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Zheng T, Zhang Z, Yu Z, Wang H, Lyu X, Han C. Investigation on the mechanisms of scorpion venom in hepatocellular carcinoma model mice via untargeted metabolomics profiling. Int Immunopharmacol 2024; 138:112578. [PMID: 38959539 DOI: 10.1016/j.intimp.2024.112578] [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: 01/28/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Metabolic reprogramming is frequently accompanied by hepatocellular carcinoma (HCC) progression. Disrupted metabolites act as potential biomarkers and drug therapeutic targets for HCC. Peptide extract of scorpion venom (PESV) induces cytotoxic anti-proliferative effects and apoptosis in tumors. However, the action mechanisms of PESV remain unknown. This study aimed to explore the serum metabolic profiles of tumor-bearing mouse model. We generated an orthotopic HCC xenograft mouse model by implanting H22 cells into the left hepatic lobe of male C57BL/6 mice. After surgery, the mice were assigned to two groups randomly: PESV (PESV-treated 40 mg/kg daily, i.g.; n = 6) and control (treated with the solvent equally for 14 d, n = 6) groups. Based on an untargeted metabolomics approach using ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry, differential metabolites were screened via univariate and multivariate data analyses. A total of 48 differential metabolites in negative ion mode and 63 in positive ion mode were identified in the serum samples. Furthermore, metabolic pathway analysis revealed that aminoacyl-tRNA biosynthesis, amino acid pathway, glutathione metabolism, protein transports, protein digestion and absorption, and cAMP signaling pathways play vital roles in PESV-induced inhibition of tumors. These findings highlight the distinct changes in the metabolic profiles of HCC-bearing mice after PESV treatment, suggesting the potential of the identified metabolic molecules as therapeutic targets for HCC.
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Affiliation(s)
- Tiancheng Zheng
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhaoxiang Zhang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zishang Yu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hengxiao Wang
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xinxing Lyu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China; Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
| | - Chen Han
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China; Department of clinical research center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
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Brival R, Ghafari N, Mingotaud AF, Fourquaux I, Gilard V, Collin F, Vicendo P, Balayssac S, Gibot L. Encapsulation of photosensitizer worsen cell responses after photodynamic therapy protocol and polymer micelles act as biomodulators on their own. Int J Pharm 2024; 663:124589. [PMID: 39147251 DOI: 10.1016/j.ijpharm.2024.124589] [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: 04/07/2024] [Revised: 08/02/2024] [Accepted: 08/13/2024] [Indexed: 08/17/2024]
Abstract
Photodynamic therapy (PDT) is a photochemical therapeutic modality used clinically for dermatological, ophthalmological and oncological applications. Pheo a was used as a model photosensitizer, either in its free form or encapsulated within poly(ethylene oxide)-block-poly(ε-caprolactone) (PEO-PCL) polymer micelles. Block copolymer micelles are water-soluble biocompatible nanocontainers with great potential for delivering hydrophobic drugs. Empty PEO-PCL micelles were also tested throughout the experiments. The goal was to conduct an in vitro investigation into human colorectal tumor HCT-116 cellular responses induced by free and encapsulated Pheo a in terms of cell architecture, plasma membrane exchanges, mitochondrial function, and metabolic disturbances. In a calibrated PDT protocol, encapsulation enhanced Pheo a penetration (flow cytometry, confocal microscopy) and cell death (Prestoblue assay), causing massive changes to cell morphology (SEM) and cytoskeleton organization (confocal), mitochondrial dysfunction and loss of integrity (TEM), rapid and massive ion fluxes across the plasma membrane (ICP-OES, ion chromatography), and metabolic alterations, including increased levels of amino acids and choline derivatives (1H NMR). The detailed investigation provides insights into the multifaceted effects of encapsulated Pheo-PDT, emphasizing the importance of considering both the photosensitizer and its delivery system in understanding therapeutic outcomes. The study also raises questions as to the broader impact of empty nanovectors per se, and encourages a more comprehensive exploration of their biological effects.
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Affiliation(s)
- Rachel Brival
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France; Centre de Microscopie Electronique Appliquée à la Biologie, Faculté de Médecine Toulouse Rangueil, Université de Toulouse, 133, route de Narbonne, 31062 Toulouse, France
| | - Nathan Ghafari
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Anne-Françoise Mingotaud
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Isabelle Fourquaux
- Centre de Microscopie Electronique Appliquée à la Biologie, Faculté de Médecine Toulouse Rangueil, Université de Toulouse, 133, route de Narbonne, 31062 Toulouse, France
| | - Véronique Gilard
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Fabrice Collin
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Patricia Vicendo
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Stéphane Balayssac
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France
| | - Laure Gibot
- Laboratoire Softmat, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 31062 Toulouse, France.
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Bartho LA, McKeating DR, Walker SP, Nijagal B, MacDonald TM, Pritchard N, Hannan NJ, Perkins AV, Tong S, Kaitu'u-Lino TJ. Plasma metabolites are altered before and after diagnosis of preeclampsia or fetal growth restriction. Sci Rep 2024; 14:15829. [PMID: 38982217 PMCID: PMC11233654 DOI: 10.1038/s41598-024-65947-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Metabolomics is the study of small molecules (metabolites), within cells, tissues and biofluids. Maternal metabolites can provide important insight into the health and development of both mother and fetus throughout pregnancy. This study assessed metabolic profiles in the maternal circulation prior to and at the time of diagnosis of preeclampsia and fetal growth restriction. Maternal plasma samples were collected from two independent cohorts: (1) Established disease cohort: 50 participants diagnosed with early-onset preeclampsia (< 34 weeks' gestation), 14 with early-onset fetal growth restriction, and 25 gestation-matched controls. (2) Prospective cohort, collected at 36 weeks' gestation before diagnosis: 17 participants later developed preeclampsia, 49 delivered infants with fetal growth restriction (birthweight < 5th centile), and 72 randomly selected controls. Metabolic evaluation was performed by Metabolomics Australia on the Agilent 6545 QTOF Mass Spectrometer. In the established disease cohort, 77 metabolites were altered in circulation from participants with preeclampsia - increased L-cysteine (3.73-fold), L-cystine (3.28-fold), L-acetylcarnitine (2.57-fold), and carnitine (1.53-fold) (p < 0.05). There were 53 metabolites dysregulated in participants who delivered a fetal growth restriction infant-including increased levulinic acid, citric acid (1.93-fold), and creatine (1.14-fold) (p < 0.05). In the prospective cohort, 30 metabolites were altered in participants who later developed preeclampsia at term - reduced glutaric acid (0.85-fold), porphobilinogen (0.77-fold) and amininohippuric acid (0.82-fold) (p < 0.05) was observed. There were 5 metabolites altered in participants who later delivered a fetal growth restriction infant - including reduced 3-methoxybenzenepropanoic acid (p < 0.05). Downstream pathway analysis revealed aminoacyl-tRNA biosynthesis to be most significantly altered in the established cohort in preeclampsia (13/48 hits, p < 0.001) and fetal growth restriction (7/48 hits, p < 0.001). The predictive cohort showed no significant pathway alterations. This study observed altered metabolites in maternal plasma collected before and after diagnosis of a preeclampsia or fetal growth restriction. While a significant number of metabolites were altered with established disease, few changes were observed in the predictive cohort. Thus, metabolites measured in this study may not be useful as predictors of preeclampsia or fetal growth restriction.
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Affiliation(s)
- Lucy A Bartho
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia.
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia.
| | - Daniel R McKeating
- School of Medical Science, Griffith University, Gold Coast Campus, Parklands Drive, Southport, QLD, 4215, Australia
| | - Susan P Walker
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Brunda Nijagal
- School of Medical Science, Griffith University, Gold Coast Campus, Parklands Drive, Southport, QLD, 4215, Australia
- Metabolomics Australia, Bio21, University of Melbourne, Parkville, VIC, Australia
| | - Teresa M MacDonald
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Natasha Pritchard
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Natalie J Hannan
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Anthony V Perkins
- School of Medical Science, Griffith University, Gold Coast Campus, Parklands Drive, Southport, QLD, 4215, Australia
| | - Stephen Tong
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Tu'uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, 163 Studley Road, Heidelberg, VIC, 3084, Australia
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, VIC, Australia
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Duan J, Zhang X, Xu J, Liu J, Zhao H. Unveiling a cuproptosis-related risk model and the role of FARSB in hepatocellular carcinoma. Heliyon 2024; 10:e32289. [PMID: 38975141 PMCID: PMC11226817 DOI: 10.1016/j.heliyon.2024.e32289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
Background Cuproptosis, a type of regulated cell death that was recently identified, has been linked to the development of a variety of diseases, among them being cancers. Nevertheless, the prognostic significance and therapeutic implications of the cuproptosis potential index in hepatocellular carcinoma (HCC) remain uncertain. Methods Single-sample gene set enrichment analysis (ssGSEA) and Weighted Gene Co-expression Network Analysis (WGCNA) methodology was conducted to ascertain the identification of modular genes that are closely linked to cuproptosis. In addition, the gene signature indicative of prognosis was formulated by employing univariate Cox regression analysis in conjunction with a random forest algorithm. The efficacy of this gene signature in predicting outcomes was confirmed through validation in both The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. Furthermore, a study was undertaken to evaluate the association between the risk score and various clinical-pathological characteristics, explore the biological processes linked to the gene signature, and analyze tumor mutational burden and somatic mutations. Lastly, potential drugs targeting the identified gene signature were identified through screening. Results The results of our comprehensive analysis across multiple cancer types demonstrated a positive correlation between an elevated cuproptosis potential index (CPI) and an accelerated rate of tumor progression. Furthermore, employing the WGCNA technique, we successfully identified 640 genes associated with cuproptosis. Among these genes, we meticulously screened and validated a seven-gene signature (TCOF1, NOP58, TMEM69, FARSB, DHX37, SLC16A3, and CBX2) that exhibited substantial prognostic significance. Using the median risk score, the division of HCC patients into cohorts with high- and low-risk highlighted significant disparities in survival results, wherein the group with higher risk exhibited a less favorable overall survival. The risk score exhibited commendable predictive efficacy. Moreover, the in vitro knockdown of FARSB significantly hindered cell viability, induced G1 phase arrest, increased apoptosis, and impaired migration in HepG2 and Huh7 cells. Conclusion Our research has successfully identified a strong seven-gene signature linked to cuproptosis, which could be utilized for prognostic evaluation and risk stratification in patients with HCC. Furthermore, the discovered gene signature, coupled with the functional analysis of FARSB, presents promising prospects as potential targets for therapeutic interventions in HCC.
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Affiliation(s)
- Junlin Duan
- Department of Clinical Laboratory, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, China
| | - Xuan Zhang
- Department of Traditional Chinese Medicine, Navy NO.905 Hospital, Navy Medical University, Shanghai, China
| | - Jingyu Xu
- Department of Traditional Chinese Medicine, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Jun Liu
- Department of Clinical Laboratory, Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, China
| | - Hetong Zhao
- Department of Traditional Chinese Medicine, Navy NO.905 Hospital, Navy Medical University, Shanghai, China
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Jayathirtha M, Jayaweera T, Whitham D, Sullivan I, Petre BA, Darie CC, Neagu AN. Two-Dimensional-PAGE Coupled with nLC-MS/MS-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in MCF7 Breast Cancer Cells Transfected for JTB Protein Silencing. Molecules 2023; 28:7501. [PMID: 38005222 PMCID: PMC10673289 DOI: 10.3390/molecules28227501] [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: 09/27/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The identification of new cancer-associated genes/proteins, the characterization of their expression variation, the interactomics-based assessment of differentially expressed genes/proteins (DEGs/DEPs), and understanding the tumorigenic pathways and biological processes involved in BC genesis and progression are necessary and possible by the rapid and recent advances in bioinformatics and molecular profiling strategies. Taking into account the opinion of other authors, as well as based on our own team's in vitro studies, we suggest that the human jumping translocation breakpoint (hJTB) protein might be considered as a tumor biomarker for BC and should be studied as a target for BC therapy. In this study, we identify DEPs, carcinogenic pathways, and biological processes associated with JTB silencing, using 2D-PAGE coupled with nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) proteomics applied to a MCF7 breast cancer cell line, for complementing and completing our previous results based on SDS-PAGE, as well as in-solution proteomics of MCF7 cells transfected for JTB downregulation. The functions of significant DEPs are analyzed using GSEA and KEGG analyses. Almost all DEPs exert pro-tumorigenic effects in the JTBlow condition, sustaining the tumor suppressive function of JTB. Thus, the identified DEPs are involved in several signaling and metabolic pathways that play pro-tumorigenic roles: EMT, ERK/MAPK, PI3K/AKT, Wnt/β-catenin, mTOR, C-MYC, NF-κB, IFN-γ and IFN-α responses, UPR, and glycolysis/gluconeogenesis. These pathways sustain cancer cell growth, adhesion, survival, proliferation, invasion, metastasis, resistance to apoptosis, tight junctions and cytoskeleton reorganization, the maintenance of stemness, metabolic reprogramming, survival in a hostile environment, and sustain a poor clinical outcome. In conclusion, JTB silencing might increase the neoplastic phenotype and behavior of the MCF7 BC cell line. The data is available via ProteomeXchange with the identifier PXD046265.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Taniya Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Isabelle Sullivan
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Brîndușa Alina Petre
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd. No. 22, 700505 Iasi, Romania
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Yin K, Wang D, Zhang Y, Lu H, Wang Y, Xing M. Dose-effect of polystyrene microplastics on digestive toxicity in chickens (Gallus gallus): Multi-omics reveals critical role of gut-liver axis. J Adv Res 2023; 52:3-18. [PMID: 36334886 PMCID: PMC10555772 DOI: 10.1016/j.jare.2022.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/19/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Microplastic pollution seriously threatens the health and safety of humans and wildlife. Avian is one of the main species endangered by microplastics. However, the damage mechanism of microplastics to the digestive system of avian is not clear. OBJECTIVES The gut-liver axis is a bidirectional channel that regulates the exchange of information between the gut and the liver and is also a key target for tissue damage caused by pollutants. This study aimed to elucidate the digestive toxicity of microplastics in avian and the key role of the gut-liver axis in it. METHODS We constructed an exposure model for microplastics in environmental concentrations and toxicological concentrations in chickens and reveal the digestive toxicity of polystyrene microplastics (PS-MPs) in avian by 16S rRNA, transcriptomics and metabolomics. RESULTS PS-MPs changed the death mode from apoptosis to necrosis and pyroptosis by upregulating Caspase 8, disrupting the intestinal vascular barrier, disturbing the intestinal flora and promoting the accumulation of lipopolysaccharide. Harmful flora and metabolites were translocated to the liver through the liver-gut axis, eliciting hepatic immune responses and promoting hepatic lipid metabolism disorders and apoptosis. Liver injury involves multiple molecular effects of mitochondrial dynamics disturbance, oxidative stress, endoplasmic reticulum stress, and cell cycle disturbance. Furthermore, metabolomics suggested that caffeine and melanin metabolites may be potential natural resistance substances for microplastics. CONCLUSION Taken together, our data demonstrate the digestive damage of PS-MPs in avian, revealing a critical role of the liver-gut axis in it. This will provide a reference for protecting the safety of avian populations.
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Affiliation(s)
- Kai Yin
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China
| | - Dongxu Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China
| | - Yue Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China
| | - Hongmin Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China
| | - Yu Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China.
| | - Mingwei Xing
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, Heilongjiang, PR China.
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Du Q, Wang X, Chen J, Wang Y, Liu W, Wang L, Liu H, Jiang L, Nie Z. Machine learning encodes urine and serum metabolic patterns for autoimmune disease discrimination, classification and metabolic dysregulation analysis. Analyst 2023; 148:4318-4330. [PMID: 37547947 DOI: 10.1039/d3an01051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
There is a wide variety of autoimmune diseases (ADs) with complex pathogenesis and their accurate diagnosis is difficult to achieve because of their vague symptoms. Metabolomics has been proven to be an efficient tool in the analysis of metabolic disorders to provide clues about the mechanism and diagnosis of diseases. Previous studies of the metabolomics analysis of ADs were not competent in their discrimination. Herein, a liquid chromatography tandem mass spectrometry (LC-MS) strategy combined with machine learning is proposed for the discrimination and classification of ADs. Urine and serum samples were collected from 267 subjects consisting of 127 healthy controls (HC) and 140 AD patients, including those with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), sicca syndrome (SS), ankylosing spondylitis (AS), systemic scleroderma (SSc) and connective tissue disease (CTD). Machine learning algorithms were encoded for the discrimination and classification of ADs with metabolomic patterns obtained by LC-MS, and satisfactory results were achieved. Notably, urine samples exhibited higher accuracy for disease differentiation and triage than serum samples. Apart from that, differential metabolites were selected and metabolite panels were evaluated to demonstrate their representativeness. Metabolic dysregulations were also investigated to gain more knowledge about the pathogenesis of ADs. This research provides a promising method for the application of metabolomics combined with machine learning in precision medicine.
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Affiliation(s)
- Qiuyao Du
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenlan Liu
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Liping Wang
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province 341000, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li J, Wen J, Hu R, Pei S, Li T, Shan B, Huang H, Zhu C. Transcriptome Responses to Different Environments in Intertidal Zones in the Peanut Worm Sipunculus nudus. BIOLOGY 2023; 12:1182. [PMID: 37759582 PMCID: PMC10525638 DOI: 10.3390/biology12091182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023]
Abstract
The peanut worm (Sipunculus nudus) is an important intertidal species worldwide. Species living in the same aquaculture area might suffer different environmental impacts. To increase knowledge of the molecular mechanisms underlying the response to environmental fluctuations, we performed a transcriptome analysis of S. nudus from different intertidal zones using a combination of the SMRT platform and the Illumina sequencing platform. (1) A total of 105,259 unigenes were assembled, and 23,063 unigenes were perfectly annotated. The results of the PacBio Iso-Seq and IIIumina RNA-Seq enriched the genetic database of S. nudus. (2) A total of 830 DEGs were detected in S. nudus from the different groups. In particular, 33 DEGs had differential expression in the top nine KEGG pathways related to pathogens, protein synthesis, and cellular immune response and signaling. The results indicate that S. nudus from different zones experience different environmental stresses. (3) Several DEGs (HSPA1, NFKBIA, eEF1A, etc.) in pathways related to pathogens (influenza A, legionellosis, measles, and toxoplasmosis) had higher expression in groups M and L. HSPA1 was clearly enriched in most of the pathways, followed by NFKBIA. The results show that the peanut worms from the M and L tidal flats might have suffered more severe environmental conditions. (4) Some DEGs (MKP, MRAS, and HSPB1) were upregulated in peanut worms from the H tidal flat, and these DEGs were mainly involved in the MAPK signaling pathway. These results indicate that the MAPK pathway may play a vital role in the immune response of the peanut worm to the effects of different intertidal flats. This study provides a valuable starting point for further studies to elucidate the molecular basis of the response to different environmental stresses in S. nudus.
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Affiliation(s)
- Junwei Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Jiufu Wen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Ruiping Hu
- Institute of Biological and Medical Engineering, Guangdong Academy of Science, Guangzhou 510316, China
| | - Surui Pei
- Corregene Biotechnology Co., Ltd., Beijing 102600, China;
| | - Ting Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Binbin Shan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Honghui Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (J.L.); (J.W.); (T.L.); (B.S.); (H.H.)
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Changbo Zhu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
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9
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Gui Z, Liu P, Zhang D, Wang W. Clinical implications and immune implications features of TARS1 in breast cancer. Front Oncol 2023; 13:1207867. [PMID: 37637061 PMCID: PMC10455957 DOI: 10.3389/fonc.2023.1207867] [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: 04/18/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Background There has been an increase in the number of women suffering from breast cancer in recent years, and discovering new therapeutic targets and efficacy predictive markers is critical for comprehensive breast cancer treatment. Methods First, we used bioinformatics methods to analyze TARS1(encoding cytoplasmicthreonyl-tRNA synthetase) expression, prognosis, and clinicopathological characteristics in TCGA database breast cancers, and then we collected breast cancer specimens from our center for validation. TARS1 was then subjected to GSEA (Gene Set Enrichment Analysis) enrichment analysis, GO/KEGG pathway enrichment analysis, and breast cancer immune infiltration characterization. As a last step, we examined TARS1's effects on breast cancer cell behavior with cellular assays. Results The overexpression of TARS1 has been found in several malignant tumors, including breast cancer, and has been linked to poor prognoses. Breast cancers with large primary tumors and negative hormone receptors are more likely to overexpress TARS1. Overexpression of TARS1 promotes the infiltration of T cells, such as Tregs and Th2s, while inhibiting the infiltration of NK cells and CD8+ T cells, which are anticancer cells in breast cancer. TARS1 was also found to be co-expressed with the majority of immune checkpoint-related genes, and breast cancer with TARS1 overexpression responded better to immunotherapy. By knocking down TARS1, breast cancer cells were prevented from proliferating and invading, as well as exhibiting other malignant biological properties. Conclusion According to our study, TARS1 may be an oncogene in breast cancer and may be a biomarker of efficacy or a target of immunotherapy in breast cancer.
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Affiliation(s)
- Zhengwei Gui
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Breast and Thyroid Surgery, Tongji Hospital, Wuhan, Hubei, China
| | - Piao Liu
- Department of General Surgery, Hubei Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Wuhan, Hubei, China
| | - Dong Zhang
- Department of General Surgery, Hubei Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Wuhan, Hubei, China
| | - Wanju Wang
- Department of General Surgery, Hubei Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Wuhan, Hubei, China
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10
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Alapati S, Fortuna G, Ramage G, Delaney C. Evaluation of Metabolomics as Diagnostic Targets in Oral Squamous Cell Carcinoma: A Systematic Review. Metabolites 2023; 13:890. [PMID: 37623834 PMCID: PMC10456490 DOI: 10.3390/metabo13080890] [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: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
In recent years, high-throughput technologies have facilitated the widespread use of metabolomics to identify biomarkers and targets for oral squamous cell carcinoma (OSCC). As a result, the primary goal of this systematic review is to identify and evaluate metabolite biomarkers and their pathways for OSCC that featured consistently across studies despite methodological variations. Six electronic databases (Medline, Cochrane, Web of Science, CINAHL, ProQuest, and Embase) were reviewed for the longitudinal studies involving OSCC patients and metabolic marker analysis (in accordance with PRISMA 2020). The studies included ranged from the inception of metabolomics in OSCC (i.e., 1 January 2007) to 30 April 2023. The included studies were then assessed for their quality using the modified version of NIH quality assessment tool and QUADOMICS. Thirteen studies were included after screening 2285 studies. The majority of the studies were from South Asian regions, and metabolites were most frequently derived from saliva. Amino acids accounted for more than quarter of the detected metabolites, with glutamate and methionine being the most prominent. The top dysregulated metabolites indicated dysregulation of six significantly enriched pathways including aminoacyl-tRNA biosynthesis, glutathione metabolism and arginine biosynthesis with the false discovery rate (FDR) <0.05. Finally, this review highlights the potential of metabolomics for early diagnosis and therapeutic targeting of OSCC. However, larger studies and standardized protocols are needed to validate these findings and make them a clinical reality.
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Affiliation(s)
- Susanth Alapati
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, University of Glasgow, 378 Sauchiehall Street, Glasgow G2 3JZ, UK; (S.A.)
| | - Giulio Fortuna
- Department of Oral Medicine, Glasgow Dental School, School of Medicine, Dentistry and Nursing, University of Glasgow, 378 Sauchiehall Street, Glasgow G2 3JZ, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, University of Glasgow, 378 Sauchiehall Street, Glasgow G2 3JZ, UK; (S.A.)
| | - Christopher Delaney
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, University of Glasgow, 378 Sauchiehall Street, Glasgow G2 3JZ, UK; (S.A.)
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11
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Liang W, Hu C, Zhu Q, Cheng X, Gao S, Liu Z, Wang H, Li P, Gao Y, Qian R. Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma. Front Oncol 2023; 13:1007198. [PMID: 37284202 PMCID: PMC10240054 DOI: 10.3389/fonc.2023.1007198] [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: 08/02/2022] [Accepted: 03/29/2023] [Indexed: 06/08/2023] Open
Abstract
Nuclear pore complex (NPC) is a major transport pivot for nucleocytoplasmic molecule exchange. Nucleoporin 205 (NUP205)-a main component of NPC-plays a key regulatory role in tumor cell proliferation; however, few reports document its effect on the pathological progression of lower-grade glioma (LGG). Therefore, we conducted an integrated analysis using 906 samples from multiple public databases to explore the effects of NUP205 on the prognosis, clinicopathological characteristics, regulatory mechanism, and tumor immune microenvironment (TIME) formation in LGG. First, multiple methods consistently showed that the mRNA and protein expression levels of NUP205 were higher in LGG tumor tissue than in normal brain tissue. This increased expression was mainly noted in the higher WHO Grade, IDH-wild type, and 1p19q non-codeleted type. Second, various survival analysis methods showed that the highly expressed NUP205 was an independent risk indicator that led to reduced survival time of patients with LGG. Third, GSEA analysis showed that NUP205 regulated the pathological progress of LGG via the cell cycle, notch signaling pathway, and aminoacyl-tRNA biosynthesis. Ultimately, immune correlation analysis suggested that high NUP205 expression was positively correlated with the infiltration of multiple immune cells, particularly M2 macrophages, and was positively correlated with eight immune checkpoints, particularly PD-L1. Collectively, this study documented the pathogenicity of NUP205 in LGG for the first time, expanding our understanding of its molecular function. Furthermore, this study highlighted the potential value of NUP205 as a target of anti-LGG immunotherapy.
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Affiliation(s)
- Wenjia Liang
- People’s Hospital of Henan University, Henan Provincial People’s Hospital, Microbiome Laboratory, Zhengzhou, Henan, China
| | - Chenchen Hu
- Intensive Care Unit, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingyun Zhu
- People’s Hospital of Henan University, Henan Provincial People’s Hospital, Microbiome Laboratory, Zhengzhou, Henan, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Shanjun Gao
- Microbiome Laboratory, Henan Provincial People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Hongbo Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Pengxu Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People’s Hospital, People’s Hospital of Henan University, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
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12
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Zhen J, Pan J, Zhou X, Yu Z, Jiang Y, Gong Y, Ding Y, Liu Y, Guo L. FARSB serves as a novel hypomethylated and immune cell infiltration related prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2937-2969. [PMID: 37074800 DOI: 10.18632/aging.204619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/09/2023] [Indexed: 04/20/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a prevalent tumor with high morbidity, and an unfavourable prognosis. FARSB is an aminoacyl tRNA synthase, and plays a key role in protein synthesis in cells. Furthermore, previous reports have indicated that FARSB is overexpressed in gastric tumor tissues and is associated with a poor prognosis and tumorigenesis. However, the function of FARSB in HCC has not been studied. RESULTS The results showed that FARSB mRNA and protein levels were upregulated in HCC and were closely related to many clinicopathological characteristics. Besides, according to multivariate Cox analysis, high FARSB expression was linked with a shorter survival time in HCC and may be an independent prognostic factor. In addition, the FARSB promoter methylation level was negatively associated with the expression of FARSB. Furthermore, enrichment analysis showed that FARSB was related to the cell cycle. And TIMER analysis revealed that the FARSB expression was closely linked to tumor purity and immune cell infiltration. The TCGA and ICGC data analysis suggested that FARSB expression is greatly related to m6A modifier related genes. Potential FARSB-related ceRNA regulatory networks were also constructed. What's more, based on the FARSB-protein interaction network, molecular docking models of FARSB and RPLP1 were constructed. Finally, drug susceptibility testing revealed that FARSB was susceptible to 38 different drugs or small molecules. CONCLUSIONS FARSB can serve as a prognostic biomarker for HCC and provide clues about immune infiltration, and m6A modification.
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Affiliation(s)
- Jing Zhen
- Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yongqi Ding
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yue Liu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Liangyun Guo
- Department of Ultrasonography, Second Affiliated Hospital of Nanchang University, Nanchang, China
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Yang M, Wu X, He C, Zhang J, Hou J, Lin D. nZVI-induced iron poisoning aggravated the toxicity of TCEP to earthworm in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120785. [PMID: 36460191 DOI: 10.1016/j.envpol.2022.120785] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Tris (2-chloroethyl) phosphate (TCEP) is a newly developed organophosphorus flame retardant that has been increasingly detected in soil as a contaminant. Nanoremediation is a potential solution for the control of TCEP, while the effectiveness and ecological risks are poorly understood. Here, we investigated the physicochemical interactions and joint toxicity of nano zero-valent iron (nZVI) (50-5000 mg/kg) and TCEP (50-5000 μg/kg) at environmental relevant concentrations to earthworms (Eisenia fetida) in soil. During a 28-d exposure, TCEP in soil was neither self-degraded nor removed by nZVI, and the individual toxicity of TCEP on the physiology of earthworms was significantly higher than that of nZVI. Notably, nZVI was found to synergize the toxicity of TCEP to earthworms without showing the classical "Trojan horse effect". Mechanically, TCEP mainly induced a typical neurotoxicity, and indirectly inhibited the food ingestion and growth performance of earthworms; nZVI induced iron poisoning aggravated the intestinal damage and directly inhibited the energy metabolism, therefore exacerbated the TCEP-induced malnutrition. Our findings provide new insights into the toxic mechanisms of nZVI-TCEP co-exposure to soil organisms, and emphasize the necessity of risk assessment and cautious usage of nanoremediation in newly emerged contaminations.
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Affiliation(s)
- Meirui Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Xinyue Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Caijiao He
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianying Zhang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China; National Demonstration Center for Experimental Environment and Resources Education (Zhejiang University), Hangzhou, 310058, China
| | - Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China.
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Ecological Civilization Academy, Anji, 313300, China
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14
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Wang F, Gu Z, Zhao X, Chen Z, Zhang Z, Sun S, Han M. Metabolic characteristics of the various incision margins for breast cancer conservation surgery. Front Oncol 2023; 12:959454. [PMID: 36686765 PMCID: PMC9846322 DOI: 10.3389/fonc.2022.959454] [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: 06/01/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Background Breast cancer (BC) has recently become the most prevalent malignancy in women. There are many alternative treatments for BC, and for aesthetic and postoperative quality of life concerns, breast-conserving surgery and corresponding adjuvant therapy have become the predominant treatment for early invasive BC. Currently, the main method used to assess the margins for breast-conserving surgery is intraoperative pathological diagnosis. However, the designation of surgical margins is controversial, and metabolomics may be a novel approach to evaluate surgical margins. Methods We collected specimens from 10 breast cancer patients and samples from its surrounding tissues and divided them into cancerous tissue and 1 mm, 2 mm, 3 mm, 5 mm and 10 mm cutting edge tissues, with a total of 60 samples. The samples were analyzed by mass spectrometry on an ultra-performance liquid chromatography-quadrupole/Orbitrap high resolution platform. The data were then statistically analyzed to detect metabolic changes in the different cutting edges and to identify possible surgical cutting edges with statistically significant findings. Abnormal metabolic pathways were identified by Kyoto Encyclopedia of Genes and Genomes (KEGG), which elucidated potential markers. Results Statistical analysis indicated that there were substantial differences between the 1 mm margin tissue and the cancer tissue, while there were no statistically significant differences between the 1 mm tissue and tissues from the other margins. The levels of 6 metabolites in the 1 mm tissue were significantly different from those in the cancer tissue and were not significantly different from those in the 2 mm tissue. The six metabolites were pyruvate, N-acetyl-L-aspartate, glutamic acid, γ-aminobutyric acid, fumaric acid, and citric acid. Metabolic pathways such as amino acid metabolism and amino t-RNA synthesis in the margin tissue were significantly distinct from those in cancer tissues based on KEGG analysis. Conclusion There was a significant difference between the 1 mm margin tissue and the cancerous tissue. Based on metabolomic analysis, the 1 mm negative margin is sufficient for surgery, and the six metabolites that we identified as abnormal, including pyruvic acid, N-acetyl-L-aspartic acid, glutamic acid, gamma-aminobutyric acid, fumaric acid and citric acid, may serve as biomarkers for a negative margin and help surgeons select an appropriate surgical margin.
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15
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Sun Z, Wu Y, Gao F, Li H, Wang C, Du L, Dong L, Jiang Y. In situ detection of exosomal RNAs for cancer diagnosis. Acta Biomater 2023; 155:80-98. [PMID: 36343908 DOI: 10.1016/j.actbio.2022.10.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Exosomes are considered as biomarkers reflecting the physiological state of the human body. Studies have revealed that the expression levels of specific exosomal RNAs are closely associated with certain cancers. Thus, detection of exosomal RNA offers a new avenue for liquid biopsy of cancers. Many exosomal RNA detection methods based on various principles have been developed, and most of the methods detect the extracted RNAs after lysing exosomes. Besides complex and time-consuming extraction steps, a major drawback of this approach is the degradation of the extracted RNAs in the absence of plasma membrane and cytosol. In addition, there is considerable loss of RNAs during their extraction. In situ detection of exosomal RNAs can avoid these drawbacks, thus allowing higher diagnostic reliability. In this paper, in situ detection of exosomal RNAs was systematically reviewed from the perspectives of detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, and involved functional materials. Furthermore, the limitations and possible improvements of the current in situ detection methods for exosomal RNAs towards the clinical diagnostic application are discussed. This review aims to provide a valuable reference for the development of in situ exosomal RNA detection strategies for non-invasive diagnosis of cancers. STATEMENT OF SIGNIFICANCE: Certain RNAs have been identified as valuable biomarkers for some cancers, and sensitive detection of cancer-related RNAs is expected to achieve better diagnostic efficacy. Currently, the detection of exosomal RNAs is receiving increasing attention due to their high stability and significant concentration differences between patients and healthy individuals. In situ detection of exosomal RNAs has greater diagnostic reliability due to the avoidance of RNA degradation and loss. However, this mode is still limited by some factors such as detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, etc. This review focuses on the progress of in situ detection of exosomal RNAs and aims to promote the development of this field.
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Affiliation(s)
- Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Yanqiu Wu
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Fucheng Gao
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Hui Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China.
| | - Lun Dong
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan 250012, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China.
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Ye Y, Yang W, Ruan X, Xu L, Cheng W, Zhao M, Wang X, Chen X, Cai D, Li G, Wang Y, Yan F, Lu X, Jiang L. Metabolism-associated molecular classification of gastric adenocarcinoma. Front Oncol 2022; 12:1024985. [DOI: 10.3389/fonc.2022.1024985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Most gastric cancers (GC) are adenocarcinomas, whereas GC is a highly heterogeneous disease due to its molecular heterogeneity. However, traditional morphology-based classification systems, including the WHO classification and Lauren’s classification, have limited utility in guiding clinical treatment. We performed nonnegative matrix factorization (NMF) clustering based on 2752 metabolism-associated genes. We characterized each of the subclasses from multiple angles, including subclass-associated metabolism signatures, immune cell infiltration, clinic10al characteristics, drug sensitivity, and pathway enrichment. As a result, four subtypes were identified: immune suppressed, metabolic, mesenchymal/immune exhausted and hypermutated. The subtypes exhibited significant prognostic differences, which suggests that the metabolism-related classification has clinical significance. Metabolic and hypermutated subtypes have better overall survival, and the hypermutated subtype is likely to be sensitive to anti-PD-1 immunotherapy. In addition, our work showed a strong connection with previously established classifications, especially Lei’s subtype, to which we provided an interpretation based on the immune cell infiltration perspective, deepening the understanding of GC heterogeneity. Finally, a 120-gene classifier was generated to determine the GC classification, and a 10-gene prognostic model was developed for survival time prediction.
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17
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Yang Y, Dai D, Jin W, Huang Y, Zhang Y, Chen Y, Wang W, Lin W, Chen X, Zhang J, Wang H, Zhang H, Teng L. Microbiota and metabolites alterations in proximal and distal gastric cancer patients. J Transl Med 2022; 20:439. [PMID: 36180919 PMCID: PMC9524040 DOI: 10.1186/s12967-022-03650-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/18/2022] [Indexed: 12/24/2022] Open
Abstract
Background Globally, gastric cancer is the third most common cancer and the third leading cause of cancer death. Proximal and distal gastric cancers have distinct clinical and biological behaviors. The microbial composition and metabolic differences in proximal and distal gastric cancers have not been fully studied and discussed. Methods In this study, the gastric microbiome of 13 proximal gastric cancer tissues, 16 distal gastric cancer tissues, and their matched non-tumor tissues were characterized using 16S rRNA amplicon sequencing. Additionally, 10 proximal gastric cancer tissues, 11 distal gastric cancer tissues, and their matched non-tumor tissues were assessed by untargeted metabolomics. Results There was no significant difference in microbial diversity and richness between the proximal and distal gastric cancer tissues. At the genus level, the abundance of Rikenellaceae_RC9_gut_group, Porphyromonas, Catonella, Proteus, Oribacterium, and Moraxella were significantly increased in Proximal T, whereas that of Methylobacterium_Methylorubrum was significantly increased in Distal T. The untargeted metabolomics analysis revealed 30 discriminative metabolites between Distal T and Distal N. In contrast, there were only 4 discriminative metabolites between Proximal T and Proximal N. In distal gastric cancer, different metabolites were scattered through multiple pathway, including the sphingolipid signaling pathway, arginine biosynthesis, protein digestion and absorption, alanine, aspartate and, glutamate metabolism, etc.In proximal gastric cancer, differential microbial metabolites were mainly related to hormone metabolism. Conclusion Methylobacterium-Methylorubrum was significantly increased in Distal T, positively correlated with cancer-promoting metabolites, and negatively correlated with cancer-inhibiting metabolites. Rikenellaceae_RC_gut_group was significantly increased in Proximal T and positively correlated with cancer-promoting metabolites. Further studies regarding the functions of the above-mentioned microorganisms and metabolites were warranted as the results may reveal the different mechanisms underlying the occurrence and development of proximal and distal gastric cancers and provide a basis for future treatments. Importance First, the differences in microbial composition and metabolites between the proximal and distal gastric cancers were described; then, the correlation between microbiota and metabolites was preliminarily discussed. These microbes and metabolites deserve further investigations as they may reveal the different mechanisms involved in the occurrence and development of proximal and distal gastric cancers and provide a basis for future treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03650-x.
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Affiliation(s)
- Yan Yang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Daofeng Dai
- Jiangxi Otorhinolaryngology Head and Neck Surgery Institute, Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Wen Jin
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yingying Huang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yingzi Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Wankun Wang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Wu Lin
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xiangliu Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jing Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Haohao Wang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Haibin Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Chen H, Huang C, Wu Y, Sun N, Deng C. Exosome Metabolic Patterns on Aptamer-Coupled Polymorphic Carbon for Precise Detection of Early Gastric Cancer. ACS NANO 2022; 16:12952-12963. [PMID: 35946596 DOI: 10.1021/acsnano.2c05355] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gastric cancer (GC) presents high mortality worldwide because of delayed diagnosis. Currently, exosome-based liquid biopsy has been applied in diagnosis and monitoring of diseases including cancers, whereas disease detection based on exosomes at the metabolic level is rarely reported. Herein, the specific aptamer-coupled Au-decorated polymorphic carbon (CoMPC@Au-Apt) is constructed for the capture of urinary exosomes from early GC patients and healthy controls (HCs) and the subsequent exosome metabolic pattern profiling without extra elution process. Combining with machine learning algorithm on all exosome metabolic patterns, the early GC patients are excellently discriminated from HCs, with an accuracy of 100% for both the discovery set and blind test. Ulteriorly, three key metabolic features with clear identities are determined as a biomarker panel, obtaining a more than 90% diagnostic accuracy for early GC in the discovery set and validation set. Moreover, the change law of the key metabolic features along with GC development is revealed through making a comparison among HCs and GC at early stage and advanced stage, manifesting their monitoring ability toward GC. This work illustrates the high specificity of exosomes and the great prospective of exosome metabolic analysis in disease diagnosis and monitoring, which will promote exosome-driven precision medicine toward practical clinical application.
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Affiliation(s)
- Haolin Chen
- Department of Chemistry, Metabolism and Integrative Biology (IMIB), Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Chuwen Huang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yonglei Wu
- Department of Chemistry, Metabolism and Integrative Biology (IMIB), Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunhui Deng
- Department of Chemistry, Metabolism and Integrative Biology (IMIB), Zhongshan Hospital, Fudan University, Shanghai 200433, China
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Chen W, Lin Y, Jiang M, Wang Q, Shu Q. Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification. Lab Invest 2022; 20:355. [PMID: 35962451 PMCID: PMC9373537 DOI: 10.1186/s12967-022-03571-9] [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: 05/19/2022] [Accepted: 08/04/2022] [Indexed: 11/12/2022]
Abstract
Background Osteosarcoma is one of the most malignant tumors, and it occurs mostly in children and adolescents. Currently, surgery and chemotherapy are the main treatments. The recurrence rate is high and the prognosis is often poor. Finding an effective target gene therapy for osteosarcoma may effectively improve its prognosis. Method In this study, genes essential for the survival of osteosarcoma cells were identified by genome-wide screening of CRISPR-Cas9 based on the DepMap database. The expression of these essential genes in osteosarcoma patients’ tissues and normal tissues was identified in the GSE19276 database. Functional pathway enrichment analysis, protein interaction network construction, and LASSO were performed to construct a prognostic risk model based on these essential genes. CCK8 assay was used to detect the effect of essential gene-LARS (Leucyl-TRNA Synthetase 1) on the proliferation of osteosarcoma. Results In this study, 785 genes critical for osteosarcoma cell proliferation were identified from the DepMap. Among these 785 essential genes, 59 DEGs were identified in osteosarcoma tissues. In the functional enrichment analysis, these 59 essential genes were mainly enriched in cell cycle-related signaling pathways. Furthermore, we established a risk score module, including LARS and DNAJC17, screened from these 59 genes, and this module could divide osteosarcoma patients into the low-risk and high-risk groups. In addition, knockdown of LARS expression inhibited the proliferative ability of osteosarcoma cells. A significant correlation was found between LARS expression and Monocytic lineage, T cells, and Fibroblasts. Conclusion In conclusion, LARS was identified as an essential gene for survival in osteosarcoma based on the DepMap database. Knockdown of LARS expression significantly inhibited the proliferation of osteosarcoma cells, suggesting that it is involved in the formation and development of osteosarcoma. The results are useful as a foundation for further studies to elucidate a potential osteosarcoma diagnostic index and therapeutic targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03571-9.
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Affiliation(s)
- Wenhao Chen
- Department of Orthopedics, The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China
| | - Qingshui Wang
- College of Life Sciences, Fujian Normal University, 8 South Xuefu Road, Fuzhou, 350117, Fujian Province, China.
| | - Qiang Shu
- The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China.
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Wusiman W, Zhang Z, Ding Q, Liu M. The pathophyiological role of aminoacyl-tRNA synthetases in digestive system diseases. Front Physiol 2022; 13:935576. [PMID: 36017335 PMCID: PMC9396140 DOI: 10.3389/fphys.2022.935576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the ligation of amino acids to their cognate transfer RNAs and are indispensable enzymes for protein biosynthesis in all the cells. Previously, ARSs were considered simply as housekeeping enzymes, however, they are now known to be involved in a variety of physiological and pathological processes, such as tumorigenesis, angiogenesis, and immune response. In this review, we summarize the role of ARSs in the digestive system, including the esophagus, stomach, small intestine, colon, as well as the auxiliary organs such as the pancreas, liver, and the gallbladder. Furthermore, we specifically focus on the diagnostic and prognostic value of ARSs in cancers, aiming to provide new insights into the pathophysiological implications of ARSs in tumorigenesis.
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Affiliation(s)
- Wugelanmu Wusiman
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zerui Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Ding
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Liu
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Mei Liu,
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21
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Deciphering the Metabolomics-Based Intervention of Yanghe Decoction on Hashimoto's Thyroiditis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6215573. [PMID: 35873647 PMCID: PMC9307328 DOI: 10.1155/2022/6215573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/18/2022]
Abstract
Background Yanghe decoction is a famous formula consisting of Rehmannia, deer horn gum, cinnamon, rue, Ephedra, ginger charcoal, and licorice. However, few studies have explored the role of the potential mechanism of Yanghe decoction in the treatment of Hashimoto's thyroiditis by metabolomics. Methods Nine mice were randomly divided into three groups: control group (group C), model group (group M), and drug administration group (group T), with three mice in each group. Mice in groups M and T were established as models of Hashimoto's thyroiditis, and group T was treated with Yanghe decoction. The metabolome of plasma samples from each group of mice was determined using mass spectrometry coupled with high-performance liquid and gas phases, and nuclear magnetic resonance. Based on the three assays, principal component analysis was performed on all samples, as well as orthogonal partial least squares-discriminant analysis and differential metabolite molecules for groups M and T. Subsequently, pathway enrichment analysis was performed, and the intersection was taken for the differential metabolites screened in the M and T groups. The levels of inflammatory factors IL-35 and IL-6 within the serum of each group of mice were detected. Results The difference analysis showed that a total of 38 differential metabolites were screened based on mass spectrometry coupled with the high-performance liquid phase, 120 differential metabolites were screened based on mass spectrometry coupled with gas phase, and a total of α-glucose and β-glucose were the differential metabolites analyzed based on NMR test results. The pathways enriched by the differential metabolites in the M and T groups were intersected, and a total of 5 common pathways were obtained (amino acid tRNA biosynthesis, D-glutamine and D-glutamate metabolism, tryptophan metabolism, nitrogen metabolism, and arginine and proline metabolism). The results also showed a significant decrease in the serum inflammatory factor IL-35 and a significant increase in IL-6 in mice from group M compared with group C, while a significant increase in the serum inflammatory factor IL-35 and a significant decrease in IL-6 in mice from group T compared with group M. Conclusion Our study reveals the metabolites as well as a metabolic network that can be altered by Yanghe decoction treatment of Hashimoto's thyroiditis and shows that Yanghe decoction can effectively reduce the level of inflammatory factors in Hashimoto's thyroid.
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22
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Liu J, Lu J, Li W, Mao W, Lu Y. Machine Learning Screens Potential Drugs Targeting a Prognostic Gene Signature Associated With Proliferation in Hepatocellular Carcinoma. Front Genet 2022; 13:900380. [PMID: 35836576 PMCID: PMC9273781 DOI: 10.3389/fgene.2022.900380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Background: This study aimed to screen potential drugs targeting a new prognostic gene signature associated with proliferation in hepatocellular carcinoma (HCC). Methods: CRISPR Library and TCGA datasets were used to explore differentially expressed genes (DEGs) related to the proliferation of HCC cells. Differential gene expression analysis, univariate COX regression analysis, random forest algorithm and multiple combinatorial screening were used to construct a prognostic gene signature. Then the predictive power of the gene signature was validated in the TCGA and ICGC datasets. Furthermore, potential drugs targeting this gene signature were screened. Results: A total of 640 DEGs related to HCC proliferation were identified. Using univariate Cox analysis and random forest algorithm, 10 hub genes were screened. Subsequently, using multiplex combinatorial screening, five hub genes (FARSB, NOP58, CCT4, DHX37 and YARS) were identified. Taking the median risk score as a cutoff value, HCC patients were divided into high- and low-risk groups. Kaplan-Meier analysis performed in the training set showed that the overall survival of the high-risk group was worse than that of the low-risk group (p < 0.001). The ROC curve showed a good predictive efficiency of the risk score (AUC > 0.699). The risk score was related to gene mutation, cancer cell stemness and immune function changes. Prediction of immunotherapy suggetsted the IC50s of immune checkpoint inhibitors including A-443654, ABT-888, AG-014699, ATRA, AUY-922, and AZ-628 in the high-risk group were lower than those in the low-risk group, while the IC50s of AMG-706, A-770041, AICAR, AKT inhibitor VIII, Axitinib, and AZD-0530 in the high-risk group were higher than those in the low-risk group. Drug sensitivity analysis indicated that FARSB was positively correlated with Hydroxyurea, Vorinostat, Nelarabine, and Lomustine, while negatively correlated with JNJ-42756493. DHX37 was positively correlated with Raltitrexed, Cytarabine, Cisplatin, Tiotepa, and Triethylene Melamine. YARS was positively correlated with Axitinib, Fluphenazine and Megestrol acetate. NOP58 was positively correlated with Vorinostat and 6-thioguanine. CCT4 was positively correlated with Nerabine. Conclusion: The five-gene signature associated with proliferation can be used for survival prediction and risk stratification for HCC patients. Potential drugs targeting this gene signature deserve further attention in the treatment of HCC.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Jianjun Lu
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Wenjie Mao
- Emergency Department, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Yamin Lu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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Galindo-Feria AS, Notarnicola A, Lundberg IE, Horuluoglu B. Aminoacyl-tRNA Synthetases: On Anti-Synthetase Syndrome and Beyond. Front Immunol 2022; 13:866087. [PMID: 35634293 PMCID: PMC9136399 DOI: 10.3389/fimmu.2022.866087] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
Anti-synthetase syndrome (ASSD) is an autoimmune disease characterized by the presence of autoantibodies targeting one of several aminoacyl t-RNA synthetases (aaRSs) along with clinical features including interstitial lung disease, myositis, Raynaud’s phenomenon, arthritis, mechanic’s hands, and fever. The family of aaRSs consists of highly conserved cytoplasmic and mitochondrial enzymes, one for each amino acid, which are essential for the RNA translation machinery and protein synthesis. Along with their main functions, aaRSs are involved in the development of immune responses, regulation of transcription, and gene-specific silencing of translation. During the last decade, these proteins have been associated with cancer, neurological disorders, infectious responses, and autoimmune diseases including ASSD. To date, several aaRSs have been described to be possible autoantigens in different diseases. The most commonly described are histidyl (HisRS), threonyl (ThrRS), alanyl (AlaRS), glycyl (GlyRS), isoleucyl (IleRS), asparaginyl (AsnRS), phenylalanyl (PheRS), tyrosyl (TyrRS), lysyl (LysRS), glutaminyl (GlnRS), tryptophanyl (TrpRS), and seryl (SerRS) tRNA synthetases. Autoantibodies against the first eight autoantigens listed above have been associated with ASSD while the rest have been associated with other diseases. This review will address what is known about the function of the aaRSs with a focus on their autoantigenic properties. We will also describe the anti-aaRSs autoantibodies and their association to specific clinical manifestations, and discuss their potential contribution to the pathogenesis of ASSD.
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Affiliation(s)
- Angeles S. Galindo-Feria
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Antonella Notarnicola
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ingrid E. Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
- *Correspondence: Begum Horuluoglu,
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Chen S, Gui R, Zhou XH, Zhang JH, Jiang HY, Liu HT, Fu YF. Combined Microbiome and Metabolome Analysis Reveals a Novel Interplay Between Intestinal Flora and Serum Metabolites in Lung Cancer. Front Cell Infect Microbiol 2022; 12:885093. [PMID: 35586253 PMCID: PMC9108287 DOI: 10.3389/fcimb.2022.885093] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
As the leading cause of cancer death, lung cancer seriously endangers human health and quality of life. Although many studies have reported the intestinal microbial composition of lung cancer, little is known about the interplay between intestinal microbiome and metabolites and how they affect the development of lung cancer. Herein, we combined 16S ribosomal RNA (rRNA) gene sequencing and liquid chromatography-mass spectrometry (LC-MS) technology to analyze intestinal microbiota composition and serum metabolism profile in a cohort of 30 lung cancer patients with different stages and 15 healthy individuals. Compared with healthy people, we found that the structure of intestinal microbiota in lung cancer patients had changed significantly (Adonis, p = 0.021). In order to determine how intestinal flora affects the occurrence and development of lung cancer, the Spearman rank correlation test was used to find the connection between differential microorganisms and differential metabolites. It was found that as thez disease progressed, L-valine decreased. Correspondingly, the abundance of Lachnospiraceae_UCG-006, the genus with the strongest association with L-valine, also decreased in lung cancer groups. Correlation analysis showed that the gut microbiome and serum metabolic profile had a strong synergy, and Lachnospiraceae_UCG-006 was closely related to L-valine. In summary, this study described the characteristics of intestinal flora and serum metabolic profiles of lung cancer patients with different stages. It revealed that lung cancer may be the result of the mutual regulation of L-valine and Lachnospiraceae_UCG-006 through the aminoacyl-tRNA biosynthesis pathway, and proposed that L-valine may be a potential marker for the diagnosis of lung cancer.
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Affiliation(s)
- Sai Chen
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Rong Gui
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiong-hui Zhou
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jun-hua Zhang
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hai-ye Jiang
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hai-ting Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yun-feng Fu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Yun-feng Fu,
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Yang Y, Li Z, Zhong Q, Zhao L, Wang Y, Chi H. Identification and validation of a novel prognostic signature based on transcription factors in breast cancer by bioinformatics analysis. Gland Surg 2022; 11:892-912. [PMID: 35694087 PMCID: PMC9177273 DOI: 10.21037/gs-22-267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 08/20/2023]
Abstract
BACKGROUND Breast cancer (BRCA) is the leading cause of cancer mortality among women, and it is associated with many tumor suppressors and oncogenes. There is increasing evidence that transcription factors (TFs) play vital roles in human malignancies, but TFs-based biomarkers for BRCA prognosis were still rare and necessary. This study sought to develop and validate a prognostic model based on TFs for BRCA patients. METHODS Differentially expressed TFs were screened from 1,109 BRCA and 113 non-tumor samples downloaded from The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis was used to identify TFs associated with overall survival (OS) of BRCA, and multivariate Cox regression analysis was performed to establish the optimal risk model. The predictive value of the TF model was established using TCGA database and validated using a Gene Expression Omnibus (GEO) data set (GSE20685). A gene set enrichment analysis was conducted to identify the enriched signaling pathways in high-risk and low-risk BRCA patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the TF target genes were also conducted separately. RESULTS A total of 394 differentially expressed TFs were screened. A 9-TF prognostic model, comprising PAX7, POU3F2, ZIC2, WT1, ALX4, FOXJ1, SPIB, LEF1 and NFE2, was constructed and validated. Compared to those in the low-risk group, patients in the high-risk group had worse clinical outcomes (P<0.001). The areas under the curve of the prognostic model for 5-year OS were 0.722 in the training cohort and 0.651 in the testing cohort. Additionally, the risk score was an independent prediction indicator for BRCA patients both in the training cohort (HR =1.757, P<0.001) and testing cohort (HR =1.401, P=0.001). It was associated with various cancer signaling pathways. Ultimately, 9 overlapping target genes were predicted by 3 prediction nomograms. The GO and KEGG enrichment analyses of these target genes suggested that the TFs in the model may regulate the activation of some classical tumor signaling pathways to control the progression of BRCA through these target genes. CONCLUSIONS Our study developed and validated a novel prognostic TF model that can effectively predict 5-year OS for BRCA patients.
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Affiliation(s)
- Yingmei Yang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Zhaoyun Li
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Qianyi Zhong
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Lei Zhao
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Yichao Wang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Hongbo Chi
- Department of Clinical Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
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Chen K, Tang R, Luo Y, Chen Y, Ei-Naggar A, Du J, Bu A, Yan Y, Lu X, Cai Y, Chang SX. Transcriptomic and metabolic responses of earthworms to contaminated soil with polypropylene and polyethylene microplastics at environmentally relevant concentrations. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128176. [PMID: 34996001 DOI: 10.1016/j.jhazmat.2021.128176] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Examining transcriptomic and metabolic responses of earthworms to microplastic-contaminated soil is critical for understanding molecular-level toxicity of microplastics; yet very little research on this topic exists. We investigated influences of environmentally relevant concentrations (ERC) of polypropylene (PP) and polyethylene (PE) microplastic-contaminated soil on earthworms at the transcriptomic, metabolic, tissue and whole-body levels to study their molecular toxicity. The addition of PP and PE at ERC induced oxidative stress on earthworms, as indicated by the high enrichment of glutathione metabolism and increased glutamine at the transcriptomic and metabolic levels. Digestive and immune systems of earthworms were damaged according to the injuries of the intestinal epithelium, partial shedding of chloragogenous tissues and unclear structure of coelom tissues, which were confirmed by pathway analysis at the transcriptomic level. Significant enrichment of arachidonic acid and glycerolipid metabolisms indicated that PP and PE disturbed the lipid metabolism in earthworms. Significantly increased betaine and myo-inositol, and decreased 2-hexyl-5-ethyl-3-furansulfonate suggested that PP and PE caused differences in osmoregulation extent. In conclusion, most similar responses of earthworm might result from special size rather than type effects of PP and PE microplastics. Contamination of soils with microplastics even at ERC has health risks to earthworms; therefore, proper management of microplastics to reduce their input to the environment is key to reducing the health risks to soil fauna.
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Affiliation(s)
- Keyi Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Ronggui Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youchao Chen
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Ali Ei-Naggar
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Department of Soil Sciences, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Jianhang Du
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Aiai Bu
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Yan
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinghang Lu
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yanjiang Cai
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Scott X Chang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta T6G 2E3, Canada
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Polyphenol Rich Forsythia suspensa Extract Alleviates DSS-Induced Ulcerative Colitis in Mice through the Nrf2-NLRP3 Pathway. Antioxidants (Basel) 2022; 11:antiox11030475. [PMID: 35326124 PMCID: PMC8944444 DOI: 10.3390/antiox11030475] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
This study systematically evaluated the effect of Forsythia suspensa extract on dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) and determined its mechanism of action. The results showed that Forsythia suspensa extract significantly inhibited DSS-induced UC in mice. In vivo mechanistic studies revealed that Forsythia suspensa extract relieved the symptoms of colitis by enhancing antioxidant activity and inhibiting pyroptosis. Further in vitro experiments on the mechanism of Forsythia suspensa showed that it reduced the level of reactive oxygen species (ROS) in J774A.1 cells. We found that Forsythia suspensa extract enhanced cellular antioxidation activity and inhibited pyroptosis. After silencing NLRP3, it was found to play an important role in pyroptosis. In addition, after Nrf2 was silenced, the inhibitory effect of Forsythia suspensa extract on cell pyroptosis was eliminated, indicating an interaction between Nrf2 and NLRP3. Metabonomics revealed that Forsythia suspensa extract significantly improved metabolic function in colitis mice by reversing the abnormal changes in the levels of 9 metabolites. The main metabolic pathways involved were glutathione metabolism, aminoacyl-tRNA biosynthesis and linoleic acid metabolism. In conclusion, we found that Forsythia suspensa extract significantly alleviated DSS-induced UC injury through the Nrf2-NLRP3 pathway and relieved metabolic dysfunction.
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