1
|
Lan T, Arastu S, Lam J, Kim H, Wang W, Wang S, Bhatt V, Lopes EC, Hu Z, Sun M, Luo X, Ghergurovich JM, Su X, Rabinowitz JD, White E, Guo JY. Glucose-6-phosphate dehydrogenase maintains redox homeostasis and biosynthesis in LKB1-deficient KRAS-driven lung cancer. Nat Commun 2024; 15:5857. [PMID: 38997257 PMCID: PMC11245543 DOI: 10.1038/s41467-024-50157-8] [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: 10/04/2023] [Accepted: 06/28/2024] [Indexed: 07/14/2024] Open
Abstract
Cancer cells depend on nicotinamide adenine dinucleotide phosphate (NADPH) to combat oxidative stress and support reductive biosynthesis. One major NADPH production route is the oxidative pentose phosphate pathway (committed step: glucose-6-phosphate dehydrogenase, G6PD). Alternatives exist and can compensate in some tumors. Here, using genetically-engineered lung cancer mouse models, we show that G6PD ablation significantly suppresses KrasG12D/+;Lkb1-/- (KL) but not KrasG12D/+;P53-/- (KP) lung tumorigenesis. In vivo isotope tracing and metabolomics reveal that G6PD ablation significantly impairs NADPH generation, redox balance, and de novo lipogenesis in KL but not KP lung tumors. Mechanistically, in KL tumors, G6PD ablation activates p53, suppressing tumor growth. As tumors progress, G6PD-deficient KL tumors increase an alternative NADPH source from serine-driven one carbon metabolism, rendering associated tumor-derived cell lines sensitive to serine/glycine depletion. Thus, oncogenic driver mutations determine lung cancer dependence on G6PD, whose targeting is a potential therapeutic strategy for tumors harboring KRAS and LKB1 co-mutations.
Collapse
Affiliation(s)
- Taijin Lan
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Sara Arastu
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Jarrick Lam
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Hyungsin Kim
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Wenping Wang
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Samuel Wang
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | | | - Eduardo Cararo Lopes
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Zhixian Hu
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Michael Sun
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | - Xuefei Luo
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
| | | | - Xiaoyang Su
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Joshua D Rabinowitz
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
- Ludwig Princeton Branch, Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Eileen White
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA
- Ludwig Princeton Branch, Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, 08544, USA
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA.
- Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, NJ, 08854, USA.
| |
Collapse
|
2
|
Dallavilla T, Galiè S, Sambruni G, Borin S, Fazio N, Fumagalli-Romario U, Manzo T, Nezi L, Schaefer MH. Differences in the molecular organisation of tumours along the colon are linked to interactions within the tumour ecosystem. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167311. [PMID: 38909851 DOI: 10.1016/j.bbadis.2024.167311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 06/25/2024]
Abstract
Tumours exhibit significant heterogeneity in their molecular profiles across patients, largely influenced by the tissue of origin, where certain driver gene mutations are predominantly associated with specific cancer types. Here, we unveil an additional layer of complexity: some cancer types display anatomic location-specific mutation profiles akin to tissue-specificity. To better understand this phenomenon, we concentrate on colon cancer. While prior studies have noted changes of the frequency of molecular alterations along the colon, the underlying reasons and whether those changes occur rather gradual or are distinct between the left and right colon, remain unclear. Developing and leveraging stringent statistical models on molecular data from 522 colorectal tumours from The Cancer Genome Atlas, we reveal disparities in molecular properties between the left and right colon affecting many genes. Interestingly, alterations in genes responsive to environmental cues and properties of the tumour ecosystem, including metabolites which we quantify in a cohort of 27 colorectal cancer patients, exhibit continuous trends along the colon. Employing network methodologies, we uncover close interactions between metabolites and genes, including drivers of colon cancer, showing continuous abundance or alteration profiles. This underscores how anatomic biases in the composition and interactions within the tumour ecosystem help explaining gradients of carcinogenesis along the colon.
Collapse
Affiliation(s)
- Tiziano Dallavilla
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Serena Galiè
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Gaia Sambruni
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Simona Borin
- Digestive Surgery, European Institute of Oncology-IRCCS, Milano, Italy
| | - Nicola Fazio
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCS, Milano, Italy
| | | | - Teresa Manzo
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Luigi Nezi
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy.
| |
Collapse
|
3
|
Hayama T, Hama K, Ozawa T, Fujiwara Y, Nozawa K, Matsuda K, Yokoyama K, Hashiguchi Y, Ochiai H, Misawa T, Fukagawa T. Ceramide synthase CERS4 gene downregulation is associated with KRAS mutation in colorectal cancer. Sci Rep 2023; 13:16249. [PMID: 37758931 PMCID: PMC10533536 DOI: 10.1038/s41598-023-43557-1] [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: 06/23/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023] Open
Abstract
Ceramide, the central molecule in sphingolipid synthesis, is a bioactive lipid that serves as a regulatory molecule in the anti-inflammatory responses, apoptosis, programmed necrosis, autophagy, and cell motility of cancer cells. In particular, the authors have reported differences in sphingolipid content in colorectal cancer tissues. The associations among genetic mutations, clinicopathological factors, and sphingolipid metabolism in colorectal cancer (CRC) have not been investigated. The objective of this study is to investigate the association between genes associated with sphingolipid metabolism, genetic variations in colorectal cancer (CRC), and clinicopathological factors in CRC patients. We enrolled 82 consecutive patients with stage I-IV CRC who underwent tumor resection at a single institution in 2019-2021. We measured the expression levels of genes related to sphingolipid metabolism and examined the relationships between CRC gene mutations and the clinicopathological data of each individual patient. The relationship between CRC gene mutations and expression levels of ceramide synthase (CERS), N-acylsphingosine amidohydrolase (ASAH), and alkaline ceramidase (ACER) genes involved in sphingolipid metabolism was examined CRES4 expression was significantly lower in the CRC KRAS gene mutation group (p = 0.004); vascular invasion was more common in colorectal cancer patients with high CERS4 expression (p = 0.0057). By examining the correlation between sphingolipid gene expression and clinical factors, we were able to identify cancer types in which sphingolipid metabolism is particularly relevant. CERS4 expression was significantly reduced in KRAS mutant CRC. Moreover, CRC with decreased CERS4 showed significantly more frequent venous invasion.
Collapse
Affiliation(s)
- Tamuro Hayama
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
- Advanced Comprehensive Research Organization (ACRO), Teikyo University, Tokyo, Japan.
| | - Kotaro Hama
- Faculty of Pharma‑Sciences, Teikyo University, Tokyo, Japan
- Advanced Comprehensive Research Organization (ACRO), Teikyo University, Tokyo, Japan
| | - Tsuyoshi Ozawa
- Kawaguchi the Institute of Proctology and Gastroenterology, Kawaguchi, Japan
| | - Yuko Fujiwara
- Faculty of Pharma‑Sciences, Teikyo University, Tokyo, Japan
| | - Keijiro Nozawa
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Keiji Matsuda
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | | | - Yojiro Hashiguchi
- Department of Surgery, Japanese Red Cross Omori Hospital, Tokyo, Japan
| | - Hiroki Ochiai
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Takeyuki Misawa
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Takeo Fukagawa
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| |
Collapse
|
4
|
Southern J, Gonzalez G, Borgas P, Poynter L, Laponogov I, Zhong Y, Mirnezami R, Veselkov D, Bronstein M, Veselkov K. Genomic-driven nutritional interventions for radiotherapy-resistant rectal cancer patient. Sci Rep 2023; 13:14862. [PMID: 37684345 PMCID: PMC10491580 DOI: 10.1038/s41598-023-41833-8] [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: 12/07/2022] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Radiotherapy response of rectal cancer patients is dependent on a myriad of molecular mechanisms including response to stress, cell death, and cell metabolism. Modulation of lipid metabolism emerges as a unique strategy to improve radiotherapy outcomes due to its accessibility by bioactive molecules within foods. Even though a few radioresponse modulators have been identified using experimental techniques, trying to experimentally identify all potential modulators is intractable. Here we introduce a machine learning (ML) approach to interrogate the space of bioactive molecules within food for potential modulators of radiotherapy response and provide phytochemically-enriched recipes that encapsulate the benefits of discovered radiotherapy modulators. Potential radioresponse modulators were identified using a genomic-driven network ML approach, metric learning and domain knowledge. Then, recipes from the Recipe1M database were optimized to provide ingredient substitutions maximizing the number of predicted modulators whilst preserving the recipe's culinary attributes. This work provides a pipeline for the design of genomic-driven nutritional interventions to improve outcomes of rectal cancer patients undergoing radiotherapy.
Collapse
Affiliation(s)
- Joshua Southern
- Department of Computing, Imperial College London, London, SW7 2BX, UK
| | - Guadalupe Gonzalez
- Department of Computing, Imperial College London, London, SW7 2BX, UK
- Prescient Design, Genentech, Basel, 4052, Switzerland
| | - Pia Borgas
- North Middlesex University Hospital, London, N18 1QX, UK
| | - Liam Poynter
- Department of Surgery and Cancer, Imperial College London, London, SW7 2BX, UK
| | - Ivan Laponogov
- Department of Surgery and Cancer, Imperial College London, London, SW7 2BX, UK
| | - Yoyo Zhong
- Department of Surgery and Cancer, Imperial College London, London, SW7 2BX, UK
| | | | - Dennis Veselkov
- Department of Computing, Imperial College London, London, SW7 2BX, UK
| | - Michael Bronstein
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Kirill Veselkov
- Prescient Design, Genentech, Basel, 4052, Switzerland.
- Department of Environmental Health Sciences, Yale University, New Haven, CT, 06510, USA.
| |
Collapse
|
5
|
Zhao Z, Bai J, Liu C, Wang Y, Wang S, Zhao F, Gu Q. Metabolomics analysis of amino acid and fatty acids in colorectal cancer patients based on tandem mass spectrometry. J Clin Biochem Nutr 2023; 73:161-171. [PMID: 37700848 PMCID: PMC10493213 DOI: 10.3164/jcbn.22-110] [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: 10/04/2022] [Accepted: 03/18/2023] [Indexed: 09/14/2023] Open
Abstract
Metabolic differences between colorectal cancer (CRC) and NI (NI) play an important role in early diagnoses and in-time treatments. We investigated the metabolic alterations between CRC patients and NI, and identified some potential biomarkers, and these biomarkers might be used as indicators for diagnosis of CRC. In this study, there were 79 NI, 50 CRC I patients, 52 CRC II patients, 56 CRC III patients, and 52 CRC IV patients. MS-MS was used to measure the metabolic alterations. Univariate and multivariate data analysis and metabolic pathway analysis were applied to analyze metabolic data and determine differential metabolites. These indicators revealed that amino acid and fatty acids could separate these groups. Several metabolites indicated an excellent variables capability in the separation of CRC patients and NI. Ornithine, arginine, octadecanoyl carnitine, palmitoyl carnitine, adipoyl carnitine, and butyryl carnitine/propanoyl carnitine were selected to distinguish the CRC patients and NI. And methionine and propanoyl carnitine, were directly linked to different stages of CRC. Receiver operating characteristics curves and variables importance in projection both represented an excellent performance of these metabolites. In conclusion, we assessed the difference between CRC patients and NI, which supports guidelines for an early diagnosis and effective treatment.
Collapse
Affiliation(s)
- Zhuo Zhao
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, China
| | - Jing Bai
- School of Pharmaceutical Sciences, Liaoning University, Shenyang, 110036, China
| | - Chang Liu
- College of Chemistry, Liaoning University, Shenyang, 110036, China
| | - Yansong Wang
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, China
| | | | | | - Qiufang Gu
- School of Nursing, Jinzhou Medical University, Jinzhou, 121001, China
| |
Collapse
|
6
|
O’Connell F, Mylod E, Donlon NE, Heeran AB, Butler C, Bhardwaj A, Ramjit S, Durand M, Lambe G, Tansey P, Welartne I, Sheahan KP, Yin X, Donohoe CL, Ravi N, Dunne MR, Brennan L, Reynolds JV, Roche HM, O’Sullivan J. Energy Metabolism, Metabolite, and Inflammatory Profiles in Human Ex Vivo Adipose Tissue Are Influenced by Obesity Status, Metabolic Dysfunction, and Treatment Regimes in Patients with Oesophageal Adenocarcinoma. Cancers (Basel) 2023; 15:cancers15061681. [PMID: 36980567 PMCID: PMC10046380 DOI: 10.3390/cancers15061681] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
Oesophageal adenocarcinoma (OAC) is a poor prognosis cancer with limited response rates to current treatment modalities and has a strong link to obesity. To better elucidate the role of visceral adiposity in this disease state, a full metabolic profile combined with analysis of secreted pro-inflammatory cytokines, metabolites, and lipid profiles were assessed in human ex vivo adipose tissue explants from obese and non-obese OAC patients. These data were then related to extensive clinical data including obesity status, metabolic dysfunction, previous treatment exposure, and tumour regression grades. Real-time energy metabolism profiles were assessed using the seahorse technology. Adipose explant conditioned media was screened using multiplex ELISA to assess secreted levels of 54 pro-inflammatory mediators. Targeted secreted metabolite and lipid profiles were analysed using Ultra-High-Performance Liquid Chromatography coupled with Mass Spectrometry. Adipose tissue explants and matched clinical data were collected from OAC patients (n = 32). Compared to visceral fat from non-obese patients (n = 16), visceral fat explants from obese OAC patients (n = 16) had significantly elevated oxidative phosphorylation metabolism profiles and an increase in Eotaxin-3, IL-17A, IL-17D, IL-3, MCP-1, and MDC and altered secretions of glutamine associated metabolites. Adipose explants from patients with metabolic dysfunction correlated with increased oxidative phosphorylation metabolism, and increases in IL-5, IL-7, SAA, VEGF-C, triacylglycerides, and metabolites compared with metabolically healthy patients. Adipose explants generated from patients who had previously received neo-adjuvant chemotherapy (n = 14) showed elevated secretions of pro-inflammatory mediators, IL-12p40, IL-1α, IL-22, and TNF-β and a decreased expression of triacylglycerides. Furthermore, decreased secreted levels of triacylglycerides were also observed in the adipose secretome of patients who received the chemotherapy-only regimen FLOT compared with patients who received no neo-adjuvant treatment or chemo-radiotherapy regimen CROSS. For those patients who showed the poorest response to currently available treatments, their adipose tissue was associated with higher glycolytic metabolism compared to patients who had good treatment responses. This study demonstrates that the adipose secretome in OAC patients is enriched with mediators that could prime the tumour microenvironment to aid tumour progression and attenuate responses to conventional cancer treatments, an effect which appears to be augmented by obesity and metabolic dysfunction and exposure to different treatment regimes.
Collapse
Affiliation(s)
- Fiona O’Connell
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Eimear Mylod
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
- Cancer Immunology and Immunotherapy Group, Department of Surgery, Trinity College Dublin, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Noel E. Donlon
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
- Cancer Immunology and Immunotherapy Group, Department of Surgery, Trinity College Dublin, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Aisling B. Heeran
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Christine Butler
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Anshul Bhardwaj
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Sinead Ramjit
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Michael Durand
- Department of Radiology, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Gerard Lambe
- Department of Radiology, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Paul Tansey
- Department of Radiology, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Ivan Welartne
- Department of Radiology, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Kevin P. Sheahan
- Department of Radiology, Beaumont Hospital, D02 YN77 Dublin, Ireland
| | - Xiaofei Yin
- UCD School of Agriculture and Food Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Claire L. Donohoe
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Narayanasamy Ravi
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Margaret R. Dunne
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
- School of Chemical & Biopharmaceutical Sciences, Technological University Dublin, Tallaght, D07 EWV4 Dublin, Ireland
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - John V. Reynolds
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Helen M. Roche
- Nutrigenomics Research Group, UCD Conway Institute, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 C1P1 Dublin, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK
| | - Jacintha O’Sullivan
- Department of Surgery, Trinity St. James’s Cancer Institute and Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College Dublin, D08 W9RT Dublin, Ireland
- Correspondence:
| |
Collapse
|
7
|
Yang J, Yang X, Guo J, Liu S. A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma. PeerJ 2023; 11:e14622. [PMID: 36632140 PMCID: PMC9828273 DOI: 10.7717/peerj.14622] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/02/2022] [Indexed: 01/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC.
Collapse
|
8
|
Efeoglu E, Henry M, Clynes M, Meleady P. Label-Free Quantitative Proteomics Analysis of Adriamycin Selected Multidrug Resistant Human Lung Cancer Cells. Biomolecules 2022; 12:biom12101401. [PMID: 36291610 PMCID: PMC9599763 DOI: 10.3390/biom12101401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
The development of drug resistance in lung cancer is a major clinical challenge, leading to a 5-year survival rate of only 18%. Therefore, unravelling the mechanisms of drug resistance and developing novel therapeutic strategies is of crucial importance. This study systematically explores the novel biomarkers of drug resistance using a lung cancer model (DLKP) with a series of drug-resistant variants. In-depth label-free quantitative mass spectrometry-based proteomics and gene ontology analysis shows that parental DLKP cells significantly differ from drug-resistant variants, and the cellular proteome changes even among the drug-resistant subpopulations. Overall, ABC transporter proteins and lipid metabolism were determined to play a significant role in the formation of drug resistance in DKLP cells. A series of membrane-related proteins such as HMOX1, TMB1, EPHX2 and NEU1 were identified to be correlated with levels of drug resistance in the DLKP subpopulations. The study also showed enrichment in biological processes and molecular functions such as drug metabolism, cellular response to the drug and drug binding. In gene ontology analysis, 18 proteins were determined to be positively or negatively correlated with resistance levels. Overall, 34 proteins which potentially have a therapeutic and diagnostic value were identified.
Collapse
Affiliation(s)
- Esen Efeoglu
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58 Dublin, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58 Dublin, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58 Dublin, Ireland
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, V94 T9PX Limerick, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58 Dublin, Ireland
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, V94 T9PX Limerick, Ireland
- School of Biotechnology, Dublin City University, D09 E432 Dublin, Ireland
- Correspondence: ; Tel.: +353-1-7005910
| |
Collapse
|
9
|
Sun R, Wang X, Chen J, Teng D, Chan S, Tu X, Wang Z, Zuo X, Wei X, Lin L, Zhang Q, Zhang X, Tang K, Zhang H, Chen W. Development and validation of a novel cellular senescence-related prognostic signature for predicting the survival and immune landscape in hepatocellular carcinoma. Front Genet 2022; 13:949110. [PMID: 36147502 PMCID: PMC9485671 DOI: 10.3389/fgene.2022.949110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 01/19/2023] Open
Abstract
Background: Cellular senescence is a typical irreversible form of life stagnation, and recent studies have suggested that long non-coding ribonucleic acids (lncRNA) regulate the occurrence and development of various tumors. In the present study, we attempted to construct a novel signature for predicting the survival of patients with hepatocellular carcinoma (HCC) and the associated immune landscape based on senescence-related (sr) lncRNAs. Method: Expression profiles of srlncRNAs in 424 patients with HCC were retrieved from The Cancer Genome Atlas database. Lasso and Cox regression analyses were performed to identify differentially expressed lncRNAs related to senescence. The prediction efficiency of the signature was checked using a receiver operating characteristic (ROC) curve, Kaplan–Meier analysis, Cox regression analyses, nomogram, and calibration. The risk groups of the gene set enrichment analysis, immune analysis, and prediction of the half-maximal inhibitory concentration (IC50) were also analyzed. Quantitative real-time polymerase chain reaction (qPCR) was used to confirm the levels of AC026412.3, AL451069.3, and AL031985.3 in normal hepatic and HCC cell lines. Results: We identified 3 srlncRNAs (AC026412.3, AL451069.3, and AL031985.3) and constructed a new risk model. The results of the ROC curve and Kaplan–Meier analysis suggested that it was concordant with the prediction. Furthermore, a nomogram model was constructed to accurately predict patient prognosis. The risk score also correlated with immune cell infiltration status, immune checkpoint expression, and chemosensitivity. The results of qPCR revealed that AC026412.3 and AL451069.3 were significantly upregulated in hepatoma cell lines. Conclusion: The novel srlncRNA (AC026412.3, AL451069.3, and AL031985.3) signatures may provide insights into new therapies and prognosis predictions for patients with HCC.
Collapse
Affiliation(s)
- Rui Sun
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xu Wang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jiajie Chen
- Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Da Teng
- Department of Hepatopancreatobiliary Surgery, Affiliated Chuzhou Hospital of Anhui Medical University, First People’s Hospital of Chuzhou, Chuzhou, China
| | - Shixin Chan
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xucan Tu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenglin Wang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaomin Zuo
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiang Wei
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Li Lin
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Qing Zhang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xiaomin Zhang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Kechao Tang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Huabing Zhang
- Department of Biochemistry and Molecular Biology, Metabolic Disease Research Center, School of Basic Medicine, Anhui Medical University, Hefei, China
- Affiliated Chuzhou Hospital of Anhui Medical University, First People’s Hospital of Chuzhou, Chuzhou, China
- *Correspondence: Huabing Zhang, ; Wei Chen, ,
| | - Wei Chen
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Huabing Zhang, ; Wei Chen, ,
| |
Collapse
|
10
|
Salita T, Rustam YH, Mouradov D, Sieber OM, Reid GE. Reprogrammed Lipid Metabolism and the Lipid-Associated Hallmarks of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14153714. [PMID: 35954376 PMCID: PMC9367418 DOI: 10.3390/cancers14153714] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is the third-most diagnosed cancer and the second-leading cause of cancer-related deaths worldwide. Limitations in early and accurate diagnosis of CRC gives rise to poor patient survival. Advancements in analytical techniques have improved our understanding of the cellular and metabolic changes occurring in CRC and potentiate avenues for improved diagnostic and therapeutic strategies. Lipids are metabolites with important biological functions; however, their role in CRC is poorly understood. Here, we provide an in-depth review of the recent literature concerning lipid alterations in CRC and propose eight lipid metabolism-associated hallmarks of CRC. Abstract Lipids have diverse structures, with multifarious regulatory functions in membrane homeostasis and bioenergetic metabolism, in mediating functional protein–lipid and protein–protein interactions, as in cell signalling and proliferation. An increasing body of evidence supports the notion that aberrant lipid metabolism involving remodelling of cellular membrane structure and changes in energy homeostasis and signalling within cancer-associated pathways play a pivotal role in the onset, progression, and maintenance of colorectal cancer (CRC) and their tumorigenic properties. Recent advances in analytical lipidome analysis technologies have enabled the comprehensive identification and structural characterization of lipids and, consequently, our understanding of the role they play in tumour progression. However, despite progress in our understanding of cancer cell metabolism and lipidomics, the key lipid-associated changes in CRC have yet not been explicitly associated with the well-established ‘hallmarks of cancer’ defined by Hanahan and Weinberg. In this review, we summarize recent findings that highlight the role of reprogrammed lipid metabolism in CRC and use this growing body of evidence to propose eight lipid metabolism-associated hallmarks of colorectal cancer, and to emphasize their importance and linkages to the established cancer hallmarks.
Collapse
Affiliation(s)
- Timothy Salita
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; (T.S.); (Y.H.R.)
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Yepy H. Rustam
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; (T.S.); (Y.H.R.)
| | - Dmitri Mouradov
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Oliver M. Sieber
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Correspondence: (O.M.S.); (G.E.R.)
| | - Gavin E. Reid
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; (T.S.); (Y.H.R.)
- School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Correspondence: (O.M.S.); (G.E.R.)
| |
Collapse
|
11
|
Zhang Y, Pang S, Sun B, Zhang M, Jiao X, Lai L, Qian Y, Yang N, Yang W. ELOVLs Predict Distinct Prognosis Value and Immunotherapy Efficacy In Patients With Hepatocellular Carcinoma. Front Oncol 2022; 12:884066. [PMID: 35912257 PMCID: PMC9334671 DOI: 10.3389/fonc.2022.884066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with high prevalence worldwide and poor prognosis. It has been verified that elongation of very-long-chain fatty acids gene family (ELOVLs), a group of genes that responsible for elongation of saturated and polyunsaturated fatty acids, participate in the pathogenesis and development of multiplex disease including cancers. However, the functions and prognosis of ELOVLs in HCC are still indistinguishable. Methods First, we searched the mRNA expression and survival data of ELOVLs in patients with HCC via the data of The Cancer Genome Atlas (TCGA). The prognosis value of ELOVLs on HCC was assessed by Kaplan–Meier plotter and Cox regression analysis. reverse transcription quantitative- polymerase chain reaction (RT-qPCR), Western blot (WB), and immunohistochemistry were applied to assess the specific mRNA and protein expression of ELOVLs in HCC clinical specimens of our cohort. Then, the functional enrichment of ELOVL1 especially the pathways relating to the immune was conducted utilizing the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analysis. Additionally, TIMER, CIBERSOR, and tumor immune dysfunction and exclusion (TIDE) were employed to evaluate the relationship between ELOVL1 and immune responses. Last, the correlation of ELOVL1 with genome heterogeneity [microsatellite instability (MSI), tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), homologous recombination deficiency (HRD), purity, ploidy, loss of heterozygosity (LOH), and neoantigens] and mutational landscape were also evaluated basing on the date in TCGA. Results Significant expression alteration was observed in ELOVLs family at the pan-cancer level. In liver cancer, ELOVL1 and ELOVL3 were strongly associated with poor prognosis of HCC by survival analysis and differential expression analysis. Immunohistochemistry microarray, WB, and RT-qPCR confirmed that ELOVL1 but not ELOVL3 played an important role in HCC. Mechanistically, functional network analysis revealed that ELOVL1 might be involved in the immune response. ELOVL1 could affect immune cell infiltration and immune checkpoint markers such as PD-1 and CTLA4 in HCC. Meanwhile, high expression of ELOVL1 would be insensitive to immunotherapy. Correlation analysis of immunotherapy markers showed that ELOVL1 has been associated with MSI, TMB, and oncogene mutations such as TP53. Conclusion ELOVLs play distinct prognostic value in HCC. ELOVL1 could predict the poor prognosis and might be a potential indicator of immunotherapy efficacy in HCC patients.
Collapse
Affiliation(s)
- Yu Zhang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shujie Pang
- Department V of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Bo Sun
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Minbo Zhang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoxiao Jiao
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Linying Lai
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yiting Qian
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ning Yang
- Department V of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- *Correspondence: Ning Yang, ; Wenzhuo Yang,
| | - Wenzhuo Yang
- Department of Gastroenterology and Hepatology, Institute of Digestive Disease, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Ning Yang, ; Wenzhuo Yang,
| |
Collapse
|
12
|
Kyselová L, Vítová M, Řezanka T. Very long chain fatty acids. Prog Lipid Res 2022; 87:101180. [PMID: 35810824 DOI: 10.1016/j.plipres.2022.101180] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Very long chain fatty acids (VLCFAs) are important components of various lipid classes in most organisms, from bacteria to higher plants and mammals, including humans. VLCFAs, or very long chain polyunsaturated fatty acids (VLCPUFAs), can be defined as fatty acids with 23 or more carbon atoms in the molecule. The main emphasis in this review is on the analysis of these acids, including obtaining standards from natural sources or their synthesis. Furthermore, the occurrence and analysis of these compounds in both lower (bacteria, invertebrates) and higher organisms (flowering plants or mammals) are discussed in detail. Attention is paid to their biosynthesis, especially the elongation of very long chain fatty acids protein (ELOVL4). This review deals with papers describing these very interesting compounds, whose chemical, biochemical and biological properties have not been fully explored.
Collapse
Affiliation(s)
- Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic.
| | - Milada Vítová
- Institute of Botany, Czech Academy of Sciences, Centre for Phycology, Dukelská 135, 379 01 Třeboň, Czech Republic.
| | - Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| |
Collapse
|
13
|
Luan G, Wang M, Yuan J, Bu X, Song J, Wang C, Zhang L. Regulatory network identified by pulmonary transcriptome and proteome profiling reveals extensive change of tumor-related genes in microRNA-21 knockout mice. J Cancer Res Clin Oncol 2022; 148:1919-1929. [PMID: 35511299 DOI: 10.1007/s00432-022-03967-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/21/2022] [Indexed: 01/08/2023]
Abstract
PURPOSE MicroRNA-21 (miR-21) is a well-known oncomiR and plays key roles in regulating various biological processes related to pulmonary diseases, especially lung carcinoma. The regulatory roles and downstream targets of miR-21 remain far from well understood. We aimed to identify miR-21-gene regulatory network in lung tissue. METHODS Transcriptome and proteome analyses were performed on lung tissues from miR-21 knockout (KO) mice and their wildtype (WT) littermates. Differentially expressed genes (DEGs) and proteins (DEPs) between miR-21KO and WT were analyzed, and correlation analysis was performed between transcriptional and translational level. DEPs were used for prediction of miR-21 target genes and construction of co-expression network. RESULTS Comparing with WT mice, 820 DEGs and 623 DEPs were identified in lung tissues of miR-21KO mice. Upregulated DEGs and DEPs were both significantly enriched in pathways of metabolism of xenobiotics by cytochrome P450, drug metabolism, and chemical carcinogenesis. Of the 31 molecules commonly identified in DEGs and DEPs, 9 upregulated genes were tumor suppressor genes while 8 downregulated genes were oncogenes, and 12 genes showed closely positive correlation between mRNA and protein expression. Real-time PCR validation results were consistent with the omics data. Among the upregulated DEPs in miR-21KO mice, 21 genes were predicted as miR-21 targets. The miR-21 regulatory network was constructed by target genes and their highly co-expressed proteins, which identified the miR-21 target Itih4 as a hub gene. CONCLUSION MiR-21-gene regulatory network was constructed in mouse lung tissue. MiR-21KO resulted in extensive upregulation of tumor suppressor genes and downregulation of oncogenes.
Collapse
Affiliation(s)
- Ge Luan
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Ming Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Jing Yuan
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Xiangting Bu
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Jing Song
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Chengshuo Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China.
| | - Luo Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China.
- Department of Allergy, Beijing TongRen Hospital, Capital Medical University, No. 1, DongJiaoMinXiang, DongCheng District, Beijing, 100730, China.
- Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
14
|
Bykanova MA, Solodilova MA, Azarova IE, Klyosova EY, Bushueva OY, Polonikova AA, Churnosov MI, Polonikov AV. Genetic variation at the catalytic subunit of glutamate cysteine ligase contributes to the susceptibility to sporadic colorectal cancer: a pilot study. Mol Biol Rep 2022; 49:6145-6154. [PMID: 35386070 DOI: 10.1007/s11033-022-07406-0] [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: 01/20/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Glutathione is a tripeptide detoxifying a variety of exogenous and endogenous free radicals and carcinogens, and a deficiency of glutathione is associated with an increased host susceptibility to oxidative stress, a pathological condition implicated in the development and progression of cancer. The catalytic subunit of glutamate-cysteine ligase (GCLC) is an enzyme responsible for the initial and rate-limiting step of glutathione biosynthesis. METHODS AND RESULTS The aim of this pilot study was to investigate whether genetic variation at the GCLC gene contributes to the risk of colorectal cancer (CRC). DNA samples from 681 unrelated Russian individuals (283 patients with CRC and 398 age- and sex-matched healthy controls) were genotyped for six common functional SNPs of the GCLC gene (SNPs) such as rs12524494, rs17883901, rs606548, rs636933, rs648595 and rs761142 of the GCLC gene using the MassARRAY-4 system. We found that genotype rs606548-C/T is significantly associated with increased risk of CRC regardless of sex and age (OR 2.24; 95% CI 1.24-4.03; P = 0.007, FDR = 0.04). Moreover, ten GCLC genotype combinations showed association with the risk of CRC (P < 0.05). Functional SNP annotation enabled establishing the CRC-associated polymorphisms are associated with a decreased GCLC expression that may be attributed to epigenetic effects of histone modifications operating in a colon-specific manner. CONCLUSIONS The present study was the first to show that genetic variation at the catalytic subunit of glutamate-cysteine ligase may contribute to the risk of colorectal cancer risk. However, further genetic association studies with a larger sample size are required to substantiate the role of GCLC gene polymorphisms in the development of sporadic colorectal cancer.
Collapse
Affiliation(s)
- Marina A Bykanova
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk, 305041, Russian Federation. .,Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041.
| | - Maria A Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041
| | - Iuliia E Azarova
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041.,Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk, Russian Federation, 305041
| | - Elena Y Klyosova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041.,Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk, Russian Federation, 305041
| | - Olga Y Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk, 305041, Russian Federation.,Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041
| | - Anna A Polonikova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041
| | - Mikhail I Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, 85 Pobedy Street, Belgorod, Russian Federation, 308015
| | - Alexey V Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk, Russian Federation, 305041.,Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk, Russian Federation, 305041
| |
Collapse
|
15
|
Krauß D, Fari O, Sibilia M. Lipid Metabolism Interplay in CRC—An Update. Metabolites 2022; 12:metabo12030213. [PMID: 35323656 PMCID: PMC8951276 DOI: 10.3390/metabo12030213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) to date still ranks as one of the deadliest cancer entities globally, and despite recent advances, the incidence in young adolescents is dramatically increasing. Lipid metabolism has recently received increased attention as a crucial element for multiple aspects of carcinogenesis and our knowledge of the underlying mechanisms is steadily growing. However, the mechanism how fatty acid metabolism contributes to CRC is still not understood in detail. In this review, we aim to summarize our vastly growing comprehension and the accompanied complexity of cellular fatty acid metabolism in CRC by describing inputs and outputs of intracellular free fatty acid pools and how these contribute to cancer initiation, disease progression and metastasis. We highlight how different lipid pathways can contribute to the aggressiveness of tumors and affect the prognosis of patients. Furthermore, we focus on the role of lipid metabolism in cell communication and interplay within the tumor microenvironment (TME) and beyond. Understanding these interactions in depth might lead to the discovery of novel markers and new therapeutic interventions for CRC. Finally, we discuss the crucial role of fatty acid metabolism as new targetable gatekeeper in colorectal cancer.
Collapse
|
16
|
Barata T, Vieira V, Rodrigues R, Neves RPD, Rocha M. Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells. Comput Biol Med 2021; 142:105177. [PMID: 35026576 DOI: 10.1016/j.compbiomed.2021.105177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023]
Abstract
Cancer Stem Cells (CSCs) contribute to cancer aggressiveness, metastasis, chemo/radio-therapy resistance, and tumor recurrence. Recent studies emphasized the importance of metabolic reprogramming of CSCs for the maintenance and progression of the cancer phenotype through both the fulfillment of the energetic requirements and the supply of substrates fundamental for fast-cell growth, as well as through metabolite-induced epigenetic regulation. Therefore, it is of paramount importance to develop therapeutic strategies tailored to target the metabolism of CSCs. In this work, we built computational Genome-Scale Metabolic Models (GSMMs) for CSCs of different tissues. Flux simulations were then used to predict metabolic phenotypes, identify potential therapeutic targets, and spot already-known Transcription Factors (TFs), miRNAs and antimetabolites that could be used as part of drug repurposing strategies against cancer. Results were in accordance with experimental evidence, provided insights of new metabolic mechanisms for already known agents, and allowed for the identification of potential new targets and compounds that could be interesting for further in vitro and in vivo validation.
Collapse
Affiliation(s)
- Tânia Barata
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - Vítor Vieira
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Rúben Rodrigues
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal.
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal; Department of Informatics, University of Minho.
| |
Collapse
|
17
|
Symeonidou V, Jakobczyk H, Bashanfer S, Malouf C, Fotopoulou F, Kotecha RS, Anderson RA, Finch AJ, Ottersbach K. Defining the fetal origin of MLL-AF4 infant leukemia highlights specific fatty acid requirements. Cell Rep 2021; 37:109900. [PMID: 34706236 PMCID: PMC8567312 DOI: 10.1016/j.celrep.2021.109900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/01/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022] Open
Abstract
Infant MLL-AF4-driven acute lymphoblastic leukemia (ALL) is a devastating disease with dismal prognosis. A lack of understanding of the unique biology of this disease, particularly its prenatal origin, has hindered improvement of survival. We perform multiple RNA sequencing experiments on fetal, neonatal, and adult hematopoietic stem and progenitor cells from human and mouse. This allows definition of a conserved fetal transcriptional signature characterized by a prominent proliferative and oncogenic nature that persists in infant ALL blasts. From this signature, we identify a number of genes in functional validation studies that are critical for survival of MLL-AF4+ ALL cells. Of particular interest are PLK1 because of the readily available inhibitor and ELOVL1, which highlights altered fatty acid metabolism as a feature of infant ALL. We identify which aspects of the disease are residues of its fetal origin and potential disease vulnerabilities.
Collapse
Affiliation(s)
- Vasiliki Symeonidou
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Hélène Jakobczyk
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Salem Bashanfer
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Camille Malouf
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Foteini Fotopoulou
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Richard A Anderson
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Andrew J Finch
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Katrin Ottersbach
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK.
| |
Collapse
|
18
|
Pakiet A, Sikora K, Kobiela J, Rostkowska O, Mika A, Sledzinski T. Alterations in complex lipids in tumor tissue of patients with colorectal cancer. Lipids Health Dis 2021; 20:85. [PMID: 34348720 PMCID: PMC8340484 DOI: 10.1186/s12944-021-01512-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/26/2021] [Indexed: 12/29/2022] Open
Abstract
Background Accumulating evidence indicates alterations in lipid metabolism and lipid composition in neoplastic tissue. Earlier nuclear magnetic resonance studies showed that the contents of major lipid groups, such as triacylglycerols, phospholipids and cholesterol, are changed in colon cancer tissue. Methods In this study, a more detailed analysis of lipids in cancer and tumor adjacent tissues from colorectal cancer patients, using liquid chromatography–mass spectrometry, allowed for comparison of 199 different lipids between cancer tissue and tumor adjacent tissue using principal component analysis. Results Significant differences were found in 67 lipid compounds between the two types of tissue; many of these lipid compounds are bioactive lipids such as ceramides, lysophospholipids or sterols and can influence the development of cancer. Additionally, increased levels of phospholipids and sphingolipids were present, which are major components of the cell membrane, and increases in these lipids can lead to changes in cell membrane properties. Conclusions This study showed that many complex lipids are significantly increased or decreased in colon cancer tissue, reflecting significant alterations in lipid metabolism. This knowledge can be used for the selection of potential molecular targets of novel anticancer strategies based on the modulation of lipid metabolism and the composition of the cell membrane in colorectal cancer cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12944-021-01512-x.
Collapse
Affiliation(s)
- Alicja Pakiet
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Kinga Sikora
- Physics-Chemistry Workshops, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Jarek Kobiela
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdansk, Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Olga Rostkowska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdansk, Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Adriana Mika
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland.
| |
Collapse
|
19
|
Peroxisomal ABC Transporters: An Update. Int J Mol Sci 2021; 22:ijms22116093. [PMID: 34198763 PMCID: PMC8201181 DOI: 10.3390/ijms22116093] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
ATP-binding cassette (ABC) transporters constitute one of the largest superfamilies of conserved proteins from bacteria to mammals. In humans, three members of this family are expressed in the peroxisomal membrane and belong to the subfamily D: ABCD1 (ALDP), ABCD2 (ALDRP), and ABCD3 (PMP70). These half-transporters must dimerize to form a functional transporter, but they are thought to exist primarily as tetramers. They possess overlapping but specific substrate specificity, allowing the transport of various lipids into the peroxisomal matrix. The defects of ABCD1 and ABCD3 are responsible for two genetic disorders called X-linked adrenoleukodystrophy and congenital bile acid synthesis defect 5, respectively. In addition to their role in peroxisome metabolism, it has recently been proposed that peroxisomal ABC transporters participate in cell signaling and cell control, particularly in cancer. This review presents an overview of the knowledge on the structure, function, and mechanisms involving these proteins and their link to pathologies. We summarize the different in vitro and in vivo models existing across the species to study peroxisomal ABC transporters and the consequences of their defects. Finally, an overview of the known and possible interactome involving these proteins, which reveal putative and unexpected new functions, is shown and discussed.
Collapse
|