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Kuriki Y, Sogawa M, Komatsu T, Kawatani M, Fujioka H, Fujita K, Ueno T, Hanaoka K, Kojima R, Hino R, Ueo H, Ueo H, Kamiya M, Urano Y. Modular Design Platform for Activatable Fluorescence Probes Targeting Carboxypeptidases Based on ProTide Chemistry. J Am Chem Soc 2024; 146:521-531. [PMID: 38110248 DOI: 10.1021/jacs.3c10086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Carboxypeptidases (CPs) are a family of hydrolases that cleave one or more amino acids from the C-terminal of peptides or proteins and play indispensable roles in various physiological and pathological processes. However, only a few highly activatable fluorescence probes for CPs have been reported, and there is a need for a flexibly tunable molecular design platform to afford a range of fluorescence probes for CPs for biological and medical research. Here, we focused on the unique activation mechanism of ProTide-based prodrugs and established a modular design platform for CP-targeting florescence probes based on ProTide chemistry. In this design, probe properties such as fluorescence emission wavelength, reactivity/stability, and target CP can be readily tuned and optimized by changing the four probe modules: the fluorophore, the substituent on the phosphorus atom, the linker amino acid at the P1 position, and the substrate amino acid at the P1' position. In particular, switching the linker amino acid at position P1 enabled us to precisely optimize the reactivity for target CPs. As a proof-of-concept, we constructed probes for carboxypeptidase M (CPM) and prostate-specific membrane antigen (also known as glutamate carboxypeptidase II). The developed probes were applicable for the imaging of CP activities in live cells and in clinical specimens from patients. This design strategy should be useful in studying CP-related biological and pathological phenomena.
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Affiliation(s)
- Yugo Kuriki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mari Sogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Minoru Kawatani
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroyoshi Fujioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kyohhei Fujita
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rumi Hino
- Department of Sports and Health Science, Daito Bunka University, 560 Iwadono, Higashimatsuyama, Saitama 355-8501, Japan
| | - Hiroki Ueo
- Ueo Breast Cancer Hospital, 1-3-5 Futamatacho, Oita, Oita 870-0887, Japan
| | - Hiroaki Ueo
- Ueo Breast Cancer Hospital, 1-3-5 Futamatacho, Oita, Oita 870-0887, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259, Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Peng M, Zhou Y, Wang Y, Yi Z, Li S, Wan C. Identified Small Open Reading Frame-Encoded Peptides in Human Serum with Nanoparticle Protein Coronas. J Proteome Res 2024; 23:368-376. [PMID: 38006349 DOI: 10.1021/acs.jproteome.3c00608] [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: 11/27/2023]
Abstract
The low-molecular-weight proteins (LMWP) in serum and plasma are related to various human diseases and can be valuable biomarkers. A small open reading frame-encoded peptide (SEP) is one kind of LMWP, which has been found to function in many bioprocesses and has also been found in human blood, making it a potential biomarker. The detection of LMWP by a mass spectrometry (MS)-based proteomic assay is often inhibited by the wide dynamic range of serum/plasma protein abundance. Nanoparticle protein coronas are a newly emerging protein enrichment method. To analyze SEPs in human serum, we have developed a protocol integrated with nanoparticle protein coronas and liquid chromatography (LC)/MS/MS. With three nanoparticles, TiO2, Fe3O4@SiO2, and Fe3O4@SiO2@TiO2, we identified 164 new SEPs in the human serum sample. Fe3O4@SiO2 and a nanoparticle mixture obtained the maximum number and the largest proportion of identified SEPs, respectively. Compared with acetonitrile-based extraction, nanoparticle protein coronas can cover more small proteins and SEPs. The magnetic nanoparticle is also fit for high-throughput parallel protein separation before LC/MS. This method is fast, efficient, reproducible, and easy to operate in 96-well plates and centrifuge tubes, which will benefit the research on SEPs and biomarkers.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yi Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Zi Yi
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Shenglan Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
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Marin AM, Batista M, Korte de Azevedo AL, Bombardelli Gomig TH, Soares Caldeira Brant R, Chammas R, Uno M, Dias Araújo D, Zanette DL, Nóbrega Aoki M. Screening of Exosome-Derived Proteins and Their Potential as Biomarkers in Diagnostic and Prognostic for Pancreatic Cancer. Int J Mol Sci 2023; 24:12604. [PMID: 37628784 PMCID: PMC10454563 DOI: 10.3390/ijms241612604] [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: 06/17/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
In the oncological area, pancreatic cancer is one of the most lethal diseases, with 5-year survival rising just 10% in high-development countries. This disease is genetically characterized by KRAS as a driven mutation followed by SMAD4, CDKN2, and TP53-associated mutations. In clinical aspects, pancreatic cancer presents unspecific clinical symptoms with the absence of screening and early plasmatic biomarker, being that CA19-9 is the unique plasmatic biomarker having specificity and sensitivity limitations. We analyzed the plasmatic exosome proteomic profile of 23 patients with pancreatic cancer and 10 healthy controls by using Nanoscale liquid chromatography coupled to tandem mass spectrometry (NanoLC-MS/MS). The pancreatic cancer patients were subdivided into IPMN and PDAC. Our findings show 33, 34, and 7 differentially expressed proteins when comparing the IPMN vs. control, PDAC-No treatment vs. control, and PDAC-No treatment vs. IPMN groups, highlighting proteins of the complement system and coagulation, such as C3, APOB, and SERPINA. Additionally, PDAC with no treatment showed 11 differentially expressed proteins when compared to Folfirinox neoadjuvant therapy or Gemcitabine adjuvant therapy. So here, we found plasmatic exosome-derived differentially expressed proteins among cancer patients (IPMN, PDAC) when comparing with healthy controls, which could represent alternative biomarkers for diagnostic and prognostic evaluation, supporting further scientific and clinical studies on pancreatic cancer.
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Affiliation(s)
- Anelis Maria Marin
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil; (A.M.M.); (M.B.); (D.L.Z.)
| | - Michel Batista
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil; (A.M.M.); (M.B.); (D.L.Z.)
- Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Alexandre Luiz Korte de Azevedo
- Laboratory of Human Cytogenetics and Oncogenetics, Genetic Department, University of Parana State (UFPR), Curitiba 80060-000, Brazil; (A.L.K.d.A.); (T.H.B.G.)
| | - Talita Helen Bombardelli Gomig
- Laboratory of Human Cytogenetics and Oncogenetics, Genetic Department, University of Parana State (UFPR), Curitiba 80060-000, Brazil; (A.L.K.d.A.); (T.H.B.G.)
| | - Rodrigo Soares Caldeira Brant
- Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Comprehensive Center for Precision Oncology (C2PO), Universidade de São Paulo, São Paulo 05508-220, Brazil; (R.C.); (M.U.); (D.D.A.)
| | - Miyuki Uno
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Comprehensive Center for Precision Oncology (C2PO), Universidade de São Paulo, São Paulo 05508-220, Brazil; (R.C.); (M.U.); (D.D.A.)
| | - Diogo Dias Araújo
- Center for Translational Research in Oncology (LIM24), Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Comprehensive Center for Precision Oncology (C2PO), Universidade de São Paulo, São Paulo 05508-220, Brazil; (R.C.); (M.U.); (D.D.A.)
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil; (A.M.M.); (M.B.); (D.L.Z.)
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil; (A.M.M.); (M.B.); (D.L.Z.)
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Discovering Breast Cancer Biomarkers Candidates through mRNA Expression Analysis Based on The Cancer Genome Atlas Database. J Pers Med 2022; 12:jpm12101753. [PMID: 36294892 PMCID: PMC9604861 DOI: 10.3390/jpm12101753] [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: 10/11/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
Background: Research on the discovery of tumor biomarkers based on big data analysis is actively being conducted. This study aimed to secure foundational data for identifying new biomarkers of breast cancer via breast cancer datasets in The Cancer Genome Atlas (TCGA). Methods: The mRNA profiles of 526 breast cancer and 60 adjacent non-cancerous breast tissues collected from TCGA datasets were analyzed via MultiExperiment Viewer and GraphPad Prism. Diagnostic performance was analyzed by identifying the pathological grades of the selected differentially expressed (DE) mRNAs and the expression patterns of molecular subtypes. Results: Via DE mRNA profile analysis, we selected 14 mRNAs with downregulated expression (HADH, CPN2, ADAM33, TDRD10, SNF1LK2, HBA2, KCNIP2, EPB42, PYGM, CEP68, ING3, EMCN, SYF2, and DTWD1) and six mRNAs with upregulated expression (ZNF8, TOMM40, EVPL, EPN3, AP1M2, and SPINT2) in breast cancer tissues compared to that in non-cancerous tissues (p < 0.001). Conclusions: In total, 20 DE mRNAs had an area under cover of 0.9 or higher, demonstrating excellent diagnostic performance in breast cancer. Therefore, the results of this study will provide foundational data for planning preliminary studies to identify new tumor biomarkers.
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Zhai G, Yang L, Luo Q, Wu K, Zhao Y, Wang F. Serum phosphopeptide profiling for colorectal cancer diagnosis using liquid chromatography-mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9316. [PMID: 35416361 DOI: 10.1002/rcm.9316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE The identification and evaluation of novel biomarkers are essential to clinical diagnosis and prognosis of colorectal cancer (CRC). Serum phosphopeptides have been recognized as a potential signature pool for cancers; therefore, we aim to profile the expression of serum phosphopeptides and to evaluate their feasibility in CRC diagnosis. METHODS We conducted the characterization and absolute quantification of endogenous phosphopeptides in sera using liquid chromatography-mass spectrometry analysis in combination with enrichment of phosphopeptides by ZrAs-Fe3 O4 @SiO2 nanoparticles and use of deuterium-labeled standards. Differentially expressed analysis of four phosphopeptides was performed, generating a two-phosphopeptide-based biomarker, LF3-4 , by logistic regression analysis, where LF3-4 is equal to (5.85 - 5.13 × [F3] - 3.57 × [F4]), and [F3] and [F4] are the concentration of phosphopeptides DpSGEGDFLAEGGGVR and ADpSGEGDFLAEGGGVR in sera, respectively. RESULTS The LF3-4 values showed significant difference in CRC cases compared with controls, and yielded a specificity of 100%, leading to correct classification of 56 (93%) out of 60 CRC patients, including 12 (92.3%) of 13 CRC cases in stage I. Double-blind validation showed that 97.5% of CRC cases were discriminated accurately. CONCLUSIONS The LF3-4 value was firstly verified to be a potential biomarker for CRC diagnosis, and may expand our view in underlying mechanisms for CRC.
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Affiliation(s)
- Guijin Zhai
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- Department of Biochemistry and Molecular Biology; Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Liping Yang
- Cancer Research Centre, Tumour Hospital Affiliated to Nantong University, Nantong, Jiangsu, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Xu T, Zhang Z, Chen H, Cai R, Yang Q, Liu Q, Fan Y, Liu W, Yao C. Carboxypeptidase N2 as a Novel Diagnostic and Prognostic Biomarker for Lung Adenocarcinoma. Front Oncol 2022; 12:843325. [PMID: 35686102 PMCID: PMC9170673 DOI: 10.3389/fonc.2022.843325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/06/2022] [Indexed: 01/05/2023] Open
Abstract
Carboxypeptidase N2 (CPN2) is a plasma metallo-protease that cleaves basic amino acids from the C-terminal of peptides and proteins. Emerging evidence showed that carboxypeptidases perform many diverse functions in the body and play key roles in tumorigenesis. However, the clinical significance and biological functions of CPN2 in lung adenocarcinoma remain unclear. Our study aimed to explore the potential role and functions of CPN2 in lung adenocarcinoma. The results showed that the transcription level of CPN2 was significantly increased in the tumor tissues of lung adenocarcinoma patients compared to the adjacent normal tissues in The Cancer Genome Atlas cohort (P < 0.05). The survival plots showed that the overall survival of patients with a high expression of CPN2 was significantly lower than that of patients with a low expression of CPN2, both in the Kaplan-Meier database and the clinical sample cohort (P < 0.05). The tissue microarray analysis found that CPN2 protein expression was significantly positively correlated with node status and tumor stage as well as tumor malignancy (P < 0.05). Further univariate and multivariate Cox regression analyses showed that CPN2 may act as an independent prognostic factor in patients with lung adenocarcinoma (P < 0.05). In addition, the analysis of co-expression genes from LinkedOmics showed that CPN2 was positively associated with many genes of fibrillar collagen family members and the PI3K-Akt pathway. The gene set enrichment analysis showed that a higher expression of CPN2 may participate in mTOR, TGF-BETA, NOTCH, TOLL-like-receptor, WNT, and MAPK signaling pathway in lung adenocarcinoma. Notably, the knockdown of CPN2 significantly inhibited the ability of cell proliferation, clone formation, invasion, and migration. Our findings suggested that the upregulation of CPN2 is associated with a worse clinical outcome in lung adenocarcinoma and cancer-related pathways, which laid the foundation for further research on CPN2 during carcinogenesis.
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Affiliation(s)
- Ting Xu
- Department of Blood Transfusion, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hongqiang Chen
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China.,Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ruili Cai
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Qian Yang
- Department of Blood Transfusion, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qi Liu
- Department of Blood Transfusion, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yahan Fan
- Department of Blood Transfusion, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wenbin Liu
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China.,Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chunyan Yao
- Department of Blood Transfusion, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Cui R, Wang C, Li T, Hua J, Zhao T, Ren L, Wang Y, Li Y. Carboxypeptidase N1 is anticipated to be a synergy metrics for chemotherapy effectiveness and prognostic significance in invasive breast cancer. Cancer Cell Int 2021; 21:571. [PMID: 34711246 PMCID: PMC8555242 DOI: 10.1186/s12935-021-02256-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence and mortality of invasive breast cancer (IBC) are increasing annually. Hence, it is urgently needed to determine reliable biomarkers for not only monitoring curative effects, but evaluating prognosis. In present study, we aim to determine the potential role of Carboxypeptidase N1 (CPN1) in IBC tissues on chemotherapeutic efficacy and poor prognosis. METHODS The expression level of CPN1 in IBC tissue samples (n = 123) was quantified by tissue microarray technique and immunohistochemical staining. Moreover, sera of IBC patients (n = 34) that underwent three to five consecutive chemotherapy sessions were collected. The patients were randomly stratified into a training (n = 15) as well as a validation group (n = 19). The expression of serum CA153 and CPN1 was quantified by electrochemiluminescence and ELISA assay, respectively. RESULTS By univariate and multivariate Cox regression analysis, we show that CPN1 expression in IBC tissues, as an independent risk factor, is related to a poor overall survival (OS) and progression-free survival (PFS) (P < 0.05). Analysis of the data revealed that CPN1 over-expression could be consistently linked to adverse clinicopathological features such as lymph node metastasis and the pathological stage (pTNM) (P < 0.05). The serum CPN1 level trajectory of individual patients generally decreased during chemotherapy. In line with these findings were changes in the follow-up ultrasonography and a consistent decrease in serum CPN1 levels. The comparison of the area under the receiver operating curves (ROC) revealed that CPN1 has a better surveillance value than CA153 in the training (AUCCPN1 = 0.834 vs. AUCCA153 = 0.724) as well as the validation set (AUCCPN1 = 0.860 vs. AUCCA153 = 0.720) when comparing cycle2 versus cycle3. CONCLUSIONS CPN1 is a suitable potential biomarker for chemotherapeutic surveillance purposes as well as being an appropriate prognostic indicator which would support an improved chemotherapy regimen.
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Affiliation(s)
- Ranliang Cui
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Chaomin Wang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Tiantian Li
- School of Medical Laboratory, Tianjin Medical University, Tianjin, China
| | - Jialei Hua
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Ting Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China.
| | - Yichao Wang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), No. 999 Donghai Road, Jiaojiang District, Taizhou, 318000, Zhejiang, China.
| | - Yueguo Li
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China.
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Al-Essa MK, Alzayadneh E, Al-Hadidi K. Assessment of Proteolysis by Pyrylium and Other Fluorogenic Reagents. Protein Pept Lett 2021; 28:809-816. [PMID: 33390107 PMCID: PMC9175085 DOI: 10.2174/0929866528999201231214954] [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: 07/27/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022]
Abstract
Aims We aim to evaluate the potential application of amine reactive fluorogenic reagents for estimating enzymatic proteolysis. Background Proteolytic enzymes play important roles in regulating many physiological processes in living organisms. Objectives
Assessment of protein degradation by using reagents for protein assay techniques. Methods We have assayed samples at the start and after 30-60 minutes incubation with trypsin by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents and NanoOrange as non-amine reactive dye. Results All BSA prepared samples with trypsin have shown significantly higher fluorescence intensity (FI) versus controls (which reflects proteolysis) when assayed by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents. However, same samples assayed with NanoOrange as non-amine reactive reagent did not show any significant variation between samples containing trypsin and controls. Conclusion These results are confirming reliability of highly sensitive protein assays utilizing amine reactive fluorogenic reagents for general estimation of proteolysis.
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Affiliation(s)
- Mohamed K Al-Essa
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Ebaa Alzayadneh
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Kamal Al-Hadidi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Cui R, Wang C, Zhao Q, Wang Y, Li Y. Serum Carboxypeptidase N1 Serves as a Potential Biomarker Complementing CA15-3 for Breast Cancer. Anticancer Agents Med Chem 2021; 20:2053-2065. [PMID: 32619179 DOI: 10.2174/1871520620666200703191135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The incidence and mortality of breast cancer are increasing annually. Breast cancer seriously threatens women's health and quality of life. We aimed to measure the clinical value of CPN1, a new serum marker of breast cancer and to evaluate the efficacy of CPN1 in combination with CA15-3. METHODS Seventy samples of breast cancer with lymph node metastasis, seventy-three samples of nonmetastatic breast cancer and twenty-five samples of healthy human serum were collected. Serum CA15-3 concentration was determined by Roche Elecsys, and serum CPN1 concentration was determined by ELISA. RESULTS In breast cancer patients, serum CPN1 concentration was positively correlated with tumour size, clinical stage and CA15-3 concentration (r = 0.376, P<0.0001). ROC curve analysis showed that the optimal critical concentration of CPN1 for breast cancer diagnosis was 32.8pg/ml. The optimal critical concentration of CPN1 in the diagnosis of metastatic breast cancer was 66.121pg/ml. CPN1 has a greater diagnostic ability for breast cancer (AUCCA15-3=0.702 vs. AUCCPN1=0.886, P<0.0001) and metastatic breast cancer (AUCCA15-3=0.629 vs. AUCCPN1=0.887, P<0.0001) than CA15-3, and the combined detection of CA15-3 and CPN1 can improve the diagnostic efficiency for breast cancer (AUCCA15-3+CPN1=0.916) and for distinguishing between metastatic and non-metastatic breast cancer (AUCCA15-3+CPN1=0.895). CONCLUSION CPN1 can be used as a new tumour marker to diagnose and evaluate the invasion and metastasis of breast cancer. The combined detection of CPN1 and CA15-3 is more accurate and has a certain value in clinical application.
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Affiliation(s)
- Ranliang Cui
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Chaomin Wang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Qi Zhao
- Tianjin Medical University, Tianjin, China
| | - Yichao Wang
- Department of Clinical Laboratory Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Yueguo Li
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
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10
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11
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G. Keller S, Kamiya M, Urano Y. Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes. Molecules 2020; 25:E5964. [PMID: 33339370 PMCID: PMC7766215 DOI: 10.3390/molecules25245964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.
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Affiliation(s)
- Sascha G. Keller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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12
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Comparative Proteomic Investigation of Plasma Reveals Novel Potential Biomarker Groups for Acute Aortic Dissection. DISEASE MARKERS 2020; 2020:4785068. [PMID: 32256857 PMCID: PMC7106916 DOI: 10.1155/2020/4785068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/03/2022]
Abstract
Acute aortic dissection (AAD) is a catastrophic cardiovascular disease with high disability and mortality due to multiple fatal complications. However, the molecular changes of the serum proteome after AAD are not very clear. Here, we performed isobaric tags for relative and absolute quantitation- (iTRAQ-) based comparative proteomic analysis to investigate the proteome profile changes after AAD by collecting plasma samples from 20 AAD patients and 20 controls. Out of the 345 identified proteins, 266 were considered as high-quality quantified proteins (95%confident peptides ≥ 2), of which 25 proteins were accumulated and 12 were reduced in AAD samples. Gene ontology enrichment analysis showed that the 25 AAD-accumulated proteins were enriched in high-density lipoprotein particles for the cellular component category and protein homodimerization acidity for the molecular function category. Protein-protein interaction network analysis showed that serum amyloid A proteins (SAAs), complement component proteins, and carboxypeptidase N catalytic chain proteins (CPNs) possessed the key nodes of the network. The expression levels of six selected AAD-accumulated proteins, B2-GP1, CPN1, F9, LBP, SAA1, and SAA2, were validated by ELISA. Moreover, ROC analysis showed that the AUCs of B2-GP1 and CPN1 were 0.808 and 0.702, respectively. Our data provide insights into molecular change profiles in proteome levels after AAD and indicate that B2-GP1 and CPN1 are potential biomarkers for AAD.
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13
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Zhang F, Lyon CJ, Walls RJ, Ning B, Fan J, Hu TY. Cathepsin B Dependent Cleavage Product of Serum Amyloid A1 Identifies Patients with Chemotherapy-Related Cardiotoxicity. ACS Pharmacol Transl Sci 2019; 2:333-341. [PMID: 32259067 DOI: 10.1021/acsptsci.9b00035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 02/08/2023]
Abstract
Improvements in long-term cancer survival rates have resulted in an increase in the prevalence of chemotherapy-linked cardiac failure, but treatment-induced cardiac injuries may not be detected until long after therapy. Monitoring cardiac function is recommended; however, cardiovascular injury in cancer patients differs from those with primary cardiac dysfunction, which limits the utility of traditional cardiac biomarkers. Here we examined plasma levels of peptides produced by cathepsin B, which is released during chemotherapy-induced cardiac injury. We applied nanotrap fractionation to enrich plasma peptides from cancer patients treated with or without chemotherapy. Peptides associated with chemotherapy-induced cardiotoxicity, but not other cardiac injury, were identified by mass spectrometry, and their dependence on cathepsin B activity was determined using enzyme inhibition experiments. We found that a peptide (SAA-1525) derived from serum amyloid A1 was significantly increased in cardiotoxicity patients, and its production was inhibited when plasma samples were pretreated with cathepsin B specific inhibitors. Plasma SAA-1525 also correlated with other markers of cardiac injury. Analysis of plasma SAA-1525 levels may hold potential as a rapid and minimally invasive method to monitor subclinical injury, thereby allowing timely intervention to mitigate further cardiac damage and avoid more severe clinical presentation.
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Affiliation(s)
- Fangfang Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Christopher J Lyon
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Robert J Walls
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Bo Ning
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jia Fan
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Tony Y Hu
- Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana 70112, United States
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14
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Abstract
The life span of cancer patients can be prolonged with appropriate therapies if detected early. Mass screening for early detection of cancer, however, requires sensitive and specific biomarkers obtainable from body fluids such as blood or urine. To date, most biomarker discovery programs focus on the proteome rather than the endogenous peptidome. It has been long-established that tumor cells and stromal cells produce tumor resident proteases (TRPs) to remodel the surrounding tumor microenvironment in support of tumor progression. In fact, proteolytic products of TRPs have been shown to correlate with malignant behavior. Being of low molecular weight, these unique peptides can pass through the endothelial barrier of the vasculature into the bloodstream. As such, the cancer peptidome has increasingly become a focus for biomarker discovery. In this review, we discuss on the various aspects of the peptidome in cancer biomarker research.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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15
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Kuriki Y, Kamiya M, Kubo H, Komatsu T, Ueno T, Tachibana R, Hayashi K, Hanaoka K, Yamashita S, Ishizawa T, Kokudo N, Urano Y. Establishment of Molecular Design Strategy To Obtain Activatable Fluorescent Probes for Carboxypeptidases. J Am Chem Soc 2018; 140:1767-1773. [DOI: 10.1021/jacs.7b11014] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Mako Kamiya
- PRESTO (Japan)
Science
and Technology Agency (JST), 4-1-8
Honcho Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hidemasa Kubo
- Division
of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | | | | | | | | | | | | | - Takeaki Ishizawa
- Department
of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Norihiro Kokudo
- Department
of Surgery, National Center for Global Health and Medicine, 1-21-1
Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Yasuteru Urano
- CREST (Japan)
Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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16
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Wu B, Ouyang Z, Lyon CJ, Zhang W, Clift T, Bone CR, Li B, Zhao Z, Kimata JT, Yu XG, Hu Y. Plasma Levels of Complement Factor I and C4b Peptides Are Associated with HIV Suppression. ACS Infect Dis 2017; 3:880-885. [PMID: 28862830 PMCID: PMC5727467 DOI: 10.1021/acsinfecdis.7b00042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Individuals who exhibit long-term
HIV suppression and CD4 T-cell preservation without antiretroviral
therapy are of great interest for HIV research. There is currently
no robust method for rapid identification of these “HIV controller”
subjects; however, HLA-B*57 (human leukocyte antigen (major histocompatibility
complex), class I, B*57) genotype exhibits modest sensitivity for
this phenotype. Complement C3b and C4b can influence HIV infection
and replication, but studies have not examined their possible link
to HIV controller status. We analyzed HLA-B*57 genotype and complement
levels in HIV-positive patients receiving suppressive antiretroviral
therapy, untreated HIV controllers, and HIV-negative subjects to identify
factors associated with HIV controller status. Our results revealed
that the plasma levels of three C4b-derived peptides and complement
factor I outperformed all other assayed biomarkers for HIV controller
identification, although we could not analyze the predictive value
of biomarker combinations with the current sample size. We believe
this rapid screening approach may prove useful for improved identification
of HIV controllers.
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Affiliation(s)
- Boyue Wu
- Biodesign Center
for Personalized Diagnostics, the Biodesign Institute, Arizona State University, 727 E. Tyler Street, Tempe, Arizona 85281, United States
- College of Laboratory Medicine, Tianjin Medical University, 1 Guangdong Road, Tianjin 300203, China
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Boston, Massachusetts 02139-3583, United States
| | - Christopher J. Lyon
- Biodesign Center
for Personalized Diagnostics, the Biodesign Institute, Arizona State University, 727 E. Tyler Street, Tempe, Arizona 85281, United States
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Wei Zhang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning 110003, China
| | - Tori Clift
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Christopher R. Bone
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
| | - Boan Li
- Center for Clinical Laboratory, 302 Military Hospital of China, 100 Middle Section of West 4th Ring Road, Beijing 100038, China
| | - Zhen Zhao
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Jason T. Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Boston, Massachusetts 02139-3583, United States
| | - Ye Hu
- Biodesign Center
for Personalized Diagnostics, the Biodesign Institute, Arizona State University, 727 E. Tyler Street, Tempe, Arizona 85281, United States
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- School of Biological and Health Systems
Engineering, Virginia G. Piper, Arizona State University, 727
E. Tyler Street, Tempe, Arizona 85281, United States
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17
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The proteins cleaved by endogenous tryptic proteases in normal EDTA plasma by C18 collection of peptides for liquid chromatography micro electrospray ionization and tandem mass spectrometry. Clin Proteomics 2017; 14:39. [PMID: 29213220 PMCID: PMC5712186 DOI: 10.1186/s12014-017-9174-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/21/2017] [Indexed: 02/08/2023] Open
Abstract
The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed. A total of 583,927 precursor ions and MS/MS spectra were correlated to 94,669 best fit peptides that reduced to 22,287 correlations to the best accession within a gene symbol and to 7174 correlations to at least 510 gene symbols with ≥ 5 independent MS/MS correlations (peptide counts) that showed FDR q-values ranging from E−9 (i.e. FDR = 0.000000001) to E−227. A set of 528 gene symbols identified by X!TANDEM and SEQUEST including C4B showed ≥ fivefold variation between ice cold versus room temperature incubation. STRING analysis of the protein gene symbols observed from endogenous peptides in normal plasma revealed an extensive protein-interaction network of cellular factors associated with cell signalling and regulation, the formation of membrane bound organelles, cellular exosomes and exocytosis network proteins. Taken together the results indicated that a pool of cellular proteins, or protein complexes, in plasma are apparently not stable and degrade soon after incubation at room temperature.
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18
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Fan J, Ning B, Lyon CJ, Hu TY. Circulating Peptidome and Tumor-Resident Proteolysis. PEPTIDOMICS OF CANCER-DERIVED ENZYME PRODUCTS 2017; 42:1-25. [DOI: 10.1016/bs.enz.2017.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Ma X, Ouyang Z. Ambient ionization and miniature mass spectrometry system for chemical and biological analysis. Trends Analyt Chem 2016; 85:10-19. [PMID: 28042191 DOI: 10.1016/j.trac.2016.04.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ambien ionization and miniaturization of mass spectrometers are two fields in mass spectrometry that have advanced significantly in the last decade. The integration of the techniques developed in these two fields is leading to the development of complete miniature analytical systems that can be used for on-site or point-of-care analysis by non-expert users. In this review, we report the current status of development in ambient ionization and miniature mass spectrometers, with an emphasis on those techniques with potential impact on the point-of-care (POC) diagnostics. The challenges in the future development of the integrated systems are discussed with possible solutions presented.
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Affiliation(s)
- Xiaoxiao Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47906
| | - Zheng Ouyang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47906
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20
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Kaisar M, van Dullemen LFA, Thézénas ML, Zeeshan Akhtar M, Huang H, Rendel S, Charles PD, Fischer R, Ploeg RJ, Kessler BM. Plasma degradome affected by variable storage of human blood. Clin Proteomics 2016; 13:26. [PMID: 27708557 PMCID: PMC5037888 DOI: 10.1186/s12014-016-9126-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/16/2016] [Indexed: 01/01/2023] Open
Abstract
Background The successful application of—omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding of disease mechanisms and may represent a source of biomarkers. However, a major confounding factor for defining disease-specific proteomic signatures in plasma is the variation in handling and processing of clinical samples leading to protein degradation. To address this, we defined a plasma proteolytic signature (degradome) reflecting pre-analytical variability in blood samples that remained at ambient temperature for different time periods after collection and prior to processing. Methods We obtained EDTA blood samples from five healthy volunteers (n = 5), and blood tubes remained at ambient temperature for 30 min, 8, 24 and 48 h prior to centrifugation and isolation of plasma. Naturally occurred peptides derived from plasma samples were compared by label-free quantitative LC–MS/MS. To profile protein degradation, we analysed pooled plasma samples at T = 30 min and 48 h using PROTOMAP analysis. The proteolytic pattern of selected protein candidates was further validated by immunoblotting. Results A total of 820 plasma proteins were surveyed by PROTOMAP, and for 4 % of these, marked degradation was observed. We show distinct proteolysis patterns for talin-1, coagulation factor XI, complement protein C1r, C3, C4 and thrombospondin, and several proteins including S100A8, A9, annexin A1, profiling-1 and platelet glycoprotein V are enriched after 48 h blood storage at ambient temperature. In particular, thrombospondin protein levels increased after 8 h and proteolytic fragments appeared after 24 h storage time. Conclusions The overall impact of blood storage at ambient temperature for variable times on the plasma proteome and degradome is relatively minor, but in some cases can cause a potential bias in identifying and assigning relevant proteomic markers. The observed effects on the plasma proteome and degradome are predominantly triggered by limited leucocyte and platelet cell activation due to blood handling and storage. The baseline plasma degradome signature presented here can help filtering candidate protein markers relevant for clinical biomarker studies. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9126-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Kaisar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,NHS Blood and Transplant, Watford, WD24 4QN UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Leon F A van Dullemen
- Surgical Research Laboratory, University Medical Center, University of Groningen, Groningen, 9713 GZ The Netherlands
| | - Marie-Laëtitia Thézénas
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - M Zeeshan Akhtar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK
| | - Honglei Huang
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Sandrine Rendel
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Rutger J Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 7LJ UK.,NHS Blood and Transplant, Watford, WD24 4QN UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
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21
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Trecate G, Sinues PML, Orlandi R. Noninvasive strategies for breast cancer early detection. Future Oncol 2016; 12:1395-411. [DOI: 10.2217/fon-2015-0071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Breast cancer screening and presurgical diagnosis are currently based on mammography, ultrasound and more sensitive imaging technologies; however, noninvasive biomarkers represent both a challenge and an opportunity for early detection of cancer. An extensive number of potential breast cancer biomarkers have been discovered by microarray hybridization or sequencing of circulating DNA, noncoding RNA and blood cell RNA; multiplex analysis of immune-related molecules and mass spectrometry-based approaches for high-throughput detection of protein, endogenous peptides, circulating and volatile metabolites. However, their medical relevance and their translation to clinics remain to be exploited. Once they will be fully validated, cancer biomarkers, used in combination with the current and emerging imaging technologies, represent an avenue to a personalized breast cancer diagnosis.
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Affiliation(s)
- Giovanna Trecate
- Department of Imaging Diagnosis & Radiotherapy, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Rosaria Orlandi
- Molecular Targeting Unit, Department of Experimental Oncology & Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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22
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Du YM, Hu Y, Xia Y, Ouyang Z. Power Normalization for Mass Spectrometry Data Analysis and Analytical Method Assessment. Anal Chem 2016; 88:3156-63. [PMID: 26882462 PMCID: PMC8135100 DOI: 10.1021/acs.analchem.5b04418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biomarker profiling using mass spectrometry plays an essential role in biological studies and is highly dependent on the data analysis for sample classification. In this study, we introduced power nomination of the mass spectra as a method for systematically altering the weights of peaks at different intensity levels. In combination with the use of support vector machine method (SVM), the impact on the sample classification has been characterized using data in four studies previously reported, including the distinctions of anomeric configurations of sugars, types of bacteria, stages of melanoma, and the types of breast cancer. Comprehensive analysis of the data with normalization at different power normalization index (PNI) was developed and analysis tools, including error-PNI plots, reference profiles, and error source profiles, were used to assess the potential of the analytical methods as well as to find the proper approaches to classify the samples.
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Affiliation(s)
- Y. Melodie Du
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Ye Hu
- Department of Nanomedicine, Houston Methodist Research Institute, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Yu Xia
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Zheng Ouyang
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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23
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Crotti S, Enzo MV, Bedin C, Pucciarelli S, Maretto I, Del Bianco P, Traldi P, Tasciotti E, Ferrari M, Rizzolio F, Toffoli G, Giordano A, Nitti D, Agostini M. Clinical predictive circulating peptides in rectal cancer patients treated with neoadjuvant chemoradiotherapy. J Cell Physiol 2015; 230:1822-8. [PMID: 25522009 DOI: 10.1002/jcp.24894] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/12/2014] [Indexed: 02/06/2023]
Abstract
Preoperative chemoradiotherapy is worldwide accepted as a standard treatment for locally advanced rectal cancer. Current standard of treatment includes administration of ionizing radiation for 45-50.4 Gy in 25-28 fractions associated with 5-fluorouracil administration during radiation therapy. Unfortunately, 40% of patients have a poor or absent response and novel predictive biomarkers are demanding. For the first time, we apply a novel peptidomic methodology and analysis in rectal cancer patients treated with preoperative chemoradiotherapy. Circulating peptides (Molecular Weight <3 kDa) have been harvested from patients' plasma (n = 33) using nanoporous silica chip and analyzed by Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometer. Peptides fingerprint has been compared between responders and non-responders. Random Forest classification selected three peptides at m/z 1082.552, 1098.537, and 1104.538 that were able to correctly discriminate between responders (n = 16) and non-responders (n = 17) before therapy (T0) providing an overall accuracy of 86% and an area under the receiver operating characteristic (ROC) curve of 0.92. In conclusion, the nanoporous silica chip coupled to mass spectrometry method was found to be a realistic method for plasma-based peptide analysis and we provide the first list of predictive circulating biomarker peptides in rectal cancer patients underwent preoperative chemoradiotherapy.
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Affiliation(s)
- Sara Crotti
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico, IRCCS National Cancer Institute, Aviano (PN), Italy; Istituto di Ricerca Pediatrica- Citt, à,, della Speranza, Corso Stati Uniti 4, Padova, Italy
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Zhao J, Hu S, Cao Y, Zhang B, Li G. Electrochemical detection of protein based on hybridization chain reaction-assisted formation of copper nanoparticles. Biosens Bioelectron 2015; 66:327-31. [DOI: 10.1016/j.bios.2014.11.039] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 12/30/2022]
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25
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Zhao H, Li Y, Hu Y. Nanotechnologies in glycoproteomics. Clin Proteomics 2014; 11:21. [PMID: 24940182 PMCID: PMC4040410 DOI: 10.1186/1559-0275-11-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/17/2014] [Indexed: 12/25/2022] Open
Abstract
Protein glycosylation, as an important post-translational modification, is implicated in a number of ailments. Applying proteomic approaches, including mass spectrometry (MS) analyses that have played a significant role in biomarker detection and early diagnosis of diseases, to the study of glycoproteins or glycopeptides will facilitate a deeper understanding of many physiological functions and biological pathways involved in cancer, inflammatory and degenerative diseases. The abundance of glycopeptides and their ionization potential are relatively lower compared to those of non-glycopeptides; therefore, sample enrichment is necessary for glycopeptides prior to MS analysis. The application of nanotechnology in the past decade has been rapidly penetrating into many diverse scientific research disciplines. Particularly in what we now refer to as the “glycoproteomics area”, nanotechnologies have enabled enhanced sensitivity and specificity of glycopeptide detection in complex biological fluids, which are critical for disease diagnosis and monitoring. In this review, we highlight some recent studies that combine the capabilities of specific nanotechnologies with the comprehensive features of glycoproteomics. In particular, we focus on the ways in which nanotechnology has facilitated the detection of glycopeptides in complex biological samples and enhanced their characterization by MS, in terms of intensity and resolution. These studies reveal an increasingly important role for nanotechnology in helping to overcome certain technical challenges in biomarker discovery, in general, and glycoproteomics research, in particular.
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Affiliation(s)
- Hu Zhao
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yaojun Li
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ye Hu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA ; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York City, NY 10021, USA
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26
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Hanash S, Schliekelman M. Proteomic profiling of the tumor microenvironment: recent insights and the search for biomarkers. Genome Med 2014; 6:12. [PMID: 24713112 PMCID: PMC3978437 DOI: 10.1186/gm529] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Although gain of oncogene functions and loss of tumor suppressor functions are driving forces in tumor development, the tumor microenvironment, comprising the extracellular matrix, surrounding stroma, signaling molecules and infiltrating immune and other cell populations, is now also recognized as crucial to tumor development and metastasis. Many interactions at the tumor cell-environment interface occur at the protein level. Proteomic approaches are contributing to the definition of the protein constituents of the microenvironment and their sources, modifications, interactions and turnover, as well as providing information on how these features relate to tumor development and progression. Recently, proteomic studies have revealed how cancer cells modulate the microenvironment through their secreted proteins and how they can alter their protein constituents to adapt to the microenvironment. Moreover, the release of proteins from the microenvironment into the circulatory system has relevance for the development of blood-based cancer diagnostics. Here, we review how proteomic approaches are being applied to studies of the tumor microenvironment to decipher tumor-stroma interactions and to elucidate the role of host cells in the tumor microenvironment.
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27
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Gronowski AM, Manson JE, Mardis ER, Mora S, Spong CY. What's Different about Women's Health? Clin Chem 2014; 60:1-3. [DOI: 10.1373/clinchem.2013.216598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ann M Gronowski
- Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Elaine R Mardis
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Samia Mora
- Divisions of Preventive Medicine and
- Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Catherine Y Spong
- Division of Extramural Research at the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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Diamandis EP. Tumor microenvironment-released peptides: could they form the basis for an early-diagnosis breast cancer test? Clin Chem 2013; 60:4-6. [PMID: 24198244 DOI: 10.1373/clinchem.2013.216143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
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