1
|
Chang Q, Chen Y, Yin J, Wang T, Dai Y, Wu Z, Guo Y, Wang L, Zhao Y, Yuan H, Song D, Zhang L. Comprehensive Urinary Proteome Profiling Analysis Identifies Diagnosis and Relapse Surveillance Biomarkers for Bladder Cancer. J Proteome Res 2024. [PMID: 38787199 DOI: 10.1021/acs.jproteome.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Bladder cancer (BCa) is the predominant malignancy of the urinary system. Herein, a comprehensive urine proteomic feature was initially established for the noninvasive diagnosis and recurrence monitoring of bladder cancer. 279 cases (63 primary BCa, 87 nontumor controls (NT), 73 relapsed BCa (BCR), and 56 nonrelapsed BCa (BCNR)) were collected to screen urinary protein biomarkers. 4761 and 3668 proteins were qualified and quantified by DDA and sequential window acquisition of all theoretical mass spectra (SWATH-MS) analysis in two discovery sets, respectively. Upregulated proteins were validated by multiple reaction monitoring (MRM) in two independent combined sets. Using the multi-support vector machine-recursive feature elimination (mSVM-RFE) algorithm, a model comprising 13 proteins exhibited good performance between BCa and NT with an AUC of 0.821 (95% CI: 0.675-0.967), 90.9% sensitivity (95% CI: 72.7-100%), and 73.3% specificity (95% CI: 53.3-93.3%) in the diagnosis test set. Meanwhile, an 11-marker classifier significantly distinguished BCR from BCNR with 75.0% sensitivity (95% CI: 50.0-100%), 81.8% specificity (95% CI: 54.5-100%), and an AUC of 0.784 (95% CI: 0.609-0.959) in the test cohort for relapse surveillance. Notably, six proteins (SPR, AK1, CD2AP, ADGRF1, GMPS, and C8A) of 24 markers were newly reported. This paper reveals novel urinary protein biomarkers for BCa and offers new theoretical insights into the pathogenesis of bladder cancer (data identifier PXD044896).
Collapse
Affiliation(s)
- Qi Chang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongqiang Chen
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jianjian Yin
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yuanheng Dai
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zixin Wu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufeng Guo
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lingang Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufen Zhao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hang Yuan
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Dongkui Song
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
2
|
Nouwen LV, Breeuwsma M, Zaal EA, van de Lest CHA, Buitendijk I, Zwaagstra M, Balić P, Filippov DV, Berkers CR, van Kuppeveld FJM. Modulation of nucleotide metabolism by picornaviruses. PLoS Pathog 2024; 20:e1012036. [PMID: 38457376 PMCID: PMC10923435 DOI: 10.1371/journal.ppat.1012036] [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: 06/28/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Viruses actively reprogram the metabolism of the host to ensure the availability of sufficient building blocks for virus replication and spreading. However, relatively little is known about how picornaviruses-a large family of small, non-enveloped positive-strand RNA viruses-modulate cellular metabolism for their own benefit. Here, we studied the modulation of host metabolism by coxsackievirus B3 (CVB3), a member of the enterovirus genus, and encephalomyocarditis virus (EMCV), a member of the cardiovirus genus, using steady-state as well as 13C-glucose tracing metabolomics. We demonstrate that both CVB3 and EMCV increase the levels of pyrimidine and purine metabolites and provide evidence that this increase is mediated through degradation of nucleic acids and nucleotide recycling, rather than upregulation of de novo synthesis. Finally, by integrating our metabolomics data with a previously acquired phosphoproteomics dataset of CVB3-infected cells, we identify alterations in phosphorylation status of key enzymes involved in nucleotide metabolism, providing insight into the regulation of nucleotide metabolism during infection.
Collapse
Affiliation(s)
- Lonneke V. Nouwen
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martijn Breeuwsma
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Esther A. Zaal
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chris H. A. van de Lest
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge Buitendijk
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Pascal Balić
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Celia R. Berkers
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section of Virology, Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
3
|
Zhang Y, Xie W, Zheng W, Qian X, Deng C. Exosome-mediated circGMPS facilitates the development of gastric cancer cells through miR-144-3p/PUM1. Cytotechnology 2024; 76:53-68. [PMID: 38304630 PMCID: PMC10828494 DOI: 10.1007/s10616-023-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/07/2023] [Indexed: 02/03/2024] Open
Abstract
In recent years, gastric cancer (GC) is still one of the major public health burdens in the world. It is reported that exosome circular RNA (circRNA) is involved in the GC progression. However, the function and potential mechanism of circGMPS in GC remains unclear and needs further exploration. In this study, we isolated and identified exosomes from serum by TEM, NTA analysis and Western blot. RNA expression was evaluated by qRT-PCR. Western blot was employed to examine protein expression. Cell proliferation was measured using CCK-8. Transwell assay was adopted to analyze cell migration and invasion. The relationship between genes was explored through bioinformatics analysis, dual-luciferase reporter gene assay and spearman correlation coefficient. We found that circGMPS was elevated in GC exosomes, tissues and cells. Poor prognosis of GC patients was related to high circGMPS expression. Both exosome co-culture with cells and insertion of circGMPS clearly promoted cell progression. Mechanically, circGMPS sponged miR-144-3p to regulate PUM1. Inhibition of PUM1 or miR-144-3p overexpression inhibited the malignant GC cell progression. Our data confirmed that exosome-derived circGMPS boosted malignant progression by miR-144-3p/PUM1 axis in GC cells, providing strong evidences for circGMPS as a clinical biomarker of GC treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-023-00597-9.
Collapse
Affiliation(s)
- Yuexin Zhang
- Department of Medical Oncology, Dan Zhou People’s Hospital, No. 21-1, Da Tong Road, Nada Town, Danzhou, 571700 Hainan China
| | - Wenrui Xie
- Department of Medical Oncology, Dan Zhou People’s Hospital, No. 21-1, Da Tong Road, Nada Town, Danzhou, 571700 Hainan China
| | - Wenhong Zheng
- Department of Medical Oncology, Dan Zhou People’s Hospital, No. 21-1, Da Tong Road, Nada Town, Danzhou, 571700 Hainan China
| | - Xiaoying Qian
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical College, Haikou, 570100 Hainan China
| | - Chengwei Deng
- Department of Medical Oncology, Dan Zhou People’s Hospital, No. 21-1, Da Tong Road, Nada Town, Danzhou, 571700 Hainan China
| |
Collapse
|
4
|
Li X, Peng X, Li Y, Wei S, He G, Liu J, Li X, Yang S, Li D, Lin W, Fang J, Yang L, Li H. Glutamine addiction in tumor cell: oncogene regulation and clinical treatment. Cell Commun Signal 2024; 22:12. [PMID: 38172980 PMCID: PMC10763057 DOI: 10.1186/s12964-023-01449-x] [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: 09/20/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
After undergoing metabolic reprogramming, tumor cells consume additional glutamine to produce amino acids, nucleotides, fatty acids, and other substances to facilitate their unlimited proliferation. As such, the metabolism of glutamine is intricately linked to the survival and progression of cancer cells. Consequently, targeting the glutamine metabolism presents a promising strategy to inhibit growth of tumor cell and cancer development. This review describes glutamine uptake, metabolism, and transport in tumor cells and its pivotal role in biosynthesis of amino acids, fatty acids, nucleotides, and more. Furthermore, we have also summarized the impact of oncogenes like C-MYC, KRAS, HIF, and p53 on the regulation of glutamine metabolism and the mechanisms through which glutamine triggers mTORC1 activation. In addition, role of different anti-cancer agents in targeting glutamine metabolism has been described and their prospective applications are assessed.
Collapse
Affiliation(s)
- Xian Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Yan Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Guangpeng He
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jiaxing Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Dai Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Weikai Lin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jianjun Fang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
| |
Collapse
|
5
|
Wei T, Liu J, Ma S, Wang M, Yuan Q, Huang A, Wu Z, Shang D, Yin P. A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach. Metabolites 2023; 13:1116. [PMID: 37999212 PMCID: PMC10673507 DOI: 10.3390/metabo13111116] [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: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients.
Collapse
Affiliation(s)
- Tianfu Wei
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Jifeng Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Shurong Ma
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Mimi Wang
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Qihang Yuan
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Anliang Huang
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Zeming Wu
- iPhenome Biotechnology (Yun Pu Kang) Inc., Dalian 116000, China
| | - Dong Shang
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Peiyuan Yin
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| |
Collapse
|
6
|
Wang J, Chen X, Zhang L, Zheng Y, Qian J, Sun N, Ding X, Cui B. Chick early amniotic fluid component improves heart function and protects against inflammation after myocardial infarction in mice. Front Cardiovasc Med 2022; 9:1042852. [DOI: 10.3389/fcvm.2022.1042852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Myocardial infarction (MI) is the major cause of mortality around the world. We recently demonstrated that chick early amniotic fluid (ceAF) can effectively rescue ischemic heart injury, indicating that it has a therapeutic function in MI. However, its functional components and the underlying mechanisms remain to be clarified. Here, we demonstrated that a fraction of ceAF, peak 8 (P8), had a protective effect on acute MI. P8 significantly decreased cardiomyocyte cross-sectional areas and cardiomyocyte apoptosis in MI mice. Using a human embryonic stem cell-derived cardiomyocyte model, which was subjected to hypoxia and reoxygenation, mimicking MI state, we found that P8 treatment reduced apoptosis and reversed myocardial contractility. Mechanistically, P8 improved cardiac function by inhibiting NF-κB signaling and downregulating inflammatory cytokine expression. Using mass spectrometry, we identified that guanosine and deoxynucleoside were the main functional components of P8 that suppressed the inflammatory response in human embryonic stem cell-derived cardiomyocytes. Collectively, our data suggest that specific components from ceAF are promising therapeutic agents for ischemic heart injury and could be a potential supplement to current medications for MI.
Collapse
|
7
|
Zhao G, Newbury P, Ishi Y, Chekalin E, Zeng B, Glicksberg BS, Wen A, Paithankar S, Sasaki T, Suri A, Nazarian J, Pacold ME, Brat DJ, Nicolaides T, Chen B, Hashizume R. Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma. Acta Neuropathol Commun 2022; 10:150. [PMID: 36274161 PMCID: PMC9590174 DOI: 10.1186/s40478-022-01463-z] [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: 03/19/2022] [Accepted: 10/13/2022] [Indexed: 11/25/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an aggressive incurable brainstem tumor that targets young children. Complete resection is not possible, and chemotherapy and radiotherapy are currently only palliative. This study aimed to identify potential therapeutic agents using a computational pipeline to perform an in silico screen for novel drugs. We then tested the identified drugs against a panel of patient-derived DIPG cell lines. Using a systematic computational approach with publicly available databases of gene signature in DIPG patients and cancer cell lines treated with a library of clinically available drugs, we identified drug hits with the ability to reverse a DIPG gene signature to one that matches normal tissue background. The biological and molecular effects of drug treatment was analyzed by cell viability assay and RNA sequence. In vivo DIPG mouse model survival studies were also conducted. As a result, two of three identified drugs showed potency against the DIPG cell lines Triptolide and mycophenolate mofetil (MMF) demonstrated significant inhibition of cell viability in DIPG cell lines. Guanosine rescued reduced cell viability induced by MMF. In vivo, MMF treatment significantly inhibited tumor growth in subcutaneous xenograft mice models. In conclusion, we identified clinically available drugs with the ability to reverse DIPG gene signatures and anti-DIPG activity in vitro and in vivo. This novel approach can repurpose drugs and significantly decrease the cost and time normally required in drug discovery.
Collapse
Affiliation(s)
- Guisheng Zhao
- grid.137628.90000 0004 1936 8753Department of Pediatrics, New York University Langone Health, 160 East 32nd St., New York, NY 10016 USA
| | - Patrick Newbury
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Yukitomo Ishi
- grid.16753.360000 0001 2299 3507Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL 60611 USA ,grid.413808.60000 0004 0388 2248Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611 USA
| | - Eugene Chekalin
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Billy Zeng
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Benjamin S. Glicksberg
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029 USA ,grid.416167.30000 0004 0442 1996Icahn School of Medicine at Mount Sinai, Hasso Plattner Institute for Digital Health at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029 USA
| | - Anita Wen
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Shreya Paithankar
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Takahiro Sasaki
- grid.16753.360000 0001 2299 3507Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL 60611 USA ,grid.412857.d0000 0004 1763 1087Department of Neurological Surgery, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Japan
| | - Amreena Suri
- grid.16753.360000 0001 2299 3507Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL 60611 USA ,grid.413808.60000 0004 0388 2248Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611 USA
| | - Javad Nazarian
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010 USA ,grid.412341.10000 0001 0726 4330University Children’s Hospital Zurich, Steinwiesstrasse 75, 8032 Zurich, Switzerland
| | - Michael E. Pacold
- grid.137628.90000 0004 1936 8753Department of Radiation Oncology, New York University Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Daniel J. Brat
- grid.16753.360000 0001 2299 3507Department of Pathology, Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611 USA
| | - Theodore Nicolaides
- grid.137628.90000 0004 1936 8753Department of Pediatrics, New York University Langone Health, 160 East 32nd St., New York, NY 10016 USA
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI, 49503, USA. .,Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue St, East Lansing, MI, 48824, USA. .,Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, MI, 48824, USA.
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL, 60611, USA. .,Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL, 60611, USA.
| |
Collapse
|
8
|
Lu J, Li J, Ren J, Ding S, Zeng Z, Huang T, Cai YD. Functional and embedding feature analysis for pan-cancer classification. Front Oncol 2022; 12:979336. [PMID: 36248961 PMCID: PMC9559388 DOI: 10.3389/fonc.2022.979336] [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: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
With the increasing number of people suffering from cancer, this illness has become a major health problem worldwide. Exploring the biological functions and signaling pathways of carcinogenesis is essential for cancer detection and research. In this study, a mutation dataset for eleven cancer types was first obtained from a web-based resource called cBioPortal for Cancer Genomics, followed by extracting 21,049 features from three aspects: relationship to GO and KEGG (enrichment features), mutated genes learned by word2vec (text features), and protein-protein interaction network analyzed by node2vec (network features). Irrelevant features were then excluded using the Boruta feature filtering method, and the retained relevant features were ranked by four feature selection methods (least absolute shrinkage and selection operator, minimum redundancy maximum relevance, Monte Carlo feature selection and light gradient boosting machine) to generate four feature-ranked lists. Incremental feature selection was used to determine the optimal number of features based on these feature lists to build the optimal classifiers and derive interpretable classification rules. The results of four feature-ranking methods were integrated to identify key functional pathways, such as olfactory transduction (hsa04740) and colorectal cancer (hsa05210), and the roles of these functional pathways in cancers were discussed in reference to literature. Overall, this machine learning-based study revealed the altered biological functions of cancers and provided a reference for the mechanisms of different cancers.
Collapse
Affiliation(s)
- Jian Lu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - JiaRui Li
- Advanced Research Computing, University of British Columbia, Vancouver, BC, Canada
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Zhenbing Zeng, ; Tao Huang, ; Yu-Dong Cai,
| |
Collapse
|
9
|
Wolff DW, Bianchi-Smiraglia A, Nikiforov MA. Compartmentalization and regulation of GTP in control of cellular phenotypes. Trends Mol Med 2022; 28:758-769. [PMID: 35718686 PMCID: PMC9420775 DOI: 10.1016/j.molmed.2022.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
Genetic or pharmacological inhibition of enzymes involved in GTP biosynthesis has substantial biological effects, underlining the need to better understand the function of GTP levels in regulation of cellular processes and the significance of targeting GTP biosynthesis enzymes for therapeutic intervention. Our current understanding of spatiotemporal regulation of GTP metabolism and its role in physiological and pathological cellular processes is far from complete. Novel methodologies such as genetically encoded sensors of free GTP offered insights into intracellular distribution and function of GTP molecules. In the current Review, we provide analysis of recent discoveries in the field of GTP metabolism and evaluate the key enzymes as molecular targets.
Collapse
Affiliation(s)
- David W Wolff
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Mikhail A Nikiforov
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
10
|
Comprehensive Analysis of Histone Modifications in Hepatocellular Carcinoma Reveals Different Subtypes and Key Prognostic Models. JOURNAL OF ONCOLOGY 2022; 2022:5961603. [PMID: 35957801 PMCID: PMC9359864 DOI: 10.1155/2022/5961603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Histone modification, an important epigenetic mechanism, is related to the carcinogenesis of hepatocellular carcinoma (HCC). In three datasets, we screened 88 epigenetic-dysregulated PCGs (epi-PCGs) , which were significantly associated with HCC survival and could cluster HCC into three molecular subtypes. These subtypes were associated with prognosis, immunomodulatory alterations, and response to different treatment strategies. Based on 88 epi-PCGs in the TCGA training set, a risk prediction model composed of 4 epi-PCGs was established. The model was closely related to the clinicopathological features and showed a strong predictive ability in different clinical subgroups. In addition, the risk prediction model was an independent prognostic factor for patients with HCC. The significance of epi-PCGs in HCC is revealed by our data analysis.
Collapse
|
11
|
Huang F, Abbas F, Fiaz S, Imran M, Yanguo K, Hassan W, Ashraf U, He Y, Cai X, Wang Z, Yu L, Ye X, Chen X. Comprehensive characterization of Guanosine monophosphate synthetase in Nicotiana tabacum. Mol Biol Rep 2022; 49:5265-5272. [PMID: 34689282 DOI: 10.1007/s11033-021-06718-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Guanosine monophosphate (GMP) synthetase is an enzyme that converts xanthosine monophosphate to GMP. GMP plays an essential role in plant development and responses to internal and external stimuli. It also plays a crucial role in several plant physiochemical processes, such as stomata closure, cation flux regulation, pathogen responses and chloroplast development. METHODS AND RESULTS The mRNA sequences of NtGMP synthase in tobacco (Nicotiana tabacum) were rapidly amplified from cDNA. The GMP synthase open reading frame contains a 1617 bp sequence encoding 538 amino acids. A sequence analysis showed that this sequence shares high homology with that of Nicotiana sylvestris, Nicotiana attenuata, N. tomentosiformis, Solanum tuberosum, Lycopersicon pennellii, L. esculentum, Capsicum annuum, C. chinense and C. baccatum GMP synthase. A BLAST analysis with a tobacco high-throughput genomic sequence database revealed that the tobacco GMP synthase gene has five introns and six exons. A phylogenetic analysis showed a close genetic evolutionary relationship with N. sylvestris GMP synthase. The tissue-specific expression profile was evaluated using quantitative real-time PCR. The data showed that NtGMP synthase was highly expressed in leaves and moderately expressed in roots, flowers, and stems. The subcellular localization was predicted using the WOLF PSORT webserver, which strongly suggested that it might be localized to the cytoplasm. CONCLUSIONS In the current study, we cloned and comprehensively characterized GMP synthase in tobacco (Nicotiana tabacum). Our results establish a basis for further research to explore the precise role of this enzyme in tobacco.
Collapse
Affiliation(s)
- Feiyan Huang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ke Yanguo
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China.
- College of Economics and Management, Kunming University, Kunming, China.
| | - Waseem Hassan
- Institute of Environment and Sustainable Development in Agricultural, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education Lahore, Punjab, Pakistan
| | - Yuansheng He
- Lincang Tobacco Corporation of Yunnan Province, Kunming, China
| | - Xuanjie Cai
- Material Procurement Center, Shanghai Tobacco Group Co., Ltd, Shanghai, 200082, China
| | - Zhijiang Wang
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China
| | - Lei Yu
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Xianwen Ye
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China.
| | - Xiaolong Chen
- Tobacco Leaf Technology Centre, China Tobacco Henan Industrial Co., Ltd, Zhengzhou, 450000, China.
| |
Collapse
|
12
|
P2Y purinergic signaling in prostate cancer: Emerging insights into pathophysiology and therapy. Biochim Biophys Acta Rev Cancer 2022; 1877:188732. [DOI: 10.1016/j.bbcan.2022.188732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/15/2022]
|
13
|
Halama A, Suhre K. Advancing Cancer Treatment by Targeting Glutamine Metabolism—A Roadmap. Cancers (Basel) 2022; 14:cancers14030553. [PMID: 35158820 PMCID: PMC8833671 DOI: 10.3390/cancers14030553] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Dysregulated glutamine metabolism is one of the metabolic features evident in cancer cells when compared to normal cells. Cancer cells utilize glutamine for energy generation as well as the synthesis of other molecules that are critical for cancer growth and progression. Therefore, drugs targeting glutamine metabolism have been extensively investigated. However, inhibition of glutamine metabolism in cancer cells results in the activation of other metabolic pathways enabling cancer cells to survive. In this review, we summarize and discuss the targets in glutamine metabolism, which has been probed in the development of anticancer drugs in preclinical and clinical studies. We further discuss pathways activated in response to glutamine metabolism inhibition, enabling cancer cells to survive the challenge. Finally, we put into perspective combined treatment strategies targeting glutamine metabolism along with other pathways as potential treatment options. Abstract Tumor growth and metastasis strongly depend on adapted cell metabolism. Cancer cells adjust their metabolic program to their specific energy needs and in response to an often challenging tumor microenvironment. Glutamine metabolism is one of the metabolic pathways that can be successfully targeted in cancer treatment. The dependence of many hematological and solid tumors on glutamine is associated with mitochondrial glutaminase (GLS) activity that enables channeling of glutamine into the tricarboxylic acid (TCA) cycle, generation of ATP and NADPH, and regulation of glutathione homeostasis and reactive oxygen species (ROS). Small molecules that target glutamine metabolism through inhibition of GLS therefore simultaneously limit energy availability and increase oxidative stress. However, some cancers can reprogram their metabolism to evade this metabolic trap. Therefore, the effectiveness of treatment strategies that rely solely on glutamine inhibition is limited. In this review, we discuss the metabolic and molecular pathways that are linked to dysregulated glutamine metabolism in multiple cancer types. We further summarize and review current clinical trials of glutaminolysis inhibition in cancer patients. Finally, we put into perspective strategies that deploy a combined treatment targeting glutamine metabolism along with other molecular or metabolic pathways and discuss their potential for clinical applications.
Collapse
|
14
|
Xiao S, Zhang H, Zhu R, Liao X, Wu Y, Mi J, Wang Y. Ammonia reduction by the gdhA and glnA genes from bacteria in laying hens. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 222:112486. [PMID: 34237637 DOI: 10.1016/j.ecoenv.2021.112486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Ammonia emissions are a high-focus pollution issue in the livestock industry. Ammonia-degrading bacteria can assimilate ammonia nitrogen as a nitrogen source to promote their growth and reproduction, providing an environmentally friendly, low-cost and safe biological way to reduce ammonia emissions from livestock. However, it remains unclear how ammonia-degrading bacteria reduce ammonia emissions from animals and what are the key ammonia assimilation genes. In the present study, two strains with ammonia nitrogen-degrading abilities (Enterococcus faecium strain C2 and Bacillus coagulans strain B1) were screened from laying chicken caecal and faecal samples and reduced ammonia emission rates by 53.60% and 31.38%, respectively. The expression levels of the ammonia assimilation genes gdhA, glnA, and GMPS increased significantly. On this basis, we successfully constructed three clone strains (PET-GDH, PET-GS, and PET-GMPS) that expressed the gdhA, glnA and GMPS genes in E. coli, respectively, to verify their ammonia-reducing activities. The results of an in vitro fermentation study showed that the ammonia production of the PET-GDH and PET-GS groups was significantly lower than that of the empty vector group (p < 0.05), with ammonia emission reduction rates of 55.5% and 54.8%, respectively. However, there was no difference between the PET-GMPS and empty vector groups. These results indicate that gdhA and glnA may be key genes involved in the bacterial-mediated regulation of ammonia emissions by laying hens, and ammonia emissions may be reduced by regulating their expression. The results of the present study provide a theoretical basis for the construction of engineered bacteria to reduce ammonia production in animals.
Collapse
Affiliation(s)
- Shasha Xiao
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Huaidan Zhang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Rongke Zhu
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Yinbao Wu
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Jiandui Mi
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China
| | - Yan Wang
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou 510642, China.
| |
Collapse
|
15
|
Marín-Aguilera M, Pereira MV, Jiménez N, Reig Ò, Cuartero A, Victoria I, Aversa C, Ferrer-Mileo L, Prat A, Mellado B. Glutamine and Cholesterol Plasma Levels and Clinical Outcomes of Patients with Metastatic Castration-Resistant Prostate Cancer Treated with Taxanes. Cancers (Basel) 2021; 13:cancers13194960. [PMID: 34638444 PMCID: PMC8507765 DOI: 10.3390/cancers13194960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Altered metabolism is a hallmark of cancer. Malignant cells metabolise glutamine to fulfil their metabolic needs. In prostate cancer, androgen receptor signalling promotes glutamine metabolism, which is also involved in cholesterol homeostasis. We aimed to determine whether the plasma glutamine levels correlate with the blood lipid profile, clinical characteristics and outcomes in patients with metastatic castration resistance prostate cancer (mCRPC) undergoing taxanes. We retrospectively assessed the glutamine and glutamate levels in plasma samples by a bioluminescent assay. Pre-treatment glutamine, glutamate, cholesterol and triglycerides levels were correlated with patients' clinical characteristics, taxanes response and clinical outcomes. Seventy-five patients with mCRPC treated with taxanes were included. The plasma glutamine levels were significantly higher in patients that received abiraterone or enzalutamide prior to taxanes (p = 0.003). Besides, patients with low glutamine levels were more likely to present a PSA response to taxanes (p = 0.048). Higher glutamine levels were significantly correlated with shorter biochemical/clinical progression-free survival (PSA/RX-PFS) (median 2.5 vs. 4.2 months; p = 0.048) and overall survival (OS) (median 12.6 vs. 20.3; p = 0.008). High cholesterol levels independently predicted early PSA/RX-PFS (p = 0.034). High glutamine and cholesterol in the plasma from patients with mCRPC were associated with adverse clinical outcomes, supporting the relevance of further research on metabolism in prostate cancer progression.
Collapse
Affiliation(s)
- Mercedes Marín-Aguilera
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Correspondence: (M.M.-A.); (B.M.); Tel.: +34-932-275-400 (ext. 4801) (M.M.-A.); +34-932-275-400 (ext. 2262) (B.M.)
| | - María V. Pereira
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Rosell Cancer Institute, 08028 Barcelona, Spain
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
| | - Natalia Jiménez
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
| | - Òscar Reig
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
| | - Anna Cuartero
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
| | - Iván Victoria
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
| | - Caterina Aversa
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
| | - Laura Ferrer-Mileo
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
- Department of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Begoña Mellado
- Translational Genomics and Targeted Therapeutics in Solid Tumors Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (M.V.P.); (N.J.); (Ò.R.); (I.V.); (A.P.)
- Medical Oncology Department, Hospital Clínic, 08036 Barcelona, Spain; (A.C.); (C.A.); (L.F.-M.)
- Fundació Clínic per a la Recerca Biomèdica, 08036 Barcelona, Spain
- Department of Medicine, University of Barcelona, 08036 Barcelona, Spain
- Correspondence: (M.M.-A.); (B.M.); Tel.: +34-932-275-400 (ext. 4801) (M.M.-A.); +34-932-275-400 (ext. 2262) (B.M.)
| |
Collapse
|
16
|
Wang J, Luo FF, Huang TJ, Mei Y, Peng LX, Qian CN, Huang BJ. The upregulated expression of RFC4 and GMPS mediated by DNA copy number alteration is associated with the early diagnosis and immune escape of ESCC based on a bioinformatic analysis. Aging (Albany NY) 2021; 13:21758-21777. [PMID: 34520390 PMCID: PMC8457608 DOI: 10.18632/aging.203520] [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: 04/12/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a malignant tumor that commonly occurs worldwide. Usually, Asia, especially China, has a high incidence of esophageal cancer. ESCC often has a poor outcome because of a late diagnosis and lack of effective treatments. To build foundations for the early diagnosis and treatment of ESCC, we used the gene expression datasets GSE20347 and GSE17351 from the GEO database and a private dataset to uncover differentially expressed genes (DEGs) and key genes in ESCC. Notably, we found that replication factor C subunit 4 (RFC4) and guanine monophosphate synthase (GMPS) were upregulated but have been rarely studied in ESCC. In particular, to the best of our knowledge, our study is the first to explore GMPS and ESCC. Furthermore, we found that high levels of RFC4 and GMPS expression may result from an increase in DNA copy number alterations. Furthermore, RFC4 and GMPS were both upregulated in the early stage and early nodal metastases of esophageal carcinoma. The expression of RFC4 was strongly correlated with GMPS. In addition, we explored the relationship between RFC4 and GMPS expression and tumor-infiltrating immune cells (TILs) in esophageal carcinoma. The results showed that the levels of RFC4 and GMPS increased with a decrease in some tumor-infiltrating cells. Upregulated RFC4 and GMPS with high TILs indicate a worse prognosis. In summary, our study shows that RFC4 and GMPS have potential as biomarkers for the early diagnosis of ESCC and may played a crucial role in the process of tumor immunity in ESCC.
Collapse
Affiliation(s)
- Jing Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Fei-Fei Luo
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Tie-Jun Huang
- Department of Nuclear Medicine, The Second People's Hospital of Shenzhen, Shenzhen 518037, People's Republic of China
| | - Yan Mei
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Li-Xia Peng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Chao-Nan Qian
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China.,Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Bi-Jun Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, People's Republic of China
| |
Collapse
|
17
|
Liao J, Song Q, Li J, Du K, Chen Y, Zou C, Mo Z. Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway. Cancer Cell Int 2021; 21:467. [PMID: 34488772 PMCID: PMC8419980 DOI: 10.1186/s12935-021-02174-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 12/30/2022] Open
Abstract
Background Prostate cancer (PCa) is still a serious male malignant disease across the world. However, no exact pathogenesis had been explained. Although adenylosuccinate lyase (ADSL) gene was identified to be important in PCa early in 1987, its comprehensive functions for PCa have not been presented. Methods The cBioPortal for Cancer Genomics, Oncomine and GEO database were retrieved to investigate the associations between of the ADSL gene and PCa. Then, the PC-3, DU145 and C4-2B cell lines were applied in vitro experiments. RNA sequencing and further western blot (WB) were applied to explore the potential mechanisms of ADSL gene in PCa. Results Based on PCa clinical datasets, we firstly found ADSL gene highly expressed in PCa tissues. Moreover, its transcript level increased in the metastatic PCa further. Elevated ADSL gene expression indicated a poor prognosis of PCa. While inhibiting the expression of ADSL with siRNA, the ability of cell proliferation and migration all declined markedly, with increased cell apoptosis inversely. Most of cells were blocked in the G0/G1 phase. Additionally, RNA sequencing also discovered the inactivity of cell cycle pathway after ADSL knockdown, which had also confirmed on the proteins levels. Conclusions Our study identified the ADSL as an oncogene of PCa through regulating the cell cycle pathway firstly, with explicit cell and clinical phenotypes. Further mechanisms were needed to confirm its carcinogenic effect. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02174-6.
Collapse
Affiliation(s)
- Jinling Liao
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Qiong Song
- Key Laboratory of Longevity and Aging-Related Disease of Chinese Ministry of Education, Center for Translational Medicine, School of Preclinical Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jie Li
- The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530218, China
| | - Kechen Du
- Key Laboratory of Longevity and Aging-Related Disease of Chinese Ministry of Education, Center for Translational Medicine, School of Preclinical Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yang Chen
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China. .,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Chunlin Zou
- Key Laboratory of Longevity and Aging-Related Disease of Chinese Ministry of Education, Center for Translational Medicine, School of Preclinical Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, No. 22 Shuangyong Road, Guangxi Zhuang Autonomous Region, Nanning, 530021, China. .,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| |
Collapse
|