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Zhou L, Lu X, Wang X, Huang Z, Wu Y, Zhou L, Meng L, Fu Q, Xia L, Meng S. A Pilot Urinary Proteome Study Reveals Widespread Influences of Circadian Rhythm Disruption by Sleep Deprivation. Appl Biochem Biotechnol 2024; 196:1992-2011. [PMID: 37458940 DOI: 10.1007/s12010-023-04666-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 04/23/2024]
Abstract
It is widely accepted that circadian rhythm disruption caused short- or long-term adverse effects on health. Although many previous studies have focused on exploration of the molecular mechanisms, there is no rapid, convenient, and non-invasive method to reveal the influence on health after circadian rhythm disruption. Here, we performed a high-resolution mass spectrometry-based data-independent acquisition (DIA) quantitative urinary proteomic approach in order to explore whether urine could reveal stress changes to those brought about by circadian rhythm disruption after sleep deprivation. After sleep deprivation, the subjects showed a significant increase in both systolic and diastolic blood pressure compared with routine sleep. More than 2000 proteins were quantified and they contained specific proteins for various organs throughout the body. And a total of 177 significantly up-regulated proteins and 68 significantly down-regulated proteins were obtained after sleep deprivation. These differentially expressed proteins (DEPs) were associated with multiple organs and pathways, which reflected widespread influences of sleep deprivation. Besides, machine learning identified a panel of five DEPs (CD300A, SCAMP3, TXN2, EFEMP1, and MYH11) that can effectively discriminate circadian rhythm disruption. Taken together, our results validate the value of urinary proteome in predicting and diagnosing the changes by circadian rhythm disruption.
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Affiliation(s)
- Li Zhou
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinyu Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaoling Wang
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhixi Huang
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yunzhe Wu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Liyang Zhou
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Liyuan Meng
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qin Fu
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Xia
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shuang Meng
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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Xing X, Cai L, Ouyang J, Wang F, Li Z, Liu M, Wang Y, Zhou Y, Hu E, Huang C, Wu L, Liu J, Liu X. Proteomics-driven noninvasive screening of circulating serum protein panels for the early diagnosis of hepatocellular carcinoma. Nat Commun 2023; 14:8392. [PMID: 38110372 PMCID: PMC10728065 DOI: 10.1038/s41467-023-44255-2] [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: 10/11/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
Early diagnosis of hepatocellular carcinoma (HCC) lacks highly sensitive and specific protein biomarkers. Here, we describe a staged mass spectrometry (MS)-based discovery-verification-validation proteomics workflow to explore serum proteomic biomarkers for HCC early diagnosis in 1002 individuals. Machine learning model determined as P4 panel (HABP2, CD163, AFP and PIVKA-II) clearly distinguish HCC from liver cirrhosis (LC, AUC 0.979, sensitivity 0.925, specificity 0.915) and healthy individuals (HC, AUC 0.992, sensitivity 0.975, specificity 1.000) in an independent validation cohort, outperforming existing clinical prediction strategies. Furthermore, the P4 panel can accurately predict LC to HCC conversion (AUC 0.890, sensitivity 0.909, specificity 0.877) with predicting HCC at a median of 11.4 months prior to imaging in prospective external validation cohorts (No.: Keshen 2018_005_02 and NCT03588442). These results suggest that proteomics-driven serum biomarker discovery provides a valuable reference for the liquid biopsy, and has great potential to improve early diagnosis of HCC.
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Affiliation(s)
- Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Linsheng Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
- Department of Hepatopancreatobiliary Surgery, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuzhou, 350000, China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Zongman Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Mingxin Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Yang Zhou
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - En Hu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China
| | - Changli Huang
- Department of Hepatopancreatobiliary Surgery, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuzhou, 350000, China
| | - Liming Wu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Jingfeng Liu
- Department of Hepatopancreatobiliary Surgery, Fujian Cancer Hospital, Clinical Oncology School of Fujian Medical University, Fuzhou, 350000, China.
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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3
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Zohud O, Lone IM, Nashef A, Iraqi FA. Towards system genetics analysis of head and neck squamous cell carcinoma using the mouse model, cellular platform, and clinical human data. Animal Model Exp Med 2023; 6:537-558. [PMID: 38129938 PMCID: PMC10757216 DOI: 10.1002/ame2.12367] [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: 08/24/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Head and neck squamous cell cancer (HNSCC) is a leading global malignancy. Every year, More than 830 000 people are diagnosed with HNSCC globally, with more than 430 000 fatalities. HNSCC is a deadly diverse malignancy with many tumor locations and biological characteristics. It originates from the squamous epithelium of the oral cavity, oropharynx, nasopharynx, larynx, and hypopharynx. The most frequently impacted regions are the tongue and larynx. Previous investigations have demonstrated the critical role of host genetic susceptibility in the progression of HNSCC. Despite the advances in our knowledge, the improved survival rate of HNSCC patients over the last 40 years has been limited. Failure to identify the molecular origins of development of HNSCC and the genetic basis of the disease and its biological heterogeneity impedes the development of new therapeutic methods. These results indicate a need to identify more genetic factors underlying this complex disease, which can be better used in early detection and prevention strategies. The lack of reliable animal models to investigate the underlying molecular processes is one of the most significant barriers to understanding HNSCC tumors. In this report, we explore and discuss potential research prospects utilizing the Collaborative Cross mouse model and crossing it to mice carrying single or double knockout genes (e.g. Smad4 and P53 genes) to identify genetic factors affecting the development of this complex disease using genome-wide association studies, epigenetics, microRNA, long noncoding RNA, lncRNA, histone modifications, methylation, phosphorylation, and proteomics.
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Affiliation(s)
- Osayd Zohud
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
| | - Iqbal M. Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
| | - Aysar Nashef
- Department of Oral and Maxillofacial SurgeryBaruch Padeh Medical CenterPoriyaIsrael
- Azrieli Faculty of MedicineBar‐Ilan UniversityRamat GanIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel AvivIsrael
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Sato Y, Futamura M, Tanaka Y, Tsuchiya H, Fukada M, Higashi T, Yasufuku I, Asai R, Tajima JY, Kiyama S, Hatakeyama H, Morishita M, Hirotsu T, Luccio ED, Ishihara T, Matsuhashi N, Yoshida K. Clinical Possibility of Caenorhabditis elegans as a Novel Evaluation Tool for Esophageal Cancer Patients Receiving Chemotherapy: A Prospective Study. Cancers (Basel) 2023; 15:3870. [PMID: 37568686 PMCID: PMC10417676 DOI: 10.3390/cancers15153870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis elegans (C. elegans) possesses a sophisticated sense of smell and is used for a novel cancer screening test that utilizes the chemotaxis index. We designed a single-institution, prospective study to confirm the ability of Nematode Nose (N-NOSE) to determine preoperative chemotherapy's efficacy for esophageal cancer patients. PATIENTS AND METHODS We investigated the predictability of N-NOSE screening for the clinical effects of preoperative chemotherapy for esophageal cancer patients receiving radical surgery. The index reduction score (IRS) was calculated via the chemotaxis of C. elegans at three points: before treatment, before surgery, and after surgery, and its clinical relevance was examined. RESULT Thirty-nine patients with esophageal cancer were enrolled from August 2020 to December 2021, and 30 patients receiving radical surgery were examined. Complete response or partial response was achieved in 23 cases (76.7%). When the target of the treatment effect was complete response only, the prediction accuracies of the IRS calculated by area under the curve was 0.85 (95% Confidence interval: 0.62-1) in clinically achieving complete response group, and the sensitivity and specificity were 1 and 0.63, respectively. CONCLUSION Index reduction score using N-NOSE screening may reflect the efficacy of chemotherapy for esophageal cancer patients. A large-scale prospective study at multiple centers is desired in the future.
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Affiliation(s)
- Yuta Sato
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Manabu Futamura
- Department of Breast Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Yoshihiro Tanaka
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Hiroshi Tsuchiya
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Masahiro Fukada
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Toshiya Higashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Itaru Yasufuku
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Ryuichi Asai
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Jesse Yu Tajima
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Shigeru Kiyama
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Hideyuki Hatakeyama
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Masayo Morishita
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Takaaki Hirotsu
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Eric di Luccio
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Takuma Ishihara
- Innovative and Clinical Research Promotion Center, Gifu University Hospital, Gifu 501-1194, Japan
| | - Nobuhisa Matsuhashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Kazuhiro Yoshida
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
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Perico D, Tong Y, Chen L, Imamichi S, Sanada Y, Ishiai M, Suzuki M, Masutani M, Mauri P. Proteomic Characterization of SAS Cell-Derived Extracellular Vesicles in Relation to Both BPA and Neutron Irradiation Doses. Cells 2023; 12:1562. [PMID: 37371031 DOI: 10.3390/cells12121562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is a selective radiotherapy based on nuclear reaction that occurs when 10B atoms accumulated in cancer cells are irradiated by thermal neutrons, triggering a nuclear fission response leading to cell death. Despite its growing importance in cancer treatment, molecular characterization of its effects is still lacking. In this context, proteomics investigation can be useful to study BNCT effect and identify potential biomarkers. Hence, we performed proteomic analysis with nanoLC-MS/MS (liquid chromatography coupled to tandem mass spectrometry) on extracellular vesicles (EVs) isolated from SAS cultures treated or not with 10B-boronophenylalanine (BPA) and different doses of neutron irradiation, to study the cellular response related to both boron administration and neutrons action. Despite the interference of fetal bovine serum in the medium, we were able to stratify BPA- and BPA+ conditions and to identify EVs-derived proteins characterizing pathways potentially related to a BNCT effect such as apoptosis, DNA repair and inflammatory response. In particular, KLF11, SERPINA1 and SERPINF2 were up-regulated in BPA+, while POLE and SERPINC1 were up-regulated in BPA-. These results provide the first proteomic investigation of EVs treated with BNCT in different conditions and highlight the potentiality of proteomics for improving biomarkers identification and mechanisms understanding of BNCT.
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Affiliation(s)
- Davide Perico
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, Italy
| | - Ying Tong
- Department of Molecular and Genomic Biomedicine, Center for Bioinformatics & Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Lichao Chen
- Central Radioisotope Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Shoji Imamichi
- Department of Molecular and Genomic Biomedicine, Center for Bioinformatics & Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Central Radioisotope Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yu Sanada
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masamichi Ishiai
- Central Radioisotope Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Minoru Suzuki
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Mitsuko Masutani
- Department of Molecular and Genomic Biomedicine, Center for Bioinformatics & Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Central Radioisotope Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Pierluigi Mauri
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, Italy
- Institute of Life Sciences, Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
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Jordaens S, Zwaenepoel K, Tjalma W, Deben C, Beyers K, Vankerckhoven V, Pauwels P, Vorsters A. Urine biomarkers in cancer detection: A systematic review of preanalytical parameters and applied methods. Int J Cancer 2023; 152:2186-2205. [PMID: 36647333 DOI: 10.1002/ijc.34434] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/25/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023]
Abstract
The aim of this review was to explore the status of urine sampling as a liquid biopsy for noninvasive cancer research by reviewing used preanalytical parameters and protocols. We searched two main health sciences databases, PubMed and Web of Science. From all eligible publications (2010-2022), information was extracted regarding: (a) study population characteristics, (b) cancer type, (c) urine preanalytics, (d) analyte class, (e) isolation method, (f) detection method, (g) comparator used, (h) biomarker type, (i) conclusion and (j) sensitivity and specificity. The search query identified 7835 records, of which 924 unique publications remained after screening the title, abstract and full text. Our analysis demonstrated that many publications did not report information about the preanalytical parameters of their urine samples, even though several other studies have shown the importance of standardization of sample handling. Interestingly, it was noted that urine is used for many cancer types and not just cancers originating from the urogenital tract. Many different types of relevant analytes have been shown to be found in urine. Additionally, future considerations and recommendations are discussed: (a) the heterogeneous nature of urine, (b) the need for standardized practice protocols and (c) the road toward the clinic. Urine is an emerging liquid biopsy with broad applicability in different analytes and several cancer types. However, standard practice protocols for sample handling and processing would help to elaborate the clinical utility of urine in cancer research, detection and disease monitoring.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Novosanis NV, Wijnegem, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Wiebren Tjalma
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Multidisciplinary Breast Clinic, Gynecological Oncology Unit, Department of Obstetrics and Gynecology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | | | - Vanessa Vankerckhoven
- Novosanis NV, Wijnegem, Belgium.,Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Alex Vorsters
- Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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Heng Z, Zhao C, Gao Y. Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice. PeerJ 2023; 11:e14737. [PMID: 36718454 PMCID: PMC9884041 DOI: 10.7717/peerj.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
Objective This study aimed to address on the most important concern of surgeons-whether to completely resect tumor. Urine can indicate early changes associated with physiological or pathophysiological processes. Based on these ideas, we conducted experiments to explore changes in the urine proteome between tumor-bearing mice and tumor-resected mice. Method The tumor-bearing mouse model was established with MC38 mouse colon cancer cells, and the mice were divided into the control group, tumor-resected group, and tumor-bearing group. Urine was collected 7 and 30 days after tumor resection. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify the urine proteome, which was analyzed for differentially expressed proteins and functional annotation. Results (1) Seven days after tumor resection, 20 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included circadian rhythm, Notch signaling pathway, leukocyte cell-cell adhesion, and heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules. (2) Thirty days after tumor resection, 33 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included cell adhesion; complement activation, the alternative pathway; the immune system process; and angiogenesis. (3) The difference in the urine proteome between the tumor-resected group and the healthy control group was smaller 30 days after tumor resection. Conclusion Changes in the urinary proteome can reflect the complete resection of MC38 tumors.
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Affiliation(s)
- Ziqi Heng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Chenyang Zhao
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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8
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Perico D, Di Silvestre D, Imamichi S, Sanada Y, Masutani M, Mauri PL. Systems Biology Approach to Investigate Biomarkers, Boron-10 Carriers, and Mechanisms Useful for Improving Boron Neutron Capture Therapy. Cancer Biother Radiopharm 2022; 38:152-159. [PMID: 36269655 DOI: 10.1089/cbr.2022.0053] [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: 11/13/2022] Open
Abstract
Systems biology approach, carried out with high-throughput omics technologies, has become a fundamental aspect of the study of complex diseases like cancer. It can molecularly characterize subjects, physiopathological conditions, and interactions, allowing a precise description, to reach personalized medicine. In particular, proteomics, typically performed with liquid chromatography coupled to mass spectrometry, is a powerful tool for systems biology, giving the possibility to perform diagnosis, patient stratification, and prediction of therapy effects. Boron Neutron Capture Therapy (BNCT) is a selective antitumoral radiotherapy based on a nuclear reaction that occurs when 10B atoms are irradiated by low-energy thermal neutrons, leading to cell death, thanks to the production of high-energy α particles. Since BNCT is recently becoming an important therapy for the treatment of different types of solid tumors such as gliomas, head and neck cancers, and others, it can take advantage of molecular investigation to improve the understanding of effects and mechanisms and so help its clinical applications. In this context, proteomics can provide a better understanding of mechanisms related to BNCT effect, identify potential biomarkers, and individuate differential responses by specific patients, stratifying responders and nonresponders. Another key aspect of BNCT is the study of new potential Boron-10 carriers to improve the selectivity of Boron delivery to tumors and proteomics can be important in this application, studying the effectiveness of new boron delivery agents, including protein-based carriers, also using computational studies that can investigate new molecules, such as boronated monoclonal antibodies, for improving BNCT.
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Affiliation(s)
- Davide Perico
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Shoji Imamichi
- Department of Molecular and Genomic Biomedicine, School of Biomedical Sciences, Nagasaki University Graduate, Nagasaki, Japan.,Central Radioisotope Division, National Cancer Center Research Institute, Tokyo, Japan.,Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Yu Sanada
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Mitsuko Masutani
- Department of Molecular and Genomic Biomedicine, School of Biomedical Sciences, Nagasaki University Graduate, Nagasaki, Japan.,Central Radioisotope Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Pier Luigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy.,Institute of Life Science, Scuola Superiore Sant'Anna, Pisa, Italy
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9
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Ponzini E, Santambrogio C, De Palma A, Mauri P, Tavazzi S, Grandori R. Mass spectrometry-based tear proteomics for noninvasive biomarker discovery. MASS SPECTROMETRY REVIEWS 2022; 41:842-860. [PMID: 33759206 PMCID: PMC9543345 DOI: 10.1002/mas.21691] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 05/05/2023]
Abstract
The lacrimal film has attracted increasing interest in the last decades as a potential source of biomarkers of physiopathological states, due to its accessibility, moderate complexity, and responsiveness to ocular and systemic diseases. High-performance liquid chromatography-mass spectrometry (LC-MS) has led to effective approaches to tear proteomics, despite the intrinsic limitations in sample amounts. This review focuses on the recent progress in strategy and technology, with an emphasis on the potential for personalized medicine. After an introduction on lacrimal-film composition, examples of applications to biomarker discovery are discussed, comparing approaches based on pooled-sample and single-tear analysis. Then, the most critical steps of the experimental pipeline, that is, tear collection, sample fractionation, and LC-MS implementation, are discussed with reference to proteome-coverage optimization. Advantages and challenges of the alternative procedures are highlighted. Despite the still limited number of studies, tear quantitative proteomics, including single-tear investigation, could offer unique contributions to the identification of low-invasiveness, sustained-accessibility biomarkers, and to the development of personalized approaches to therapy and diagnosis.
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Affiliation(s)
- Erika Ponzini
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
| | - Carlo Santambrogio
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Antonella De Palma
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Pierluigi Mauri
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Silvia Tavazzi
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
- COMiBUniversity of Milano‐BicoccaMilanItaly
| | - Rita Grandori
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
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10
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Clinical Viability of Boron Neutron Capture Therapy for Personalized Radiation Treatment. Cancers (Basel) 2022; 14:cancers14122865. [PMID: 35740531 PMCID: PMC9221296 DOI: 10.3390/cancers14122865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Usually, for dose planning in radiotherapy, the tumor is delimited as a volume on the image of the patient together with other clinical considerations based on populational evidence. However, the same prescription dose can provide different results, depending on the patient. Unfortunately, the biological aspects of the tumor are hardly considered in dose planning. Boron Neutron Capture Radiotherapy enables targeted treatment by incorporating boron-10 at the cellular level and irradiating with neutrons of a certain energy so that they produce nuclear reactions locally and almost exclusively damage the tumor cell. This technique is not new, but modern neutron generators and more efficient boron carriers have reactivated the clinical interest of this technique in the pursuit of more precise treatments. In this work, we review the latest technological facilities and future possibilities for the clinical implementation of BNCT and for turning it into a personalized therapy. Abstract Boron Neutron Capture Therapy (BNCT) is a promising binary disease-targeted therapy, as neutrons preferentially kill cells labeled with boron (10B), which makes it a precision medicine treatment modality that provides a therapeutic effect exclusively on patient-specific tumor spread. Contrary to what is usual in radiotherapy, BNCT proposes cell-tailored treatment planning rather than to the tumor mass. The success of BNCT depends mainly on the sufficient spatial biodistribution of 10B located around or within neoplastic cells to produce a high-dose gradient between the tumor and healthy tissue. However, it is not yet possible to precisely determine the concentration of 10B in a specific tissue in real-time using non-invasive methods. Critical issues remain to be resolved if BNCT is to become a valuable, minimally invasive, and efficient treatment. In addition, functional imaging technologies, such as PET, can be applied to determine biological information that can be used for the combined-modality radiotherapy protocol for each specific patient. Regardless, not only imaging methods but also proteomics and gene expression methods will facilitate BNCT becoming a modality of personalized medicine. This work provides an overview of the fundamental principles, recent advances, and future directions of BNCT as cell-targeted cancer therapy for personalized radiation treatment.
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11
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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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12
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Importance of radiobiological studies for the advancement of boron neutron capture therapy (BNCT). Expert Rev Mol Med 2022; 24:e14. [PMID: 35357286 DOI: 10.1017/erm.2022.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Boron neutron capture therapy (BNCT) is a tumour selective particle radiotherapy, based on the administration of boron carriers incorporated preferentially by tumour cells, followed by irradiation with a thermal or epithermal neutron beam. BNCT clinical results to date show therapeutic efficacy, associated with an improvement in patient quality of life and prolonged survival. Translational research in adequate experimental models is necessary to optimise BNCT for different pathologies. This review recapitulates some examples of BNCT radiobiological studies for different pathologies and clinical scenarios, strategies to optimise boron targeting, enhance BNCT therapeutic effect and minimise radiotoxicity. It also describes the radiobiological mechanisms induced by BNCT, and the importance of the detection of biomarkers to monitor and predict the therapeutic efficacy and toxicity of BNCT alone or combined with other strategies. Besides, there is a brief comment on the introduction of accelerator-based neutron sources in BNCT. These sources would expand the clinical BNCT services to more patients, and would help to make BNCT a standard treatment modality for various types of cancer. Radiobiological BNCT studies have been of utmost importance to make progress in BNCT, being essential to design novel, safe and effective clinical BNCT protocols.
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13
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Giamougiannis P, Silva RVO, Freitas DLD, Lima KMG, Anagnostopoulos A, Angelopoulos G, Naik R, Wood NJ, Martin-Hirsch PL, Martin FL. Raman spectroscopy of blood and urine liquid biopsies for ovarian cancer diagnosis: identification of chemotherapy effects. JOURNAL OF BIOPHOTONICS 2021; 14:e202100195. [PMID: 34296515 DOI: 10.1002/jbio.202100195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Blood plasma and serum Raman spectroscopy for ovarian cancer diagnosis has been applied in pilot studies, with promising results. Herein, a comparative analysis of these biofluids, with a novel assessment of urine, was conducted by Raman spectroscopy application in a large patient cohort. Spectra were obtained through samples measurements from 116 ovarian cancer patients and 307 controls. Principal component analysis identified significant spectral differences between cancers without previous treatment (n = 71) and following neo-adjuvant chemotherapy (NACT), (n = 45). Application of five classification algorithms achieved up to 73% sensitivity for plasma, high specificities and accuracies for both blood biofluids, and lower performance for urine. A drop in sensitivities for the NACT group in plasma and serum, with an opposite trend in urine, suggest that Raman spectroscopy could identify chemotherapy-related changes. This study confirms that biofluids' Raman spectroscopy can contribute in ovarian cancer's diagnostic work-up and demonstrates its potential in monitoring treatment response.
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Affiliation(s)
- Panagiotis Giamougiannis
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - Raissa V O Silva
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Daniel L D Freitas
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kássio M G Lima
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Antonios Anagnostopoulos
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Georgios Angelopoulos
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Raj Naik
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Nicholas J Wood
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
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14
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Urinary exosomal long noncoding RNAs serve as biomarkers for early detection of non-small cell lung cancer. Biosci Rep 2021; 41:229852. [PMID: 34580719 PMCID: PMC8521532 DOI: 10.1042/bsr20210908] [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: 04/22/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/31/2022] Open
Abstract
Objective: Increasing the efficiency of early diagnosis using noninvasive biomarkers is crucial for enhancing the survival rate of lung cancer patients. We explore the differential expression of non-small cell lung cancer (NSCLC)-related long noncoding RNAs (lncRNAs) in urinary exosomes in NSCLC patients and normal controls to diagnose lung cancer. Methods: A differential expression analysis between NSCLC patients and healthy controls was performed using microarrays. Gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to predict potential functions of lncRNAs in NSCLC. quantitative real-time PCR (QT-PCR) was used to verify microarray results. Results: A total of 640 lncRNAs (70 up- and 570 down-regulated) were differentially expressed in NSCLC patients in comparison to healthy controls. Six lncRNAs were detected by QT-PCR. GO term and KEGG pathway analyses showed that differential lncRNAs were enriched in cellular component organization or biogenesis, as well as other biological processes and signaling pathways, such as the PI3K-AKT, FOXO, p53, and fatty acid biosynthesis. Conclusions: The differential lncRNAs in urinary exosomes are potential diagnostic biomarkers of NSCLC. The lncRNAs enriched in specific pathways may be associated with tumor cell proliferation, tumor cell apoptosis, and the cell cycle involved in the pathogenesis of NSCLC.
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15
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Wang W, Wu J, Liu P, Tang X, Pang H, Xie T, Xu F, Shao J, Chen Y, Liu B, Zheng Y. Urinary Proteomics Identifying Novel Biomarkers for the Diagnosis and Phenotyping of Carotid Artery Stenosis. Front Mol Biosci 2021; 8:714706. [PMID: 34447787 PMCID: PMC8383446 DOI: 10.3389/fmolb.2021.714706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/26/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Carotid artery stenosis (CAS) is caused by the formation of atherosclerotic plaques inside the arterial wall and accounts for 20–30% of all strokes. The development of an early, noninvasive diagnostic method and the identification of high-risk patients for ischemic stroke is essential to the management of CAS in clinical practice. Methods: We used the data-independent acquisition (DIA) technique to conduct a urinary proteomic study in patients with CAS and healthy controls. We identified the potential diagnosis and risk stratification biomarkers of CAS. And Ingenuity pathway analysis was used for functional annotation of differentially expressed proteins (DEPs). Furthermore, receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic values of DEPs. Results: A total of 194 DEPs were identified between CAS patients and healthy controls by DIA quantification. The bioinformatics analysis showed that these DEPs were correlated with the pathogenesis of CAS. We further identified 32 DEPs in symptomatic CAS compared to asymptomatic CAS, and biological function analysis revealed that these proteins are mainly related to immune/inflammatory pathways. Finally, a biomarker panel of six proteins (ACP2, PLD3, HLA-C, GGH, CALML3, and IL2RB) exhibited potential diagnostic value in CAS and good discriminative power for differentiating symptomatic and asymptomatic CAS with high sensitivity and specificity. Conclusions: Our study identified novel potential urinary biomarkers for noninvasive early screening and risk stratification of CAS.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Wu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyue Tang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyu Pang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Xu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Shao
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuexin Chen
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bao Liu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehong Zheng
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Theranostics in Boron Neutron Capture Therapy. Life (Basel) 2021; 11:life11040330. [PMID: 33920126 PMCID: PMC8070338 DOI: 10.3390/life11040330] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/15/2022] Open
Abstract
Boron neutron capture therapy (BNCT) has the potential to specifically destroy tumor cells without damaging the tissues infiltrated by the tumor. BNCT is a binary treatment method based on the combination of two agents that have no effect when applied individually: 10B and thermal neutrons. Exclusively, the combination of both produces an effect, whose extent depends on the amount of 10B in the tumor but also on the organs at risk. It is not yet possible to determine the 10B concentration in a specific tissue using non-invasive methods. At present, it is only possible to measure the 10B concentration in blood and to estimate the boron concentration in tissues based on the assumption that there is a fixed uptake of 10B from the blood into tissues. On this imprecise assumption, BNCT can hardly be developed further. A therapeutic approach, combining the boron carrier for therapeutic purposes with an imaging tool, might allow us to determine the 10B concentration in a specific tissue using a non-invasive method. This review provides an overview of the current clinical protocols and preclinical experiments and results on how innovative drug development for boron delivery systems can also incorporate concurrent imaging. The last section focuses on the importance of proteomics for further optimization of BNCT, a highly precise and personalized therapeutic approach.
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17
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Virreira Winter S, Karayel O, Strauss MT, Padmanabhan S, Surface M, Merchant K, Alcalay RN, Mann M. Urinary proteome profiling for stratifying patients with familial Parkinson's disease. EMBO Mol Med 2021; 13:e13257. [PMID: 33481347 PMCID: PMC7933820 DOI: 10.15252/emmm.202013257] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
The prevalence of Parkinson's disease (PD) is increasing but the development of novel treatment strategies and therapeutics altering the course of the disease would benefit from specific, sensitive, and non‐invasive biomarkers to detect PD early. Here, we describe a scalable and sensitive mass spectrometry (MS)‐based proteomic workflow for urinary proteome profiling. Our workflow enabled the reproducible quantification of more than 2,000 proteins in more than 200 urine samples using minimal volumes from two independent patient cohorts. The urinary proteome was significantly different between PD patients and healthy controls, as well as between LRRK2 G2019S carriers and non‐carriers in both cohorts. Interestingly, our data revealed lysosomal dysregulation in individuals with the LRRK2 G2019S mutation. When combined with machine learning, the urinary proteome data alone were sufficient to classify mutation status and disease manifestation in mutation carriers remarkably well, identifying VGF, ENPEP, and other PD‐associated proteins as the most discriminating features. Taken together, our results validate urinary proteomics as a valuable strategy for biomarker discovery and patient stratification in PD.
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Affiliation(s)
- Sebastian Virreira Winter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Matthew Surface
- Department of Neurology, Columbia University, New York, NY, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. Molecules 2020; 25:molecules25133028. [PMID: 32630776 PMCID: PMC7411631 DOI: 10.3390/molecules25133028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.
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19
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Plasma-Based Proteomics Profiling of Patients with Hyperthyroidism after Antithyroid Treatment. Molecules 2020; 25:molecules25122831. [PMID: 32575434 PMCID: PMC7356574 DOI: 10.3390/molecules25122831] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
Thyroid hormones critically modulate body homeostasis and haemostasis by regulating energy and metabolism. Previous studies have focused on individual pathways or proteins that are affected by increases in thyroid hormone levels, while an overall plasma proteomic signature of this increased level is lacking. Herein, an integrated untargeted proteomic approach with network analysis was used to identify changes in circulating proteins in the plasma proteome between hyperthyroid and euthyroid states. Plasma from 10 age-matched subjects at baseline (hyperthyroid) and post treatment with carbimazole (euthyroid) was compared by difference gel electrophoresis (DIGE) and matrix-assisted laser desorption/ionization time of flight (MALDI TOF) mass spectrometry (MS). A total of 20 proteins were identified with significant difference in abundance (analysis of variance (ANOVA) test, p ≤ 0.05; fold-change ≥ 1.5) between the two states (12 increased and 8 decreased in abundance in the hyperthyroid state). Twelve protein spots corresponding to ten unique proteins were significantly more abundant in the hyperthyroid state compared with the euthyroid state. These increased proteins were haptoglobin (HP), hemopexin (HPX), clusterin (CLU), apolipoprotein L1 (APOL1), alpha-1-B glycoprotein (A1BG), fibrinogen gamma chain (FGG), Ig alpha-1 chain C region (IGHA1), complement C6 (C6), leucine rich alpha 2 glycoprotein (LRG1), and carboxypeptidase N catalytic chain (CPN1). Eight protein spots corresponding to six unique proteins were significantly decreased in abundance in the hyperthyroid samples compared with euthyroid samples. These decreased proteins were apolipoprotein A1 (APOA1), inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), plasminogen (PLG), alpha-1 antitrypsin (SERPINA1), fibrinogen beta chain (FGB), and complement C1r subcomponent (C1R). The differentially abundant proteins were investigated by ingenuity pathway analysis (IPA). The network pathway identified related to infectious disease, inflammatory disease, organismal injury and abnormalities, and the connectivity map focused around two central nodes, namely the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and p38 mitogen-activated protein kinase (MAPK) pathways. The plasma proteome of patients with hyperthyroidism revealed differences in the abundance of proteins involved in acute phase response signaling, and development of a hypercoagulable and hypofibrinolytic state. Our findings enhance our existing knowledge of the altered proteins and associated biochemical pathways in hyperthyroidism.
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20
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Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH. Urine Proteomics: Evaluation of Different Sample Preparation Workflows for Quantitative, Reproducible, and Improved Depth of Analysis. J Proteome Res 2020; 19:1857-1862. [DOI: 10.1021/acs.jproteome.9b00772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hua Ding
- Proteomics Core Facility, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Hossein Fazelinia
- Proteomics Core Facility, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Lynn A. Spruce
- Proteomics Core Facility, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Dana A. Weiss
- Division of Urology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Stephen A. Zderic
- Division of Urology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Steven H. Seeholzer
- Proteomics Core Facility, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
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21
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Zhang Y, Gao Y, Gao Y. Early changes in the urine proteome in a rat liver tumour model. PeerJ 2020; 8:e8462. [PMID: 32095334 PMCID: PMC7017802 DOI: 10.7717/peerj.8462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/26/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Urine, as a potential biomarker source among body fluids, can accumulate many early changes in the body due to the lack of mechanisms to maintain a homeostatic state. This study aims to detect early changes in the urinary proteome in a rat liver tumour model. METHODS The tumour model was established with the Walker-256 carcinosarcoma cell line (W256). Urinary proteins at days 3, 5, 7 and 11 were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with controls, differential proteins were selected. Associations of differential proteins with cancer were retrieved. RESULTS At days 3, 5, 7 and 11, five, fifteen, eleven and twelve differential proteins were identified, respectively. Some of the differential proteins were reported to be associated with liver cancer. This differential urinary protein pattern was different from the patterns in W256 subcutaneous, lung metastasis and intracerebral tumour models. CONCLUSIONS This study demonstrates that (1) early changes in urinary proteins can be found in the rat liver tumour model; (2) urinary proteins can be used to differentiate the same tumour cells grown in different organs.
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Affiliation(s)
- Yameng Zhang
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Yufei Gao
- College of Information Science and Technology, Beijing Normal University, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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Kusumoto H, Tashiro K, Shimaoka S, Tsukasa K, Baba Y, Furukawa S, Furukawa J, Suenaga T, Kitazono M, Tanaka S, Niihara T, Hirotsu T, Uozumi T. Behavioural Response Alteration in Caenorhabditis elegans to Urine After Surgical Removal of Cancer: Nematode-NOSE (N-NOSE) for Postoperative Evaluation. BIOMARKERS IN CANCER 2019; 11:1179299X19896551. [PMID: 31903024 PMCID: PMC6931140 DOI: 10.1177/1179299x19896551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 12/17/2022]
Abstract
The technique used for cancer monitoring is essential for effective cancer
therapy. Currently, several methods such as diagnostic imaging and biochemical
markers have been used for cancer monitoring, but these are invasive and show
low sensitivity. A previous study reported that Caenorhabditis
elegans sensitively discriminated patients with cancer from healthy
subjects, based on the smell of a urine sample. However, whether C.
elegans olfaction can detect the removal of cancerous tumours
remains unknown. This study was conducted to examine C. elegans
olfactory behaviour to urine samples collected from 78 patients before and after
surgery. The diagnostic ability of the technique termed Nematode-NOSE (N-NOSE)
was evaluated by receiver operating characteristic (ROC) analysis. The ROC curve
of N-NOSE was higher than those of classic tumour markers. Furthermore, we
examined the change in C. elegans olfactory behaviour following
exposure to preoperative and postoperative samples. The results suggest that a
reduction in attraction indicates the removal of the cancerous tumour. This
study may lead to the development of a noninvasive and highly sensitive tool for
evaluating postoperative cancer patients.
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Affiliation(s)
| | - Kotaro Tashiro
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | - Syunji Shimaoka
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | - Koichiro Tsukasa
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | - Yukiko Baba
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | - Saori Furukawa
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | | | - Toyokuni Suenaga
- Department of Gastrointestinal Surgery, Nanpuh Hospital, Kagoshima, Japan
| | - Masaki Kitazono
- Department of Gastrointestinal Surgery, Nanpuh Hospital, Kagoshima, Japan
| | - Sadao Tanaka
- Department of Diagnostic Pathology, Nanpuh Hospital, Kagoshima, Japan
| | - Toru Niihara
- Department of Gastroenterology, Nanpuh Hospital, Kagoshima, Japan
| | - Takaaki Hirotsu
- R&D Center, Hirotsu Bio Science Inc., Tokyo, Japan.,Department of Biology, Graduate School of Sciences, Kyushu University, Fukuoka, Japan.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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Special Issue: Mass Spectrometric Proteomics. Molecules 2019; 24:molecules24061133. [PMID: 30901962 PMCID: PMC6472213 DOI: 10.3390/molecules24061133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 12/27/2022] Open
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