1
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Zeng Q, Jiang T. The role of FHL1 in tumors. Gene 2024; 911:148347. [PMID: 38458365 DOI: 10.1016/j.gene.2024.148347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Affiliation(s)
- Qun Zeng
- Department of Biochemistry and Molecular Biology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Tingting Jiang
- Department of Clinical Laboratory, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
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2
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Wang Z, Wang H, Zhou Y, Li L, Lyu M, Wu C, He T, Tan L, Zhu Y, Guo T, Wu H, Zhang H, Sun Y. An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma. Nat Commun 2024; 15:3560. [PMID: 38671151 PMCID: PMC11053152 DOI: 10.1038/s41467-024-47926-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: 06/02/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Pediatric papillary thyroid carcinomas (PPTCs) exhibit high inter-tumor heterogeneity and currently lack widely adopted recurrence risk stratification criteria. Hence, we propose a machine learning-based objective method to individually predict their recurrence risk. We retrospectively collect and evaluate the clinical factors and proteomes of 83 pediatric benign (PB), 85 pediatric malignant (PM) and 66 adult malignant (AM) nodules, and quantify 10,426 proteins by mass spectrometry. We find 243 and 121 significantly dysregulated proteins from PM vs. PB and PM vs. AM, respectively. Function and pathway analyses show the enhanced activation of the inflammatory and immune system in PM patients compared with the others. Nineteen proteins are selected to predict recurrence using a machine learning model with an accuracy of 88.24%. Our study generates a protein-based personalized prognostic prediction model that can stratify PPTC patients into high- or low-recurrence risk groups, providing a reference for clinical decision-making and individualized treatment.
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Affiliation(s)
- Zhihong Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - He Wang
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Yan Zhou
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lu Li
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Mengge Lyu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Chunlong Wu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Tianen He
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lingling Tan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Yi Zhu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Tiannan Guo
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Hongkun Wu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China.
| | - Yaoting Sun
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, China.
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3
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Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res 2024. [PMID: 38572503 DOI: 10.1021/acs.jproteome.3c00781] [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: 04/05/2024]
Abstract
The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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Affiliation(s)
- Md Yasir Arafat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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4
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Qiao X, Qi X, Xing P, Liu T, Hao H, Yang X, Jiang B, Cui M, Su X. Tandem Mass Tag-Based Proteomic Profiling Identifies Biomarkers in Drainage Fluid for Early Detection of Anastomotic Leakage after Rectal Cancer Resection. J Proteome Res 2023; 22:3559-3569. [PMID: 37793102 DOI: 10.1021/acs.jproteome.3c00394] [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: 10/06/2023]
Abstract
Anastomotic leakage (AL), one of the most severe complications in rectal surgery, is often diagnosed late because of the low specificity of the clinical symptoms and limitations of current clinical investigations. Identification of patients with early AL remains challenging. Here, we explored the protein expression profiles of AL patients to provide potential biomarkers to identify AL in patients who undergo surgery for rectal cancer. We screened differentially expressed proteins (DEPs) in drainage fluid from AL and non-AL patients using a tandem mass tag method. A total of 248 DEPs, including 98 upregulated and 150 downregulated proteins, were identified between AL and non-AL groups. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that DEPs were enriched in neutrophil degranulation, bacterial infection, proteolysis, hemostasis, and complement and coagulation cascades. The results of enzyme-linked immunosorbent assay validated that the expression of the top three upregulated DEPs, AMY2A, RETN, and CELA3A, was significantly increased in the drainage fluid of AL patients, compared with that of non-AL patients (AMY2A, P = 0.001; RETN, P < 0.0001; and CELA3A, P = 0.023). Thus, our findings provide several potential biomarkers for the early diagnosis of AL after rectal cancer resection.
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Affiliation(s)
- Xiaowen Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinyu Qi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Pu Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Tianqi Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Hao Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xinying Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Beihai Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ming Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiangqian Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing 100142, China
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5
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Yang S, Zhu G, He R, Fang D, Feng J. Advances in transcriptomics and proteomics in differentiated thyroid cancer: An updated perspective (Review). Oncol Lett 2023; 26:396. [PMID: 37600346 PMCID: PMC10433702 DOI: 10.3892/ol.2023.13982] [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: 02/14/2023] [Accepted: 05/25/2023] [Indexed: 08/22/2023] Open
Abstract
Thyroid cancer (TC) is a broad classification of neoplasms that includes differentiated thyroid cancer (DTC) as a common histological subtype. DTC is characterized by an increased mortality rate in advanced stages, which contributes to the overall high mortality rate of DTC. This progression is mainly attributed to alterations in molecular driver genes, resulting in changes in phenotypes such as invasion, metastasis and dedifferentiation. Clinical management of DTC is challenging due to insufficient diagnostic and therapeutic options. The advent of-omics technology has presented a promising avenue for the diagnosis and treatment of DTC. Identifying molecular markers that can predict the early progression of DTC to a late adverse outcome is essential for precise diagnosis and treatment. The present review aimed to enhance our understanding of DTC by integrating big data with biological systems through-omics technology, specifically transcriptomics and proteomics, which can shed light on the molecular mechanisms underlying carcinogenesis.
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Affiliation(s)
- Shici Yang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Gaohong Zhu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Rui He
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Dong Fang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jiaojiao Feng
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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6
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Liu R, Cao Z, Pan M, Wu M, Li X, Yuan H, Liu Z. A novel prognostic model for papillary thyroid cancer based on epithelial-mesenchymal transition-related genes. Cancer Med 2022; 11:4703-4720. [PMID: 35608185 PMCID: PMC9741981 DOI: 10.1002/cam4.4836] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/08/2022] [Accepted: 05/04/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The frequent incidence of postsurgical recurrence issues in papillary thyroid cancer (PTC) patients is a primary concern considering the low cancer-related mortality. Previous studies have demonstrated that epithelial-mesenchymal transition (EMT) activation is closely related to PTC progression and invasion. In this study, we aimed to develop a novel EMT signature and ancillary nomogram to improve personalized prediction of progression-free interval (PFI). METHODS First, we carried out a differential analysis of PTC samples and pairwise normal thyroid samples to explore the differentially expressed genes (DEGs). The intersection of the DEGs with EMT-related genes (ERGs) were identified as differentially expressed EMT-related genes (DE-ERGs). We determined PFI-related DE-ERGs by Cox regression analysis and then established a novel gene classifier by LASSO regression analysis. We validated the signature in external datasets and in multiple cell lines. Further, we used uni- and multivariate analyses to identify independent prognostic characters. RESULTS We identified 244 prognosis-related DE-ERGs. The 244 DE-ERGs were associated with several pivotal oncogenic processes. We also constructed a novel 10-gene signature and relevant prognostic model for recurrence prediction of PTC. The 10-gene signature had a C-index of 0.723 and the relevant nomogram had a C-index of 0.776. The efficacy of the signature and nomogram was satisfying and closely correlated with relevant clinical parameters. Furthermore, the signature also had a unique potential in differentiating anaplastic thyroid cancer (ATC) samples. CONCLUSIONS The novel EMT signature and nomogram are useful and convenient for personalized management for thyroid cancer.
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Affiliation(s)
- Rui Liu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Zhen Cao
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Meng Pan
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Xiaobin Li
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Hongwei Yuan
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
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7
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Mass Spectrometry and Mass Spectrometry Imaging-based Thyroid Cancer Analysis. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-022-00218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Zhong X, Yang Y, Li B, Liang P, Huang Y, Zheng Q, Wang Y, Xiao X, Mo Y, Zhang Z, Zhou X, Huang G, Zhao W. Downregulation of SLC27A6 by DNA Hypermethylation Promotes Proliferation but Suppresses Metastasis of Nasopharyngeal Carcinoma Through Modulating Lipid Metabolism. Front Oncol 2022; 11:780410. [PMID: 35047398 PMCID: PMC8761909 DOI: 10.3389/fonc.2021.780410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/01/2021] [Indexed: 12/14/2022] Open
Abstract
Lipid is the building block and an important source of energy, contributing to the malignant behavior of tumor cells. Recent studies suggested that lipid droplets (LDs) accumulations were associated with nasopharyngeal carcinoma (NPC) progression. Solute carrier family 27 member 6 (SLC27A6) mediates the cellular uptake of long-chain fatty acid (LCFA), a necessary lipid component. However, the functions of SLC27A6 in NPC remain unknown. Here, we found a significant reduction of SLC27A6 mRNA in NPC tissues compared with normal nasopharyngeal epithelia (NNE). The promoter methylation ratio of SLC27A6 was greater in NPC than in non-cancerous tissues. The demethylation reagent 5-aza-2'-deoxycytidine (5-aza-dC) remarkably restored the mRNA expression of SLC27A6, suggesting that this gene was downregulated in NPC owing to DNA promoter hypermethylation. Furthermore, SLC27A6 overexpression level in NPC cell lines led to significant suppression of cell proliferation, clonogenicity in vitro, and tumorigenesis in vivo. Higher SLC27A6 expression, on the other hand, promoted NPC cell migration and invasion. In particular, re-expression of SLC27A6 faciliated epithelial-mesenchymal transition (EMT) signals in xenograft tumors. Furthermore, we observed that SLC27A6 enhanced the intracellular amount of triglyceride (TG) and total cholesterol (T-CHO) in NPC cells, contributing to lipid biosynthesis and increasing metastatic potential. Notably, the mRNA level of SLC27A6 was positively correlated with cancer stem cell (CSC) markers, CD24 and CD44. In summary, DNA promoter hypermethylation downregulated the expression of SLC27A6. Furthermore, re-expression of SLC27A6 inhibited the growth capacity of NPC cells but strengthened the CSC markers. Our findings revealed the dual role of SLC27A6 in NPC and shed novel light on the link between lipid metabolism and CSC maintenance.
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Affiliation(s)
- Xuemin Zhong
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China.,Guangxi Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Nanning, China
| | - Yanping Yang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China.,Guangxi Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Nanning, China
| | - Bo Li
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Pan Liang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China.,Guangxi Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Nanning, China
| | - Yiying Huang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qian Zheng
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Yifang Wang
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Xue Xiao
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingxi Mo
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zhe Zhang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoying Zhou
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Guangwu Huang
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China.,Guangxi Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Nanning, China
| | - Weilin Zhao
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
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9
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Neto V, Esteves-Ferreira S, Inácio I, Alves M, Dantas R, Almeida I, Guimarães J, Azevedo T, Nunes A. Metabolic Profile Characterization of Different Thyroid Nodules Using FTIR Spectroscopy: A Review. Metabolites 2022; 12:metabo12010053. [PMID: 35050174 PMCID: PMC8777789 DOI: 10.3390/metabo12010053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Thyroid cancer’s incidence has increased in the last decades, and its diagnosis can be a challenge. Further and complementary testing based in biochemical alterations may be important to correctly identify thyroid cancer and prevent unnecessary surgery. Fourier-transform infrared (FTIR) spectroscopy is a metabolomic technique that has already shown promising results in cancer metabolome analysis of neoplastic thyroid tissue, in the identification and classification of prostate tumor tissues and of breast carcinoma, among others. This work aims to gather and discuss published information on the ability of FTIR spectroscopy to be used in metabolomic studies of the thyroid, including discriminating between benign and malignant thyroid samples and grading and classifying different types of thyroid tumors.
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Affiliation(s)
- Vanessa Neto
- Department of Medical Sciences, iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (V.N.); (I.A.)
| | - Sara Esteves-Ferreira
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Isabel Inácio
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Márcia Alves
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Rosa Dantas
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Idália Almeida
- Department of Medical Sciences, iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (V.N.); (I.A.)
| | - Joana Guimarães
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Teresa Azevedo
- Centro Hospitalar do Baixo Vouga, CHBV—Endocrinology Department, 3810-164 Aveiro, Portugal; (S.E.-F.); (I.I.); (M.A.); (R.D.); (J.G.); (T.A.)
| | - Alexandra Nunes
- Department of Medical Sciences, iBiMED—Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal; (V.N.); (I.A.)
- Correspondence:
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10
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Wang X, Zhang L, Chen H, Wang P, Yin Y, Jin J, Xu J, Wen J. Rational Proteomic Analysis of a New Domesticated Klebsiella pneumoniae x546 Producing 1,3-Propanediol. Front Microbiol 2021; 12:770109. [PMID: 34899654 PMCID: PMC8662357 DOI: 10.3389/fmicb.2021.770109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
In order to improve the capability of Klebsiella pneumoniae to produce an important chemical raw material, 1,3-propanediol (1,3-PDO), a new type of K. pneumoniae x546 was obtained by glycerol acclimation and subsequently was used to produce 1,3-PDO. Under the control of pH value using Na+ pH neutralizer, the 1,3-PDO yield of K. pneumoniae x546 in a 7.5-L fermenter was 69.35 g/L, which was 1.5-fold higher than the original strain (45.91 g/L). After the addition of betaine, the yield of 1,3-PDO reached up to 74.44 g/L at 24 h, which was 40% shorter than the original fermentation time of 40 h. To study the potential mechanism of the production improvement of 1,3-PDO, the Tandem Mass Tags (TMT) technology was applied to investigate the production of 1,3-PDO in K. pneumoniae. Compared with the control group, 170 up-regulated proteins and 291 down-regulated proteins were identified. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, it was found that some proteins [such as homoserine kinase (ThrB), phosphoribosylglycinamide formyltransferase (PurT), phosphoribosylaminoimidazolesuccinocarboxamide synthase (PurC), etc.] were involved in the fermentation process, whereas some other proteins (such as ProX, ProW, ProV, etc.) played a significant role after the addition of betaine. Moreover, combined with the metabolic network of K. pneumoniae during 1,3-PDO, the proteins in the biosynthesis of 1,3-PDO [such as DhaD, DhaK, lactate dehydrogenase (LDH), BudC, etc.] were analyzed. The process of 1,3-PDO production in K. pneumoniae was explained from the perspective of proteome for the first time, which provided a theoretical basis for genetic engineering modification to improve the yield of 1,3-PDO. Because of the use of Na+ pH neutralizer in the fermentation, the subsequent environmental pollution treatment cost was greatly reduced, showing high potential for industry application in the future.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Department of Chemistry, National University of Singapore, Singapore, Singapore.,Institute of Materials Research and Engineering, Singapore, Singapore
| | - Lin Zhang
- Dalian Petrochemical Research Institute of Sinopec, Dalian, China
| | - Hong Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jiaqi Jin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianwei Xu
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,Institute of Materials Research and Engineering, Singapore, Singapore
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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11
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Feng K, Ma R, Li H, Yin K, Du G, Chen X, Liu Z, Yin D. Upregulated SLC27A2/FATP2 in differentiated thyroid carcinoma promotes tumor proliferation and migration. J Clin Lab Anal 2021; 36:e24148. [PMID: 34854499 PMCID: PMC8761402 DOI: 10.1002/jcla.24148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
Background Differentiated thyroid carcinoma (DTC) accounts for the vast majority of thyroid cancer (TC) cases. The rapidly increasing incidence of TC requires the urgent identification of new diagnostic and therapeutic targets. Solute carrier family 27 member 2 (SLC27A2/FATP2) plays an essential role in lipid biosynthesis and fatty acid transport. Recent studies have confirmed its involvement in a variety of diseases, including cancer. Methods In this study, the expression of SLC27A2 was analyzed in cancer and paracancerous tissue samples from 98 thyroid cancer patients, and we performed ROC analysis to confirm the diagnostic value. CCK8, Transwell, and other methods were used to study its effect on DTC, and the mechanism of SLC27A2 was investigated by RNA sequencing and Western blot. Results The expression of SLC27A2 was upregulated in both DTC tissues and cell lines and was correlated with clinical progression. In vitro studies further confirmed that SLC27A2 knockdown attenuated the proliferation and invasion of DTC cells. Through RNA sequence analysis and gene set enrichment analysis, we found that the MAPK pathway is the main downstream signaling pathway for the regulation by SLC27A2. SLC27A2 affects cell proliferation and differentiation by inducing changes in the proto‐oncogene C‐FOS. Conclusions Our results show that SLC27A2 plays an important role in tumor proliferation and migration, providing a new putative target for the diagnosis and treatment of TC.
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Affiliation(s)
- Kaixiang Feng
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Runsheng Ma
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China
| | - Keyu Yin
- College of Nursing, Lanzhou University, Lanzhou, China
| | - Gongbo Du
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xin Chen
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China
| | - Zhen Liu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, China
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12
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Su X, Guo Y, Fang T, Jiang X, Wang D, Li D, Bai P, Zhang B, Wang J, Liu C. Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis. Front Microbiol 2021; 12:701265. [PMID: 34512577 PMCID: PMC8429793 DOI: 10.3389/fmicb.2021.701265] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.
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Affiliation(s)
- Xiaolei Su
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Yinghua Guo
- Medical School of Chinese PLA, Beijing, China.,College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Tingzheng Fang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xuege Jiang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Dapeng Wang
- Medical School of Chinese PLA, Beijing, China.,Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Diangeng Li
- Department of Academic Research, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Po Bai
- Respiratory Diseases Department, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Bin Zhang
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, China
| | - Junfeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Changting Liu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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Niu R, Wang J, Geng C, Li Y, Dong L, Liu L, Chang Y, Shen J, Nie Z, Zhang Y, Hu B. Tandem mass tag-based proteomic analysis reveals cathepsin-mediated anti-autophagic and pro-apoptotic effects under proliferative diabetic retinopathy. Aging (Albany NY) 2020; 13:973-990. [PMID: 33293479 PMCID: PMC7835038 DOI: 10.18632/aging.202217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 04/20/2023]
Abstract
Proliferative diabetic retinopathy (PDR) is a severe complication of diabetes and can cause blindness. However, the available therapeutic modalities to PDR have unsatisfactory efficacies and incur adverse effects, which is due to the paucity in the understanding of pathogenic mechanisms responsible for the disease. In this study, tandem mass tag labeling technology combined with liquid chromatography and tandem mass spectrometry were utilized to identify differentially expressed proteins in vitreous humor of patients with rhegmatogenous retinal detachment and PDR. The data are available via ProteomeXchange with identifier PXD021788. Afterwards, the downregulated protein expression of Cathepsin B, D, and L was verified in vitreous and serum of another cohort. The gene expression profiling of the 3 cathepsins was confirmed in blood cells of an extra cohort. Furthermore, in high glucose (HG)-treated retinal vascular endothelial cell cultures recapitulating the cathepsin expression patterns, Cathepsin B or D downregulation mediated the HG-induced anti-autophagic and pro-apoptotic effects, thereby may contribute to vascular lesions under hyperglycemia. This study demonstrates previously undescribed expression patterns of cathepsins, reveals a novel cathepsin-involved pathogenic mechanism under PDR, and sheds light on potential therapeutic targets to this debilitating retinal disease.
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Affiliation(s)
- Rui Niu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Jindan Wang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Chao Geng
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yahong Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Lijie Dong
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Lin Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yuwen Chang
- Hetian District People's Hospital, Xinjiang, China
| | - Jianqun Shen
- Hetian District People's Hospital, Xinjiang, China
| | - Zetong Nie
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Bojie Hu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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