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Fu L, Li M, Lv J, Yang C, Zhang Z, Qin S, Li W, Wang X, Chen L. Deep neural network for discovering metabolism-related biomarkers for lung adenocarcinoma. Front Endocrinol (Lausanne) 2023; 14:1270772. [PMID: 37955007 PMCID: PMC10634586 DOI: 10.3389/fendo.2023.1270772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Lung cancer is a major cause of illness and death worldwide. Lung adenocarcinoma (LUAD) is its most common subtype. Metabolite-mRNA interactions play a crucial role in cancer metabolism. Thus, metabolism-related mRNAs are potential targets for cancer therapy. Methods This study constructed a network of metabolite-mRNA interactions (MMIs) using four databases. We retrieved mRNAs from the Tumor Genome Atlas (TCGA)-LUAD cohort showing significant expressional changes between tumor and non-tumor tissues and identified metabolism-related differential expression (DE) mRNAs among the MMIs. Candidate mRNAs showing significant contributions to the deep neural network (DNN) model were mined. Using MMIs and the results of function analysis, we created a subnetwork comprising candidate mRNAs and metabolites. Results Finally, 10 biomarkers were obtained after survival analysis and validation. Their good prognostic value in LUAD was validated in independent datasets. Their effectiveness was confirmed in the TCGA and an independent Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset by comparison with traditional machine-learning models. Conclusion To summarize, 10 metabolism-related biomarkers were identified, and their prognostic value was confirmed successfully through the MMI network and the DNN model. Our strategy bears implications to pave the way for investigating metabolic biomarkers in other cancers.
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Affiliation(s)
- Lei Fu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Manshi Li
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chengcheng Yang
- Department of Respiratory, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zihan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shimei Qin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xinyan Wang
- Department of Respiratory, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Martino F, Lupi M, Giraudo E, Lanzetti L. Breast cancers as ecosystems: a metabolic perspective. Cell Mol Life Sci 2023; 80:244. [PMID: 37561190 PMCID: PMC10415483 DOI: 10.1007/s00018-023-04902-9] [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: 06/01/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
Breast cancer (BC) is the most frequently diagnosed cancer and one of the major causes of cancer death. Despite enormous progress in its management, both from the therapeutic and early diagnosis viewpoints, still around 700,000 patients succumb to the disease each year, worldwide. Late recurrency is the major problem in BC, with many patients developing distant metastases several years after the successful eradication of the primary tumor. This is linked to the phenomenon of metastatic dormancy, a still mysterious trait of the natural history of BC, and of several other types of cancer, by which metastatic cells remain dormant for long periods of time before becoming reactivated to initiate the clinical metastatic disease. In recent years, it has become clear that cancers are best understood if studied as ecosystems in which the impact of non-cancer-cell-autonomous events-dependent on complex interaction between the cancer and its environment, both local and systemic-plays a paramount role, probably as significant as the cell-autonomous alterations occurring in the cancer cell. In adopting this perspective, a metabolic vision of the cancer ecosystem is bound to improve our understanding of the natural history of cancer, across space and time. In BC, many metabolic pathways are coopted into the cancer ecosystem, to serve the anabolic and energy demands of the cancer. Their study is shedding new light on the most critical aspect of BC management, of metastatic dissemination, and that of the related phenomenon of dormancy and fostering the application of the knowledge to the development of metabolic therapies.
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Affiliation(s)
- Flavia Martino
- Department of Oncology, University of Torino Medical School, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Mariadomenica Lupi
- Department of Oncology, University of Torino Medical School, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Enrico Giraudo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
- Department of Science and Drug Technology, University of Torino, Turin, Italy
| | - Letizia Lanzetti
- Department of Oncology, University of Torino Medical School, Turin, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
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Tambay V, Raymond VA, Goossens C, Rousseau L, Turcotte S, Bilodeau M. Metabolomics-Guided Identification of a Distinctive Hepatocellular Carcinoma Signature. Cancers (Basel) 2023; 15:3232. [PMID: 37370840 DOI: 10.3390/cancers15123232] [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: 04/27/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major contributor to cancer-related morbidity and mortality burdens globally. Given the fundamental metabolic activity of hepatocytes within the liver, hepatocarcinogenesis is bound to be characterized by alterations in metabolite profiles as a manifestation of metabolic reprogramming. METHODS HCC and adjacent non-tumoral liver specimens were obtained from patients after HCC resection. Global patterns in tissue metabolites were identified using non-targeted 1H Nuclear Magnetic Resonance (1H-NMR) spectroscopy whereas specific metabolites were quantified using targeted liquid chromatography-mass spectrometry (LC/MS). RESULTS Principal component analysis (PCA) within our 1H-NMR dataset identified a principal component (PC) one of 53.3%, along which the two sample groups were distinctively clustered. Univariate analysis of tissue specimens identified more than 150 metabolites significantly altered in HCC compared to non-tumoral liver. For LC/MS, PCA identified a PC1 of 45.2%, along which samples from HCC tissues and non-tumoral tissues were clearly separated. Supervised analysis (PLS-DA) identified decreases in tissue glutathione, succinate, glycerol-3-phosphate, alanine, malate, and AMP as the most important contributors to the metabolomic signature of HCC by LC/MS. CONCLUSIONS Together, 1H-NMR and LC/MS metabolomics have the capacity to distinguish HCC from non-tumoral liver. The characterization of such distinct profiles of metabolite abundances underscores the major metabolic alterations that result from hepatocarcinogenesis.
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Affiliation(s)
- Vincent Tambay
- Laboratoire d'Hépatologie Cellulaire, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Valérie-Ann Raymond
- Laboratoire d'Hépatologie Cellulaire, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Corentine Goossens
- Laboratoire d'Hépatologie Cellulaire, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Louise Rousseau
- Biobanque et Base de Données Hépatobiliaire et Pancréatique, Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0C1, Canada
| | - Simon Turcotte
- Biobanque et Base de Données Hépatobiliaire et Pancréatique, Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0C1, Canada
- Département de Chirurgie, Service de Transplantation Hépatique et de Chirurgie Hépatobiliaire et Pancréatique, Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0C1, Canada
| | - Marc Bilodeau
- Laboratoire d'Hépatologie Cellulaire, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H3T1J4, Canada
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Lipid Metabolism Heterogeneity and Crosstalk with Mitochondria Functions Drive Breast Cancer Progression and Drug Resistance. Cancers (Basel) 2022; 14:cancers14246267. [PMID: 36551752 PMCID: PMC9776509 DOI: 10.3390/cancers14246267] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is a heterogeneous disease that can be triggered by genetic alterations in mammary epithelial cells, leading to diverse disease outcomes in individual patients. The metabolic heterogeneity of BC enhances its ability to adapt to changes in the tumor microenvironment and metabolic stress, but unfavorably affects the patient's therapy response, prognosis and clinical effect. Extrinsic factors from the tumor microenvironment and the intrinsic parameters of cancer cells influence their mitochondrial functions, which consequently alter their lipid metabolism and their ability to proliferate, migrate and survive in a harsh environment. The balanced interplay between mitochondria and fatty acid synthesis or fatty acid oxidation has been attributed to a combination of environmental factors and to the genetic makeup, oncogenic signaling and activities of different transcription factors. Hence, understanding the mechanisms underlying lipid metabolic heterogeneity and alterations in BC is gaining interest as a major target for drug resistance. Here we review the major recent reports on lipid metabolism heterogeneity and bring to light knowledge on the functional contribution of diverse lipid metabolic pathways to breast tumorigenesis and therapy resistance.
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Beyond Genetics: Metastasis as an Adaptive Response in Breast Cancer. Int J Mol Sci 2022; 23:ijms23116271. [PMID: 35682953 PMCID: PMC9181003 DOI: 10.3390/ijms23116271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 01/27/2023] Open
Abstract
Metastatic disease represents the primary cause of breast cancer (BC) mortality, yet it is still one of the most enigmatic processes in the biology of this tumor. Metastatic progression includes distinct phases: invasion, intravasation, hematogenous dissemination, extravasation and seeding at distant sites, micro-metastasis formation and metastatic outgrowth. Whole-genome sequencing analyses of primary BC and metastases revealed that BC metastatization is a non-genetically selected trait, rather the result of transcriptional and metabolic adaptation to the unfavorable microenvironmental conditions which cancer cells are exposed to (e.g., hypoxia, low nutrients, endoplasmic reticulum stress and chemotherapy administration). In this regard, the latest multi-omics analyses unveiled intra-tumor phenotypic heterogeneity, which determines the polyclonal nature of breast tumors and constitutes a challenge for clinicians, correlating with patient poor prognosis. The present work reviews BC classification and epidemiology, focusing on the impact of metastatic disease on patient prognosis and survival, while describing general principles and current in vitro/in vivo models of the BC metastatic cascade. The authors address here both genetic and phenotypic intrinsic heterogeneity of breast tumors, reporting the latest studies that support the role of the latter in metastatic spreading. Finally, the review illustrates the mechanisms underlying adaptive stress responses during BC metastatic progression.
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Roda N, Blandano G, Pelicci PG. Blood Vessels and Peripheral Nerves as Key Players in Cancer Progression and Therapy Resistance. Cancers (Basel) 2021; 13:cancers13174471. [PMID: 34503281 PMCID: PMC8431382 DOI: 10.3390/cancers13174471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The interactions between cancer cells and the surrounding blood vessels and peripheral nerves are critical in all the phases of tumor development. Accordingly, therapies that specifically target vessels and nerves represent promising anticancer approaches. The first aim of this review is to document the importance of blood vessels and peripheral nerves in both cancer onset and local or distant growth of tumoral cells. We then focus on the state-of-the-art therapies that limit cancer progression through the impairment of blood vessels and peripheral nerves. The mentioned literature is helpful for the scientific community to appreciate the recent advances in these two fundamental components of tumors. Abstract Cancer cells continuously interact with the tumor microenvironment (TME), a heterogeneous milieu that surrounds the tumor mass and impinges on its phenotype. Among the components of the TME, blood vessels and peripheral nerves have been extensively studied in recent years for their prominent role in tumor development from tumor initiation. Cancer cells were shown to actively promote their own vascularization and innervation through the processes of angiogenesis and axonogenesis. Indeed, sprouting vessels and axons deliver several factors needed by cancer cells to survive and proliferate, including nutrients, oxygen, and growth signals, to the expanding tumor mass. Nerves and vessels are also fundamental for the process of metastatic spreading, as they provide both the pro-metastatic signals to the tumor and the scaffold through which cancer cells can reach distant organs. Not surprisingly, continuously growing attention is devoted to the development of therapies specifically targeting these structures, with promising initial results. In this review, we summarize the latest evidence that supports the importance of blood vessels and peripheral nerves in cancer pathogenesis, therapy resistance, and innovative treatments.
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Affiliation(s)
- Niccolò Roda
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (N.R.); (G.B.)
| | - Giada Blandano
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (N.R.); (G.B.)
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (N.R.); (G.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
- Correspondence:
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Cancer Metabolism as a New Real Target in Tumor Therapy. Cells 2021; 10:cells10061393. [PMID: 34198722 PMCID: PMC8227542 DOI: 10.3390/cells10061393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
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Metabolic Classification and Intervention Opportunities for Tumor Energy Dysfunction. Metabolites 2021; 11:metabo11050264. [PMID: 33922558 PMCID: PMC8146396 DOI: 10.3390/metabo11050264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive view of cell metabolism provides a new vision of cancer, conceptualized as tissue with cellular-altered metabolism and energetic dysfunction, which can shed light on pathophysiological mechanisms. Cancer is now considered a heterogeneous ecosystem, formed by tumor cells and the microenvironment, which is molecularly, phenotypically, and metabolically reprogrammable. A wealth of evidence confirms metabolic reprogramming activity as the minimum common denominator of cancer, grouping together a wide variety of aberrations that can affect any of the different metabolic pathways involved in cell physiology. This forms the basis for a new proposed classification of cancer according to the altered metabolic pathway(s) and degree of energy dysfunction. Enhanced understanding of the metabolic reprogramming pathways of fatty acids, amino acids, carbohydrates, hypoxia, and acidosis can bring about new therapeutic intervention possibilities from a metabolic perspective of cancer.
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