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Hemmati M, Wudy SI, Hackbarth F, Mittermeier-Kleßinger VK, Coleman OI, Haller D, Ludwig C, Dawid C, Kleigrewe K. Development of a Global Metabo-Lipid-Prote-omics Workflow to Compare Healthy Proximal and Distal Colonic Epithelium in Mice. J Proteome Res 2024; 23:3124-3140. [PMID: 39052308 DOI: 10.1021/acs.jproteome.3c00771] [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] [Indexed: 07/27/2024]
Abstract
A multimetabo-lipid-prote-omics workflow was developed to characterize the molecular interplay within proximal (PC) and distal (DC) colonic epithelium of healthy mice. This multiomics data set lays the foundation to better understand the two tissue types and can be used to study, for example, colon-related diseases like colorectal cancer or inflammatory bowel disease. First, the methyl tert-butyl ether extraction method was optimized, so that from a single tissue biopsy >350 reference-matched metabolites, >1850 reference-matched lipids, and >4500 proteins were detected by using targeted and untargeted metabolomics, untargeted lipidomics, and proteomics. Next, each omics-data set was analyzed individually and then merged with the additional omics disciplines to generate a deep understanding of the underlying complex regulatory network within the colon. Our data demonstrates, for example, differences in mucin formation, detected on substrate level as well as on enzyme level, and altered lipid metabolism by the detection of phospholipases hydrolyzing sphingomyelins to ceramides. In conclusion, the combination of the three mass spectrometry-based omics techniques can better entangle the functional and regional differences between PC and DC tissue compared to each single omics technique.
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Affiliation(s)
- Maryam Hemmati
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Susanne I Wudy
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Franziska Hackbarth
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Verena K Mittermeier-Kleßinger
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Olivia I Coleman
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Corinna Dawid
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Professorship for Functional Phytometabolomics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Wang JY, Cai YY, Li L, Zhu XM, Shen ZF, Wang ZH, Liao J, Lu JP, Liu XH, Lin FC. Dihydroorotase MoPyr4 is required for development, pathogenicity, and autophagy in rice blast fungus. Cell Commun Signal 2024; 22:362. [PMID: 39010102 PMCID: PMC11247805 DOI: 10.1186/s12964-024-01741-4] [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: 03/29/2024] [Accepted: 07/06/2024] [Indexed: 07/17/2024] Open
Abstract
Dihydroorotase (DHOase) is the third enzyme in the six enzymatic reaction steps of the endogenous pyrimidine nucleotide de novo biosynthesis pathway, which is a metabolic pathway conserved in both bacteria and eukaryotes. However, research on the biological function of DHOase in plant pathogenic fungi is very limited. In this study, we identified and named MoPyr4, a homologous protein of Saccharomyces cerevisiae DHOase Ura4, in the rice blast fungus Magnaporthe oryzae and investigated its ability to regulate fungal growth, pathogenicity, and autophagy. Deletion of MoPYR4 led to defects in growth, conidiation, appressorium formation, the transfer and degradation of glycogen and lipid droplets, appressorium turgor accumulation, and invasive hypha expansion in M. oryzae, which eventually resulted in weakened fungal pathogenicity. Long-term replenishment of exogenous uridine-5'-phosphate (UMP) can effectively restore the phenotype and virulence of the ΔMopyr4 mutant. Further study revealed that MoPyr4 also participated in the regulation of the Pmk1-MAPK signaling pathway, co-localized with peroxisomes for the oxidative stress response, and was involved in the regulation of the Osm1-MAPK signaling pathway in response to hyperosmotic stress. In addition, MoPyr4 interacted with MoAtg5, the core protein involved in autophagy, and positively regulated autophagic degradation. Taken together, our results suggested that MoPyr4 for UMP biosynthesis was crucial for the development and pathogenicity of M. oryzae. We also revealed that MoPyr4 played an essential role in the external stress response and pathogenic mechanism through participation in the Pmk1-MAPK signaling pathway, peroxisome-related oxidative stress response mechanism, the Osm1-MAPK signaling pathway and the autophagy pathway.
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Affiliation(s)
- Jing-Yi Wang
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Ying Cai
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lin Li
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xue-Ming Zhu
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zi-Fang Shen
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zi-He Wang
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jian Liao
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Ping Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Hong Liu
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fu-Cheng Lin
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Xianghu Laboratory, State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Mullen NJ, Shukla SK, Thakur R, Kollala SS, Wang D, Chaika N, Santana JF, Miklavcic WR, LaBreck DA, Mallareddy JR, Price DH, Natarajan A, Mehla K, Sykes DB, Hollingsworth MA, Singh PK. DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation. eLife 2024; 12:RP87292. [PMID: 38973593 PMCID: PMC11230627 DOI: 10.7554/elife.87292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Pyrimidine nucleotide biosynthesis is a druggable metabolic dependency of cancer cells, and chemotherapy agents targeting pyrimidine metabolism are the backbone of treatment for many cancers. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme in the de novo pyrimidine biosynthesis pathway that can be targeted by clinically approved inhibitors. However, despite robust preclinical anticancer efficacy, DHODH inhibitors have shown limited single-agent activity in phase 1 and 2 clinical trials. Therefore, novel combination therapy strategies are necessary to realize the potential of these drugs. To search for therapeutic vulnerabilities induced by DHODH inhibition, we examined gene expression changes in cancer cells treated with the potent and selective DHODH inhibitor brequinar (BQ). This revealed that BQ treatment causes upregulation of antigen presentation pathway genes and cell surface MHC class I expression. Mechanistic studies showed that this effect is (1) strictly dependent on pyrimidine nucleotide depletion, (2) independent of canonical antigen presentation pathway transcriptional regulators, and (3) mediated by RNA polymerase II elongation control by positive transcription elongation factor B (P-TEFb). Furthermore, BQ showed impressive single-agent efficacy in the immunocompetent B16F10 melanoma model, and combination treatment with BQ and dual immune checkpoint blockade (anti-CTLA-4 plus anti-PD-1) significantly prolonged mouse survival compared to either therapy alone. Our results have important implications for the clinical development of DHODH inhibitors and provide a rationale for combination therapy with BQ and immune checkpoint blockade.
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Affiliation(s)
- Nicholas J Mullen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Surendra K Shukla
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Ravi Thakur
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Dezhen Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Nina Chaika
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, University of IowaIowa CityUnited States
| | - William R Miklavcic
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Drew A LaBreck
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - David H Price
- Department of Biochemistry and Molecular Biology, University of IowaIowa CityUnited States
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Kamiya Mehla
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General HospitalBostonUnited States
- Harvard Stem Cell InstituteCambridgeUnited States
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Pankaj K Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
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Dsouza L, Pant A, Pope B, Yang Z. Role of vaccinia virus growth factor in stimulating the mTORC1-CAD axis of the de novo pyrimidine pathway under different nutritional cues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601567. [PMID: 39005450 PMCID: PMC11245005 DOI: 10.1101/2024.07.02.601567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Vaccinia virus (VACV), the prototype poxvirus, actively reprograms host cell metabolism upon infection. However, the nature and molecular mechanisms remain largely elusive. Given the diverse nutritional exposures of cells in different physiological contexts, it is essential to understand how VACV may alter various metabolic pathways in different nutritional conditions. In this study, we established the importance of de novo pyrimidine biosynthesis in VACV infection. We elucidated the significance of vaccinia growth factor (VGF), a viral early protein and a homolog of cellular epidermal growth factor, in enabling VACV to phosphorylate the key enzyme CAD of the de novo pyrimidine pathway at serine 1859, a site known to positively regulate CAD activity. While nutrient-poor conditions typically inhibit mTORC1 activation, VACV activates CAD via mTORC1-S6K1 signaling axis, in conditions where glutamine and asparagine are absent. However, unlike its cellular homolog, epidermal growth factor (EGF), VGF peptide alone in the absence of VACV infection has minimal ability to activate CAD, suggestive of the involvement of other viral factor(s) and differential functions to EGF acquired during poxvirus evolution. Our research provides a foundation for understanding the regulation of a significant metabolic pathway, namely, de novo pyrimidine synthesis during VACV infection, shedding new light on viral regulation under distinct nutritional environments. This study not only has the potential to contribute to the advancement of antiviral treatments but also improve the development of VACV as an oncolytic agent and vaccine vector.
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Affiliation(s)
- Lara Dsouza
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Anil Pant
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Blake Pope
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Zhilong Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
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5
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Zhang S, Tuo P, Ji Y, Huang Z, Xiong Z, Li H, Ruan C. Identification of 1-Methylnicotinamide as a specific biomarker for the progression of cirrhosis to hepatocellular carcinoma. J Cancer Res Clin Oncol 2024; 150:310. [PMID: 38890166 PMCID: PMC11189347 DOI: 10.1007/s00432-024-05848-6] [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: 04/15/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a prevalent malignant tumor, often arising from hepatitis induced by the hepatitis B virus (HBV) in China. However, effective biomarkers for early diagnosis are lacking, leading to a 5-year overall survival rate of less than 20% among patients with advanced HCC. This study aims to identify serum biomarkers for early HCC diagnosis to enhance patient survival rates. METHODS We established an independent cohort comprising 27 healthy individuals, 13 patients with HBV-induced cirrhosis, 13 patients with hepatitis B-type HCC, and 8 patients who progressed from cirrhosis to hepatocellular carcinoma during follow-up. Serum metabolic abnormalities during the progression from cirrhosis to HCC were studied using untargeted metabolomics. Liquid chromatography-mass spectrometry-based metabolomics methods characterized the subjects' serum metabolic profiles. Partial least squares discriminant analysis (PLS-DA) was employed to elucidate metabolic profile changes during the progression from cirrhosis to HCC. Differentially expressed metabolites (DEMs) between cirrhosis and HCC groups were identified using the LIMMA package in the R language. Two machine learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), and Random Forest Classifier (RF), were used to identify key metabolic biomarkers involved in the progression from cirrhosis to HCC. Key metabolic biomarkers were further validated using targeted metabolomics in a new independent validation cohort comprising 25 healthy individuals and 25 patients with early-stage hepatocellular carcinoma. RESULTS A total of 155 serum metabolites were identified, of which 21/54 metabolites exhibited significant changes in HCC patients compared with cirrhosis patients and healthy individuals, respectively. PLS-DA clustering results demonstrated a significant change trend in the serum metabolic profile of patients with HBV-induced cirrhosis during the progression to HCC. Utilizing LASSO regression and RF algorithms, we confirmed 10 key metabolic biomarkers. Notably, 1-Methylnicotinamide (1-MNAM) exhibited a persistent and significant decrease in healthy individuals, cirrhosis, and HCC patients. Moreover, 1-MNAM levels in developing patients were significantly higher during the cirrhosis stage than in the HCC stage. Targeted metabolomic validation in an external cohort further confirmed the good diagnostic performance of 1-MNAM in early HCC detection. CONCLUSION Our findings imply that 1-MNAM may be a specific biomarker for the progression of cirrhosis to HCC.
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Affiliation(s)
- Sijia Zhang
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Ping Tuo
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Yuanye Ji
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Zuoan Huang
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Zi Xiong
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Hongshan Li
- Liver Disease Department of Integrative Medicine, Ningbo No. 2 Hospital, Ningbo, 315010, China.
| | - Chunyan Ruan
- Centre for Medical Research, Ningbo No. 2 Hospital, Ningbo, 315010, China.
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Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. TARO: tree-aggregated factor regression for microbiome data integration. Bioinformatics 2024; 40:btae321. [PMID: 38788190 PMCID: PMC11193058 DOI: 10.1093/bioinformatics/btae321] [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: 09/21/2023] [Revised: 03/16/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
MOTIVATION Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns. RESULTS We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the taxonomic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances. AVAILABILITY AND IMPLEMENTATION The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package.
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Affiliation(s)
- Aditya K Mishra
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Christine B Peterson
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
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Shi Q, Xue C, Zeng Y, Yuan X, Chu Q, Jiang S, Wang J, Zhang Y, Zhu D, Li L. Notch signaling pathway in cancer: from mechanistic insights to targeted therapies. Signal Transduct Target Ther 2024; 9:128. [PMID: 38797752 PMCID: PMC11128457 DOI: 10.1038/s41392-024-01828-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/31/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Notch signaling, renowned for its role in regulating cell fate, organ development, and tissue homeostasis across metazoans, is highly conserved throughout evolution. The Notch receptor and its ligands are transmembrane proteins containing epidermal growth factor-like repeat sequences, typically necessitating receptor-ligand interaction to initiate classical Notch signaling transduction. Accumulating evidence indicates that the Notch signaling pathway serves as both an oncogenic factor and a tumor suppressor in various cancer types. Dysregulation of this pathway promotes epithelial-mesenchymal transition and angiogenesis in malignancies, closely linked to cancer proliferation, invasion, and metastasis. Furthermore, the Notch signaling pathway contributes to maintaining stem-like properties in cancer cells, thereby enhancing cancer invasiveness. The regulatory role of the Notch signaling pathway in cancer metabolic reprogramming and the tumor microenvironment suggests its pivotal involvement in balancing oncogenic and tumor suppressive effects. Moreover, the Notch signaling pathway is implicated in conferring chemoresistance to tumor cells. Therefore, a comprehensive understanding of these biological processes is crucial for developing innovative therapeutic strategies targeting Notch signaling. This review focuses on the research progress of the Notch signaling pathway in cancers, providing in-depth insights into the potential mechanisms of Notch signaling regulation in the occurrence and progression of cancer. Additionally, the review summarizes pharmaceutical clinical trials targeting Notch signaling for cancer therapy, aiming to offer new insights into therapeutic strategies for human malignancies.
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Affiliation(s)
- Qingmiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yifan Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shuwen Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jinzhi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yaqi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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8
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Feng Z, Wu Z, Zhang Y. Integration of bioinformatics and machine learning approaches for the validation of pyrimidine metabolism-related genes and their implications in immunotherapy for osteoporosis. BMC Musculoskelet Disord 2024; 25:402. [PMID: 38778304 PMCID: PMC11110368 DOI: 10.1186/s12891-024-07512-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Osteoporosis (OP), the "silent epidemic" of our century, poses a significant challenge to public health, predominantly affecting postmenopausal women and the elderly. It evolves from mild symptoms to pronounced severity, stabilizing eventually. Unique among OP's characteristics is the altered metabolic profile of affected cells, particularly in pyrimidine metabolism (PyM), a crucial pathway for nucleotide turnover and pyrimidine decomposition. While metabolic adaptation is acknowledged as a therapeutic target in various diseases, the specific role of PyM genes (PyMGs) in OP's molecular response remains to be clarified. METHODS In pursuit of elucidating and authenticating PyMGs relevant to OP, we embarked on a comprehensive bioinformatics exploration. This entailed the integration of Weighted Gene Co-expression Network Analysis (WGCNA) with a curated list of 37 candidate PyMGs, followed by the examination of their biological functions and pathways via Gene Set Variation Analysis (GSVA). The Least Absolute Shrinkage and Selection Operator (LASSO) technique was harnessed to identify crucial hub genes. We evaluated the diagnostic prowess of five PyMGs in OP detection and explored their correlation with OP's clinical traits, further validating their expression profiles through independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956). RESULTS Our analytical rigor unveiled five PyMGs-IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N-with significant ties to OP. A deeper dive into their biological functions highlighted their roles in estrogen response modulation, cytosolic calcium ion concentration regulation, and GABAergic synaptic transmission. Remarkably, these PyMGs emerged as potent diagnostic biomarkers for OP, distinguishing affected individuals with substantial accuracy. CONCLUSIONS This investigation brings to light five PyMGs intricately associated with OP, heralding new avenues for biomarker discovery and providing insights into its pathophysiological underpinnings. These findings not only deepen our comprehension of OP's complexity but also herald the advent of more refined diagnostic and therapeutic modalities.
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Affiliation(s)
- Zichen Feng
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Yongchen Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China.
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Choi YJ, Lee K, Lee SY, Kwon Y, Woo J, Jeon CY, Ko SG. p53 activation enhances the sensitivity of non-small cell lung cancer to the combination of SH003 and docetaxel by inhibiting de novo pyrimidine synthesis. Cancer Cell Int 2024; 24:156. [PMID: 38704578 PMCID: PMC11069295 DOI: 10.1186/s12935-024-03337-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Identifying molecular biomarkers for predicting responses to anti-cancer drugs can enhance treatment precision and minimize side effects. This study investigated the novel cancer-targeting mechanism of combining SH003, an herbal medicine, with docetaxel in non-small cell lung cancer (NSCLC) cells. Also, the present study aimed to identify the genetic characteristics of cancer cells susceptible to this combination. METHODS Cell viability was analyzed by WST-8 assay. Apoptosis induction, BrdU incorporation, and cell cycle analysis were performed using flow cytometry. Metabolites were measured by LC-MS/MS analysis. Real-time PCR and western blotting evaluated RNA and protein expression. DNA damage was quantified through immunofluorescence. cBioPortal and GEPIA data were utilized to explore the mutual co-occurrence of TP53 and UMPS and UMPS gene expression in NSCLC. RESULTS The combination treatment suppressed de novo pyrimidine nucleotide biosynthesis by reducing the expression of related enzymes. This blockade of pyrimidine metabolism led to DNA damage and subsequent apoptosis, revealing a novel mechanism for inducing lung cancer cell death with this combination. However, some lung cancer cells exhibited distinct responses to the combination treatment that inhibited pyrimidine metabolism. The differences in sensitivity in lung cancer cells were determined by the TP53 gene status. TP53 wild-type lung cancer cells were effectively inhibited by the combination treatment through p53 activation, while TP53 mutant- or null-type cells exhibited lower sensitivity. CONCLUSIONS This study, for the first time, established a link between cancer cell genetic features and treatment response to simultaneous SH003 and docetaxel treatment. It highlights the significance of p53 as a predictive factor for susceptibility to this combination treatment. These findings also suggest that p53 status could serve as a crucial criterion in selecting appropriate therapeutic strategies for targeting pyrimidine metabolism in lung cancer.
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Affiliation(s)
- Yu-Jeong Choi
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Kangwook Lee
- Department of Food and Biotechnology, Korea University, Sejong, Korea
| | - Seo Yeon Lee
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Youngbin Kwon
- Department of Korean Medicine, Graduate School, Kyung Hee University, Seoul, Korea
| | - Jaehyuk Woo
- Department of Korean Medicine, Graduate School, Kyung Hee University, Seoul, Korea
| | - Chan-Yong Jeon
- Department of Internal Medicine, College of Korean Medicine, Gachon University, Gyeonggi-Do, Korea
| | - Seong-Gyu Ko
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
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10
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Chen W, Toda E, Takeuchi K, Sawa Y, Wakamatsu K, Kuwahara N, Ishikawa A, Igarashi Y, Terasaki M, Kunugi S, Terasaki Y, Yamada K, Terashima Y, Shimizu A. Disulfiram treatment suppresses antibody-producing reactions by inhibiting macrophage activation and B cell pyrimidine metabolism. Commun Biol 2024; 7:488. [PMID: 38649462 PMCID: PMC11035657 DOI: 10.1038/s42003-024-06183-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Antibody responses, involving B cells, CD4 + T cells, and macrophages, are implicated in autoimmune diseases and organ transplant rejection. We have previously shown that inhibiting FROUNT with disulfiram (DSF) suppresses macrophage activation and migration, effectively treating inflammatory diseases. In this study, we investigated the effectiveness of DSF in antibody-producing reactions. Using a heart transplantation mouse model with antibody-mediated rejection, we administered anti-CD8 antibody to exclude cellular rejection. DSF directly inhibited B cell responses in vitro and significantly reduced plasma donor-specific antibodies and graft antibody deposition in vivo, resulting in prolonged survival of the heart graft. DSF also mediated various effects, including decreased macrophage infiltration and increased Foxp3+ regulatory T-cells in the grafts. Additionally, DSF inhibited pyrimidine metabolism-related gene expression induced by B-cell stimulation. These findings demonstrate that DSF modulates antibody production in the immune response complexity by regulating B-cell and macrophage responses.
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Affiliation(s)
- Weili Chen
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Etsuko Toda
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan.
- Laboratory for Morphological and Biomolecular Imaging, Nippon Medical School, Tokyo, Japan.
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan.
| | - Kazuhiro Takeuchi
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
- Division of Organ Replacement and Xenotransplantation Surgery, Center for Advanced Biomedical Science and Swine Research, Kagoshima University, Kagoshima, Japan
| | - Yurika Sawa
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Kyoko Wakamatsu
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Naomi Kuwahara
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Arimi Ishikawa
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Yuri Igarashi
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Mika Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Shinobu Kunugi
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | | | - Kazuhiko Yamada
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Yuya Terashima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Akira Shimizu
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan.
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11
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Squires E, Walshe IH, Cheung W, Bowerbank SL, Dean JR, Wood J, McHugh MP, Plattner S, Howatson G. Plasma-Induced Changes in the Metabolome Following Vistula Tart Cherry Consumption. Nutrients 2024; 16:1023. [PMID: 38613057 PMCID: PMC11013268 DOI: 10.3390/nu16071023] [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: 02/15/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Evidence suggests that tart cherry (TC) supplementation has beneficial effects on health indices and recovery following strenuous exercise. However, little is known about the mechanisms and how TC might modulate the human metabolome. The aim of this study was to evaluate the influence of an acute high- and low-dose of Vistula TC supplementation on the metabolomic profile in humans. In a randomised, double-blind, placebo controlled, cross-over design, 12 healthy participants (nine male and three female; mean ± SD age, stature, and mass were 29 ± 7 years old, 1.75 ± 0.1 m, and 77.3 ± 10.5 kg, respectively) visited the laboratory on three separate occasions (high dose; HI, low dose; LO, or placebo), separated by at least seven days. After an overnight fast, a baseline venous blood sample was taken, followed by consumption of a standardised breakfast and dose conditions (HI, LO, or placebo). Subsequent blood draws were taken 1, 2, 3, 5, and 8 h post consumption. Following sample preparation, an untargeted metabolomics approach was adopted, and the extracts analysed by LCMS/MS. When all time points were collated, a principal component analysis showed a significant difference between the conditions (p < 0.05), such that the placebo trial had homogeneity, and HI showed greater heterogeneity. In a sub-group analysis, cyanidine-3-O-glucoside (C3G), cyanidine-3-O-rutinoside (C3R), and vanillic acid (VA) were detected in plasma and showed significant differences (p < 0.05) following acute consumption of Vistula TC, compared to the placebo group. These results provide evidence that phenolics are bioavailable in plasma and induce shifts in the metabolome following acute Vistula TC consumption. These data could be used to inform future intervention studies where changes in physiological outcomes could be influenced by metabolomic shifts following acute supplementation.
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Affiliation(s)
- Emma Squires
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - Ian H. Walshe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - William Cheung
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - Samantha L. Bowerbank
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - John R. Dean
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - Jacob Wood
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
| | - Malachy P. McHugh
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
- Nicholas Institute of Sports Medicine and Athletic Trauma, Northwell Health, New York, NY 10065, USA
| | | | - Glyn Howatson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; (E.S.); (I.H.W.); (W.C.); (S.L.B.); (J.R.D.); (J.W.); (M.P.M.)
- Water Research Group, North West University, Potchefstroom 2531, South Africa
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12
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Watanabe T, Yamamoto Y, Kurahashi Y, Kawasoe K, Kidoguchi K, Ureshino H, Kamachi K, Yoshida-Sakai N, Fukuda-Kurahashi Y, Nakamura H, Okada S, Sueoka E, Kimura S. Reprogramming of pyrimidine nucleotide metabolism supports vigorous cell proliferation of normal and malignant T cells. Blood Adv 2024; 8:1345-1358. [PMID: 38190613 PMCID: PMC10945144 DOI: 10.1182/bloodadvances.2023011131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024] Open
Abstract
ABSTRACT Adult T-cell leukemia/lymphoma (ATL) is triggered by infection with human T-cell lymphotropic virus-1 (HTLV-1). Here, we describe the reprogramming of pyrimidine biosynthesis in both normal T cells and ATL cells through regulation of uridine-cytidine kinase 2 (UCK2), which supports vigorous proliferation. UCK2 catalyzes the monophosphorylation of cytidine/uridine and their analogues during pyrimidine biosynthesis and drug metabolism. We found that UCK2 was overexpressed aberrantly in HTLV-1-infected T cells but not in normal T cells. T-cell activation via T-cell receptor (TCR) signaling induced expression of UCK2 in normal T cells. Somatic alterations and epigenetic modifications in ATL cells activate TCR signaling. Therefore, we believe that expression of UCK2 in HTLV-1-infected cells is induced by dysregulated TCR signaling. Recently, we established azacitidine-resistant (AZA-R) cells showing absent expression of UCK2. AZA-R cells proliferated normally in vitro, whereas UCK2 knockdown inhibited ATL cell growth. Although uridine and cytidine accumulated in AZA-R cells, possibly because of dysfunction of pyrimidine salvage biosynthesis induced by loss of UCK2 expression, the amount of UTP and CTP was almost the same as in parental cells. Furthermore, AZA-R cells were more susceptible to an inhibitor of dihydroorotic acid dehydrogenase, which performs the rate-limiting enzyme of de novo pyrimidine nucleotide biosynthesis, and more resistant to dipyridamole, an inhibitor of pyrimidine salvage biosynthesis, suggesting that AZA-R cells adapt to UCK2 loss by increasing de novo pyrimidine nucleotide biosynthesis. Taken together, the data suggest that fine-tuning pyrimidine biosynthesis supports vigorous cell proliferation of both normal T cells and ATL cells.
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Affiliation(s)
- Tatsuro Watanabe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuta Yamamoto
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- OHARA Pharmaceutical Co, Ltd, Shiga, Japan
| | - Kazunori Kawasoe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Keisuke Kidoguchi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Ureshino
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kazuharu Kamachi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Nao Yoshida-Sakai
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Fukuda-Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- OHARA Pharmaceutical Co, Ltd, Shiga, Japan
| | - Hideaki Nakamura
- Department of Transfusion Medicine, Saga University Hospital, Saga, Japan
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Eisaburo Sueoka
- Department of Clinical Laboratory Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Shinya Kimura
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
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13
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Bu F, Qin X, Wang T, Li N, Zheng M, Wu Z, Ma K. Unlocking potential biomarkers bridging coronary atherosclerosis and pyrimidine metabolism-associated genes through an integrated bioinformatics and machine learning approach. BMC Cardiovasc Disord 2024; 24:148. [PMID: 38454353 PMCID: PMC10921789 DOI: 10.1186/s12872-024-03819-w] [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: 11/10/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND This study delves into the intricate landscape of atherosclerosis (AS), a chronic inflammatory disorder with significant implications for cardiovascular health. AS poses a considerable burden on global healthcare systems, elevating both mortality and morbidity rates. The pathological underpinnings of AS involve a marked metabolic disequilibrium, particularly within pyrimidine metabolism (PyM), a crucial enzymatic network central to nucleotide synthesis and degradation. While the therapeutic relevance of pyrimidine metabolism in diverse diseases is acknowledged, the explicit role of pyrimidine metabolism genes (PyMGs) in the context of AS remains elusive. Utilizing bioinformatics methodologies, this investigation aims to reveal and substantiate PyMGs intricately linked with AS. METHODS A set of 41 candidate PyMGs was scrutinized through differential expression analysis. GSEA and GSVA were employed to illuminate potential biological pathways and functions associated with the identified PyMGs. Simultaneously, Lasso regression and SVM-RFE were utilized to distill core genes and assess the diagnostic potential of four quintessential PyMGs (CMPK1, CMPK2, NT5C2, RRM1) in discriminating AS. The relationship between key PyMGs and clinical presentations was also explored. Validation of the expression levels of the four PyMGs was performed using the GSE43292 and GSE9820 datasets. RESULTS This investigation identified four PyMGs, with NT5C2 and RRM1 emerging as key players, intricately linked to AS pathogenesis. Functional analysis underscored their critical involvement in metabolic processes, including pyrimidine-containing compound metabolism and nucleotide biosynthesis. Diagnostic evaluation of these PyMGs in distinguishing AS showcased promising results. CONCLUSION In conclusion, this exploration has illuminated a constellation of four PyMGs with a potential nexus to AS pathogenesis. These findings unveil emerging biomarkers, paving the way for novel approaches to disease monitoring and progression, and providing new avenues for therapeutic intervention in the realm of atherosclerosis.
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Affiliation(s)
- Fanli Bu
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Xiao Qin
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Tiantian Wang
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Na Li
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Man Zheng
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China
| | - Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kai Ma
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, People's Republic of China.
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14
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Shapiro BD, Battle A. Bayesian Multi-View Clustering given complex inter-view structure. F1000Res 2024; 11:1460. [PMID: 38495778 PMCID: PMC10940850 DOI: 10.12688/f1000research.126215.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 03/19/2024] Open
Abstract
Multi-view datasets are becoming increasingly prevalent. These datasets consist of different modalities that provide complementary characterizations of the same underlying system. They can include heterogeneous types of information with complex relationships, varying degrees of missingness, and assorted sample sizes, as is often the case in multi-omic biological studies. Clustering multi-view data allows us to leverage different modalities to infer underlying systematic structure, but most existing approaches are limited to contexts in which entities are the same across views or have clear one-to-one relationships across data types with a common sample size. Many methods also make strong assumptions about the similarities of clusterings across views. We propose a Bayesian multi-view clustering approach (BMVC) which can handle the realities of multi-view datasets that often have complex relationships and diverse structure. BMVC incorporates known and complex many-to-many relationships between entities via a probabilistic graphical model that enables the joint inference of clusterings specific to each view, but where each view informs the others. Additionally, BMVC estimates the strength of the relationships between each pair of views, thus moderating the degree to which it imposes dependence constraints. We benchmarked BMVC on simulated data to show that it accurately estimates varying degrees of inter-view dependence when inter-view relationships are not limited to one-to-one correspondence. Next, we demonstrated its ability to capture visually interpretable inter-view structure in a public health survey of individuals and households in Puerto Rico following Hurricane Maria. Finally, we showed that BMVC clusters integrate the complex relationships between multi-omic profiles of breast cancer patient data, improving the biological homogeneity of clusters and elucidating hypotheses for functional biological mechanisms. We found that BMVC leverages complex inter-view structure to produce higher quality clusters than those generated by standard approaches. We also showed that BMVC is a valuable tool for real-world discovery and hypothesis generation.
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Affiliation(s)
- Benjamin D. Shapiro
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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15
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Abo-Hammam RH, Salah M, Shabayek S, Hanora A, Zakeer S, Khattab RH. Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study. AIMS Microbiol 2024; 10:148-160. [PMID: 38525041 PMCID: PMC10955169 DOI: 10.3934/microbiol.2024008] [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: 09/30/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 03/26/2024] Open
Abstract
One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.
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Affiliation(s)
- Rana H. Abo-Hammam
- Forensic toxicologist and narcotics expert, Ministry of Justice, Tanta, Egypt
| | - Mohammed Salah
- Department of Microbiology and Immunology, Faculty of pharmacy, Port-Said University, Port-Said, Egypt
| | - Sarah Shabayek
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
| | - Randa H. Khattab
- Department of Microbiology and Immunology, Al-Salam University, Tanta, Egypt
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16
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Guo H, Liu D, Liu K, Hou Y, Li C, Li Q, Ding X, Verstegen MMA, Zhang J, Wang L, Ding Y, Tang R, Pan X, Zheng K, van der Laan LJW, Pan Q, Wang W. Drug repurposing screen identifies vidofludimus calcium and pyrazofurin as novel chemical entities for the development of hepatitis E interventions. Virol Sin 2024; 39:123-133. [PMID: 37984761 PMCID: PMC10877426 DOI: 10.1016/j.virs.2023.11.006] [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: 08/05/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Hepatitis E virus (HEV) infection can cause severe complications and high mortality, particularly in pregnant women, organ transplant recipients, individuals with pre-existing liver disease and immunosuppressed patients. However, there are still unmet needs for treating chronic HEV infections. Herein, we screened a best-in-class drug repurposing library consisting of 262 drugs/compounds. Upon screening, we identified vidofludimus calcium and pyrazofurin as novel anti-HEV entities. Vidofludimus calcium is the next-generation dihydroorotate dehydrogenase (DHODH) inhibitor in the phase 3 pipeline to treat autoimmune diseases or SARS-CoV-2 infection. Pyrazofurin selectively targets uridine monophosphate synthetase (UMPS). Their anti-HEV effects were further investigated in a range of cell culture models and human liver organoids models with wild type HEV strains and ribavirin treatment failure-associated HEV strains. Encouragingly, both drugs exhibited a sizeable therapeutic window against HEV. For instance, the IC50 value of vidofludimus calcium is 4.6-7.6-fold lower than the current therapeutic doses in patients. Mechanistically, their anti-HEV mode of action depends on the blockage of pyrimidine synthesis. Notably, two drugs robustly inhibited ribavirin treatment failure-associated HEV mutants (Y1320H, G1634R). Their combination with IFN-α resulted in synergistic antiviral activity. In conclusion, we identified vidofludimus calcium and pyrazofurin as potent candidates for the treatment of HEV infections. Based on their antiviral potency, and also the favorable safety profile identified in clinical studies, our study supports the initiation of clinical studies to repurpose these drugs for treating chronic hepatitis E.
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Affiliation(s)
- Hongbo Guo
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Dan Liu
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Kuan Liu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, NL-3015 CN, the Netherlands; Department of Surgery, Erasmus MC Transplant Institute, University Medical Center, Rotterdam, 3015CE, NL-3015 CN, the Netherlands
| | - Yao Hou
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Chunyang Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiudi Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiaohui Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center, Rotterdam, 3015CE, NL-3015 CN, the Netherlands
| | - Jikai Zhang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Lingli Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yibo Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Renxian Tang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiucheng Pan
- Department of Infectious Diseases, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Kuiyang Zheng
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center, Rotterdam, 3015CE, NL-3015 CN, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, NL-3015 CN, the Netherlands.
| | - Wenshi Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, 221004, China.
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17
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Hamid A, Mäser P, Mahmoud AB. Drug Repurposing in the Chemotherapy of Infectious Diseases. Molecules 2024; 29:635. [PMID: 38338378 PMCID: PMC10856722 DOI: 10.3390/molecules29030635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Repurposing is a universal mechanism for innovation, from the evolution of feathers to the invention of Velcro tape. Repurposing is particularly attractive for drug development, given that it costs more than a billion dollars and takes longer than ten years to make a new drug from scratch. The COVID-19 pandemic has triggered a large number of drug repurposing activities. At the same time, it has highlighted potential pitfalls, in particular when concessions are made to the target product profile. Here, we discuss the pros and cons of drug repurposing for infectious diseases and analyze different ways of repurposing. We distinguish between opportunistic and rational approaches, i.e., just saving time and money by screening compounds that are already approved versus repurposing based on a particular target that is common to different pathogens. The latter can be further distinguished into divergent and convergent: points of attack that are divergent share common ancestry (e.g., prokaryotic targets in the apicoplast of malaria parasites), whereas those that are convergent arise from a shared lifestyle (e.g., the susceptibility of bacteria, parasites, and tumor cells to antifolates due to their high rate of DNA synthesis). We illustrate how such different scenarios can be capitalized on by using examples of drugs that have been repurposed to, from, or within the field of anti-infective chemotherapy.
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Affiliation(s)
- Amal Hamid
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
| | - Pascal Mäser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, 4123 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Abdelhalim Babiker Mahmoud
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
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18
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Mullen NJ, Shukla SK, Thakur R, Kollala SS, Wang D, Chaika N, Santana JF, Miklavcic WR, LaBreck DA, Mallareddy JR, Price DH, Natarajan A, Mehla K, Sykes DB, Hollingsworth MA, Singh PK. DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.03.535399. [PMID: 37066260 PMCID: PMC10103971 DOI: 10.1101/2023.04.03.535399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pyrimidine nucleotide biosynthesis is a druggable metabolic dependency of cancer cells, and chemotherapy agents targeting pyrimidine metabolism are the backbone of treatment for many cancers. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme in the de novo pyrimidine biosynthesis pathway that can be targeted by clinically approved inhibitors. However, despite robust preclinical anticancer efficacy, DHODH inhibitors have shown limited single-agent activity in phase 1 and 2 clinical trials. Therefore, novel combination therapy strategies are necessary to realize the potential of these drugs. To search for therapeutic vulnerabilities induced by DHODH inhibition, we examined gene expression changes in cancer cells treated with the potent and selective DHODH inhibitor brequinar (BQ). This revealed that BQ treatment causes upregulation of antigen presentation pathway genes and cell surface MHC class I expression. Mechanistic studies showed that this effect is 1) strictly dependent on pyrimidine nucleotide depletion, 2) independent of canonical antigen presentation pathway transcriptional regulators, and 3) mediated by RNA polymerase II elongation control by positive transcription elongation factor B (P-TEFb). Furthermore, BQ showed impressive single-agent efficacy in the immunocompetent B16F10 melanoma model, and combination treatment with BQ and dual immune checkpoint blockade (anti-CTLA-4 plus anti-PD-1) significantly prolonged mouse survival compared to either therapy alone. Our results have important implications for the clinical development of DHODH inhibitors and provide a rationale for combination therapy with BQ and immune checkpoint blockade.
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Affiliation(s)
- Nicholas J. Mullen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Surendra K. Shukla
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Ravi Thakur
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Dezhen Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Nina Chaika
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Juan F. Santana
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, USA
| | - William R. Miklavcic
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Drew A. LaBreck
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - David H. Price
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Kamiya Mehla
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - David B. Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Michael A. Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Pankaj K. Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
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19
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Du Y, Li YY, Choi BY, Fernadez R, Su KJ, Sharma K, Qi L, Yin Z, Zhao Q, Shen H, Qiu C, Zhao LJ, Luo Z, Wu L, Tian Q, Deng HW. Metabolomic profiles associated with physical activity in White and African American adult men. PLoS One 2023; 18:e0289077. [PMID: 37943870 PMCID: PMC10635561 DOI: 10.1371/journal.pone.0289077] [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: 12/09/2022] [Accepted: 07/11/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Physical activity (PA) is associated with various health benefits, especially in improving chronic health conditions. However, the metabolic changes in host metabolism in response to PA remain unclear, especially in racially/ethnically diverse populations. OBJECTIVE This study is to assess the metabolic profiles associated with the frequency of PA in White and African American (AA) men. METHODS Using the untargeted metabolomics data collected from 698 White and AA participants (mean age: 38.0±8.0, age range: 20-50) from the Louisiana Osteoporosis Study (LOS), we conducted linear regression models to examine metabolites that are associated with PA levels (assessed by self-reported regular exercise frequency levels: 0, 1-2, and ≥3 times per week) in White and AA men, respectively, as well as in the pooled sample. Covariates considered for statistical adjustments included race (only for the pooled sample), age, BMI, waist circumstance, smoking status, and alcohol drinking. RESULTS Of the 1133 untargeted compounds, we identified 7 metabolites associated with PA levels in the pooled sample after covariate adjustment with a false discovery rate of 0.15. Specifically, compared to participants who did not exercise, those who exercised at a frequency ≥3 times/week showed higher abundances in uracil, orotate, 1-(1-enyl-palmitoyl)-2-oleoyl-GPE (P-16:0/18:1) (GPE), threonate, and glycerate, but lower abundances in salicyluric glucuronide and adenine in the pooled sample. However, in Whites, salicyluric glucuronide and orotate were not significant. Adenine, GPE, and threonate were not significant in AAs. In addition, the seven metabolites were not significantly different between participants who exercised ≥3 times/week and 1-2 times/week, nor significantly different between participants with 1-2 times/week and 0/week in the pooled sample and respective White and AA groups. CONCLUSIONS Metabolite responses to PA are dose sensitive and may differ between White and AA populations. The identified metabolites may help advance our knowledge of guiding precision PA interventions. Studies with rigorous study designs are warranted to elucidate the relationship between PA and metabolites.
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Affiliation(s)
- Yan Du
- School of Nursing, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Yuan-Yuan Li
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, North Carolina, United States of America
| | - Byeong Yeob Choi
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Roman Fernadez
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Kumar Sharma
- Center for Precision Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University; New Orleans, LA, United States of America
| | - Zenong Yin
- Department of Public Health, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Qi Zhao
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Chuan Qiu
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Zhe Luo
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Li Wu
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University; New Orleans, LA, United States of America
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20
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Shao L, Wang W, Gong X, Yu Y, Xue J, Zeng X, Liu J. The Toxicity Differences of Fluralaner against the Red Imported Fire Ant ( Solenopsis invicta) at Different Developmental Stages. Int J Mol Sci 2023; 24:15627. [PMID: 37958611 PMCID: PMC10649654 DOI: 10.3390/ijms242115627] [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: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The red imported fire ant (RIFA), Solenopsis invicta, is an invasive pest that causes damage to agricultural and ecological environments worldwide. Fluralaner is a new isoxazoline pesticide with the potential to become a control agent against RIFA. However, it is not clear whether S. invicta responds the same way to fluralaner at different reproductive stages. The present study firstly evaluated the toxicity of fluralaner to S. invicta at different developmental stages, finding that fourth instar larvae (LD50, 1744.23 mg/kg) and worker ants (LD50, 8.62 mg/kg) were differently susceptible to fluralaner, while the mortality rate of fourth instar larvae was significantly lower at the same concentration of 10 mg/L (5.56 ± 3.14%) than that of worker ants (62.22 ± 3.14%), demonstrating a greater tolerance to fluralaner. Subsequently, the metabolic responses of worker and larval ants to fluralaner stress (10 mg/L) were investigated using non-targeted metabolomics, which indicated that the amount of differential metabolites and the KEGG metabolic pathways enriched were different between workers and larvae when exposed to the same dose (10 mg/L) of fluralaner. Differential metabolites of larvae and worker ants under fluralaner stress were mainly concentrated in organic acids and their derivatives, lipids and lipid-like molecules, nucleosides, nucleotides, and analogues, combined with the enriched metabolic pathways, revealed that the differential metabolic responses of larvae and worker ants were mainly in energy metabolism, detoxification metabolism, and neurotransmitter ligands. Workers consumed more substrates in the arginine synthesis pathway (l-glutamic acid, l-aspartic acid, and fumaric acid) to provide energy for the detoxification (glutathione) of pesticides when exposed to fluralaner stress, and the high accumulation of l-aspartic acid induced excitotoxicity in the worker ants. Larval ants consumed more arachidonic acid to synthesize PG D2, and changes in the metabolism of antioxidants such as catechins, hesperidin, and l-ascorbic acid suggested that larvae were more capable of scavenging the ROS response than worker ants. The results of non-targeted metabolomics successfully revealed differences in the sensitivity of larvae and workers to fluralaner agents, providing insights into the fluralaner control of Solenopsis invicta.
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Affiliation(s)
| | | | | | | | | | | | - Jiali Liu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (L.S.); (W.W.); (X.G.); (Y.Y.); (J.X.); (X.Z.)
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21
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Mishra AK, Mahmud I, Lorenzi PL, Jenq RR, Wargo JA, Ajami NJ, Peterson CB. TARO: tree-aggregated factor regression for microbiome data integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562792. [PMID: 37904958 PMCID: PMC10614880 DOI: 10.1101/2023.10.17.562792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Motivation Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns. Results We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the phylogenetic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances. Availability and implementation The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package .
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22
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Vignon M, Bastide A, Attina A, David A, Bousquet P, Orti V, Vialaret J, Lehmann S, Periere DD, Hirtz C. Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis. J Periodontal Res 2023; 58:959-967. [PMID: 37349891 DOI: 10.1111/jre.13155] [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: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVE To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS). BACKGROUND The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date. MATERIALS AND METHODS Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS. RESULTS Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary. CONCLUSION The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.
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Affiliation(s)
- Margaux Vignon
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Aurore Attina
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Philippe Bousquet
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Valérie Orti
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Jérôme Vialaret
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | - Sylvain Lehmann
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Christophe Hirtz
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
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23
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Wu Z, Li X, Gu Z, Xia X, Yang J. Pyrimidine metabolism regulator-mediated molecular subtypes display tumor microenvironmental hallmarks and assist precision treatment in bladder cancer. Front Oncol 2023; 13:1102518. [PMID: 37664033 PMCID: PMC10470057 DOI: 10.3389/fonc.2023.1102518] [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: 11/19/2022] [Accepted: 03/20/2023] [Indexed: 09/05/2023] Open
Abstract
Background Bladder cancer (BLCA) is a common urinary system malignancy with a significant morbidity and death rate worldwide. Non-muscle invasive BLCA accounts for over 75% of all BLCA cases. The imbalance of tumor metabolic pathways is associated with tumor formation and proliferation. Pyrimidine metabolism (PyM) is a complex enzyme network that incorporates nucleoside salvage, de novo nucleotide synthesis, and catalytic pyrimidine degradation. Metabolic reprogramming is linked to clinical prognosis in several types of cancer. However, the role of pyrimidine metabolism Genes (PyMGs) in the BLCA-fighting process remains poorly understood. Methods Predictive PyMGs were quantified in BLCA samples from the TCGA and GEO datasets. TCGA and GEO provided information on stemness indices (mRNAsi), gene mutations, CNV, TMB, and corresponding clinical features. The prediction model was built using Lasso regression. Co-expression analysis was conducted to investigate the relationship between gene expression and PyM. Results PyMGs were overexpressed in the high-risk sample in the absence of other clinical symptoms, demonstrating their predictive potential for BLCA outcome. Immunological and tumor-related pathways were identified in the high-risk group by GSWA. Immune function and m6a gene expression varied significantly between the risk groups. In BLCA patients, DSG1, C6orf15, SOST, SPRR2A, SERPINB7, MYBPH, and KRT1 may participate in the oncology process. Immunological function and m6a gene expression differed significantly between the two groups. The prognostic model, CNVs, single nucleotide polymorphism (SNP), and drug sensitivity all showed significant gene connections. Conclusions BLCA-associated PyMGs are available to provide guidance in the prognostic and immunological setting and give evidence for the formulation of PyM-related molecularly targeted treatments. PyMGs and their interactions with immune cells in BLCA may serve as therapeutic targets.
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Affiliation(s)
- Zixuan Wu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaohuan Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenchang Gu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinhua Xia
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Jing Yang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
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24
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Sarwar MS, Ramirez CN, Dina Kuo HC, Chou P, Wu R, Sargsyan D, Yang Y, Shannar A, Mary Peter R, Yin R, Wang Y, Su X, Kong AN. The environmental carcinogen benzo[a]pyrene regulates epigenetic reprogramming and metabolic rewiring in a two-stage mouse skin carcinogenesis model. Carcinogenesis 2023; 44:436-449. [PMID: 37100755 PMCID: PMC10414144 DOI: 10.1093/carcin/bgad024] [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: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Non-melanoma skin cancer (NMSC) is the most common cancer in the world. Environmental exposure to carcinogens is one of the major causes of NMSC initiation and progression. In the current study, we utilized a two-stage skin carcinogenesis mouse model generated by sequential exposure to cancer-initiating agent benzo[a]pyrene (BaP) and promoting agent 12-O-tetradecanoylphorbol-13-acetate (TPA), to study epigenetic, transcriptomic and metabolic changes at different stages during the development of NMSC. BaP/TPA caused significant alterations in DNA methylation and gene expression profiles in skin carcinogenesis, as evidenced by DNA-seq and RNA-seq analysis. Correlation analysis between differentially expressed genes and differentially methylated regions found that the mRNA expression of oncogenes leucine rich repeat LGI family member 2 (Lgi2), kallikrein-related peptidase 13 (Klk13) and SRY-Box transcription factor (Sox5) are correlated with the promoter CpG methylation status, indicating BaP/TPA regulates these oncogenes through regulating their promoter methylation at different stages of NMSC. Pathway analysis identified that the modulation of macrophage-stimulating protein-recepteur d'origine nantais and high-mobility group box 1 signaling pathways, superpathway of melatonin degradation, melatonin degradation 1, sirtuin signaling and actin cytoskeleton signaling pathways are associated with the development of NMSC. The metabolomic study showed BaP/TPA regulated cancer-associated metabolisms like pyrimidine and amino acid metabolisms/metabolites and epigenetic-associated metabolites, such as S-adenosylmethionine, methionine and 5-methylcytosine, indicating a critical role in carcinogen-mediated metabolic reprogramming and its consequences on cancer development. Altogether, this study provides novel insights integrating methylomic, transcriptomic and metabolic-signaling pathways that could benefit future skin cancer treatment and interception studies.
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Affiliation(s)
- Md. Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christina N Ramirez
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pochung Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuqing Yang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ahmad Shannar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rebecca Mary Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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25
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Mahé M, Rios-Fuller TJ, Karolin A, Schneider RJ. Genetics of enzymatic dysfunctions in metabolic disorders and cancer. Front Oncol 2023; 13:1230934. [PMID: 37601653 PMCID: PMC10433910 DOI: 10.3389/fonc.2023.1230934] [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: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Inherited metabolic disorders arise from mutations in genes involved in the biogenesis, assembly, or activity of metabolic enzymes, leading to enzymatic deficiency and severe metabolic impairments. Metabolic enzymes are essential for the normal functioning of cells and are involved in the production of amino acids, fatty acids and nucleotides, which are essential for cell growth, division and survival. When the activity of metabolic enzymes is disrupted due to mutations or changes in expression levels, it can result in various metabolic disorders that have also been linked to cancer development. However, there remains much to learn regarding the relationship between the dysregulation of metabolic enzymes and metabolic adaptations in cancer cells. In this review, we explore how dysregulated metabolism due to the alteration or change of metabolic enzymes in cancer cells plays a crucial role in tumor development, progression, metastasis and drug resistance. In addition, these changes in metabolism provide cancer cells with a number of advantages, including increased proliferation, resistance to apoptosis and the ability to evade the immune system. The tumor microenvironment, genetic context, and different signaling pathways further influence this interplay between cancer and metabolism. This review aims to explore how the dysregulation of metabolic enzymes in specific pathways, including the urea cycle, glycogen storage, lysosome storage, fatty acid oxidation, and mitochondrial respiration, contributes to the development of metabolic disorders and cancer. Additionally, the review seeks to shed light on why these enzymes represent crucial potential therapeutic targets and biomarkers in various cancer types.
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Affiliation(s)
| | | | | | - Robert J. Schneider
- Department of Microbiology, Grossman NYU School of Medicine, New York, NY, United States
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Yamanaka C, Uki S, Kaitoh K, Iwata M, Yamanishi Y. De novo drug design based on patient gene expression profiles via deep learning. Mol Inform 2023; 42:e2300064. [PMID: 37475603 DOI: 10.1002/minf.202300064] [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: 03/16/2023] [Revised: 05/25/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Computational de novo drug design is a challenging issue in medicine, and it is desirable to consider all of the relevant information of the biological systems in a disease state. Here, we propose a novel computational method to generate drug candidate molecular structures from patient gene expression profiles via deep learning, which we call DRAGONET. Our model can generate new molecules that are likely to counteract disease-specific gene expression patterns in patients, which is made possible by exploring the latent space constructed by a transformer-based variational autoencoder and integrating the substructures of disease-correlated molecules. We applied DRAGONET to generate drug candidate molecules for gastric cancer, atopic dermatitis, and Alzheimer's disease, and demonstrated that the newly generated molecules were chemically similar to registered drugs for each disease. This approach is applicable to diseases with unknown therapeutic target proteins and will make a significant contribution to the field of precision medicine.
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Affiliation(s)
- Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Shunya Uki
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
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27
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Jatana S, Ponti AK, Johnson EE, Rebert NA, Smith JL, Fulmer CG, Maytin EV, Achkar JP, Fernandez AP, McDonald C. A novel murine model of pyoderma gangrenosum reveals that inflammatory skin-gut crosstalk is mediated by IL-1β-primed neutrophils. Front Immunol 2023; 14:1148893. [PMID: 37475852 PMCID: PMC10354730 DOI: 10.3389/fimmu.2023.1148893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Pyoderma gangrenosum (PG) is a debilitating skin condition often accompanied by inflammatory bowel disease (IBD). Strikingly, ~40% of patients that present with PG have underlying IBD, suggesting shared but unknown mechanisms of pathogenesis. Impeding the development of effective treatments for PG is the absence of an animal model that exhibits features of both skin and gut manifestations. This study describes the development of the first experimental drug-induced mouse model of PG with concomitant intestinal inflammation. Topical application of pyrimidine synthesis inhibitors on wounded mouse skin generates skin ulcers enriched in neutrophil extracellular traps (NETs) as well as pro-inflammatory cellular and soluble mediators mimicking human PG. The mice also develop spontaneous intestinal inflammation demonstrated by histologic damage. Further investigations revealed increased circulating low density IL-1β primed neutrophils that undergo enhanced NETosis at inflamed tissue sites supported by an increase in circulatory citrullinated histone 3, a marker of aberrant NET formation. Granulocyte depletion dampens the intestinal inflammation in this model, further supporting the notion that granulocytes contribute to the skin-gut crosstalk in PG mice. We anticipate that this novel murine PG model will enable researchers to probe common disease mechanisms and identify more effective targets for treatment for PG patients with IBD.
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Affiliation(s)
- Samreen Jatana
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - András K. Ponti
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Erin E. Johnson
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Biology, John Carroll University, University Heights, OH, United States
| | - Nancy A. Rebert
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Jordyn L. Smith
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Clifton G. Fulmer
- Department of Pathology, Pathology & Laboratory Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Edward V. Maytin
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Dermatology, Dermatology & Plastic Surgery Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Jean-Paul Achkar
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Gastroenterology, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Anthony P. Fernandez
- Department of Pathology, Pathology & Laboratory Medicine, Cleveland Clinic, Cleveland, OH, United States
- Department of Dermatology, Dermatology & Plastic Surgery Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Christine McDonald
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
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28
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Azizan A, Venter L, Jansen van Rensburg PJ, Ericson JA, Ragg NLC, Alfaro AC. Metabolite Changes of Perna canaliculus Following a Laboratory Marine Heatwave Exposure: Insights from Metabolomic Analyses. Metabolites 2023; 13:815. [PMID: 37512522 PMCID: PMC10385441 DOI: 10.3390/metabo13070815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Temperature is considered to be a major abiotic factor influencing aquatic life. Marine heatwaves are emerging as threats to sustainable shellfish aquaculture, affecting the farming of New Zealand's green-lipped mussel [Perna canaliculus (Gmelin, 1791)]. In this study, P. canaliculus were gradually exposed to high-temperature stress, mimicking a five-day marine heatwave event, to better understand the effects of heat stress on the metabolome of mussels. Following liquid chromatography-tandem mass spectrometry analyses of haemolymph samples, key sugar-based metabolites supported energy production via the glycolysis pathway and TCA cycle by 24 h and 48 h of heat stress. Anaerobic metabolism also fulfilled the role of energy production. Antioxidant molecules acted within thermally stressed mussels to mitigate oxidative stress. Purine metabolism supported tissue protection and energy replenishment. Pyrimidine metabolism supported the protection of nucleic acids and protein synthesis. Amino acids ensured balanced intracellular osmolality at 24 h and ammonia detoxification at 48 h. Altogether, this work provides evidence that P. canaliculus has the potential to adapt to heat stress up to 24 °C by regulating its energy metabolism, balancing nucleotide production, and implementing oxidative stress mechanisms over time. The data reported herein can also be used to evaluate the risks of heatwaves and improve mitigation strategies for aquaculture.
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Affiliation(s)
- Awanis Azizan
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | | | | | | | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
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Skubisz K, Dąbkowski K, Samborowska E, Starzyńska T, Deskur A, Ambrozkiewicz F, Karczmarski J, Radkiewicz M, Kusnierz K, Kos-Kudła B, Sulikowski T, Cybula P, Paziewska A. Serum Metabolite Biomarkers for Pancreatic Tumors: Neuroendocrine and Pancreatic Ductal Adenocarcinomas-A Preliminary Study. Cancers (Basel) 2023; 15:3242. [PMID: 37370852 DOI: 10.3390/cancers15123242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Pancreatic cancer is the most common pancreatic solid malignancy with an aggressive clinical course and low survival rate. There are a limited number of reliable prognostic biomarkers and a need to understand the pathogenesis of pancreatic tumors; neuroendocrine (PNET) and pancreatic ductal adenocarcinomas (PDAC) encouraged us to analyze the serum metabolome of pancreatic tumors and disturbances in the metabolism of PDAC and PNET. METHODS Using the AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) with liquid chromatography-mass spectrometry (LC-MS), we identified changes in metabolite profiles and disrupted metabolic pathways serum of NET and PDAC patients. RESULTS The concentration of six metabolites showed statistically significant differences between the control group and PDAC patients (p.adj < 0.05). Glutamine (Gln), acetylcarnitine (C2), and citrulline (Cit) presented a lower concentration in the serum of PDAC patients, while phosphatidylcholine aa C32:0 (PC aa C32:0), sphingomyelin C26:1 (SM C26:1), and glutamic acid (Glu) achieved higher concentrations compared to serum samples from healthy individuals. Five of the tested metabolites: C2 (FC = 8.67), and serotonin (FC = 2.68) reached higher concentration values in the PNET serum samples compared to PDAC, while phosphatidylcholine aa C34:1 (PC aa C34:1) (FC = -1.46 (0.68)) had a higher concentration in the PDAC samples. The area under the curves (AUC) of the receiver operating characteristic (ROC) curves presented diagnostic power to discriminate pancreatic tumor patients, which were highest for acylcarnitines: C2 with AUC = 0.93, serotonin with AUC = 0.85, and PC aa C34:1 with AUC = 0.86. CONCLUSIONS The observations presented provide better insight into the metabolism of pancreatic tumors, and improve the diagnosis and classification of tumors. Serum-circulating metabolites can be easily monitored without invasive procedures and show the present clinical patients' condition, helping with pharmacological treatment or dietary strategies.
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Affiliation(s)
- Karolina Skubisz
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Pediatric Hospital of Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Krzysztof Dąbkowski
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Emilia Samborowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Teresa Starzyńska
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Anna Deskur
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, 32300 Pilsen, Czech Republic
| | - Jakub Karczmarski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Mariusz Radkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Katarzyna Kusnierz
- The Department of Gastrointestinal Surgery, Medical University of Silesia, 40-752 Katowice, Poland
| | - Beata Kos-Kudła
- Department of Endocrinology and Neuroendocrine Tumours, Department of Pathophysiology and Endocrinology, Medical University of Silesia, 40-752 Katowice, Poland
| | - Tadeusz Sulikowski
- Department of General, Minimally Invasive and Gastroenterological Surgery, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Patrycja Cybula
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Molecular Biology Laboratory, Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland
| | - Agnieszka Paziewska
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
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30
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Fernandez Garcia E, Paudel U, Noji MC, Bowman CE, Rustgi AK, Pitarresi JR, Wellen KE, Arany Z, Weissenrieder JS, Foskett JK. The mitochondrial Ca 2+ channel MCU is critical for tumor growth by supporting cell cycle progression and proliferation. Front Cell Dev Biol 2023; 11:1082213. [PMID: 37363724 PMCID: PMC10285664 DOI: 10.3389/fcell.2023.1082213] [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: 10/27/2022] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: The mitochondrial uniporter (MCU) Ca2+ ion channel represents the primary means for Ca2+ uptake by mitochondria. Mitochondrial matrix Ca2+ plays critical roles in mitochondrial bioenergetics by impinging upon respiration, energy production and flux of biochemical intermediates through the TCA cycle. Inhibition of MCU in oncogenic cell lines results in an energetic crisis and reduced cell proliferation unless media is supplemented with nucleosides, pyruvate or α-KG. Nevertheless, the roles of MCU-mediated Ca2+ influx in cancer cells remain unclear, in part because of a lack of genetic models. Methods: MCU was genetically deleted in transformed murine fibroblasts for study in vitro and in vivo. Tumor formation and growth were studied in murine xenograft models. Proliferation, cell invasion, spheroid formation and cell cycle progression were measured in vitro. The effects of MCU deletion on survival and cell-death were determined by probing for live/death markers. Mitochondrial bioenergetics were studied by measuring mitochondrial matrix Ca2+ concentration, membrane potential, global dehydrogenase activity, respiration, ROS production and inactivating-phosphorylation of pyruvate dehydrogenase. The effects of MCU rescue on metabolism were examined by tracing of glucose and glutamine utilization for fueling of mitochondrial respiration. Results: Transformation of primary fibroblasts in vitro was associated with increased MCU expression, enhanced MCU-mediated Ca2+ uptake, altered mitochondrial matrix Ca2+ concentration responses to agonist stimulation, suppression of inactivating-phosphorylation of pyruvate dehydrogenase and a modest increase of mitochondrial respiration. Genetic MCU deletion inhibited growth of HEK293T cells and transformed fibroblasts in mouse xenograft models, associated with reduced proliferation and delayed cell-cycle progression. MCU deletion inhibited cancer stem cell-like spheroid formation and cell invasion in vitro, both predictors of metastatic potential. Surprisingly, mitochondrial matrix [Ca2+], membrane potential, global dehydrogenase activity, respiration and ROS production were unaffected. In contrast, MCU deletion elevated glycolysis and glutaminolysis, strongly sensitized cell proliferation to glucose and glutamine limitation, and altered agonist-induced cytoplasmic Ca2+ signals. Conclusion: Our results reveal a dependence of tumorigenesis on MCU, mediated by a reliance on MCU for cell metabolism and Ca2+ dynamics necessary for cell-cycle progression and cell proliferation.
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Affiliation(s)
- Emily Fernandez Garcia
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Usha Paudel
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael C. Noji
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Medicine, Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Caitlyn E. Bowman
- Department of Medicine, Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Anil K. Rustgi
- Division of Digestive and Liver Diseases, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, United States
| | - Jason R. Pitarresi
- Division of Hematology/Oncology, Departments of Medicine and Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Kathryn E. Wellen
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zolt Arany
- Department of Medicine, Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Jillian S. Weissenrieder
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - J. Kevin Foskett
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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31
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Funke VLE, Walter C, Melcher V, Wei L, Sandmann S, Hotfilder M, Varghese J, Jäger N, Kool M, Jones DTW, Pfister SM, Milde T, Mynarek M, Rutkowski S, Seggewiss J, Jeising D, de Faria FW, Marquardt T, Albert TK, Schüller U, Kerl K. Group-specific cellular metabolism in Medulloblastoma. J Transl Med 2023; 21:363. [PMID: 37277823 DOI: 10.1186/s12967-023-04211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Cancer metabolism influences multiple aspects of tumorigenesis and causes diversity across malignancies. Although comprehensive research has extended our knowledge of molecular subgroups in medulloblastoma (MB), discrete analysis of metabolic heterogeneity is currently lacking. This study seeks to improve our understanding of metabolic phenotypes in MB and their impact on patients' outcomes. METHODS Data from four independent MB cohorts encompassing 1,288 patients were analysed. We explored metabolic characteristics of 902 patients (ICGC and MAGIC cohorts) on bulk RNA level. Moreover, data from 491 patients (ICGC cohort) were searched for DNA alterations in genes regulating cell metabolism. To determine the role of intratumoral metabolic differences, we examined single-cell RNA-sequencing (scRNA-seq) data from 34 additional patients. Findings on metabolic heterogeneity were correlated to clinical data. RESULTS Established MB groups exhibit substantial differences in metabolic gene expression. By employing unsupervised analyses, we identified three clusters of group 3 and 4 samples with distinct metabolic features in ICGC and MAGIC cohorts. Analysis of scRNA-seq data confirmed our results of intertumoral heterogeneity underlying the according differences in metabolic gene expression. On DNA level, we discovered clear associations between altered regulatory genes involved in MB development and lipid metabolism. Additionally, we determined the prognostic value of metabolic gene expression in MB and showed that expression of genes involved in metabolism of inositol phosphates and nucleotides correlates with patient survival. CONCLUSION Our research underlines the biological and clinical relevance of metabolic alterations in MB. Thus, distinct metabolic signatures presented here might be the first step towards future metabolism-targeted therapeutic options.
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Affiliation(s)
- Viktoria L E Funke
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Carolin Walter
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Lanying Wei
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Marc Hotfilder
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, 48149, Münster, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Jochen Seggewiss
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Daniela Jeising
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Flavia W de Faria
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Thorsten Marquardt
- Department of General Pediatrics, Metabolic Diseases, University Children's Hospital Münster, 48149, Münster, Germany
| | - Thomas K Albert
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Research Institute Children's Cancer Center, 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
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32
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García EF, Paudel U, Noji MC, Bowman CE, Pitarresi JR, Rustgi AK, Wellen KE, Arany Z, Weissenrieder JS, Foskett JK. The mitochondrial Ca 2+ channel MCU is critical for tumor growth by supporting cell cycle progression and proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538295. [PMID: 37163088 PMCID: PMC10168388 DOI: 10.1101/2023.04.26.538295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The mitochondrial uniporter (MCU) Ca 2+ ion channel represents the primary means for Ca 2+ uptake into mitochondria. Here we employed in vitro and in vivo models with MCU genetically eliminated to understand how MCU contributes to tumor formation and progression. Transformation of primary fibroblasts in vitro was associated with increased MCU expression, enhanced mitochondrial Ca 2+ uptake, suppression of inactivating-phosphorylation of pyruvate dehydrogenase, a modest increase of basal mitochondrial respiration and a significant increase of acute Ca 2+ -dependent stimulation of mitochondrial respiration. Inhibition of mitochondrial Ca 2+ uptake by genetic deletion of MCU markedly inhibited growth of HEK293T cells and of transformed fibroblasts in mouse xenograft models. Reduced tumor growth was primarily a result of substantially reduced proliferation and fewer mitotic cells in vivo , and slower cell proliferation in vitro associated with delayed progression through S-phase of the cell cycle. MCU deletion inhibited cancer stem cell-like spheroid formation and cell invasion in vitro , both predictors of metastatic potential. Surprisingly, mitochondrial matrix Ca 2+ concentration, membrane potential, global dehydrogenase activity, respiration and ROS production were unchanged by genetic deletion of MCU in transformed cells. In contrast, MCU deletion elevated glycolysis and glutaminolysis, strongly sensitized cell proliferation to glucose and glutamine limitation, and altered agonist-induced cytoplasmic Ca 2+ signals. Our results reveal a dependence of tumorigenesis on MCU, mediated by a reliance on mitochondrial Ca 2+ uptake for cell metabolism and Ca 2+ dynamics necessary for cell-cycle progression and cell proliferation.
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33
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E. coli Secretome Metabolically Modulates MDA-MB-231 Breast Cancer Cells' Energy Metabolism. Int J Mol Sci 2023; 24:ijms24044219. [PMID: 36835626 PMCID: PMC9964955 DOI: 10.3390/ijms24044219] [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: 11/30/2022] [Revised: 01/26/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer (BC) is commonly diagnosed in women. BC cells are associated with altered metabolism, which is essential to support their energetic requirements, cellular proliferation, and continuous survival. The altered metabolism of BC cells is a result of the genetic abnormalities of BC cells. Risk factors can also enhance it, including age, lifestyle, hormone disturbances, etc. Other unknown BC-promoting risk factors are under scientific investigation. One of these investigated factors is the microbiome. However, whether the breast microbiome found in the BC tissue microenvironment can impact BC cells has not been studied. We hypothesized that E. coli, part of a normal breast microbiome with more presence in BC tissue, secretes metabolic molecules that could alter BC cells' metabolism to maintain their survival. Thus, we directly examined the impact of the E. coli secretome on the metabolism of BC cells in vitro. MDA-MB-231 cells, an in vitro model of aggressive triple-negative BC cells, were treated with the E. coli secretome at different time points, followed by untargeted metabolomics analyses via liquid chromatography-mass spectrometry to identify metabolic alterations in the treated BC cell lines. MDA-MB-231 cells that were not treated were used as controls. Moreover, metabolomic analyses were performed on the E. coli secretome to profile the most significant bacterial metabolites affecting the metabolism of the treated BC cell lines. The metabolomics results revealed about 15 metabolites that potentially have indirect roles in cancer metabolism that were secreted from E. coli in the culture media of MDA-MB-231 cells. The cells treated with the E. coli secretome showed 105 dysregulated cellular metabolites compared to controls. The dysregulated cellular metabolites were involved in the metabolism of fructose and mannose, sphingolipids, amino acids, fatty acids, amino sugar, nucleotide sugar, and pyrimidine, which are vital pathways required for the pathogenesis of BC. Our findings are the first to show that the E. coli secretome modulates the BC cells' energy metabolism, highlighting insights into the possibility of altered metabolic events in BC tissue in the actual BC tissue microenvironment that are potentially induced by the local bacteria. Our study provides metabolic data that could be as a basis for future studies searching for the underlying mechanisms mediated by bacteria and their secretome to alter the metabolism of BC cells.
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Untargeted Metabolomics Based Prediction of Therapeutic Potential for Apigenin and Chrysin. Int J Mol Sci 2023; 24:ijms24044066. [PMID: 36835484 PMCID: PMC9967419 DOI: 10.3390/ijms24044066] [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: 12/27/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
The prominent flavonoids apigenin and chrysin have been demonstrated to have systemic benefits. Our previous work was first to establish the impact of apigenin and chrysin on cellular transcriptome. In the current study, we have revealed the ability of apigenin and chrysin to alter the cellular metabolome based on our untargeted metabolomics. Based on our metabolomics data, both these structurally related flavonoids demonstrate diverging and converging properties. Apigenin demonstrated the potential to possess anti-inflammatory and vasorelaxant properties through the upregulation of intermediate metabolites of alpha-linolenic acid and linoleic acid pathways. Chrysin, on the other hand, exhibited abilities to inhibit protein and pyrimidine synthesis along with downregulation of gluconeogenesis pathways based on the altered metabolites detected. Chrysin-mediated metabolite changes are mostly due to its ability to modulate L-alanine metabolism and the urea cycle. On the other hand, both the flavonoids also demonstrated converging properties. Apigenin and chrysin were able to downregulate metabolites involved in cholesterol biosynthesis and uric acid synthesis, namely 7-dehydrocholesterol and xanthosine, respectively. This work will provide understanding regarding the diverse therapeutic potential of these naturally occurring flavonoids and help us in curbing an array of metabolic complications.
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The Role of PI3K/AKT/mTOR Signaling in Hepatocellular Carcinoma Metabolism. Int J Mol Sci 2023; 24:ijms24032652. [PMID: 36768977 PMCID: PMC9916527 DOI: 10.3390/ijms24032652] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths in the world. Metabolic reprogramming is considered a new hallmark of cancer, but it remains unclearly described in HCC. The dysregulation of the PI3K/AKT/mTOR signaling pathway is common in HCC and is, therefore, a topic of further research and the concern of developing a novel target for liver cancer therapy. In this review, we illustrate mechanisms by which this signaling network is accountable for regulating HCC cellular metabolism, including glucose metabolism, lipid metabolism, amino acid metabolism, pyrimidine metabolism, and oxidative metabolism, and summarize the ongoing clinical trials based on the inhibition of the PI3K/AKT/mTOR pathway in HCC.
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36
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Yu Y, Yu J, Ge S, Su Y, Fan X. Novel insight into metabolic reprogrammming in cancer radioresistance: A promising therapeutic target in radiotherapy. Int J Biol Sci 2023; 19:811-828. [PMID: 36778122 PMCID: PMC9910008 DOI: 10.7150/ijbs.79928] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Currently, cancer treatment mainly consists of surgery, radiotherapy, chemotherapy, immunotherapy, and molecular targeted therapy, of which radiotherapy is one of the major pillars. However, the occurrence of radioresistance largely limits its therapeutic effect. Metabolic reprogramming is an important hallmark in cancer progression and treatment resistance. In radiotherapy, DNA breakage is the major mechanism of cell damage, and in turn, cancer cells are prone to increase the metabolic flux of glucose, glutamine, serine, arginine, fatty acids etc., thus providing sufficient substrates and energy for DNA damage repair. Therefore, studying the linkage between metabolic reprogramming and cancer radioresistance may provide new ideas for improving the efficacy of tumor therapy. This review mainly focuses on the role of metabolic alterations, including glucose, amino acid, lipid, nucleotide and other ion metabolism, in radioresistance, and proposes possible therapeutic targets to improve the efficacy of cancer radiotherapy.
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Affiliation(s)
- Yilin Yu
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
| | - Jie Yu
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
| | - Yun Su
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
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37
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Hyroššová P, Milošević M, Škoda J, Vachtenheim Jr J, Rohlena J, Rohlenová K. Effects of metabolic cancer therapy on tumor microenvironment. Front Oncol 2022; 12:1046630. [PMID: 36582801 PMCID: PMC9793001 DOI: 10.3389/fonc.2022.1046630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Targeting tumor metabolism for cancer therapy is an old strategy. In fact, historically the first effective cancer therapeutics were directed at nucleotide metabolism. The spectrum of metabolic drugs considered in cancer increases rapidly - clinical trials are in progress for agents directed at glycolysis, oxidative phosphorylation, glutaminolysis and several others. These pathways are essential for cancer cell proliferation and redox homeostasis, but are also required, to various degrees, in other cell types present in the tumor microenvironment, including immune cells, endothelial cells and fibroblasts. How metabolism-targeted treatments impact these tumor-associated cell types is not fully understood, even though their response may co-determine the overall effectivity of therapy. Indeed, the metabolic dependencies of stromal cells have been overlooked for a long time. Therefore, it is important that metabolic therapy is considered in the context of tumor microenvironment, as understanding the metabolic vulnerabilities of both cancer and stromal cells can guide new treatment concepts and help better understand treatment resistance. In this review we discuss recent findings covering the impact of metabolic interventions on cellular components of the tumor microenvironment and their implications for metabolic cancer therapy.
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Affiliation(s)
- Petra Hyroššová
- Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czechia
| | - Mirko Milošević
- Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czechia,Faculty of Science, Charles University, Prague, Czechia
| | - Josef Škoda
- Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czechia
| | - Jiří Vachtenheim Jr
- 3rd Department of Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
| | - Jakub Rohlena
- Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czechia,*Correspondence: Kateřina Rohlenová, ; Jakub Rohlena,
| | - Kateřina Rohlenová
- Institute of Biotechnology of the Czech Academy of Sciences, Prague, Czechia,*Correspondence: Kateřina Rohlenová, ; Jakub Rohlena,
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38
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Schild T, Keshari KR. Revealing de novo pyrimidine synthesis as a key vulnerability in brain tumors. Cancer Cell 2022; 40:1457-1458. [PMID: 36400017 DOI: 10.1016/j.ccell.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Brain tumors are notoriously difficult to treat. Three recent Cancer Cell articles aim to uncover novel druggable targets in IDH mutant gliomas, diffuse midline gliomas, and medulloblastomas, respectively, and show that these brain tumor types shift their metabolism to become reliant on de novo pyrimidine synthesis.
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Affiliation(s)
- Tanya Schild
- Department of Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kayvan R Keshari
- Department of Radiology and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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39
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Kim DH, Kim JS, Mok CS, Chang EH, Choi J, Lim J, Kim CH, Park AR, Bae YJ, Koo BS, Lee HC. dTMP imbalance through thymidylate 5'-phosphohydrolase activity induces apoptosis in triple-negative breast cancers. Sci Rep 2022; 12:20027. [PMID: 36414668 PMCID: PMC9681768 DOI: 10.1038/s41598-022-24706-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Immunotherapy has a number of advantages over traditional anti-tumor therapy but can cause severe adverse reactions due to an overactive immune system. In contrast, a novel metabolic treatment approach can induce metabolic vulnerability through multiple cancer cell targets. Here, we show a therapeutic effect by inducing nucleotide imbalance and apoptosis in triple negative breast cancer cells (TNBC), by treating with cytosolic thymidylate 5'-phosphohydrolase (CT). We show that a sustained consumption of dTMP by CT could induce dNTP imbalance, leading to apoptosis as tricarboxylic acid cycle intermediates were depleted to mitigate this imbalance. These cytotoxic effects appeared to be different, depending on substrate specificity of the 5' nucleotide or metabolic dependency of the cancer cell lines. Using representative TNBC cell lines, we reveal how the TNBC cells were affected by CT-transfection through extracellular acidification rate (ECAR)/oxygen consumption rate (OCR) analysis and differential transcription/expression levels. We suggest a novel approach for treating refractory TNBC by an mRNA drug that can exploit metabolic dependencies to exacerbate cell metabolic vulnerability.
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Affiliation(s)
- Dae-Ho Kim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea ,grid.251916.80000 0004 0532 3933Department of Molecular Science and Technology, Ajou University, Suwon, 16499 Republic of Korea ,grid.251916.80000 0004 0532 3933Department of Otolaryngology, Ajou University School of Medicine, Suwon, 16499 Republic of Korea
| | - Jin-Sook Kim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Chang-Soo Mok
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea ,grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University Biomedi Campus, Gyeonggi-do, 10326 Republic of Korea
| | - En-Hyung Chang
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Jiwon Choi
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Junsub Lim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Chul-Ho Kim
- grid.251916.80000 0004 0532 3933Department of Otolaryngology, Ajou University School of Medicine, Suwon, 16499 Republic of Korea
| | | | | | - Bong-Seong Koo
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Hyeon-Cheol Lee
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
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40
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Schölermann B, Bonowski J, Grigalunas M, Burhop A, Xie Y, Hoock JGF, Liu J, Dow M, Nelson A, Nowak C, Pahl A, Sievers S, Ziegler S. Identification of Dihydroorotate Dehydrogenase Inhibitors Using the Cell Painting Assay. Chembiochem 2022; 23:e202200475. [PMID: 36134475 PMCID: PMC9828254 DOI: 10.1002/cbic.202200475] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/21/2022] [Indexed: 02/03/2023]
Abstract
Profiling approaches have been increasingly employed for the characterization of disease-relevant phenotypes or compound perturbation as they provide a broad, unbiased view on impaired cellular states. We report that morphological profiling using the cell painting assay (CPA) can detect modulators of de novo pyrimidine biosynthesis and of dihydroorotate dehydrogenase (DHODH) in particular. The CPA can differentiate between impairment of pyrimidine and folate metabolism, which both affect cellular nucleotide pools. The identified morphological signature is shared by inhibitors of DHODH and the functionally tightly coupled complex III of the mitochondrial respiratory chain as well as by UMP synthase, which is downstream of DHODH. The CPA appears to be particularly suited for the detection of DHODH inhibitors at the site of their action in cells. As DHODH is a validated therapeutic target, the CPA will enable unbiased identification of DHODH inhibitors and inhibitors of de novo pyrimidine biosynthesis for biological research and drug discovery.
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Affiliation(s)
- Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jana Bonowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Annina Burhop
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Yusheng Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Joseph G. F. Hoock
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jie Liu
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Mark Dow
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Adam Nelson
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Christine Nowak
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
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41
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Peter TK, Withanage MHH, Comnick CL, Pendleton C, Dabdoub S, Ganesan S, Drake D, Banas J, Xie XJ, Zeng E. Systematic review and meta-analysis of oral squamous cell carcinoma associated oral microbiome. Front Microbiol 2022; 13:968304. [PMID: 36338051 PMCID: PMC9632422 DOI: 10.3389/fmicb.2022.968304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022] Open
Abstract
The intersection between the human oral microbiome and oral health is an emerging area of study which has gained momentum over the last decade. This momentum has motivated a search for associations between the oral microbiome and oral cancer, in hopes of identifying possible biomarkers that facilitate earlier diagnosis and improved prognosis for patients with that disease. The present study examined the relationship between the microbiome in the human oral cavity and oral squamous cell carcinoma (OSCC). We searched the literature for case-control studies which focused on the relationship between the human oral microbiome and OSCC. We aggregated three types of data from these studies: bacteriome data at the genus level, predicted functional pathway data, and gene abundance data. From these data, we noted several microbial genera which may be associated with oral cancer status, including Fusobacterium. We also identified functional pathways which merit further investigation, including RNA degradation (ko03018) and primary immunodeficiency (ko05340). In addition, our analysis of gene abundance data identified the gene K06147 (ATP-binding cassette, subfamily B, bacterial) as being over abundant in OSCC samples. Our results are generalizations which identified some currents that we believe could guide further research. Our work faced several limitations related to the heterogeneity of the available data. Wide variation in methods for sample collection, methods for controlling for known behavioral risk factors, computing platform choice, and methods for case-control design all posed confounding factors in this work. We examined the current methods of data collection, data processing, and data reporting in order to offer suggestions toward the establishment of best practices within this field. We propose that these limitations should be addressed through the implementation of standardized data analytic practices that will conform to the rigor and reproducibility standards required of publicly funded research.
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Affiliation(s)
- Tabitha K. Peter
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Miyuraj H. H. Withanage
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Carissa L. Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Chandler Pendleton
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Shareef Dabdoub
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Sukirth Ganesan
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - David Drake
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Jeffrey Banas
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Pediatric Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Xian Jin Xie
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Preventative and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Preventative and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States,*Correspondence: Erliang Zeng
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Lackner M, Neef SK, Winter S, Beer-Hammer S, Nürnberg B, Schwab M, Hofmann U, Haag M. Untargeted stable isotope-resolved metabolomics to assess the effect of PI3Kβ inhibition on metabolic pathway activities in a PTEN null breast cancer cell line. Front Mol Biosci 2022; 9:1004602. [PMID: 36310598 PMCID: PMC9614656 DOI: 10.3389/fmolb.2022.1004602] [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: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
The combination of high-resolution LC-MS untargeted metabolomics with stable isotope-resolved tracing is a promising approach for the global exploration of metabolic pathway activities. In our established workflow we combine targeted isotopologue feature extraction with the non-targeted X13CMS routine. Metabolites, detected by X13CMS as differentially labeled between two biological conditions are subsequently integrated into the original targeted library. This strategy enables monitoring of changes in known pathways as well as the discovery of hitherto unknown metabolic alterations. Here, we demonstrate this workflow in a PTEN (phosphatase and tensin homolog) null breast cancer cell line (MDA-MB-468) exploring metabolic pathway activities in the absence and presence of the selective PI3Kβ inhibitor AZD8186. Cells were fed with [U-13C] glucose and treated for 1, 3, 6, and 24 h with 0.5 µM AZD8186 or vehicle, extracted by an optimized sample preparation protocol and analyzed by LC-QTOF-MS. Untargeted differential tracing of labels revealed 286 isotope-enriched features that were significantly altered between control and treatment conditions, of which 19 features could be attributed to known compounds from targeted pathways. Other 11 features were unambiguously identified based on data-dependent MS/MS spectra and reference substances. Notably, only a minority of the significantly altered features (11 and 16, respectively) were identified when preprocessing of the same data set (treatment vs. control in 24 h unlabeled samples) was performed with tools commonly used for label-free (i.e. w/o isotopic tracer) non-targeted metabolomics experiments (Profinder´s batch recursive feature extraction and XCMS). The structurally identified metabolites were integrated into the existing targeted isotopologue feature extraction workflow to enable natural abundance correction, evaluation of assay performance and assessment of drug-induced changes in pathway activities. Label incorporation was highly reproducible for the majority of isotopologues in technical replicates with a RSD below 10%. Furthermore, inter-day repeatability of a second label experiment showed strong correlation (Pearson R2 > 0.99) between tracer incorporation on different days. Finally, we could identify prominent pathway activity alterations upon PI3Kβ inhibition. Besides pathways in central metabolism, known to be changed our workflow revealed additional pathways, like pyrimidine metabolism or hexosamine pathway. All pathways identified represent key metabolic processes associated with cancer metabolism and therapy.
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Affiliation(s)
- Marcel Lackner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sylvia K. Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Sandra Beer-Hammer
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute for Experimental and Clinical Pharmacology and Pharmacogenomics, Interfaculty Center for Pharmacogenomics and Drug Research (ICePhA), University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Bernd Nürnberg
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute for Experimental and Clinical Pharmacology and Pharmacogenomics, Interfaculty Center for Pharmacogenomics and Drug Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- *Correspondence: Mathias Haag,
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Hamidi M, Eriz A, Mitxelena J, Fernandez-Ares L, Aurrekoetxea I, Aspichueta P, Iglesias-Ara A, Zubiaga AM. Targeting E2F Sensitizes Prostate Cancer Cells to Drug-Induced Replication Stress by Promoting Unscheduled CDK1 Activity. Cancers (Basel) 2022; 14:cancers14194952. [PMID: 36230876 PMCID: PMC9564059 DOI: 10.3390/cancers14194952] [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: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary E2F1 and E2F2 are highly expressed in many cancer types, but their contribution to malignancy is not well understood. Here we aimed to define the impact of E2F1/E2F2 deregulation in prostate cancer. We show that inhibition of E2F sensitizes prostate cancer cells to drug-induced replication stress and cell death. We found that E2F target genes involved in nucleotide biosynthesis contribute to maintaining genome stability in prostate cancer cells, but their enzymatic activity is insufficient to prevent replication stress after E2F1/E2F2 depletion. Instead, E2F1/E2F2 hinder premature CDK1 activation during S phase, which is key to ensure genome stability and viability of prostate cancer cells. From a therapeutic perspective, inhibiting E2F activity provokes catastrophic levels of replication stress and blunts xenograft growth in combination with drugs targeting nucleotide biosynthesis or DNA repair. Our results highlight the suitability of targeting E2F for the treatment of prostate cancer. Abstract E2F1/E2F2 expression correlates with malignancy in prostate cancer (PCa), but its functional significance remains unresolved. To define the mechanisms governed by E2F in PCa, we analyzed the contribution of E2F target genes to the control of genome integrity, and the impact of modulating E2F activity on PCa progression. We show that silencing or inhibiting E2F1/E2F2 induces DNA damage during S phase and potentiates 5-FU-induced replication stress and cellular toxicity. Inhibition of E2F downregulates the expression of E2F targets involved in nucleotide biosynthesis (TK1, DCK, TYMS), whose expression is upregulated by 5-FU. However, their enzymatic products failed to rescue DNA damage of E2F1/E2F2 knockdown cells, suggesting additional mechanisms for E2F function. Interestingly, targeting E2F1/E2F2 in PCa cells reduced WEE1 expression and resulted in premature CDK1 activation during S phase. Inhibition of CDK1/CDK2 prevented DNA damage induced by E2F loss, suggesting that E2F1/E2F2 safeguard genome integrity by restraining CDK1/CDK2 activity. Importantly, combined inhibition of E2F and ATR boosted replication stress and dramatically reduced tumorigenic capacity of PCa cells in xenografts. Collectively, inhibition of E2F in combination with drugs targeting nucleotide biosynthesis or DNA repair is a promising strategy to provoke catastrophic levels of replication stress that could be applied to PCa treatment.
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Affiliation(s)
- Mohaddase Hamidi
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
| | - Ainhoa Eriz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
| | - Jone Mitxelena
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
- Ikerbasque—Basque Foundation for Science, 48009 Bilbao, Spain
| | - Larraitz Fernandez-Ares
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
| | - Igor Aurrekoetxea
- Department of Physiology, Faculty of Medicine and Nursing, University of Basque Country UPV/EHU, 48080 Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Patricia Aspichueta
- Department of Physiology, Faculty of Medicine and Nursing, University of Basque Country UPV/EHU, 48080 Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Ainhoa Iglesias-Ara
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
- Correspondence: (A.I.-A.); (A.M.Z.); Tel.: +34-94-601-5799 (A.I.-A.); +34-94-601-2603 (A.M.Z.); Fax: +34-94-601-3143 (A.M.Z.)
| | - Ana M. Zubiaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain
- Correspondence: (A.I.-A.); (A.M.Z.); Tel.: +34-94-601-5799 (A.I.-A.); +34-94-601-2603 (A.M.Z.); Fax: +34-94-601-3143 (A.M.Z.)
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Oncogenic β-catenin stimulation of AKT2-CAD-mediated pyrimidine synthesis is targetable vulnerability in liver cancer. Proc Natl Acad Sci U S A 2022; 119:e2202157119. [PMID: 36122209 PMCID: PMC9522414 DOI: 10.1073/pnas.2202157119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
β-Catenin encoding gene CTNNB1 is known as the most frequently mutated proto-oncogene in liver cancer. We report that active β-catenin is essential in initiation and advancement of hepatocarcinogenesis. As a transcriptional activator of AKT2, β-catenin potentiates AKT2 phosphorylation of CAD, which in return stimulates de novo pyrimidine synthesis and liver cancer development. β-Catenin, AKT2, and pyrimidine synthesis inhibitors are promising therapeutics for the treatment of oncogenic β-catenin–associated cancer. CTNNB1, encoding β-catenin protein, is the most frequently altered proto-oncogene in hepatic neoplasms. In this study, we studied the significance and pathological mechanism of CTNNB1 gain-of-function mutations in hepatocarcinogenesis. Activated β-catenin not only triggered hepatic tumorigenesis but also exacerbated Tp53 deletion or hepatitis B virus infection–mediated liver cancer development in mouse models. Using untargeted metabolomic profiling, we identified boosted de novo pyrimidine synthesis as the major metabolic aberration in β-catenin mutant cell lines and livers. Oncogenic β-catenin transcriptionally stimulated AKT2, which then phosphorylated the rate-limiting de novo pyrimidine synthesis enzyme CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, dihydroorotase) on S1406 and S1859 to potentiate nucleotide synthesis. Moreover, inhibition of β-catenin/AKT2-stimulated pyrimidine synthesis axis preferentially repressed β-catenin mutant cell proliferation and tumor formation. Therefore, β-catenin active mutations are oncogenic in various preclinical liver cancer models. Stimulation of β-catenin/AKT2/CAD signaling cascade on pyrimidine synthesis is an essential and druggable vulnerability for β-catenin mutant liver cancer.
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Sudan S, Zhan X, Li J. A Novel Probiotic Bacillus subtilis Strain Confers Cytoprotection to Host Pig Intestinal Epithelial Cells during Enterotoxic Escherichia coli Infection. Microbiol Spectr 2022; 10:e0125721. [PMID: 35736372 PMCID: PMC9430607 DOI: 10.1128/spectrum.01257-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/26/2022] [Indexed: 01/13/2023] Open
Abstract
Enteric infections caused by enterotoxic Escherichia coli (ETEC) negatively impact the growth performance of piglets during weaning, resulting in significant economic losses for the producers. With the ban on antibiotic usage in livestock production, probiotics have gained a lot of attention as a potential alternative. However, strain specificity and limited knowledge on the host-specific targets limit their efficacy in preventing ETEC-related postweaning enteric infections. We recently isolated and characterized a novel probiotic Bacillus subtilis bacterium (CP9) that demonstrated antimicrobial activity. Here, we report anti-ETEC properties of CP9 and its impact on metabolic activity of swine intestinal epithelial (IPEC-J2) cells. Our results showed that pre- or coincubation with CP9 protected IPEC-J2 cells from ETEC-induced cytotoxicity. CP9 significantly attenuated ETEC-induced inflammatory response by reducing ETEC-induced nitric oxide production and relative mRNA expression of the Toll-like receptors (TLRs; TLR2, TLR4, and TLR9), proinflammatory tumor necrosis factor alpha, interleukins (ILs; IL-6 and IL-8), augmenting anti-inflammatory granulocyte-macrophage colony-stimulating factor and host defense peptide mucin 1 (MUC1) mRNA levels. We also show that CP9 significantly (P < 0.05) reduced caspase-3 activity, reinstated cell proliferation and increased relative expression of tight junction genes, claudin-1, occludin, and zona occludens-1 in ETEC-infected cells. Finally, metabolomic analysis revealed that CP9 exposure induced metabolic modulation in IPEC J2 cells with the greatest impact seen in alanine, aspartate, and glutamate metabolism; pyrimidine metabolism; nicotinate and nicotinamide metabolism; glutathione metabolism; the citrate cycle (TCA cycle); and arginine and proline metabolism. Our study shows that CP9 incubation attenuated ETEC-induced cytotoxicity in IPEC-J2 cells and offers insight into potential application of this probiotic for ETEC infection control. IMPORTANCE ETEC remains one of the leading causes of postweaning diarrhea and mortality in swine production. Due to the rising concerns with the antibiotic use in livestock, alternative interventions need to be developed. In this study, we analyzed the cytoprotective effect of a novel probiotic strain in combating ETEC infection in swine intestinal cells, along with assessing its mechanism of action. To our knowledge, this is also the first study to analyze the metabolic impact of a probiotic on intestinal cells. Results from this study should provide effective cues in developing a probiotic intervention for ameliorating ETEC infection and improving overall gut health in swine production.
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Affiliation(s)
- Sudhanshu Sudan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Xiaoshu Zhan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Julang Li
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
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DNA methylome and single-cell transcriptome analyses reveal CDA as a potential druggable target for ALK inhibitor-resistant lung cancer therapy. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1236-1249. [PMID: 35999456 PMCID: PMC9440127 DOI: 10.1038/s12276-022-00836-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 11/08/2022]
Abstract
Acquired resistance to inhibitors of anaplastic lymphoma kinase (ALK) is a major clinical challenge for ALK fusion-positive non-small-cell lung cancer (NSCLC). In the absence of secondary ALK mutations, epigenetic reprogramming is one of the main mechanisms of drug resistance, as it leads to phenotype switching that occurs during the epithelial-to-mesenchymal transition (EMT). Although drug-induced epigenetic reprogramming is believed to alter the sensitivity of cancer cells to anticancer treatments, there is still much to learn about overcoming drug resistance. In this study, we used an in vitro model of ceritinib-resistant NSCLC and employed genome-wide DNA methylation analysis in combination with single-cell (sc) RNA-seq to identify cytidine deaminase (CDA), a pyrimidine salvage pathway enzyme, as a candidate drug target. CDA was hypomethylated and upregulated in ceritinib-resistant cells. CDA-overexpressing cells were rarely but definitively detected in the naïve cell population by scRNA-seq, and their abundance was increased in the acquired-resistance population. Knockdown of CDA had antiproliferative effects on resistant cells and reversed the EMT phenotype. Treatment with epigenome-related nucleosides such as 5-formyl-2'-deoxycytidine selectively ablated CDA-overexpressing resistant cells via accumulation of DNA damage. Collectively, our data suggest that targeting CDA metabolism using epigenome-related nucleosides represents a potential new therapeutic strategy for overcoming ALK inhibitor resistance in NSCLC.
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Inhibitors of Nucleotide Biosynthesis as Candidates for a Wide Spectrum of Antiviral Chemotherapy. Microorganisms 2022; 10:microorganisms10081631. [PMID: 36014049 PMCID: PMC9413629 DOI: 10.3390/microorganisms10081631] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Emerging and re-emerging viruses have been a challenge in public health in recent decades. Host-targeted antivirals (HTA) directed at cellular molecules or pathways involved in virus multiplication represent an interesting strategy to combat viruses presently lacking effective chemotherapy. HTA could provide a wide range of agents with inhibitory activity against current and future viruses that share similar host requirements and reduce the possible selection of antiviral-resistant variants. Nucleotide metabolism is one of the more exploited host metabolic pathways as a potential antiviral target for several human viruses. This review focuses on the antiviral properties of the inhibitors of pyrimidine and purine nucleotide biosynthesis, with an emphasis on the rate-limiting enzymes dihydroorotate dehydrogenase (DHODH) and inosine monophosphate dehydrogenase (IMPDH) for which there are old and new drugs active against a broad spectrum of pathogenic viruses.
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Feng M, Hou T, Zhou M, Cen Q, Yi T, Bai J, Zeng Y, Liu Q, Zhang C, Zhang Y. Gut microbiota may be involved in Alzheimer’s disease pathology by dysregulating pyrimidine metabolism in APP/PS1 mice. Front Aging Neurosci 2022; 14:967747. [PMID: 35992591 PMCID: PMC9382084 DOI: 10.3389/fnagi.2022.967747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionAlzheimer’s disease (AD) is the most common form of dementia worldwide. The biological mechanisms underlying the pathogenesis of AD aren’t completely clear. Studies have shown that the gut microbiota could be associated with AD pathogenesis; however, the pathways involved still need to be investigated.AimsTo explore the possible pathways of the involvement of gut microbiota in AD pathogenesis through metabolites and to identify new AD biomarkers.MethodsSeven-month-old APP/PS1 mice were used as AD models. The Morris water maze test was used to examine learning and memory ability. 16S rRNA gene sequencing and widely targeted metabolomics were used to identify the gut microbiota composition and fecal metabolic profile, respectively, followed by a combined analysis of microbiomics and metabolomics.ResultsImpaired learning abilities were observed in APP/PS1 mice. Statistically significant changes in the gut microbiota were detected, including a reduction in β-diversity, a higher ratio of Firmicutes/Bacteroidota, and multiple differential bacteria. Statistically significant changes in fecal metabolism were also detected, with 40 differential fecal metabolites and perturbations in the pyrimidine metabolism. Approximately 40% of the differential fecal metabolites were markedly associated with the gut microbiota, and the top two bacteria associated with the most differential metabolites were Bacillus firmus and Rikenella. Deoxycytidine, which causes changes in the pyrimidine metabolic pathway, was significantly correlated with Clostridium sp. Culture-27.ConclusionsGut microbiota may be involved in the pathological processes associated with cognitive impairment in AD by dysregulating pyrimidine metabolism. B. firmus, Rikenella, Clostridium sp. Culture-27, and deoxyuridine may be important biological markers for AD. Our findings provide new insights into the host-microbe crosstalk in AD pathology and contribute to the discovery of diagnostic markers and therapeutic targets for AD.
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Affiliation(s)
- Min Feng
- School of Rehabilitation Medicine and Healthcare, Hunan University of Medicine, Huaihua, China
| | - Tianshu Hou
- Department of Preventive Traditional Chinese Medicine, Chengdu Integrated TCM, Western Medical Hospital, Chengdu, China
| | - Mingze Zhou
- Health and Rehabilitation School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiuyu Cen
- Health and Rehabilitation School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ting Yi
- Health and Rehabilitation School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jinfeng Bai
- School of Rehabilitation Medicine and Healthcare, Hunan University of Medicine, Huaihua, China
| | - Yun Zeng
- School of Rehabilitation Medicine and Healthcare, Hunan University of Medicine, Huaihua, China
| | - Qi Liu
- Acupuncture and Tuina School, Shaanxi University of Chinese Medicine, Xianyang, China
- *Correspondence: Qi Liu,
| | - Chengshun Zhang
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Chengshun Zhang,
| | - Yingjun Zhang
- School of Clinical Medicine, Hunan University of Medicine, Huaihua, China
- Yingjun Zhang,
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Jayarathna DK, Rentería ME, Batra J, Gandhi NS. A supervised machine learning approach identifies gene-regulating factor-mediated competing endogenous RNA networks in hormone-dependent cancers. J Cell Biochem 2022; 123:1394-1408. [PMID: 35757968 PMCID: PMC9542250 DOI: 10.1002/jcb.30300] [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: 04/21/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Competing endogenous RNAs (ceRNAs) have become an emerging topic in cancer research due to their role in gene regulatory networks. To date, traditional ceRNA bioinformatic studies have investigated microRNAs as the only factor regulating gene expression. Growing evidence suggests that genomic (e.g., copy number alteration [CNA]), transcriptomic (e.g., transcription factors [TFs]), and epigenomic (e.g., DNA methylation [DM]) factors can influence ceRNA regulatory networks. Herein, we used the Least absolute shrinkage and selection operator regression, a machine learning approach, to integrate DM, CNA, and TFs data with RNA expression to infer ceRNA networks in cancer risk. The gene‐regulating factors‐mediated ceRNA networks were identified in four hormone‐dependent (HD) cancer types: prostate, breast, colorectal, and endometrial. The shared ceRNAs across HD cancer types were further investigated using survival analysis, functional enrichment analysis, and protein–protein interaction network analysis. We found two (BUB1 and EXO1) and one (RRM2) survival‐significant ceRNA(s) shared across breast‐colorectal‐endometrial and prostate–colorectal–endometrial combinations, respectively. Both BUB1 and BUB1B genes were identified as shared ceRNAs across more than two HD cancers of interest. These genes play a critical role in cell division, spindle‐assembly checkpoint signalling, and correct chromosome alignment. Furthermore, shared ceRNAs across multiple HD cancers have been involved in essential cancer pathways such as cell cycle, p53 signalling, and chromosome segregation. Identifying ceRNAs' roles across multiple related cancers will improve our understanding of their shared disease biology. Moreover, it contributes to the knowledge of RNA‐mediated cancer pathogenesis.
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Affiliation(s)
- Dulari K Jayarathna
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Miguel E Rentería
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Woolloongabba, QLD, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalized Health, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, Australia.,Cancer and Ageing Research Program, Translational Research Institute, Woolloongabba, QLD, Australia
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Matchett EC, Ambrose EC, Kornbluth J. Characterization of uridine-cytidine kinase like-1 nucleoside kinase activity and its role in tumor growth. Biochem J 2022; 479:1149-1164. [PMID: 35583288 PMCID: PMC9246348 DOI: 10.1042/bcj20210770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/26/2022] [Accepted: 05/18/2022] [Indexed: 11/27/2022]
Abstract
Uridine-cytidine kinase like-1 (UCKL-1) is a largely uncharacterized protein with high sequence similarity to other uridine-cytidine kinases (UCKs). UCKs play an important role in the pyrimidine salvage pathway, catalyzing the phosphorylation of uridine and cytidine to UMP and CMP, respectively. Only two human UCKs have been identified, UCK1 and UCK2. Previous studies have shown both enzymes phosphorylate uridine and cytidine using ATP as the phosphate donor. No studies have evaluated the kinase potential of UCKL-1. We cloned and purified UCKL-1 and found that it successfully phosphorylated uridine and cytidine using ATP as the phosphate donor. The catalytic efficiency (calculated as kcat/KM) was 1.2 × 104 s-1, M-1 for uridine and 0.7 × 104 s-1, M-1 for cytidine. Our lab has previously shown that UCKL-1 is up-regulated in tumor cells, providing protection against natural killer (NK) cell killing activity. We utilized small interfering RNA (siRNA) to down-regulate UCKL-1 in vitro and in vivo to determine the effect of UCKL-1 on tumor growth and metastasis. The down-regulation of UCKL-1 in YAC-1 lymphoma cells in vitro resulted in decreased cell counts and increased apoptotic activity. Down-regulation of UCKL-1 in K562 leukemia cells in vivo led to decreased primary tumor growth and less tumor cell dissemination and metastasis. These results identify UCKL-1 as a bona fide pyrimidine kinase with the therapeutic potential to be a target for tumor growth inhibition and for diminishing or preventing metastasis.
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Affiliation(s)
- Emily C. Matchett
- Department of Pathology, Saint Louis University School of Medicine, St. Louis, MO, U.S.A
| | - Elise C. Ambrose
- Department of Pathology, Saint Louis University School of Medicine, St. Louis, MO, U.S.A
| | - Jacki Kornbluth
- Department of Pathology, Saint Louis University School of Medicine, St. Louis, MO, U.S.A
- VA St. Louis Health Care System, St. Louis, MO, U.S.A
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