1
|
Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
Collapse
Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| |
Collapse
|
2
|
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
|
3
|
Yao C, Lv D, Zhou X, Fu P, Sun W, Chen J, Lin H. Exploring urinary modified nucleosides as biomarkers for diabetic retinopathy: Development and validation of a ultra performance liquid chromatography-tandem mass spectrometry method. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1232:123968. [PMID: 38150972 DOI: 10.1016/j.jchromb.2023.123968] [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: 08/17/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023]
Abstract
The dynamic modification of RNA plays a crucial role in biological regulation and is strongly linked to human disease development and progression. Notably, modified nucleosides in urine have shown promising potential as early diagnostic biomarkers for various conditions. In this study, we developed and validated a rapid, sensitive, and accurate UPLC-MS/MS method for quantifying eight types of modified nucleosides (N1-methyladenosine (m1A), N6-methyladenosine (m6A), 5-methyluridine (m5U), 5-taurinomethyl-2-thiouridine (τm5s2U), 5-methylcytidine (m5C), 2'-O-methylcytidine (Cm), N1-methylguanosine (m1G), and N7-methylguanosine (m7G) in human urine. Using the method, we measured the urinary concentrations of m1A, m6A, m5U, τm5s2U, m5C, Cm, m1G, and m7G in a total of 21 control individuals and 23 patients diagnosed with diabetic retinopathy (DR). Cm levels showed promise as a diagnostic marker for diabetic retinopathy (DR), with a significant value (P < 0.01) and an AUC of 0.735. Other modified nucleosides also exhibited significant differences within specific subpopulations. As non-proliferative diabetic retinopathy (NPDR) signifies the latent early stage of diabetic retinopathy, we developed a multivariate linear model that integrates patients' sex, age, height, and urinary concentration of modified nucleosides which aims to predict and differentiate between healthy individuals, NPDR patients, and proliferative diabetic retinopathy (PDR) patients. Encouragingly, the model achieved satisfactory accuracy rates: healthy (81%), NPDR (75%), and PDR (80%). Our findings provide valuable insights into the development of an early, cost-effective, and noninvasive diagnostic approach for diabetic retinopathy.
Collapse
Affiliation(s)
- Chen Yao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, PR China; School of Life Sciences, Hainan University, Haikou 570228, PR China.
| | - Daizhu Lv
- Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China.
| | - Xueqing Zhou
- Analysis and Testing Center, Hainan University, Haikou 570228, PR China.
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, PR China.
| | - Wen Sun
- Hainan Traditional Chinese Medicine Hospital, Hospital of Chinese Medicine Affiliated by Hainan Medical College, Haikou 570203, PR China.
| | - Jinlian Chen
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Haikou 570311, PR China.
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, PR China.
| |
Collapse
|
4
|
Artymowicz M, Struck-Lewicka W, Wiczling P, Markuszewski M, Markuszewski MJ, Siluk D. Targeted quantitative metabolomics with a linear mixed-effect model for analysis of urinary nucleosides and deoxynucleosides from bladder cancer patients before and after tumor resection. Anal Bioanal Chem 2023; 415:5511-5528. [PMID: 37460824 PMCID: PMC10444683 DOI: 10.1007/s00216-023-04826-0] [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: 04/14/2023] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 08/23/2023]
Abstract
In the present study, we developed and validated a fast, simple, and sensitive quantitative method for the simultaneous determination of eleven nucleosides and deoxynucleosides from urine samples. The analyses were performed with the use of liquid chromatography coupled with triple quadrupole mass spectrometry. The sample pretreatment procedure was limited to centrifugation, vortex mixing of urine samples with a methanol/water solution (1:1, v/v), evaporation and dissolution steps. The analysis lasted 20 min and was performed in dynamic multiple reaction monitoring mode (dMRM) in positive polarity. Process validation was conducted to determine the linearity, precision, accuracy, limit of quantification, stability, recovery and matrix effect. All validation procedures were carried out in accordance with current FDA and EMA regulations. The validated method was applied for the analysis of 133 urine samples derived from bladder cancer patients before tumor resection and 24 h, 2 weeks, and 3, 6, 9, and 12 months after the surgery. The obtained data sets were analyzed using a linear mixed-effect model. The analysis revealed that concentration level of 2-methylthioadenosine was decreased, while for inosine, it was increased 24 h after tumor resection in comparison to the preoperative state. The presented quantitative longitudinal study of urine nucleosides and deoxynucleosides before and up to 12 months after bladder tumor resection brings additional prospective insight into the metabolite excretion pattern in bladder cancer disease. Moreover, incurred sample reanalysis was performed proving the robustness and repeatability of the developed targeted method.
Collapse
Affiliation(s)
- Małgorzata Artymowicz
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Aleja Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Wiktoria Struck-Lewicka
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Aleja Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Paweł Wiczling
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Aleja Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Marcin Markuszewski
- Department of Urology, Medical University of Gdańsk, Mariana Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Michał J Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Aleja Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Danuta Siluk
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Aleja Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| |
Collapse
|
5
|
Yang M, Liu X, Tang X, Sun W, Ji Z. LC-MS based urine untargeted metabolomic analyses to identify and subdivide urothelial cancer. Front Oncol 2023; 13:1160965. [PMID: 37256175 PMCID: PMC10226587 DOI: 10.3389/fonc.2023.1160965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Urine metabolomics has been a promising technique in the liquid biopsy of urothelial cancer (UC). The comparison of upper tract urothelial cancer (UTUC), lower tract urothelial cancer (BCa), and healthy controls (HCs) need to be performed to find related biomarkers. Methods In our investigation, urine samples from 35 UTUCs, 44 BCas, and 53 gender- and age-matched HCs were analyzed using liquid chromatography-high resolution mass spectrometry (LC-HRMS). In different groups, the differential metabolites and the disturbed metabolism pathways were explored. Transcriptomics and urine metabolomics are combined to identify the probably disturbed gene in BCa. Results With an area under the curve (AUC) of 0.815, the panel consisting of prostaglandin I2, 5-methyldeoxycytidine, 2,6-dimethylheptanoyl carnitine, and deoxyinosine was able to discriminate UC from HCs. With an AUC of 0.845, the validation group also demonstrated strong predictive ability. UTUC and BCa without hematuria could be distinguished using the panel of 5'-methylthioadenosine, L-beta-aspartyl-L-serine, dehydroepiandrosterone sulfate, and N'-formylkynurenine (AUC=0.858). The metabolite panel comprising aspartyl-methionine, 7-methylinosine, and alpha-CEHC glucuronide could discriminate UTUC from BCa with hematuria with an AUC of 0.83. Fatty acid biosynthesis, purine metabolism, tryptophan metabolism, pentose and glucuronate interconversions, and arachidonic acid metabolism were dysregulated when comparing UC with HCs. PTGIS and BCHE, the genes related to the metabolism of prostaglandin I2 and myristic acid respectively, were significantly associated with the survival of BCa. Discussion Not only could LC-HRMS urine metabolomic investigations distinguish UC from HCs, but they could also identify UTUC from BCa. Additionally, urine metabolomics combined with transcriptomics can find out the potential aberrant genes in the metabolism.
Collapse
Affiliation(s)
- Ming Yang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaoyue Tang
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| |
Collapse
|