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Zhou S, Lin N, Yu L, Su X, Liu Z, Yu X, Gao H, Lin S, Zeng Y. Single-cell multi-omics in the study of digestive system cancers. Comput Struct Biotechnol J 2024; 23:431-445. [PMID: 38223343 PMCID: PMC10787224 DOI: 10.1016/j.csbj.2023.12.007] [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: 08/04/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.
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Affiliation(s)
- Shuang Zhou
- The Second Clinical Medical School of Fujian Medical University, Quanzhou, Fujian Province, China
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Nanfei Lin
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, & Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Xiaowan Yu
- Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
- Fujian Provincial Key Laboratory of Lung Stem Cells, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, China
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2
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Ali HR, West RB. Spatial Biology of Breast Cancer. Cold Spring Harb Perspect Med 2024; 14:a041335. [PMID: 38110242 PMCID: PMC11065165 DOI: 10.1101/cshperspect.a041335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Spatial findings have shaped on our understanding of breast cancer. In this review, we discuss how spatial methods, including spatial transcriptomics and proteomics and the resultant understanding of spatial relationships, have contributed to concepts regarding cancer progression and treatment. In addition to discussing traditional approaches, we examine how emerging multiplex imaging technologies have contributed to the field and how they might influence future research.
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Affiliation(s)
- H Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert B West
- Department of Pathology, Stanford University Medical Center, Stanford, California 94305, USA
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3
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Goulden T, Bodachivskyi I, Padula MP, Williams DBG. Concentrated ionic liquids for proteomics: Caveat emptor! Int J Biol Macromol 2023; 253:127438. [PMID: 37839603 DOI: 10.1016/j.ijbiomac.2023.127438] [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: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.
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Affiliation(s)
- Thomas Goulden
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - Iurii Bodachivskyi
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar St, Kyiv 02094, Ukraine
| | - Matthew P Padula
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - D Bradley G Williams
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; University of Wollongong, School of Chemistry and Molecular Bioscience, Wollongong, NSW 2522, Australia.
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4
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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5
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Bennett NR, Coventry B, Goreshnik I, Huang B, Allen A, Vafeados D, Peng YP, Dauparas J, Baek M, Stewart L, DiMaio F, De Munck S, Savvides SN, Baker D. Improving de novo protein binder design with deep learning. Nat Commun 2023; 14:2625. [PMID: 37149653 PMCID: PMC10163288 DOI: 10.1038/s41467-023-38328-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/24/2023] [Indexed: 05/08/2023] Open
Abstract
Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the augmentation of energy-based protein binder design using deep learning. We find that using AlphaFold2 or RoseTTAFold to assess the probability that a designed sequence adopts the designed monomer structure, and the probability that this structure binds the target as designed, increases design success rates nearly 10-fold. We find further that sequence design using ProteinMPNN rather than Rosetta considerably increases computational efficiency.
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Affiliation(s)
- Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Aza Allen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ying Po Peng
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Steven De Munck
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Savvas N Savvides
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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6
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Firdous P, Hassan T, Farooq S, Nissar K. Applications of proteomics in cancer diagnosis. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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7
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Huang Z, Zhao X, Hu J, Zhang C, Xie X, Liu R, Lv Y. Single-Nanoparticle Differential Immunoassay for Multiplexed Gastric Cancer Biomarker Monitoring. Anal Chem 2022; 94:12899-12906. [PMID: 36069220 DOI: 10.1021/acs.analchem.2c03013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Precision medicine demands the best application of multiple unambiguous biomarkers to bring uniform decisions in disease prognosis. The remarkable development of heterogeneous immunoassay greatly promotes precision medicine when combined with the biomarker combination strategy. Nevertheless, the cumbersome washing steps in heterogeneous immunoassay have inevitably compromised the accuracy because of the sample losses and nature change of the matrix, challenging the further exploration of a more facile and lower limit-of-detection analysis. The new methodologies with high throughputs and specificity are never out of date to provide simultaneous evaluations and uniform decisions on multiple analytes through a simple process. Herein, we propose a new wash-free immunoassay, named differential assay, for multiplexed biomarker monitoring. The method is based on counting the number difference of unbound nanoparticle tags before and after immunoreactions from a solid support (i.e., magnetic microsphere) by single-particle inductively coupled plasma mass spectrometry (sp-ICP-MS), discarding the tedious washing steps. We primarily explore the proof-of-concept proposal within two types (sandwich and competitive assay), demonstrating the good feasibility for further facile clinical practice. To provide efficient multiplexed evaluations, we synthesized PtNPs with four diameters and screened the most suitable size for efficient differential immunoassay. The wash-free strategy was successfully utilized in simultaneous serological biomarker (CA724, CA199, and CEA) evaluation, with results in good accordance with those measured by the clinical routine method. Potentially, the proposed differential bioassay can be regarded as a more facile and valuable tool in malignancy prognosis and cancer recurrence monitoring.
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Affiliation(s)
- Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Xin Zhao
- Department of Clinical Laboratory, Chengdu Seventh People's Hospital, Chengdu 610041, Sichuan, P. R. China
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Chengchao Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Xiaobo Xie
- Analytical & Testing Center, Sichuan University, Chengdu 610064, P. R. China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu 610064, P. R. China
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8
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Kim SY, Park KH, Kim HJ, Kim YM, Ahn K, Lee KN. Inflammation-related immune proteins in maternal plasma as potential predictive biomarkers for rescue cerclage outcome in women with cervical insufficiency. Am J Reprod Immunol 2022; 88:e13557. [PMID: 35499384 DOI: 10.1111/aji.13557] [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: 09/28/2021] [Revised: 02/04/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
PROBLEM This study aimed to determine whether various novel plasma mediators of immune regulation associated with inflammation could independently predict the clinical outcome of rescue cerclage in patients with cervical insufficiency (CI). METHOD OF STUDY A total of 41 singleton pregnant women (17-25 weeks) who underwent rescue cerclage for CI were retrospectively evaluated. Stored plasma samples were assayed for IGFBP-1, -2, -3, IL-6, latexin, LBP, lipocalin-2, M-CSF, MIP-1α, MMP-8, -9, pentraxin 3, resistin, S100A8, S100A8/A9, thrombospondin-2, TIMP-1, and TNFR2 levels. The primary outcome measures were spontaneous preterm birth (SPTB) at < 28 and < 34 weeks after cerclage placement. RESULTS Multivariate Firth's logistic regression analysis revealed that high levels of IGFBP-3 and S100A8/A9, and low levels of MIP-1α were significantly associated with SPTB at < 28 weeks after cerclage placement, whereas only low MIP-1α levels were significantly associated with SPTB at < 34 weeks, even after adjustment for baseline clinical covariates (e.g., cervical dilatation). For the prediction of SPTB at < 28 weeks, the area under the curves (AUC) of IGFBP-3, MIP-1α, and S100A8/A9 were of .686, .691, and .693, respectively. Similarly, the AUC of MIP-1 α was of .659 to predict SPTB at < 34 weeks. CONCLUSIONS These findings suggest that plasma IGFBP-3, MIP-1α, and S100A8/A9 can represent noninvasive independent biomarkers for identifying women with CI at high risk for SPTB following rescue cerclage. Nonetheless, further in large, multicenter clinical studies should be performed to confirm the clinical value of these biomarkers.
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Affiliation(s)
- So Yeon Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, South Korea.,Department of Obstetrics and Gynecology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, South Korea.,Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hyeon Ji Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Yu Mi Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kwanghee Ahn
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kyong-No Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, South Korea
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Marino D, Pizzi M, Kotova I, Schmidt R, Schröder C, Guzzardo V, Talli I, Peroni E, Finotto S, Scapinello G, Dei Tos AP, Piazza F, Trentin L, Zagonel V, Piovan E. High ETV6 Levels Support Aggressive B Lymphoma Cell Survival and Predict Poor Outcome in Diffuse Large B-Cell Lymphoma Patients. Cancers (Basel) 2022; 14:cancers14020338. [PMID: 35053500 PMCID: PMC8774128 DOI: 10.3390/cancers14020338] [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: 11/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
The identification of prognostic factors for aggressive B-cell lymphomas still represents an unmet clinical need. We used forward phase protein arrays (FFPA) to identify proteins associated with overall survival (OS) from diagnostic formalin-fixed paraffin-embedded material of diffuse large B-cell lymphoma (DLBCL) patients (n = 47). Univariate Cox regression analysis identified numerous proteins, including immune check-point molecules (PDCD1, PDCD2 and PD1L2) and BCL2 to be significantly associated with OS. However, only ETV6 and PIM2 proteins persisted following multivariate Cox analysis. Independent validation studies by immunohistochemistry and analysis of public gene expression profiles of DLBCL confirmed a prognostic role for high ETV6 and ETV6/PIM2 ratios in DLBCL. ETV6 is a recurrently mutated/deleted gene in DLBCL for which its function in this disease entity is currently unknown. We find that ETV6 is upregulated during oncogenic transformation of germinal center B-cells and that it regulates DLBCL survival, as its acute loss results in marked apoptosis. Fluctuations in survivin (BIRC5) expression levels were associated with this phenomenon. Furthermore, an inverse correlation between ETV6 and BIRC5 expression levels was found and correlated with a response to the BIRC5 inhibitor, YM155. In conclusion, we present evidence for an oncogenic function of ETV6 in DLBCL.
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Affiliation(s)
- Dario Marino
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Marco Pizzi
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Iuliia Kotova
- Sciomics GmbH, 69151 Neckargemünd, Germany; (I.K.); (R.S.); (C.S.)
| | - Ronny Schmidt
- Sciomics GmbH, 69151 Neckargemünd, Germany; (I.K.); (R.S.); (C.S.)
| | | | - Vincenza Guzzardo
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Ilaria Talli
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy;
| | - Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy;
| | - Silvia Finotto
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Greta Scapinello
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Angelo Paolo Dei Tos
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Francesco Piazza
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Livio Trentin
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Vittorina Zagonel
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Erich Piovan
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy;
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy;
- Correspondence: ; Tel.: +39-(049)-8215895
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10
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Liu H, Wang Y, Fu R, Zhou J, Liu Y, Zhao Q, Yao J, Cui Y, Wang C, Jiao B, He Y. A multicolor enzyme-linked immunoassay method for visual readout of carbendazim. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4256-4265. [PMID: 34591948 DOI: 10.1039/d1ay01028j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzyme-linked immunosorbent assay (ELISA) with high specificity and sensitivity is one of the most popular techniques for detecting carbendazim (CBD), a commonly used benzimidazole fungicide in agriculture. However, the traditional ELISA based on the horseradish peroxidase (HRP)-3,3',5,5'-tetramethylbenzidine (TMB) system for CBD only displays the yellow color of TMB2+ from deep to light, making it difficult for the naked eye to judge whether CBD in fruits and vegetables exceeds the maximum residue limit. In this article, we intend to improve the traditional ELISA method to establish a multicolor signal output ELISA to achieve visual semiquantitative detection of CBD. This method is based on the optical properties of gold nanorods (AuNRs). After introducing AuNRs into TMB2+ solution, which was produced by the HRP-TMB system of traditional ELISA, AuNRs were quickly etched by TMB2+. Consequently, the longitudinal localized surface plasmon resonance peak of AuNRs shows a clear blue shift and a vivid color change. Different concentrations of CBD generate different amounts of TMB2+, which in turn leads to different etching degrees of AuNRs, and ultimately results in a rainbow-like color change. As a result, CBD from 0.08 to 100 ng mL-1 can be easily distinguished by the naked eye, which does not require any large instruments. Moreover, the colors displayed by 0.49 ng mL-1 (purple) and 0 ng mL-1 (pink) are significantly different from each other. It should be noted that 0.49 ng mL-1 is far below the most stringent maximum residue limit of CBD in the world. Additionally, the quantitative determination of CBD spiked in canned citrus, citrus fruits, chives, and cabbage samples showed satisfactory recoveries. The good performance of the AuNR-based ELISA makes it have a wide range of application prospects in food safety and international trade.
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Affiliation(s)
- Haoran Liu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Yiwen Wang
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Ruijie Fu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Jing Zhou
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Yanlin Liu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Qiyang Zhao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Jingjing Yao
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro Products, Wuhan 430064, Hubei, P. R. China.
| | - Yongliang Cui
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Chengqiu Wang
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Bining Jiao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
| | - Yue He
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Chongqing, 400712, P. R. China
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11
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Correa Rojo A, Heylen D, Aerts J, Thas O, Hooyberghs J, Ertaylan G, Valkenborg D. Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. Front Physiol 2021; 12:723510. [PMID: 34512391 PMCID: PMC8427610 DOI: 10.3389/fphys.2021.723510] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomics data. Furthermore, we highlight the current challenges to put quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data with genomics data for future applications in precision medicine.
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Affiliation(s)
- Alejandro Correa Rojo
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dries Heylen
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Jan Aerts
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Olivier Thas
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), Wollongong, NSW, Australia
| | - Jef Hooyberghs
- Flemish Institute for Technological Research (VITO), Mol, Belgium.,Theoretical Physics, Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Gökhan Ertaylan
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dirk Valkenborg
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
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12
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Fordham AM, Ekert PG, Fleuren EDG. Precision medicine and phosphoproteomics for the identification of novel targeted therapeutic avenues in sarcomas. Biochim Biophys Acta Rev Cancer 2021; 1876:188613. [PMID: 34390800 DOI: 10.1016/j.bbcan.2021.188613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022]
Abstract
Rapid advances in genomic technologies have enabled in-depth interrogation of cancer genomes, revealing novel and unexpected therapeutic targets in many cancer types. Identifying actionable dependencies in the diverse and heterogeneous group of sarcomas, particularly those that occur in children or adolescents and young adults (AYAs), remains especially challenging. These patients rarely harbor actionable genomic aberrations, no targeted agent is approved, and outcomes have remained poor for the past decades. This underlines a clear need to refine our methods for target identification. Phosphoproteomics studies in sarcoma showed the power of such analyses to capture novel actionable drivers that are not accompanied by mutational events or gene amplifications. This Review makes the case that incorporating phosphoproteomic molecular profiling alongside (functional) genomics technologies can significantly expand therapeutic target identification, and pinpoint drug mechanisms of action, in pediatric and AYA sarcoma patients. We explore the utility and prospects of phosphoproteomics in personalized medicine.
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Affiliation(s)
- Ashleigh M Fordham
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia; School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia; School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia.
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13
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Zimmer A, Korem Y, Rappaport N, Wilmanski T, Baloni P, Jade K, Robinson M, Magis AT, Lovejoy J, Gibbons SM, Hood L, Price ND. The geometry of clinical labs and wellness states from deeply phenotyped humans. Nat Commun 2021; 12:3578. [PMID: 34117230 PMCID: PMC8196202 DOI: 10.1038/s41467-021-23849-8] [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: 08/17/2020] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. For thousands of people, we have collected longitudinal multi-omics data. To analyze, interpret and visualize this extremely high-dimensional data, we use the Pareto Task Inference (ParTI) method. We find that the clinical labs data fall within a tetrahedron. We then use all other data types to characterize the four archetypes. We find that the tetrahedron comprises three wellness states, defining a wellness triangular plane, and one aberrant health state that captures aspects of commonality in movement away from wellness. We reveal the tradeoffs that shape the data and their hierarchy, and use longitudinal data to observe individual trajectories. We then demonstrate how the movement on the tetrahedron can be used for detecting unexpected trajectories, which might indicate transitions from health to disease and reveal abnormal conditions, even when all individual blood measurements are in the norm.
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Affiliation(s)
- Anat Zimmer
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Yael Korem
- grid.13992.300000 0004 0604 7563Weizmann Institute, Rehovot, Israel
| | - Noa Rappaport
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Tomasz Wilmanski
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Priyanka Baloni
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Kathleen Jade
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Max Robinson
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Andrew T. Magis
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Jennifer Lovejoy
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Sean M. Gibbons
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Leroy Hood
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA ,Providence St Joseph Health, Seattle, WA USA
| | - Nathan D. Price
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
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14
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Zhang C, Wei Y, Mardinoglu A, Zhang P. Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer. Front Mol Biosci 2021; 8:668146. [PMID: 34124153 PMCID: PMC8193925 DOI: 10.3389/fmolb.2021.668146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Adil Mardinoglu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
- Faculty of Dentistry, Oral & Craniofacial Sciences, Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom
| | - Peng Zhang
- Department of Surgery, School of Medicine, University of Maryland, College Park, MD, United States
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15
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Schulte C, Khayenko V, Nordblom NF, Tippel F, Peck V, Gupta AJ, Maric HM. High-throughput determination of protein affinities using unmodified peptide libraries in nanomolar scale. iScience 2021; 24:101898. [PMID: 33364586 PMCID: PMC7753147 DOI: 10.1016/j.isci.2020.101898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/02/2022] Open
Abstract
Protein-protein interactions (PPIs) are of fundamental importance for our understanding of physiology and pathology. PPIs involving short, linear motifs play a major role in immunological recognition, signaling, and regulation and provide attractive starting points for pharmaceutical intervention. Yet, state-of-the-art protein-peptide affinity determination approaches exhibit limited throughput and sensitivity, often resulting from ligand immobilization, labeling, or synthesis. Here, we introduce a high-throughput method for in-solution analysis of protein-peptide interactions using a phenomenon called temperature related intensity change (TRIC). We use TRIC for the identification and fine-mapping of low- and high-affinity protein interaction sites and the definition of sequence binding requirements. Validation is achieved by microarray-based studies using wild-type and mutated recombinant protein and the native protein within tissue lysates. On-chip neutralization and strong correlation with structural data establish TRIC as a quasi-label-free method to determine binding affinities of unmodified peptide libraries with large dynamic range.
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Affiliation(s)
- Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Vladimir Khayenko
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Noah Frieder Nordblom
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Franziska Tippel
- Nanotemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany
| | - Violetta Peck
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Amit Jean Gupta
- Nanotemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
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16
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Huang Z, Li Z, Jiang M, Liu R, Lv Y. Homogeneous Multiplex Immunoassay for One-Step Pancreatic Cancer Biomarker Evaluation. Anal Chem 2020; 92:16105-16112. [DOI: 10.1021/acs.analchem.0c03780] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ziyan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Min Jiang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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17
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Kang TH, Seong BL. Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms. Front Microbiol 2020; 11:1927. [PMID: 33101218 PMCID: PMC7546209 DOI: 10.3389/fmicb.2020.01927] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (VH) and light (VL) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of VH-VL pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, South Korea
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18
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Liu Y, Jia Y, Yang K, Wang Z. Heterogeneous Strategies to Eliminate Intracellular Bacterial Pathogens. Front Microbiol 2020; 11:563. [PMID: 32390959 PMCID: PMC7192003 DOI: 10.3389/fmicb.2020.00563] [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: 12/15/2019] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Antibiotic tolerance in bacterial pathogens that are genetically susceptible, but phenotypically tolerant to treatment, represents a growing crisis for public health. In particular, the intracellular bacteria-mediated antibiotic tolerance by acting as “Trojan horses” play a critical and underappreciated role in the disease burden of bacterial infections. Thus, more intense efforts are required to tackle this problem. In this review, we firstly provide a brief overview of modes of action of bacteria invasion and survival in macrophage or non-professional phagocytic cells. Furthermore, we summarize our current knowledge about promising strategies to eliminate these intracellular bacterial pathogens, including direct bactericidal agents, antibiotic delivery to infection sites by various carriers, and activation of host immune functions. Finally, we succinctly discuss the challenges faced by bringing them into clinical trials and our constructive perspectives.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Kangni Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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19
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Zhang W, Besford QA, Christofferson AJ, Charchar P, Richardson JJ, Elbourne A, Kempe K, Hagemeyer CE, Field MR, McConville CF, Yarovsky I, Caruso F. Cobalt-Directed Assembly of Antibodies onto Metal-Phenolic Networks for Enhanced Particle Targeting. NANO LETTERS 2020; 20:2660-2666. [PMID: 32155075 DOI: 10.1021/acs.nanolett.0c00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The orientation-specific immobilization of antibodies onto nanoparticles, to preserve antibody-antigen recognition, is a key challenge in developing targeted nanomedicines. Herein, we report the targeting ability of metal-phenolic network (MPN)-coated gold nanoparticles with surface-physisorbed antibodies against respective antigens. The MPN coatings were self-assembled from metal ions (FeIII, CoII, CuII, NiII, or ZnII) cross-linked with tannic acid. Upon physisorption of antibodies, all particle systems exhibited enhanced association with target antigens, with CoII systems demonstrating more than 2-fold greater association. These systems contained more metal atoms distributed in a way to specifically interact with antibodies, which were investigated by molecular dynamics simulations. A model antibody fragment crystallizable (Fc) region in solution with CoII-tannic acid complexes revealed that the solvent-exposed CoII can directly coordinate to the histidine-rich portion of the Fc region. This one-pot interaction suggests anchoring of the antibody Fc region to the MPN on nanoparticles, allowing for enhanced targeting.
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Affiliation(s)
- Wenjie Zhang
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Quinn A Besford
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Patrick Charchar
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Joseph J Richardson
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aaron Elbourne
- Nanobiotechnology Laboratory, School of Science, RMIT University, Melbourne Victoria 3001, Australia
| | - Kristian Kempe
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Christoph E Hagemeyer
- NanoBiotechnology Laboratory, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Matthew R Field
- RMIT Microscopy & Microanalysis Facility, RMIT University, Melbourne, Victoria 3001, Australia
| | - Chris F McConville
- College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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20
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Yaghoobi V, Martinez-Morilla S, Liu Y, Charette L, Rimm DL, Harigopal M. Advances in quantitative immunohistochemistry and their contribution to breast cancer. Expert Rev Mol Diagn 2020; 20:509-522. [PMID: 32178550 DOI: 10.1080/14737159.2020.1743178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Automated image analysis provides an objective, quantitative, and reproducible method of measurement of biomarkers. Image quantification is particularly well suited for the analysis of tissue microarrays which has played a major pivotal role in the rapid assessment of molecular biomarkers. Data acquired from grinding up bulk tissue samples miss spatial information regarding cellular localization; therefore, methods that allow for spatial cell phenotyping at high resolution have proven to be valuable in many biomarker discovery assays. Here, we focus our attention on breast cancer as an example of a tumor type that has benefited from quantitative biomarker studies using tissue microarray format.Areas covered: The history of immunofluorescence and immunohistochemistry and the current status of these techniques, including multiplexing technologies (spectral and non-spectral) and image analysis software will be addressed. Finally, we will turn our attention to studies that have provided proof-of-principle evidence that have been impacted from the use of these techniques.Expert opinion: Assessment of prognostic and predictive biomarkers on tissue sections and TMA using Quantitative immunohistochemistry is an important advancement in the investigation of biologic markers. The challenges in standardization of quantitative technologies for accurate assessment are required for adoption into routine clinical practice.
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Affiliation(s)
- Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lori Charette
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Malini Harigopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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21
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Lee Y, Kang BH, Kang M, Chung DR, Yi GS, Lee LP, Jeong KH. Nanoplasmonic On-Chip PCR for Rapid Precision Molecular Diagnostics. ACS APPLIED MATERIALS & INTERFACES 2020; 12:12533-12540. [PMID: 32101396 DOI: 10.1021/acsami.9b23591] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Emerging molecular diagnosis requires ultrafast polymerase chain reaction (PCR) on chip for rapid precise detection of infectious diseases in the point-of-care test. Here, we report nanoplasmonic on-chip PCR for rapid precision molecular diagnostics. The nanoplasmonic pillar arrays (NPA) comprise gold nanoislands on the top and sidewall of large-scale glass nanopillar arrays. The nanoplasmonic pillars enhance light absorption of a white light-emitting diode (LED) over the whole visible range due to strong electromagnetic hotspots between the nanoislands. As a result, they effectively induce photothermal heating for ultrafast PCR thermal cycling. The temperature profile of NPA exhibits 30 cycles between 98 and 60 °C for a total of 3 min and 30 s during the cyclic excitation of white LED light. The experimental results also demonstrate the rapid DNA amplification of both 0.1 ng μL-1 of λ-DNA in 20 thermal cycles and 0.1 ng μL-1 of complementary DNA of Middle East respiratory syndrome coronavirus in 30 thermal cycles using a conventional PCR volume of 15 μL. This nanoplasmonic PCR technique provides a new opportunity for rapid precision molecular diagnostics.
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Affiliation(s)
- Youngseop Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Byoung-Hoon Kang
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
- Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Disease, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
- Center for Infection Prevention and Control, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
- Asia Pacific Foundation for infectious Diseases (APFID), 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California 94720, United States
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California 94720, United States
- Biophysics Graduate Program, University of California, Berkeley, California 94720, United States
| | - Ki-Hun Jeong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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22
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Engelen W, Zhu K, Subedi N, Idili A, Ricci F, Tel J, Merkx M. Programmable Bivalent Peptide-DNA Locks for pH-Based Control of Antibody Activity. ACS CENTRAL SCIENCE 2020; 6:22-31. [PMID: 31989023 PMCID: PMC6978833 DOI: 10.1021/acscentsci.9b00964] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Indexed: 05/11/2023]
Abstract
The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide-DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from a tight-binding bivalent peptide-DNA lock into a weaker-binding monovalent ligand. Different designs are introduced that allow antibody activation at both basic and acidic pHs, either autonomously or in the presence of an additional oligonucleotide trigger. The pH of antibody activation could be precisely tuned by changing the DNA triple helix sequence. The peptide-DNA locks allowed pH-dependent antibody targeting of tumor cells both in bulk and for single cells confined in water-in-oil microdroplets. The latter approach enables high-throughput antibody-mediated detection of single tumor cells based on their distinctive metabolic activity.
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Affiliation(s)
- Wouter Engelen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Kwankwan Zhu
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Nikita Subedi
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Andrea Idili
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Jurjen Tel
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- E-mail:
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Xu YW, Chen H, Hong CQ, Chu LY, Yang SH, Huang LS, Guo H, Chen LY, Liu CT, Huang XY, Lin LH, Chen SL, Wu ZY, Peng YH, Xu LY, Li EM. Serum IGFBP-1 as a potential biomarker for diagnosis of early-stage upper gastrointestinal tumour. EBioMedicine 2020; 51:102566. [PMID: 31901863 PMCID: PMC6956950 DOI: 10.1016/j.ebiom.2019.11.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Early detection would improve upper gastrointestinal cancer prognosis. We aimed to identify serum protein biomarker for the detection of early-stage upper gastrointestinal cancer. METHODS We performed a three-tiered study including 2028 participants from three medical centres. First, we applied two different antibody arrays to screen candidate serum proteins that increased in 20 patients with oesophageal squamous cell carcinoma (ESCC) compared with 20 normal controls. We then evaluated the selected protein by enzyme-linked immunosorbent assay in 1064 participants including 731 upper gastrointestinal cancer patients (287 ESCCs, 237 oesophagogastric junction adenocarcinomas (EJAs), and 207 stomach cancers) and 333 normal controls. The diagnostic value of the selected protein was finally validated in two independent cohorts of ESCC patients and controls (n=472 and 452, respectively). The receiver operating characteristic was used to calculate diagnostic accuracy. FINDINGS Serum insulin-like growth factor binding protein-1 (IGFBP-1) identified in both antibody arrays showed significantly elevated levels in upper gastrointestinal cancers, compared with normal controls. Serum IGFBP-1 provided high diagnostic accuracy of early-stage ESCC, EJA, stomach and cancer (areas under the curve: 0·898, 0·936 and 0·864, respectively). This protein maintained diagnostic performance for early-stage ESCC in independent cohorts 1 and 2 (0·849 and 0·911, respectively). Additionally, serum levels of IGFBP-1 dropped significantly after surgical resection of primary tumours, compared with the corresponding pre-operative ESCC samples (p < 0·05). INTERPRETATION Serum IGFBP-1 represents a promising diagnostic biomarker to detect early-stage upper gastrointestinal cancer.
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Affiliation(s)
- Yi-Wei Xu
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou, China; Precision Medicine Research Centre, Shantou University Medical College, Shantou, China; Guangdong Oesophageal Cancer Research Institute, Shantou University Medical College, Shantou, China
| | - Hao Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Chao-Qun Hong
- Department of Oncological Laboratory Research, The Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Ling-Yu Chu
- Precision Medicine Research Centre, Shantou University Medical College, Shantou, China
| | - Shi-Han Yang
- Department of Dermatology and Venereology, Shantou Central Hospital, Shantou, China
| | - Li-Sheng Huang
- Department of Radiation Oncology, The Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Hong Guo
- Department of Radiation Oncology, The Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Liu-Yi Chen
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Can-Tong Liu
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou, China; Precision Medicine Research Centre, Shantou University Medical College, Shantou, China
| | - Xin-Yi Huang
- Precision Medicine Research Centre, Shantou University Medical College, Shantou, China
| | - Lie-Hao Lin
- Department of surgery, Shantou Nan'ao People's Hospital, Shantou, China
| | - Shu-Lin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Zhi-Yong Wu
- Department of Surgical Oncology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China.
| | - Yu-Hui Peng
- Department of Clinical Laboratory Medicine, the Cancer Hospital of Shantou University Medical College, Shantou, China; Precision Medicine Research Centre, Shantou University Medical College, Shantou, China; Guangdong Oesophageal Cancer Research Institute, Shantou University Medical College, Shantou, China.
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, China.
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China.
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24
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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25
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Method Validation by CPTAC Guidelines for Multi-protein Marker Assays Using Multiple Reaction Monitoring-mass Spectrometry. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Chakkarapani SK, Lee S, Park B, Seo HY, Kang SH. Plasmon-Amplified Endogenous Fluorescence Nanospectroscopic Sensor Based on Inherent Elastic Scattering for Ultratrace Ratiometric Detection of Capsaicinoids. ACS Sens 2019; 4:953-960. [PMID: 30844242 DOI: 10.1021/acssensors.9b00058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Endogenous fluorescence imaging techniques are key for modern single-molecule quantification without the use of additional labeling probes. However, the drawback of weak fluorescence signal is the primary challenge in meeting the ever-increasing demands of single-molecule detection. Here, we report a simple and reliable method that provides up to ∼100-fold uniform fluorescence enhancement of endogenous fluorescence of the capsaicinoid molecule. The method is based on a single nanoparticle plasmon-amplified endogenous fluorescence nanospectroscopic sensor (PAEFS). This work demonstrated the applicability of PAEFS in refining sensitivity at the single-molecule level by showing ultralow limits of detection (106 times lower than previous reports) of fluorescence-based capsaicinoids with a wide range of linear response (18 zM to 85 pM). Spectrally overlapped capsaicinoid analogues were quantified ratiometrically to detect the analogue percentages in real samples. The novel endogenous fluorescence enhancement approach presented here represents a universal sensor for enhanced detection of single molecules using existing techniques without altering the original molecular features or using add-on labeling probes.
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Affiliation(s)
- Suresh Kumar Chakkarapani
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Boyeon Park
- World Institute of Kimchi, Kimchiro 86, Namgu, Gwangju 61755, Republic of Korea
| | - Hye-Young Seo
- World Institute of Kimchi, Kimchiro 86, Namgu, Gwangju 61755, Republic of Korea
| | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
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27
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Rafea M, Elkafrawy P, Nasef MM, Elnemr R, Jamal AT. Applying Machine Learning of Erythrocytes Dynamic Antigens Store in Medicine. Front Mol Biosci 2019; 6:19. [PMID: 31001536 PMCID: PMC6456707 DOI: 10.3389/fmolb.2019.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Erythrocytes Dynamic Antigens Store (EDAS) is a new discovery. EDAS consists of self-antigens and foreign (non-self) antigens. In patients with infectious diseases or malignancies, antigens of infection microorganism or malignant tumor exist in EDAS. Storing EDAS of normal individuals and patients in a database has, at least, two benefits. First, EDAS can be mined to determine biomarkers representing diseases which can enable researchers to develop a new line of laboratory diagnostic tests and vaccines. Second, EDAS can be queried, directly, to reach a precise diagnosis without the need to do many laboratory tests. The target is to find the minimum set of proteins that can be used as biomarkers for a particular disease. A hypothetical EDAS is created. Hundred-thousand records are randomly generated. The mathematical model of hypothetical EDAS together with the proposed techniques for biomarker discovery and direct diagnosis are described. The different possibilities that may occur in reality are experimented. Biomarkers' proteins are identified for pathogens and malignancies, which can be used to diagnose conditions that are difficult to diagnose. The presented tool can be used in clinical laboratories to diagnose disease disorders.
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Affiliation(s)
- Mahmoud Rafea
- Central Lab of Agriculture Expert Systems, Giza, Egypt
| | - Passant Elkafrawy
- Mathematics and Computer Science Department, Faculty of Science, Menoufia University, Shibin El Kom, Egypt
| | - Mohammed M Nasef
- Mathematics and Computer Science Department, Faculty of Science, Menoufia University, Shibin El Kom, Egypt
| | - Rasha Elnemr
- Central Lab of Agriculture Expert Systems, Giza, Egypt
| | - Amani Tariq Jamal
- Computer Science Department, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
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28
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29
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Lin Y, Jia J, Yang R, Chen D, Wang J, Luo F, Guo L, Qiu B, Lin Z. Ratiometric Immunosensor for GP73 Detection Based on the Ratios of Electrochemiluminescence and Electrochemical Signal Using DNA Tetrahedral Nanostructure as the Carrier of Stable Reference Signal. Anal Chem 2019; 91:3717-3724. [DOI: 10.1021/acs.analchem.9b00013] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yue Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jinpeng Jia
- Department of Orthopaedics, General Hospital of Chinese People’s Liberation Army, 28 Fuxing Road, Beijing 100853, China
| | - Rui Yang
- Central Laboratory, The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Road 48, Huaishu Street, Wuxi, Jiangshu 214002, China
| | - Daozhen Chen
- Central Laboratory, The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Road 48, Huaishu Street, Wuxi, Jiangshu 214002, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Longhua Guo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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Liang J, Cui Y, Meng Y, Li X, Wang X, Liu W, Huang L, Du H. Integrated analysis of transcription factors and targets co-expression profiles reveals reduced correlation between transcription factors and target genes in cancer. Funct Integr Genomics 2018; 19:191-204. [PMID: 30251028 DOI: 10.1007/s10142-018-0636-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]
Abstract
Transcription factors are recognized as the key regulators of gene expression. However, the changes in the correlation of transcription factors and their target genes between normal and tumor tissues are usually ignored. In this research, we used mRNA expression profile data from The Cancer Genome Atlas which included 5726 samples across 11 major human cancers to perform co-expression analysis by the Pearson correlation coefficients. Then, integrating 81,357 pairs of transcription factors and target genes from transcription factors databases to find out the changes in the co-expression correlation of these gene pairs from normal to tumor tissues. Based on the changes in the number of co-expressed TF-TG pairs and changes in the level of co-expression, we found the generally reduced correlation between transcription factors and their target genes in cancer. Additionally, we screened out universal and specific transcription factors-target genes pairs which may significant influence particular cancer. Then, we obtained 423 cancer cell line expression profiles from Broad Institute Cancer Cell Line Encyclopedia to verify our results. Some of these pairs like XRCC5-XRCC6 have been reported to involve in multiple cancers, while pairs like IRF1-PSMB9 without any previous articles related to tumor but involve in the biological processes of cancer, which are of great potential to be therapeutic targets. Our research may provide insights to better understand the tumor development mechanisms and find potential therapeutic targets.
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Affiliation(s)
- Jinsheng Liang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Ying Cui
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Yuhuan Meng
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xingsong Li
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanli Liu
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China.
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31
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Luan J, Morrissey JJ, Wang Z, Derami HG, Liu KK, Cao S, Jiang Q, Wang C, Kharasch ED, Naik RR, Singamaneni S. Add-on plasmonic patch as a universal fluorescence enhancer. LIGHT, SCIENCE & APPLICATIONS 2018; 7:29. [PMID: 30839611 PMCID: PMC6107004 DOI: 10.1038/s41377-018-0027-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/09/2018] [Accepted: 04/25/2018] [Indexed: 05/13/2023]
Abstract
Fluorescence-based techniques are the cornerstone of modern biomedical optics, with applications ranging from bioimaging at various scales (organelle to organism) to detection and quantification of a wide variety of biological species of interest. However, the weakness of the fluorescence signal remains a persistent challenge in meeting the ever-increasing demand to image, detect, and quantify biological species with low abundance. Here, we report a simple and universal method based on a flexible and conformal elastomeric film with adsorbed plasmonic nanostructures, which we term a "plasmonic patch," that provides large (up to 100-fold) and uniform fluorescence enhancement on a variety of surfaces through simple transfer of the plasmonic patch to the surface. We demonstrate the applications of the plasmonic patch in improving the sensitivity and limit of detection (by more than 100 times) of fluorescence-based immunoassays implemented in microtiter plates and in microarray format. The novel fluorescence enhancement approach presented here represents a disease, biomarker, and application agnostic ubiquitously applicable fundamental and enabling technology to immediately improve the sensitivity of existing analytical methodologies in an easy-to-handle and cost-effective manner, without changing the original procedures of the existing techniques.
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Affiliation(s)
- Jingyi Luan
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Zheyu Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Hamed Gholami Derami
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Keng-Ku Liu
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Sisi Cao
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Qisheng Jiang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Congzhou Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
| | - Evan D. Kharasch
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110 USA
- The Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine, St. Louis, MO USA
| | - Rajesh R. Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433 USA
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO 63130 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
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32
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In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation. Mod Pathol 2018; 31:253-263. [PMID: 28937142 DOI: 10.1038/modpathol.2017.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 02/07/2023]
Abstract
Antibodies are important tools in anatomical pathology and research, but the quality of in situ protein detection by immunohistochemistry greatly depends on the choice of antibodies and the abundance of the targeted proteins. Many antibodies used in scientific research do not meet requirements for specificity and sensitivity. Accordingly, methods that improve antibody performance and produce quantitative data can greatly advance both scientific investigations and clinical diagnostics based on protein expression and in situ localization. We demonstrate here protocols for antibody labeling that allow specific protein detection in tissues via bright-field in situ proximity ligation assays, where each protein molecule must be recognized by two antibodies. We further demonstrate that single polyclonal antibodies or purified serum preparations can be used for these dual recognition assays. The requirement for protein recognition by pairs of antibody conjugates can significantly improve specificity of protein detection over single-binder assays.
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33
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Mulrane L, Gallagher WM, O'Connor DP. Assessment of Significance of Novel Proteins in Breast Cancer Using Tissue Microarray Technology. Methods Mol Biol 2018; 1501:311-325. [PMID: 27796961 DOI: 10.1007/978-1-4939-6475-8_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The arraying of formalin-fixed paraffin-embedded (FFPE) tissue, or less commonly frozen tissue, in tissue microarrays (TMAs) is an invaluable method with which to assess the association of novel proteins with a myriad of diseases in large cohorts of patients allowing high throughput evaluation as potential biomarkers. TMAs are most frequently used in cancer studies although they are not limited to this application. The most common method of evaluation of TMAs is via immunohistochemistry (IHC) which is an antibody-based protein localisation method routinely used in the clinical laboratory. However, significant issues still exist with respect to the validation of antibodies for use on TMA sections, with a large number of published studies failing to do so correctly [O'Hurley et al. Mol Oncol, doi:10.1016/j.molonc.2014.03.008, 2014]. Here, we present a method to determine the antibody specificity for use in immunohistochemistry (IHC), as well as the analysis and interpretation of results from an IHC-stained TMA.
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Affiliation(s)
- Laoighse Mulrane
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Darran P O'Connor
- RCSI Molecular & Cellular Therapeutics (MCT), Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland.
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34
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Pinto G, Radulovic M, Godovac-Zimmermann J. Spatial perspectives in the redox code-Mass spectrometric proteomics studies of moonlighting proteins. MASS SPECTROMETRY REVIEWS 2018; 37:81-100. [PMID: 27186965 DOI: 10.1002/mas.21508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
The Redox Code involves specific, reversible oxidative changes in proteins that modulate protein tertiary structure, interactions, trafficking, and activity, and hence couple the proteome to the metabolic/oxidative state of cells. It is currently a major focus of study in cell biology. Recent studies of dynamic cellular spatial reorganization with MS-based subcellular-spatial-razor proteomics reveal that protein constituents of many subcellular structures, including mitochondria, the endoplasmic reticulum, the plasma membrane, and the extracellular matrix, undergo changes in their subcellular abundance/distribution in response to oxidative stress. These proteins are components of a diverse variety of functional processes spatially distributed across cells. Many of the same proteins are involved in response to suppression of DNA replication indicate that oxidative stress is strongly intertwined with DNA replication/proliferation. Both are replete with networks of moonlighting proteins that show coordinated changes in subcellular location and that include primary protein actuators of the redox code involved in the processing of NAD+ /NADH, NADP+ /NADPH, Cys/CySS, and GSH/GSSG redox couples. Small groups of key proteins such as {KPNA2, KPNB1, PCNA, PTMA, SET} constitute "spatial switches" that modulate many nuclear processes. Much of the functional response involves subcellular protein trafficking, including nuclear import/export processes, vesicle-mediated trafficking, the endoplasmic reticulum/Golgi pathway, chaperone-assisted processes, and other transport systems. This is not visible to measurements of total protein abundance by transcriptomics or proteomics. Comprehensive pictures of cellular function will require collection of data on the subcellular transport and local functions of many moonlighting proteins, especially of those with critical roles in spatial coordination across cells. The proteome-wide analysis of coordinated changes in abundance and trafficking of proteins offered by MS-based proteomics has a unique, crucial role to play in deciphering the complex adaptive systems that underlie cellular function. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Gabriella Pinto
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
| | - Marko Radulovic
- Insitute of Oncology and Radiology, Pasterova 14, Belgrade, 11000, Serbia
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, Center for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London, NW3 2PF, United Kingdom
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Peng L, Cantor DI, Huang C, Wang K, Baker MS, Nice EC. Tissue and plasma proteomics for early stage cancer detection. Mol Omics 2018; 14:405-423. [PMID: 30251724 DOI: 10.1039/c8mo00126j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pursuit of novel and effective biomarkers is essential in the struggle against cancer, which is a leading cause of mortality worldwide. Here we discuss the relative advantages and disadvantages of the most frequently used proteomics techniques, concentrating on the latest advances and application of tissue and plasma proteomics for novel cancer biomarker discovery.
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Affiliation(s)
- Liyuan Peng
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - David I. Cantor
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Macquarie University
- New South Wales
- Australia
| | - Canhua Huang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Kui Wang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University
- Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
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36
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Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson P, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F. A pathology atlas of the human cancer transcriptome. Science 2017; 357:357/6352/eaan2507. [PMID: 28818916 DOI: 10.1126/science.aan2507] [Citation(s) in RCA: 2127] [Impact Index Per Article: 303.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/02/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022]
Abstract
Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. .,Center for Biosustainability, Danish Technical University, Copenhagen, Denmark.,School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sunjae Lee
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Gholamreza Bidkhori
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Rui Benfeitas
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Zhengtao Liu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kemal Sanli
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Bengt Glimelius
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Ponten
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Oxidative Stress in Kidney Diseases: The Cause or the Consequence? Arch Immunol Ther Exp (Warsz) 2017; 66:211-220. [PMID: 29214330 PMCID: PMC5956016 DOI: 10.1007/s00005-017-0496-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022]
Abstract
Exaggerated oxidative stress (OS) is usually considered as a disturbance in regular function of an organism. The excessive levels of OS mediators may lead to major damage within the organism’s cells and tissues. Therefore, the OS-associated biomarkers may be considered as new diagnostic tools of various diseases. In nephrology, researchers are looking for alternative methods replacing the renal biopsy in patients with suspicion of chronic kidney disease (CKD). Currently, CKD is a frequent health problem in world population, which can lead to progressive loss of kidney function and eventually to end-stage renal disease. The course of CKD depends on the primary disease. It is assumed that one of the factors influencing the course of CKD might be OS. In the current work, we review whether monitoring the OS-associated biomarkers in nephrology patients can support the decision-making process regarding diagnosis, prognostication and treatment initiation.
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Kitayama Y, Yoshikawa K, Takeuchi T. Post-Cross-Linked Molecular Imprinting with Functional Polymers as a Universal Building Block for Artificial Polymeric Receptors. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yukiya Kitayama
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuki Yoshikawa
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Toshifumi Takeuchi
- Graduate School of Engineering, Kobe University, 1-1
Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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39
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Optomechanical devices for deep plasma cancer proteomics. Semin Cancer Biol 2017; 52:26-38. [PMID: 28867489 DOI: 10.1016/j.semcancer.2017.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/22/2017] [Accepted: 08/30/2017] [Indexed: 12/27/2022]
Abstract
Most of the cancer deaths could be avoided by early detection of the tumor when it is confined to its primary site and it has not metastasized. To this aim, one of the most promising strategies is the discovery and detection of protein biomarkers shed by the young tumor to the bloodstream. Proteomic technologies, mainly mass spectrometry and multiplexed immunoassays, have rapidly developed during last years with improved limits of detection and multiplexing capability. Unfortunately, these developments together major investments and large international efforts have not resulted into new useful protein biomarkers. Here, we analyze the potential and limitations of current proteomic technologies for detecting protein biomarkers released into circulation by the tumor. We find that these technologies can hardly probe the deepest region of the plasma proteome, at concentrations below the pg/mL level, where protein biomarkers for early cancer detection may exist. This clearly indicates the need of incorporating novel ultrasensitive techniques to the proteomic tool-box that can cover the inaccessible regions of the plasma proteome. We here propose biological detectors based on nanomechanical systems for discovery and detection of cancer protein biomarkers in plasma. We review the modes of operation of these devices, putting our focus on recent developments on nanomechanical sandwich immunoassays and nanomechanical spectrometry. The first technique enables reproducible immunodetection of proteins at concentrations well below the pg/mL level, with a limit of detection on the verge of 10 ag/mL. This technology can potentially detect low abundance tumor-associated proteins in plasma at the very early stages of the tumor. The second technique enables the identification of individual intact proteins by two physical coordinates, the mass and stiffness, instead of the mass-to-charge ratio of the protein constituents. This technology enormously simplifies the identification of proteins and it can provide useful information on interactions and posttranslational modifications, that otherwise is lost in mass spectrometry.
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40
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Kim H, Yu SJ, Yeo I, Cho YY, Lee DH, Cho Y, Cho EJ, Lee JH, Kim YJ, Lee S, Jun J, Park T, Yoon JH, Kim Y. Prediction of Response to Sorafenib in Hepatocellular Carcinoma: A Putative Marker Panel by Multiple Reaction Monitoring-Mass Spectrometry (MRM-MS). Mol Cell Proteomics 2017; 16:1312-1323. [PMID: 28550167 DOI: 10.1074/mcp.m116.066704] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/10/2017] [Indexed: 12/11/2022] Open
Abstract
Sorafenib is the only standard treatment for unresectable hepatocellular carcinoma (HCC), but it provides modest survival benefits over placebo, necessitating predictive biomarkers of the response to sorafenib. Serum samples were obtained from 115 consecutive patients with HCC before sorafenib treatment and analyzed by multiple reaction monitoring-mass spectrometry (MRM-MS) and ELISA to quantify candidate biomarkers. We verified a triple-marker panel to be predictive of the response to sorafenib by MRM-MS, comprising CD5 antigen-like (CD5L), immunoglobulin J (IGJ), and galectin-3-binding protein (LGALS3BP), in HCC patients. This panel was a significant predictor (AUROC > 0.950) of the response to sorafenib treatment, having the best cut-off value (0.4) by multivariate analysis. In the training set, patients who exceeded this cut-off value had significantly better overall survival (median, 21.4 months) than those with lower values (median, 8.6 months; p = 0.001). Further, a value that was lower than this cutoff was an independent predictor of poor overall survival [hazard ratio (HR), 2.728; 95% confidence interval (CI), 1.312-5.672; p = 0.007] and remained an independent predictive factor of rapid progression (HR, 2.631; 95% CI, 1.448-4.780; p = 0.002). When applied to the independent validation set, levels of the cut-off value for triple-marker panel maintained their prognostic value for poor clinical outcomes. On the contrast, the triple-marker panel was not a prognostic factor for patients who were treated with transarterial chemoembolization (TACE). The discriminatory signature of a triple-marker panel provides new insights into targeted proteomic biomarkers for individualized sorafenib therapy.
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Affiliation(s)
- Hyunsoo Kim
- From the ‡Department of Biomedical Engineering.,§Institute of Medical and Biological Engineering, Medical Research Center, and
| | - Su Jong Yu
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Injun Yeo
- From the ‡Department of Biomedical Engineering
| | - Young Youn Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Dong Hyeon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yuri Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Eun Ju Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Jeong-Hoon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yoon Jun Kim
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | | | - Jongsoo Jun
- **Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Taesung Park
- ‖Interdisciplinary program in Bioinformatics and.,**Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Jung-Hwan Yoon
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea;
| | - Youngsoo Kim
- From the ‡Department of Biomedical Engineering; .,§Institute of Medical and Biological Engineering, Medical Research Center, and
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41
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Borrebaeck CAK. Precision diagnostics: moving towards protein biomarker signatures of clinical utility in cancer. Nat Rev Cancer 2017; 17:199-204. [PMID: 28154374 DOI: 10.1038/nrc.2016.153] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Interest in precision diagnostics has been fuelled by the concept that early detection of cancer would benefit patients; that is, if detected early, more tumours should be resectable and treatment more efficacious. Serum contains massive amounts of potentially diagnostic information, and affinity proteomics has risen as an accurate approach to decipher this, to generate actionable information that should result in more precise and evidence-based options to manage cancer. To achieve this, we need to move from single to multiplex biomarkers, a so-called signature, that can provide significantly increased diagnostic accuracy. This Opinion article focuses on the progress being made in identifying protein biomarker signatures of clinical utility, using blood-based proteomics.
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Affiliation(s)
- Carl A K Borrebaeck
- Department of Immunotechnology, CREATE Health Translational Cancer Center, Medicon Village (Bldg 406), Lund University, 223 81 Lund, Sweden
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42
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Salvucci M, Würstle ML, Morgan C, Curry S, Cremona M, Lindner AU, Bacon O, Resler AJ, Murphy ÁC, O'Byrne R, Flanagan L, Dasgupta S, Rice N, Pilati C, Zink E, Schöller LM, Toomey S, Lawler M, Johnston PG, Wilson R, Camilleri-Broët S, Salto-Tellez M, McNamara DA, Kay EW, Laurent-Puig P, Van Schaeybroeck S, Hennessy BT, Longley DB, Rehm M, Prehn JHM. A Stepwise Integrated Approach to Personalized Risk Predictions in Stage III Colorectal Cancer. Clin Cancer Res 2017; 23:1200-1212. [PMID: 27649552 DOI: 10.1158/1078-0432.ccr-16-1084] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/02/2016] [Accepted: 08/15/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Apoptosis is essential for chemotherapy responses. In this discovery and validation study, we evaluated the suitability of a mathematical model of apoptosis execution (APOPTO-CELL) as a stand-alone signature and as a constituent of further refined prognostic stratification tools.Experimental Design: Apoptosis competency of primary tumor samples from patients with stage III colorectal cancer (n = 120) was calculated by APOPTO-CELL from measured protein concentrations of Procaspase-3, Procaspase-9, SMAC, and XIAP. An enriched APOPTO-CELL signature (APOPTO-CELL-PC3) was synthesized to capture apoptosome-independent effects of Caspase-3. Furthermore, a machine learning Random Forest approach was applied to APOPTO-CELL-PC3 and available molecular and clinicopathologic data to identify a further enhanced signature. Association of the signature with prognosis was evaluated in an independent colon adenocarcinoma cohort (TCGA COAD, n = 136).Results: We identified 3 prognostic biomarkers (P = 0.04, P = 0.006, and P = 0.0004 for APOPTO-CELL, APOPTO-CELL-PC3, and Random Forest signatures, respectively) with increasing stratification accuracy for patients with stage III colorectal cancer.The APOPTO-CELL-PC3 signature ranked highest among all features. The prognostic value of the signatures was independently validated in stage III TCGA COAD patients (P = 0.01, P = 0.04, and P = 0.02 for APOPTO-CELL, APOPTO-CELL-PC3, and Random Forest signatures, respectively). The signatures provided further stratification for patients with CMS1-3 molecular subtype.Conclusions: The integration of a systems-biology-based biomarker for apoptosis competency with machine learning approaches is an appealing and innovative strategy toward refined patient stratification. The prognostic value of apoptosis competency is independent of other available clinicopathologic and molecular factors, with tangible potential of being introduced in the clinical management of patients with stage III colorectal cancer. Clin Cancer Res; 23(5); 1200-12. ©2016 AACR.
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Affiliation(s)
- Manuela Salvucci
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maximilian L Würstle
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Clare Morgan
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medical Oncology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sarah Curry
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Mattia Cremona
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medical Oncology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas U Lindner
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Orna Bacon
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Alexa J Resler
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Áine C Murphy
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Robert O'Byrne
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lorna Flanagan
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sonali Dasgupta
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Nadege Rice
- Faculté de Médecine, Université Paris Descartes, Paris, France
| | - Camilla Pilati
- INSERM UMR-S1147, Personalized Medicine, Pharmacogenomics, Therapeutic Optimization, Université Paris Descartes, Paris, France
| | - Elisabeth Zink
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lisa M Schöller
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinead Toomey
- Department of Medical Oncology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Patrick G Johnston
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Richard Wilson
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | | | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elaine W Kay
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Pierre Laurent-Puig
- INSERM UMR-S1147, Personalized Medicine, Pharmacogenomics, Therapeutic Optimization, Université Paris Descartes, Paris, France
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Bryan T Hennessy
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medical Oncology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Markus Rehm
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | - Jochen H M Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics. Sci Rep 2017; 7:41929. [PMID: 28167817 PMCID: PMC5294601 DOI: 10.1038/srep41929] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/05/2017] [Indexed: 01/25/2023] Open
Abstract
The human blood proteome is frequently assessed by protein abundance profiling using a combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS). In traditional sequence database search, many good-quality MS/MS data remain unassigned. Here we uncover the hidden part of the blood proteome via novel SpotLight approach. This method combines de novo MS/MS sequencing of enriched antibodies and co-extracted proteins with subsequent label-free quantification of new and known peptides in both enriched and unfractionated samples. In a pilot study on differentiating early stages of Alzheimer’s disease (AD) from Dementia with Lewy Bodies (DLB), on peptide level the hidden proteome contributed almost as much information to patient stratification as the apparent proteome. Intriguingly, many of the new peptide sequences are attributable to antibody variable regions, and are potentially indicative of disease etiology. When the hidden and apparent proteomes are combined, the accuracy of differentiating AD (n = 97) and DLB (n = 47) increased from ≈85% to ≈95%. The low added burden of SpotLight proteome analysis makes it attractive for use in clinical settings.
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44
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Tagit O, Hildebrandt N. Fluorescence Sensing of Circulating Diagnostic Biomarkers Using Molecular Probes and Nanoparticles. ACS Sens 2017; 2:31-45. [PMID: 28722447 DOI: 10.1021/acssensors.6b00625] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interplay of photonics, nanotechnology, and biochemistry has significantly improved the identification and characterization of multiple types of biomarkers by optical biosensors. Great achievements in fluorescence-based technologies have been realized, for example, by the advancement of multiplexing techniques or the introduction of nanoparticles to biochemical and clinical research. This review presents a concise overview of recent advances in fluorescence sensing techniques for the detection of circulating disease biomarkers. Detection principles of representative approaches, including fluorescence detection using molecular fluorophores, quantum dots, and metallic and silica nanoparticles, are explained and illustrated by pertinent examples from the recent literature. Advanced detection technologies and material development play a major role in modern biosensing and consistently provide significant improvements toward robust, sensitive, and versatile platforms for early detection of circulating diagnostic biomarkers.
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Affiliation(s)
- Oya Tagit
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
- Department
of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Niko Hildebrandt
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
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45
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A universal multicolor immunosensor for semiquantitative visual detection of biomarkers with the naked eyes. Biosens Bioelectron 2017; 87:122-128. [DOI: 10.1016/j.bios.2016.08.021] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/07/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023]
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46
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Magnusson K, Gremel G, Rydén L, Pontén V, Uhlén M, Dimberg A, Jirström K, Pontén F. ANLN is a prognostic biomarker independent of Ki-67 and essential for cell cycle progression in primary breast cancer. BMC Cancer 2016; 16:904. [PMID: 27863473 PMCID: PMC5116155 DOI: 10.1186/s12885-016-2923-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/02/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Anillin (ANLN), an actin-binding protein required for cytokinesis, has recently been presented as part of a prognostic marker panel in breast cancer. The objective of the current study was to further explore the prognostic and functional value of ANLN as a single biomarker in breast cancer. METHODS Immunohistochemical assessment of ANLN protein expression was performed in two well characterized breast cancer cohorts (n = 484) with long-term clinical follow-up data and the results were further validated at the mRNA level in a publicly available transcriptomics dataset. The functional relevance of ANLN was investigated in two breast cancer cell lines using RNA interference. RESULTS High nuclear fraction of ANLN in breast tumor cells was significantly associated with large tumor size, high histological grade, high proliferation rate, hormone receptor negative tumors and poor prognosis in both examined cohorts. Multivariable analysis showed that the association between ANLN and survival was significantly independent of age in cohort I and significantly independent of proliferation, as assessed by Ki-67 expression in tumor cells, age, tumor size, ER and PR status, HER2 status and nodal status in cohort II. Analysis of ANLN mRNA expression confirmed that high expression of ANLN was significantly correlated to poor overall survival in breast cancer patients. Consistent with the role of ANLN during cytokinesis, transient knock-down of ANLN protein expression in breast cancer cell lines resulted in an increase of senescent cells and an accumulation of cells in the G2/M phase of the cell cycle with altered cell morphology including large, poly-nucleated cells. Moreover, ANLN siRNA knockdown also resulted in decreased expression of cyclins D1, A2 and B1. CONCLUSIONS ANLN expression in breast cancer cells plays an important role during cell division and a high fraction of nuclear ANLN expression in tumor cells is correlated to poor prognosis in breast cancer patients, independent of Ki-67, tumor size, hormone receptor status, HER2 status, nodal status and age.
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Affiliation(s)
- Kristina Magnusson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriela Gremel
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lisa Rydén
- Department of Clinical Sciences, Division of Surgery, Lund University, Lund, Sweden
| | - Victor Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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47
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Magalhães P, Schanstra JP, Carrick E, Mischak H, Zürbig P. Urinary biomarkers for renal tract malformations. Expert Rev Proteomics 2016; 13:1121-1129. [PMID: 27791437 DOI: 10.1080/14789450.2016.1254555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications. Areas covered: In this review, we summarized relevant studies identified in "Pubmed" using the keywords "urinary biomarkers" and "proteomics" and "renal tract malformations" or "hydronephrosis" or "ureteropelvic junction obstruction" or "posterior urethral valves" or "vesicoureteral reflux". These publications represent studies on potential protein-based biomarkers, either individually or combined in panels, of RTMs in human and animal models. Expert commentary: Successful use in the clinic of these protein-based biomarkers will need to involve larger scale studies to reach sufficient power. Improved performance will potentially come from combining immunoassay- and MS-based markers.
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Affiliation(s)
- Pedro Magalhães
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,b Department of Pediatric Nephrology, Hannover Medical School , Hannover , Germany
| | - Joost P Schanstra
- c Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease , Toulouse , France.,d Université Toulouse III Paul-Sabatier , Toulouse , France
| | - Emma Carrick
- e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Harald Mischak
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Petra Zürbig
- a Mosaiques Diagnostics GmbH , Hannover , Germany
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Oh S, Kim HS. Emerging power of proteomics for delineation of intrinsic tumor subtypes and resistance mechanisms to anti-cancer therapies. Expert Rev Proteomics 2016; 13:929-939. [PMID: 27599289 DOI: 10.1080/14789450.2016.1233063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Despite extreme genetic heterogeneity, tumors often show similar alterations in the expression, stability, and activation of proteins important in oncogenic signaling pathways. Thus, classifying tumor samples according to shared proteomic features may help facilitate the identification of cancer subtypes predictive of therapeutic responses and prognostic for patient outcomes. Meanwhile, understanding mechanisms of intrinsic and acquired resistance to anti-cancer therapies at the protein level may prove crucial to devising reversal strategies. Areas covered: Herein, we review recent advances in quantitative proteomic technology and their applications in studies to identify intrinsic tumor subtypes of various tumors, to illuminate mechanistic aspects of pharmacological and oncogenic adaptations, and to highlight interaction targets for anti-cancer compounds and cancer-addicted proteins. Expert commentary: Quantitative proteomic technologies are being successfully employed to classify tumor samples into distinct intrinsic subtypes, to improve existing DNA/RNA based classification methods, and to evaluate the activation status of key signaling pathways.
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Affiliation(s)
- Sejin Oh
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
| | - Hyun Seok Kim
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
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Yu KH, Snyder M. Omics Profiling in Precision Oncology. Mol Cell Proteomics 2016; 15:2525-36. [PMID: 27099341 PMCID: PMC4974334 DOI: 10.1074/mcp.o116.059253] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/15/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer causes significant morbidity and mortality worldwide, and is the area most targeted in precision medicine. Recent development of high-throughput methods enables detailed omics analysis of the molecular mechanisms underpinning tumor biology. These studies have identified clinically actionable mutations, gene and protein expression patterns associated with prognosis, and provided further insights into the molecular mechanisms indicative of cancer biology and new therapeutics strategies such as immunotherapy. In this review, we summarize the techniques used for tumor omics analysis, recapitulate the key findings in cancer omics studies, and point to areas requiring further research on precision oncology.
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Affiliation(s)
- Kun-Hsing Yu
- From the ‡Department of Genetics, Stanford University School of Medicine, Stanford, California; §Biomedical Informatics Program, Stanford University School of Medicine, Stanford, California
| | - Michael Snyder
- From the ‡Department of Genetics, Stanford University School of Medicine, Stanford, California;
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Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays. MICROARRAYS 2016; 5:microarrays5030019. [PMID: 27600085 PMCID: PMC5040966 DOI: 10.3390/microarrays5030019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 12/26/2022]
Abstract
In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much fewer molecules than the numbers usually identified in studies comparing tumor to healthy control tissues. Insulin-like growth factor-binding protein 7 (IGFBP7), S100 calcium binding protein A9 (S100A9), interleukin-10 (IL‐10) and mucin 6 (MUC6) exhibited the most profound variations. For an evaluation of the proteins’ capacity for discriminating gastric cancer, a Receiver Operating Characteristic curve analysis was performed, yielding an accuracy (area under the curve) value of 89.2% for distinguishing tumor from non-tumorous tissue. For confirmation, immunohistological analyses were done on tissue slices prepared from another cohort of patients with gastric cancer. The utility of the 17 marker proteins, and particularly the four molecules with the highest specificity for gastric adenocarcinoma, is discussed for them to act as candidates for diagnosis, even in serum, and targets for therapeutic approaches.
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