proposed methodology could help guide personalized treatment selection in clinical practice.
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Affiliation(s)
- Alex N. Mueller
- School of Medicine, University of Louisville, Louisville, KY, USA
| | - Samantha Morrisey
- Division of Immunotherapy, Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Hunter A. Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Xiaoling Hu
- Division of Immunotherapy, Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Rohit Kumar
- School of Medicine, University of Louisville, Louisville, KY, USA
- UofL Health – Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Phuong T. Ngo
- School of Medicine, University of Louisville, Louisville, KY, USA
- UofL Health – Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Jun Yan
- Division of Immunotherapy, Department of Surgery, University of Louisville, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- UofL Health – Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Hermann B. Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- UofL Health – Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Center for Predictive Medicine, University of Louisville, Louisville, KY, USA
- Department of Bioengineering, University of Louisville, Louisville, KY, USA
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18
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Miller HA, Rai SN, Yin X, Zhang X, Chesney JA, van Berkel VH, Frieboes HB. Lung cancer metabolomic data from tumor core biopsies enables risk-score calculation for progression-free and overall survival. Metabolomics 2022; 18:31. [PMID: 35567637 PMCID: PMC9724684 DOI: 10.1007/s11306-022-01891-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/19/2022] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Metabolomics has emerged as a powerful method to provide insight into cancer progression, including separating patients into low- and high-risk groups for overall (OS) and progression-free survival (PFS). However, survival prediction based mainly on metabolites obtained from biofluids remains elusive. OBJECTIVES This proof-of-concept study evaluates metabolites as biomarkers obtained directly from tumor core biopsies along with covariates age, sex, pathological stage at diagnosis (I/II vs. III/VI), histological subtype, and treatment vs. no treatment to risk stratify lung cancer patients in terms of OS and PFS. METHODS Tumor core biopsy samples obtained during routine lung cancer patient care at the University of Louisville Hospital and Norton Hospital were evaluated with high-resolution 2DLC-MS/MS, and the data were analyzed by Kaplan-Meier survival analysis and Cox proportional hazards regression. A linear equation was developed to stratify patients into low and high risk groups based on log-transformed intensities of key metabolites. Sparse partial least squares discriminant analysis (SPLS-DA) was performed to predict OS and PFS events. RESULTS Univariable Cox proportional hazards regression model coefficients divided by the standard errors were used as weight coefficients multiplied by log-transformed metabolite intensity, then summed to generate a risk score for each patient. Risk scores based on 10 metabolites for OS and 5 metabolites for PFS were significant predictors of survival. Risk scores were validated with SPLS-DA classification model (AUROC 0.868 for OS and AUROC 0.755 for PFS, when combined with covariates). CONCLUSION Metabolomic analysis of lung tumor core biopsies has the potential to differentiate patients into low- and high-risk groups based on OS and PFS events and probability.
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Affiliation(s)
- Hunter A Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
| | - Shesh N Rai
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, USA
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, USA
| | - Jason A Chesney
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, USA
- Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, USA
| | - Victor H van Berkel
- James Graham Brown Cancer Center, University of Louisville, Louisville, USA
- Department of Cardiovascular and Thoracic Surgery, University of Louisville, Louisville, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, USA.
- James Graham Brown Cancer Center, University of Louisville, Louisville, USA.
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, USA.
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19
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Pang H, Hu K, Li F, Duan H, Chen Y, Hu Y, Wang D, Jiang M. Untargeted metabolomics profiling in a mouse model of lung cancer treated with thermal ablation. Bioengineered 2022; 13:11258-11268. [PMID: 35481548 PMCID: PMC9208470 DOI: 10.1080/21655979.2022.2065742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Thermal ablation is widely used in the treatment of lung cancer and is beneficial for the overall survival of patients in clinic. However, there is barely a priority in which ablation system should be chosen under different periods of tumor progression in lung cancer. The present study investigated different modes of thermal ablation systems in mice with transplanted Lewis lung carcinoma tumors and their various biological effects in local regions using untargeted metabolomics. The results showed that thermal ablation could significantly suppress tumor growth and the differentially expressed metabolites of tumors after ablation relative to untreated tumors concentrated on organic compounds, organic acids and derivatives, nucleosides, nucleotides, and lipids. The upregulated metabolites indicated an inflammatory reaction in the ablation groups at an early stage after ablation. Steroid hormone and tryptophan metabolism, which are associated with immune responses, were modulated after both cryoablation and hyperthermal ablation. Characteristically, the results also indicated that cryoablation suppressed glucose oxidation and carbohydrate metabolism of tumor, while hyperthermal ablation suppressed lipid metabolism of tumor. In conclusion, thermal ablation could inhibit tumor growth under either freezing or heating modes with characteristic different biological effects on tumors.
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Affiliation(s)
- Haoyue Pang
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Kaiwen Hu
- Department of Oncology, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Fuyao Li
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Hua Duan
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Yu Chen
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Yaqi Hu
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Dan Wang
- Department of Hemooncology, Dongzhimen Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Min Jiang
- Department of Oncology, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
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20
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Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data. Ann Biomed Eng 2022; 50:314-329. [PMID: 35083584 PMCID: PMC9743982 DOI: 10.1007/s10439-022-02904-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/01/2022] [Indexed: 12/15/2022]
Abstract
Advances in omic technologies have provided insight into cancer progression and treatment response. However, the nonlinear characteristics of cancer growth present a challenge to bridge from the molecular- to the tissue-scale, as tumor behavior cannot be encapsulated by the sum of the individual molecular details gleaned experimentally. Mathematical modeling and computational simulation have been traditionally employed to facilitate analysis of nonlinear systems. In this study, for the first time tumor metabolomic data are linked via mathematical modeling to the tumor tissue-scale behavior, showing the capability to mechanistically simulate cancer progression personalized to omic information obtainable from patient tumor core biopsy analysis. Generally, a higher degree of metabolic dysregulation has been correlated with more aggressive tumor behavior. Accordingly, key parameters influenced by metabolomic data in this model include tumor proliferation, vascularization, aggressiveness, lactic acid production, monocyte infiltration and macrophage polarization, and drug effect. The model enables evaluating interactions of interest between these parameters which drive tumor growth based on the metabolomic data. The results show that the model can group patients consistently with the clinically observed outcomes of response/non-response to chemotherapy. This modeling approach provides a first step towards evaluation of tumor growth based on tumor-specific metabolomic data.
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21
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Yin X, Yang J, Zhang M, Wang X, Xu W, Price CAH, Huang L, Liu W, Su H, Wang W, Chen H, Hou G, Walker M, Zhou Y, Shen Z, Liu J, Qian K, Di W. Serum Metabolic Fingerprints on Bowl-Shaped Submicroreactor Chip for Chemotherapy Monitoring. ACS NANO 2022; 16:2852-2865. [PMID: 35099942 PMCID: PMC9007521 DOI: 10.1021/acsnano.1c09864] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemotherapy is a primary cancer treatment strategy, the monitoring of which is critical to enhancing the survival rate and quality of life of cancer patients. However, current chemotherapy monitoring mainly relies on imaging tools with inefficient sensitivity and radiation invasiveness. Herein, we develop the bowl-shaped submicroreactor chip of Au-loaded 3-aminophenol formaldehyde resin (denoted as APF-bowl&Au) with a specifically designed structure and Au loading content. The obtained APF-bowl&Au, used as the matrix of laser desorption/ionization mass spectrometry (LDI MS), possesses an enhanced localized electromagnetic field for strengthened small metabolite detection. The APF-bowl&Au enables the extraction of serum metabolic fingerprints (SMFs), and machine learning of the SMFs achieves chemotherapy monitoring of ovarian cancer with area-under-the-curve (AUC) of 0.81-0.98. Furthermore, a serum metabolic biomarker panel is preliminarily identified, exhibiting gradual changes as the chemotherapy cycles proceed. This work provides insights into the development of nanochips and contributes to a universal detection platform for chemotherapy monitoring.
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Affiliation(s)
- Xia Yin
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
| | - Jing Yang
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Mengji Zhang
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Xinyao Wang
- State
Key Laboratory of Catalysis, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
| | - Wei Xu
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Cameron-Alexander H. Price
- The
University of Manchester at Harwell, Diamond
Light Source, Didcot, Oxfordshire OX11 0DE, U.K.
- UK Catalysis
Hub, Research Complex at Harwell, Rutherford
Appleton Laboratories, Harwell Campus, Didcot, Oxfordshire OX11 0FA, U.K.
| | - Lin Huang
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Wanshan Liu
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Haiyang Su
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Wenjing Wang
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
| | - Hongyu Chen
- State
Key Laboratory of Catalysis, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
| | - Guangjin Hou
- State
Key Laboratory of Catalysis, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
| | - Mark Walker
- Department
of Obstetrics and Gynecology, University
of Ottawa, Ottawa, Ontario ON K1H 8L6, Canada
| | - Ying Zhou
- Department
of Obstetrics and Gynecology, The First Affiliated Hospital of USTC,
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Auhui 230001, P.R. China
| | - Zhen Shen
- Department
of Obstetrics and Gynecology, The First Affiliated Hospital of USTC,
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Auhui 230001, P.R. China
| | - Jian Liu
- State
Key Laboratory of Catalysis, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P.R. China
- DICP-Surrey
Joint Centre for Future Materials, Department of Chemical and Process
Engineering, and Advanced Technology Institute, University of Surrey, Guilford, Surrey GU2 7XH, U.K.
| | - Kun Qian
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
- School
of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China
| | - Wen Di
- State
Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory
of Gynecologic Oncology, Department of Obstetrics and Gynecology,
Renji Hospital, School of Medicine, Shanghai
Jiao Tong University, Shanghai, 200127, P.R. China
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22
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Miller HA, Emam R, Lynch CM, Bockhorst S, Frieboes HB. Discrepancies in metabolomic biomarker identification from patient-derived lung cancer revealed by combined variation in data pre-treatment and imputation methods. Metabolomics 2021; 17:37. [PMID: 33772663 PMCID: PMC8138701 DOI: 10.1007/s11306-021-01787-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The identification of metabolomic biomarkers predictive of cancer patient response to therapy and of disease stage has been pursued as a "holy grail" of modern oncology, relying on the metabolic dysfunction that characterizes cancer progression. In spite of the evaluation of many candidate biomarkers, however, determination of a consistent set with practical clinical utility has proven elusive. OBJECTIVE In this study, we systematically examine the combined role of data pre-treatment and imputation methods on the performance of multivariate data analysis methods and their identification of potential biomarkers. METHODS Uniquely, we are able to systematically evaluate both unsupervised and supervised methods with a metabolomic data set obtained from patient-derived lung cancer core biopsies with true missing values. Eight pre-treatment methods, ten imputation methods, and two data analysis methods were applied in combination. RESULTS The combined choice of pre-treatment and imputation methods is critical in the definition of candidate biomarkers, with deficient or inappropriate selection of these methods leading to inconsistent results, and with important biomarkers either being overlooked or reported as a false positive. The log transformation appeared to normalize the original tumor data most effectively, but the performance of the imputation applied after the transformation was highly dependent on the characteristics of the data set. CONCLUSION The combined choice of pre-treatment and imputation methods may need careful evaluation prior to metabolomic data analysis of human tumors, in order to enable consistent identification of potential biomarkers predictive of response to therapy and of disease stage.
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Affiliation(s)
- Hunter A Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Ramy Emam
- Department of Bioengineering, University of Louisville, Louisville, KY, USA
| | - Chip M Lynch
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, USA
| | - Samuel Bockhorst
- Department of Medicine, University of Louisville, Louisville, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA.
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, KY, USA.
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
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