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Zhong Z, Sun MM, He M, Huang HP, Hu GY, Ma SQ, Zheng HZ, Li MY, Yao L, Cong DY, Wang HF. Proteomics and its application in the research of acupuncture: An updated review. Heliyon 2024; 10:e33233. [PMID: 39022010 PMCID: PMC11253069 DOI: 10.1016/j.heliyon.2024.e33233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
As a complementary and alternative therapy, acupuncture is widely used in the prevention and treatment of various diseases. However, the understanding of the mechanism of acupuncture effects is still limited due to the lack of systematic biological validation. Notably, proteomics technologies in the field of acupuncture are rapidly evolving, and these advances are greatly contributing to the research of acupuncture. In this study, we review the progress of proteomics research in analyzing the molecular mechanisms of acupuncture for neurological disorders, pain, circulatory disorders, digestive disorders, and other diseases, with an in-depth discussion around acupoint prescription and acupuncture manipulation modalities. The study found that proteomics has great potential in understanding the mechanisms of acupuncture. This study will help explore the mechanisms of acupuncture from a proteomic perspective and provide information to support future clinical decisions.
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Affiliation(s)
- Zhen Zhong
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Meng Sun
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Min He
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Peng Huang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Guan-Yu Hu
- The Third Affiliated Hospital of Southern Medical University, No.183, West of Zhongshan Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, China
| | - Shi-Qi Ma
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Zhu Zheng
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Yuan Li
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Lin Yao
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - De-Yu Cong
- Department of Tuina, Traditional Chinese Medicine Hospital of Jilin Province, 130000, Changchun, China
| | - Hong-Feng Wang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
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Martín-García D, García-Aranda M, Redondo M. Biomarker Identification through Proteomics in Colorectal Cancer. Int J Mol Sci 2024; 25:2283. [PMID: 38396959 PMCID: PMC10888664 DOI: 10.3390/ijms25042283] [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: 01/26/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Colorectal cancer (CRC) is a devastating disease that ranks third in diagnosis and as the second leading cause of cancer-related deaths. The early detection of CRC has been shown to be the most effective strategy to improve treatment outcomes and patient survival. Therefore, current lines of research focus on the development of reliable diagnostic tools. Targeted therapies, in combination with standard chemotherapy and immune checkpoint inhibitors, have emerged as promising treatment protocols in CRC. However, their effectiveness is linked to the molecular characteristics of each patient. The importance of discovering biomarkers that help predict response to therapies and assess prognosis is evident as they allow for a fundamental step towards personalized care and successful treatments. Among the ongoing efforts to identify them, mass spectrometry-based translational proteomics presents itself as a unique opportunity as it enables the discovery and application of protein biomarkers that may revolutionize the early detection and treatment of CRC. Our objective is to show the most recent studies focused on the identification of CRC-related protein markers, as well as to provide an updated view of advances in the field of proteomics and cancer.
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Affiliation(s)
- Desirée Martín-García
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Málaga, Spain;
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
| | - Marilina García-Aranda
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
| | - Maximino Redondo
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Málaga, Spain;
- Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), 29590 Málaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Málaga, Spain
- Research and Innovation Unit, Hospital Universitario Costa del Sol, 29602 Marbella, Spain
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Ding Z, Wang N, Ji N, Chen ZS. Proteomics technologies for cancer liquid biopsies. Mol Cancer 2022; 21:53. [PMID: 35168611 PMCID: PMC8845389 DOI: 10.1186/s12943-022-01526-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/31/2022] [Indexed: 02/07/2023] Open
Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
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Affiliation(s)
- Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Gangxing 3rd Rd, High-Tech and Innovation Zone, Bldg. 2, Rm. 2201, Jinan City, Shandong Province 250101 P. R. China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Gangxing 3rd Rd, High-Tech and Innovation Zone, Bldg. 2, Rm. 2201, Jinan City, Shandong Province 250101 P. R. China
| | - Ning Ji
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Institute for Biotechnology, St. John’s University, 8000 Utopia Parkway, Queens, New York, 11439 USA
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060 China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Institute for Biotechnology, St. John’s University, 8000 Utopia Parkway, Queens, New York, 11439 USA
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Paramanantham A, Jung EJ, Go SIL, Jeong BK, Jung JM, Hong SC, Kim GS, Lee WS. Activated ERK Signaling Is One of the Major Hub Signals Related to the Acquisition of Radiotherapy-Resistant MDA-MB-231 Breast Cancer Cells. Int J Mol Sci 2021; 22:ijms22094940. [PMID: 34066541 PMCID: PMC8124562 DOI: 10.3390/ijms22094940] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is one of the major causes of deaths due to cancer, especially in women. The crucial barrier for breast cancer treatment is resistance to radiation therapy, one of the important local regional therapies. We previously established and characterized radio-resistant MDA-MB-231 breast cancer cells (RT-R-MDA-MB-231 cells) that harbor a high expression of cancer stem cells (CSCs) and the EMT phenotype. In this study, we performed antibody array analysis to identify the hub signaling mechanism for the radiation resistance of RT-R-MDA-MB-231 cells by comparing parental MDA-MB-231 (p-MDA-MB-231) and RT-R-MDA-MB-231 cells. Antibody array analysis unveiled that the MAPK1 protein was the most upregulated protein in RT-R-MDA-MB-231 cells compared to in p-MDA-MB-231 cells. The pathway enrichment analysis also revealed the presence of MAPK1 in almost all enriched pathways. Thus, we used an MEK/ERK inhibitor, PD98059, to block the MEK/ERK pathway and to identify the role of MAPK1 in the radio-resistance of RT-R-MDA-MB-231 cells. MEK/ERK inhibition induced cell death in both p-MDA-MB-231 and RT-R-MDA-MB-231 cells, but the death mechanism for each cell was different; p-MDA-MB-231 cells underwent apoptosis, showing cell shrinkage and PARP-1 cleavage, while RT-R-MDA-MB-231 cells underwent necroptosis, showing mitochondrial dissipation, nuclear swelling, and an increase in the expressions of CypA and AIF. In addition, MEK/ERK inhibition reversed the radio-resistance of RT-R-MDA-MB-231 cells and suppressed the increased expression of CSC markers (CD44 and OCT3/4) and the EMT phenotype (β-catenin and N-cadherin/E-cadherin). Taken together, this study suggests that activated ERK signaling is one of the major hub signals related to the radio-resistance of MDA-MB-231 breast cancer cells.
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Affiliation(s)
- Anjugam Paramanantham
- Departments of Internal Medicine, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea; (A.P.); (E.J.J.); (S.-I.G.)
- School of Veterinary and Institute of Life Science, Gyeongsang National University, 900 Gajwadong, Jinju 660-701, Korea
| | - Eun Joo Jung
- Departments of Internal Medicine, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea; (A.P.); (E.J.J.); (S.-I.G.)
| | - Se-IL Go
- Departments of Internal Medicine, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea; (A.P.); (E.J.J.); (S.-I.G.)
| | - Bae Kwon Jeong
- Departments of Radiation Oncology, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea;
| | - Jin-Myung Jung
- Departments of Neurosurgery, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea;
| | - Soon Chan Hong
- Departments of Surgery, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea;
| | - Gon Sup Kim
- School of Veterinary and Institute of Life Science, Gyeongsang National University, 900 Gajwadong, Jinju 660-701, Korea
- Correspondence: (G.S.K.); (W.S.L.); Tel.: +82-55-772-2356 (G.S.K.); +82-55-750-8733 (W.S.L.); Fax: +82-55-758-9122 (W.S.L.)
| | - Won Sup Lee
- Departments of Internal Medicine, Institute of Health Sciences and Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 90 Chilam-dong, Jinju 660-702, Korea; (A.P.); (E.J.J.); (S.-I.G.)
- Correspondence: (G.S.K.); (W.S.L.); Tel.: +82-55-772-2356 (G.S.K.); +82-55-750-8733 (W.S.L.); Fax: +82-55-758-9122 (W.S.L.)
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Uzdensky AB. Apoptosis regulation in the penumbra after ischemic stroke: expression of pro- and antiapoptotic proteins. Apoptosis 2020; 24:687-702. [PMID: 31256300 DOI: 10.1007/s10495-019-01556-6] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ischemic stroke is the leading cause of human disability and mortality in the world. The main problem in stroke therapy is the search of efficient neuroprotector capable to rescue neurons in the potentially salvageable transition zone (penumbra), which is expanding after brain damage. The data on molecular mechanisms of penumbra formation and expression of diverse signaling proteins in the penumbra during first 24 h after ischemic stroke are discussed. Two basic features of cell death regulation in the ischemic penumbra were observed: (1) both apoptotic and anti-apoptotic proteins are simultaneously over-expressed in the penumbra, so that the fate of individual cells is determined by the balance between these opposite tendencies. (2) Similtaneous and concerted up-regulation in the ischemic penumbra of proteins that execute apoptosis (caspases 3, 6, 7; Bcl-10, SMAC/DIABLO, AIF, PSR), signaling proteins that regulate different apoptosis pathways (p38, JNK, DYRK1A, neurotrophin receptor p75); transcription factors that control expression of various apoptosis regulation proteins (E2F1, p53, c-Myc, GADD153); and proteins, which are normally involved in diverse cellular functions, but stimulate apoptosis in specific situations (NMDAR2a, Par4, GAD65/67, caspase 11). Hence, diverse apoptosis initiation and regulation pathways are induced simultaneously in penumbra from very different initial positions. Similarly, various anti-apoptotic proteins (Bcl-x, p21/WAF-1, MDM2, p63, PKBα, ERK1, RAF1, ERK5, MAKAPK2, protein phosphatases 1α and MKP-1, estrogen and EGF receptors, calmodulin, CaMKII, CaMKIV) are upregulated. These data provide an integral view of neurodegeneration and neuroprotection in penumbra. Some discussed proteins may serve as potential targets for anti-stroke therapy.
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Affiliation(s)
- Anatoly B Uzdensky
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, 194/1 Stachky Prospect, Rostov-on-Don, Russia, 344090.
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Jaeschke A, Eckert H, Bray LJ. proMAD: semiquantitative densitometric measurement of protein microarrays. BMC Bioinformatics 2020; 21:72. [PMID: 32093608 PMCID: PMC7041094 DOI: 10.1186/s12859-020-3402-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein microarrays are a versatile and widely used tool for analyzing complex protein mixtures. Membrane arrays utilize antibodies which are captured on a membrane to specifically immobilize several proteins of interest at once. Using detection antibodies, the bound protein-antibody-complex is converted into visual signals, which can be quantified using densitometry. The reliability of such densitometric assessments depends on a variety of factors, not only sample preparation and the choice of acquisition device but also the selected analysis software and the algorithms used for readout and processing data. Currently available software packages use a single image of a membrane at an optimal exposure time selected for that specific experimental framework. This selection is based on a user's best guess and is subject to inter-user variability or the acquisition device algorithm. With modern image acquisition systems proving the capacity to collect signal development over time, this information can be used to improve densitometric measurements. Here we introduce proMAD, a toolkit for protein microarray analysis providing a novel systemic approach for the quantification of membrane arrays based on the kinetics of the analytical reaction. RESULTS Briefly, our toolkit ensures an exact membrane alignment, utilizing basic computer vision techniques. It also provides a stable method to estimate the background light level. Finally, we model the light production over time, utilizing the knowledge about the reaction kinetics of the underlying horseradish peroxidase-based signal detection method. CONCLUSION proMAD incorporates the reaction kinetics of the enzyme to model the signal development over time for each membrane creating an individual, self-referencing concept. Variations of membranes within a given experimental set up can be accounted for, allowing for a better comparison of such. While the open-source library can be implemented in existing workflows and used for highly user-tailored analytic setups, the web application, on the other hand, provides easy platform-independent access to the core algorithm to a wide range of researchers. proMAD's inherent flexibility has the potential to cover a wide range of use-cases and enables the automation of data analytic tasks.
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Affiliation(s)
- Anna Jaeschke
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, 4059 Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Kelvin Grove, Queensland, 4059 Australia
| | - Hagen Eckert
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, Dresden, Germany
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, Dresden, Germany
| | - Laura J. Bray
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, 4059 Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Kelvin Grove, Queensland, 4059 Australia
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Tiemann K, Garri C, Wang J, Clarke L, Kani K. Assessment of Resistance to Tyrosine Kinase Inhibitors by an Interrogation of Signal Transduction Pathways by Antibody Arrays. J Vis Exp 2018. [PMID: 30295648 DOI: 10.3791/57779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cancer patients with an aberrant regulation of the protein phosphorylation networks are often treated with the tyrosine kinase inhibitors. Response rates approaching 85% are common. Unfortunately, patients often become refractory to the treatment by altering their signal transduction pathways. An implementation of the expression profiling with microarrays can identify the overall mRNA-level changes, and proteomics can identify the overall changes in protein levels or can identify the proteins involved, but the activity of the signal transduction pathways can only be established by interrogating post-translational modifications of the proteins. As a result, the ability to identify whether a drug treatment is successful or whether resistance arose, or the ability to characterize any alterations in the signaling pathways, is an important clinical challenge. Here, we provide a detailed explanation of antibody arrays as a tool which can identify system-wide alterations in various post-translational modifications (e.g., phosphorylation). One of the advantages of using antibody arrays includes their accessibility (an array does not require either an expert in proteomics or costly equipment) and speed. The availability of arrays targeting a combination of post-translational modifications is the primary limitation. In addition, unbiased approaches (phosphoproteomics) may be more suitable for the novel discovery, whereas antibody arrays are ideal for the most widely characterized targets.
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Affiliation(s)
- Katrin Tiemann
- Lawrence J. Ellison Institute for Transformative Medicine, Center for Applied Molecular Medicine, University of Southern California
| | - Carolina Garri
- Lawrence J. Ellison Institute for Transformative Medicine, Center for Applied Molecular Medicine, University of Southern California
| | - Jeffrey Wang
- Lawrence J. Ellison Institute for Transformative Medicine, Center for Applied Molecular Medicine, University of Southern California
| | - Lauren Clarke
- Lawrence J. Ellison Institute for Transformative Medicine, Center for Applied Molecular Medicine, University of Southern California
| | - Kian Kani
- Lawrence J. Ellison Institute for Transformative Medicine, Center for Applied Molecular Medicine, University of Southern California;
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Huang W, Luo S, Burgess R, Yi YH, Huang GF, Huang RP. New Insights into the Tumor Microenvironment Utilizing Protein Array Technology. Int J Mol Sci 2018; 19:ijms19020559. [PMID: 29438283 PMCID: PMC5855781 DOI: 10.3390/ijms19020559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/22/2017] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
The tumor microenvironment (TME) is a considerably heterogeneous niche, which is created by tumor cells, the surrounding tumor stroma, blood vessels, infiltrating immune cells, and a variety of associated stromal cells. Intercellular communication within this niche is driven by soluble proteins synthesized by local tumor and stromal cells and include chemokines, growth factors, interferons, interleukins, and angiogenic factors. The interaction of tumor cells with their microenvironment is essential for tumorigenesis, tumor progression, growth, and metastasis, and resistance to drug therapy. Protein arrays enable the parallel detection of hundreds of proteins in a small amount of biological sample. Recent data have demonstrated that the application of protein arrays may yield valuable information regarding the structure and functional mechanisms of the TME. In this review, we will discuss protein array technologies and their applications in TME analysis to discern pathways involved in promoting the tumorigenic phenotype.
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Affiliation(s)
- Wei Huang
- RayBiotech, Inc., Guangzhou, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- South China Biochip Research Center, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
| | - Shuhong Luo
- RayBiotech, Inc., Guangzhou, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- South China Biochip Research Center, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- RayBiotech, Inc., 3607 Parkway Lane, Norcross, GA 30092, USA.
| | - Rob Burgess
- RayBiotech, Inc., 3607 Parkway Lane, Norcross, GA 30092, USA.
| | - Yu-Hua Yi
- RayBiotech, Inc., Guangzhou, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- South China Biochip Research Center, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
| | - Gordon F Huang
- RayBiotech, Inc., 3607 Parkway Lane, Norcross, GA 30092, USA.
| | - Ruo-Pan Huang
- RayBiotech, Inc., Guangzhou, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- South China Biochip Research Center, 79 Ruihe Road, Huangpu District, Guangzhou 510600, China.
- RayBiotech, Inc., 3607 Parkway Lane, Norcross, GA 30092, USA.
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Kupcova Skalnikova H, Cizkova J, Cervenka J, Vodicka P. Advances in Proteomic Techniques for Cytokine Analysis: Focus on Melanoma Research. Int J Mol Sci 2017; 18:E2697. [PMID: 29236046 PMCID: PMC5751298 DOI: 10.3390/ijms18122697] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Melanoma is a skin cancer with permanently increasing incidence and resistance to therapies in advanced stages. Reports of spontaneous regression and tumour infiltration with T-lymphocytes makes melanoma candidate for immunotherapies. Cytokines are key factors regulating immune response and intercellular communication in tumour microenvironment. Cytokines may be used in therapy of melanoma to modulate immune response. Cytokines also possess diagnostic and prognostic potential and cytokine production may reflect effects of immunotherapies. The purpose of this review is to give an overview of recent advances in proteomic techniques for the detection and quantification of cytokines in melanoma research. Approaches covered span from mass spectrometry to immunoassays for single molecule detection (ELISA, western blot), multiplex assays (chemiluminescent, bead-based (Luminex) and planar antibody arrays), ultrasensitive techniques (Singulex, Simoa, immuno-PCR, proximity ligation/extension assay, immunomagnetic reduction assay), to analyses of single cells producing cytokines (ELISpot, flow cytometry, mass cytometry and emerging techniques for single cell secretomics). Although this review is focused mainly on cancer and particularly melanoma, the discussed techniques are in general applicable to broad research field of biology and medicine, including stem cells, development, aging, immunology and intercellular communication.
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Affiliation(s)
- Helena Kupcova Skalnikova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
| | - Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 16500 Prague, Czech Republic.
| | - Jakub Cervenka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12843 Prague 4, Czech Republic.
| | - Petr Vodicka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
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10
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Shah KG, Yager P. Wavelengths and Lifetimes of Paper Autofluorescence: A Simple Substrate Screening Process to Enhance the Sensitivity of Fluorescence-Based Assays in Paper. Anal Chem 2017; 89:12023-12029. [PMID: 29048155 DOI: 10.1021/acs.analchem.7b02424] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Porous media made of nitrocellulose and glass fiber are common "paper" substrates for lateral flow assays, microfluidic paper analytical devices and other point-of-care diagnostic assays. Such assays commonly use optical labels such as gold nanoparticles, latex beads, or fluorescent nanoparticles to visualize the presence of analytes. Fluorescent labels are commonly used in bioassays to enhance sensitivity, but autoluminescence of the paper substrate worsens signal-to-noise ratios of fluorescence-based assays. To date, there exists no systematic investigation of autoluminescence wavelengths or lifetimes of porous membranes used in lateral flow assays. In response, we quantified the autoluminescence of commonly used porous materials across the visible spectrum via excitation-emission spectroscopy and time-resolved fluorescence spectroscopy, and demonstrate that autoluminescence is solely due to autofluorescence with lifetimes of about 5 ns in the visible spectrum. Counterintuitively, we found that spectroscopy alone does not provide sufficient information to select candidate paper substrates for fluorophore-labeled assays. Therefore, we developed a simple quantitative framework to select a low-fluorescence substrate that minimizes both the overlap of paper and fluorophore emission spectra and the fluorescence intensity on an imaging system of interest (such as a gel imager). Use of this framework was shown to lower the limit of detection of an influenza A nucleoprotein immunoassay by over 50%. The tools developed in this manuscript enable assay developers to screen appropriate, low-fluorescence porous substrates and enhance the sensitivity of membrane-based fluorescence assays.
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Affiliation(s)
- Kamal G Shah
- Department of Bioengineering, University of Washington , Box 355061, Seattle, Washington 98195, United States
| | - Paul Yager
- Department of Bioengineering, University of Washington , Box 355061, Seattle, Washington 98195, United States
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11
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Divya KP, Dharuman V. Supported binary liposome vesicle-gold nanoparticle for enhanced label free DNA and protein sensing. Biosens Bioelectron 2017; 95:168-173. [DOI: 10.1016/j.bios.2017.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 01/05/2023]
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12
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Neiswinger J, Uzoma I, Cox E, Rho H, Song G, Paul C, Jeong JS, Lu KY, Chen CS, Zhu H. Protein Microarrays: Flexible Tools for Scientific Innovation. Cold Spring Harb Protoc 2016; 2016:2016/10/pdb.top081471. [PMID: 27698245 DOI: 10.1101/pdb.top081471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be performed in a parallel and unbiased manner. The first high-density protein microarray, dubbed the "yeast proteome array," consisted of approximately 5800 full-length yeast proteins and was initially used to identify protein-lipid interactions. Further assays were subsequently developed to allow measurement of protein-DNA, protein-RNA, and protein-protein interactions, as well as four well-known posttranslational modifications: phosphorylation, acetylation, ubiquitylation, and SUMOylation. In this introduction, we describe the advent of high-density protein microarrays, as well as current methods for assessing a wide variety of protein interactions and posttranslational modifications.
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Affiliation(s)
- Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Ijeoma Uzoma
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Eric Cox
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - HeeSool Rho
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Corry Paul
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Jun Seop Jeong
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Kuan-Yi Lu
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
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Cayer DM, Nazor KL, Schork NJ. Mission critical: the need for proteomics in the era of next-generation sequencing and precision medicine. Hum Mol Genet 2016; 25:R182-R189. [DOI: 10.1093/hmg/ddw214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
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Fasolo J, Im H, Snyder MP. Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions. J Vis Exp 2015:e51872. [PMID: 26274875 DOI: 10.3791/51872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an affinity purified yeast kinase fusion protein containing a V5-epitope tag for read-out. Purified kinase is obtained through culture of a yeast strain optimized for high copy protein production harboring a plasmid containing a Kinase-V5 fusion construct under a GAL inducible promoter. The yeast is grown in restrictive media with a neutral carbon source for 6 hr followed by induction with 2% galactose. Next, the culture is harvested and kinase is purified using standard affinity chromatographic techniques to obtain a highly purified protein kinase for use in the assay. The purified kinase is diluted with kinase buffer to an appropriate range for the assay and the protein microarrays are blocked prior to hybridization with the protein microarray. After the hybridization, the arrays are probed with monoclonal V5 antibody to identify proteins bound by the kinase-V5 protein. Finally, the arrays are scanned using a standard microarray scanner, and data is extracted for downstream informatics analysis to determine a high confidence set of protein interactions for downstream validation in vivo.
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Affiliation(s)
| | - Hogune Im
- Department of Genetics, Stanford University
| | - Michael P Snyder
- Department of Genetics, Stanford University; Stanford Center for Genomics and Personalized Medicine, Stanford University;
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15
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Kim J, Bae S, Song S, Chung K, Kwon S. Fiber composite slices for multiplexed immunoassays. BIOMICROFLUIDICS 2015; 9:044109. [PMID: 26339310 PMCID: PMC4522008 DOI: 10.1063/1.4927590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/17/2015] [Indexed: 05/11/2023]
Abstract
Fabrication methods for the development of multiplexed immunoassay platforms primarily depend on the individual functionalization of reaction chambers to achieve a heterogeneous reacting substrate composition, which increases the overall manufacturing time and cost. Here, we describe a new type of low-cost fabrication method for a scalable immunoassay platform based on cotton threads. The manufacturing process involves the fabrication of functionalized fibers and the arrangement of these fibers into a bundle; this bundle is then sectioned to make microarray-like particles with a predefined surface architecture. With these sections, composed of heterogeneous thread fragments with different types of antibodies, we demonstrated quantitative and 7-plex immunoassays. We expect that this methodology will prove to be a versatile, low-cost, and highly scalable method for the fabrication of multiplexed bioassay platforms.
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Affiliation(s)
- Jiyun Kim
- Nano Systems Institute, Seoul National University , Seoul 151-744, South Korea
| | | | | | - Keumsim Chung
- QuantaMatrix Inc., Se oul National University , Seoul 151-744, South Korea
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16
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Chen JQ, Wakefield LM, Goldstein DJ. Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics. J Transl Med 2015; 13:182. [PMID: 26048678 PMCID: PMC4467619 DOI: 10.1186/s12967-015-0537-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/14/2015] [Indexed: 12/17/2022] Open
Abstract
There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed.
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Affiliation(s)
- Jin-Qiu Chen
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 2140, Bethesda, MD, 20892, USA.
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - David J Goldstein
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Lee MS, Kim JH, Lee JS, Yun SJ, Kim WJ, Ahn H, Park J. Prognostic Significance of CREB-Binding Protein and CD81 Expression in Primary High Grade Non-Muscle Invasive Bladder Cancer: Identification of Novel Biomarkers for Bladder Cancer Using Antibody Microarray. PLoS One 2015; 10:e0125405. [PMID: 25915404 PMCID: PMC4411067 DOI: 10.1371/journal.pone.0125405] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/23/2015] [Indexed: 12/15/2022] Open
Abstract
High-grade (HG) bladder cancers (BCs) are genetically unstable and have an unpredictable course. The identification of prognostic factors in HG non-muscle invasive BC (NMIBC) is crucial for improving patients’ quality of life and preventing BC-specific mortality. Here, we used an antibody microarray (AbM) to identify novel candidate biomarkers in primary HG NMIBC and validated the prognostic significance of the candidate biomarkers. Three pairs of tissue samples from primary HG NMIBC and normal urothelium were analyzed using an AbM kit containing 656 antibodies, and differentially expressed proteins were identified. Among the 42 upregulated and 14 downregulated proteins with statistical significance in BC tissues, CREB-binding protein and CD81 were selected as representative upregulated and downregulated candidate biomarkers, respectively. We then validated the expression of these candidate biomarkers in primary human urothelial cells and BC cell lines by western blotting and immunofluorescence assays, and the results were consistent with the AbM expression profiles. Additionally, Kaplan-Meier survival using immunohistochemical data from an independent primary HG NMIBC cohort comprising 113 patients showed that expression of the 2 biomarkers was significantly associated with recurrence-free and progression-free survival. In multivariate analysis, the 2 biomarkers remained significant predictors for recurrence-free survival. Taken together, our findings suggest that expression of CREB-binding protein and CD81 in BC tissue specimens may have prognostic value in patients with primary HG NMIBC.
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Affiliation(s)
- Myung-Shin Lee
- Department of Microbiology, Eulji University School of Medicine, Daejeon, South Korea
| | - Joo Heon Kim
- Department of Pathology, Eulji University School of Medicine, Daejeon, South Korea
| | - Ji-Su Lee
- Department of Microbiology, Eulji University School of Medicine, Daejeon, South Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, South Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, South Korea
| | - Hanjong Ahn
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jinsung Park
- Department of Urology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, South Korea
- * E-mail:
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Abstract
All of life is regulated by complex and organized chemical reactions that help dictate when to grow, to move, to reproduce, and to die. When these processes go awry, or are interrupted by pathological agents, diseases such as cancer, autoimmunity, or infections can result. Cytokines, chemokines, growth factors, adipokines, and other chemical moieties make up a vast subset of these chemical reactions that are altered in disease states, and monitoring changes in these molecules could provide for the identification of disease biomarkers. From the first identification of carcinoembryonic antigen, to the discovery of prostate-specific antigen, to numerous others described within, biomarkers of disease are detectable in a plethora of sample types. The growing number of biomarkers for infection, autoimmunity, and cancer allow for increasingly early detection, to identification of novel drug targets, to prognostic indicators of disease outcome. However, more and more studies are finding that a single cytokine or growth factor is insufficient as a true disease biomarker and that a more global perspective is needed to understand true disease biology. Such a broad view requires a multiplexed platform for chemical detection, and antibody arrays meet and exceed this need by performing this detection in a high-throughput fashion. Herein, we will discuss how antibody arrays have evolved, and how they have helped direct new drug target design, helped identify therapeutic disease markers, and helped in earlier disease detection. From asthma to renal disease, and neurological dysfunction to immunologic disorders, antibody arrays afford a bright future for new biomarkers discovery.
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Emirbekov EZ, Pashaeva ME. Expression of cytoskeleton proteins in hypothalamic cells in winter sleeping ground squirrels Citellus pygmaeus Pallas during hibernation. NEUROCHEM J+ 2014. [DOI: 10.1134/s1819712414020032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Photopatterning of self assembled monolayers on oxide surfaces for the selective attachment of biomolecules. Biosens Bioelectron 2014; 53:82-9. [DOI: 10.1016/j.bios.2013.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 11/21/2022]
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21
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Cluster of differentiation antibody microarrays on plasma immersion ion implanted polycarbonate. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 35:434-40. [DOI: 10.1016/j.msec.2013.11.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/10/2013] [Accepted: 11/22/2013] [Indexed: 01/07/2023]
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Haselgrübler T, Haider M, Ji B, Juhasz K, Sonnleitner A, Balogi Z, Hesse J. High-throughput, multiparameter analysis of single cells. Anal Bioanal Chem 2013; 406:3279-96. [PMID: 24292433 DOI: 10.1007/s00216-013-7485-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 12/23/2022]
Abstract
Heterogeneity of cell populations in various biological systems has been widely recognized, and the highly heterogeneous nature of cancer cells has been emerging with clinical relevance. Single-cell analysis using a combination of high-throughput and multiparameter approaches is capable of reflecting cell-to-cell variability, and at the same time of unraveling the complexity and interdependence of cellular processes in the individual cells of a heterogeneous population. In this review, analytical methods and microfluidic tools commonly used for high-throughput, multiparameter single-cell analysis of DNA, RNA, and proteins are discussed. Applications and limitations of currently available technologies for cancer research and diagnostics are reviewed in the light of the ultimate goal to establish clinically applicable assays.
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Affiliation(s)
- Thomas Haselgrübler
- Center for Advanced Bioanalysis GmbH, Gruberstraße 40-42, 4020, Linz, Austria,
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23
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Zhang X, Soori G, Dobleman TJ, Xiao GG. The application of monoclonal antibodies in cancer diagnosis. Expert Rev Mol Diagn 2013; 14:97-106. [PMID: 24308340 DOI: 10.1586/14737159.2014.866039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer becomes the second leading cause of death in the world. An effective strategy for early diagnosis of the disease is key to reduce the mortality and morbidity. Development of effective monoclonal antibody (mAb)-based assays or diagnostic imaging techniques for detection of antigens and small molecules that are released from cancerous cells will enhance modern diagnostic medicine of cancer significantly. Although mAb technology is still under development, recent advances in preparation of recombinant antigen and antibody engineering techniques have dramatically enhanced the applications of this technology in cancer diagnosis. Compared with other methods, mAb-based assays may provide spatial, temporal, accurate and quantitative measurement for diagnosis of the disease. This review summarizes the progress of the mAb-based assays in the field of molecular diagnosis of cancer.
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Affiliation(s)
- Xuemei Zhang
- The Medical College of Dalian University, Dalian Economic & Technical Development Zone, Dalian 116622, People's Republic of China, China
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24
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Abstract
Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post-translational modifications, the analysis of host-microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases.
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Affiliation(s)
- F X Reymond Sutandy
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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Abstract
BACKGROUND The cancer biomarkers field is being enriched by molecular profiling obtained by high-throughput approaches. In the context of other proteomic technologies, targeted antibody arrays are contributing strongly to the identification of protein cancer biomarker candidates. OBJECTIVE To describe innovative strategies multiplexing protein measurements of protein extracts of cultured cells, tissue and body fluids using antibody arrays that, combined with appropriate validation approaches, are enabling the discovery of cancer-associated biomarkers. METHOD The strategies and cancer biomarker candidates identified using antibody arrays reported so far that may assist in the diagnosis, surveillance and prognosis, and potentially for predictive and therapeutic purposes for patients affected with solid and hematological neoplasias. RESULTS/CONCLUSION Owing to their versatility, novel technological and experimental design implementations are broadening the applications of antibody arrays also for biomarker discovery. However, the cancer biomarker candidates delivered so far using this technology are still at an early developmental phase, requiring validation with many specimens focusing on specific clinical end points.
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Affiliation(s)
- Marta Sanchez-Carbayo
- Group Leader Spanish National Cancer Research Center, Tumor Markers Group, 308A, Melchor Fernandez Almagro 3, E-28029 Madrid, Spain +34 91 7328053 ; +34 91 224 6972 ;
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Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012; 6:548-62. [PMID: 23027439 PMCID: PMC3600421 DOI: 10.1002/prca.201200041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
Abstract
Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology.
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Affiliation(s)
- Heng Zhu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, MD, USA.
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Singh S, Srivastava A, Oh HM, Ahn CY, Choi GG, Asthana RK. Recent trends in development of biosensors for detection of microcystin. Toxicon 2012; 60:878-94. [DOI: 10.1016/j.toxicon.2012.06.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 05/08/2012] [Accepted: 06/06/2012] [Indexed: 01/14/2023]
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Tan HT, Lee YH, Chung MCM. Cancer proteomics. MASS SPECTROMETRY REVIEWS 2012; 31:583-605. [PMID: 22422534 DOI: 10.1002/mas.20356] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.
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Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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29
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Uzdensky A, Kristiansen B, Moan J, Juzeniene A. Dynamics of signaling, cytoskeleton and cell cycle regulation proteins in glioblastoma cells after sub-lethal photodynamic treatment: antibody microarray study. Biochim Biophys Acta Gen Subj 2012; 1820:795-803. [PMID: 22484521 DOI: 10.1016/j.bbagen.2012.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Photodynamic therapy (PDT) that induces oxidative stress and cell death is used for tumor destruction in oncology. To characterize early molecular events in photosensitized glioblastoma cells, we studied expression of 224 proteins after sublethal PDT that doesn't kill but wounds cells. METHODS Cultured glioblastoma D54Mg cells were photosensitized with 5-aminolevulinic acid so that cell survival was 95-100%. At following 0.5-5.5h protein expression and phosphorylation was assayed using proteomic antibody microarrays. RESULTS Within the first post-treatment hour we observed phosphorylation of protein kinase Raf, adhesion-related kinases FAK and Pyk2, and microtubule-associated protein tau. Protein kinase Cγ and microtubule-associated protein MAP-1B were overexpressed. Dystrophin, calponin, and vinculin, components of the actin cytoskeleton scaffold, microtubule-associated proteins MAP2 and CNP, cytokeratins 4 and 7 were down-regulated that indicated changes in adhesion and cell shape. Down-regulation of cyclins A, D1 and D3, c-Myc, checkpoint proteins chk1/2 and up-regulation of Smad4 could arrest the cell cycle. Overexpression of Bcl-xL and down-regulation of caspase 9 demonstrated anti-apoptotic response. At 2h post-treatment protein expression changed lesser but at 5.5h levels of PKCγ and β-synuclein and phosphorylation of Raf, FAK, Pyk2, and tau increased again. CONCLUSIONS Sub-lethal PDT induces complex response of glioblastoma cells including changes in activity and expression of proteins involved in adhesion-mediated signaling, signal transduction, cytoskeleton remodeling, cell cycle regulation and anti-apoptotic processes. GENERAL SIGNIFICANCE Multiple reactions of various cellular subsystems including adhesion, cytoskeleton, signal transduction, cell cycle, and apoptosis are integrated into the general cell response to a sublethal impact.
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Affiliation(s)
- Anatoly Uzdensky
- Department of Biophysics, Southern Federal University, Stachky 194/1, 344090, Rostov-on-Don, Russia.
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30
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Abstract
The cancer biomarkers field is being enriched by molecular profiling obtained by high-throughput approaches. Targeted antibody arrays are strongly contributing to the identification of protein cancer -biomarker candidates and functional proteomic analyses. Due to their versatility, novel technological and experimental design implementations are broadening the applications of antibody arrays. However, the cancer biomarker candidates delivered to date using this technology are still in their early developmental phase, requiring validation with high number of specimens focusing on specific clinical endpoints. Innovative strategies multiplexing protein measurements of protein extracts of cultured cells, tissue and body fluids using antibody arrays combined with appropriate validation approaches are enabling the -discovery of cancer-associated biomarkers. This review describes these strategies and cancer biomarker candidates reported to date that may assist in the diagnosis, surveillance, prognosis, and potentially for predictive and therapeutic purposes for patients affected with solid and hematological neoplasias.
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31
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Stuchlý J, Kanderová V, Fišer K, Černá D, Holm A, Wu W, Hrušák O, Lund-Johansen F, Kalina T. An automated analysis of highly complex flow cytometry-based proteomic data. Cytometry A 2011; 81:120-9. [DOI: 10.1002/cyto.a.22011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 01/08/2023]
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Early diagnostic protein biomarkers for breast cancer: how far have we come? Breast Cancer Res Treat 2011; 134:1-12. [PMID: 22179926 DOI: 10.1007/s10549-011-1907-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/29/2011] [Indexed: 12/22/2022]
Abstract
Many studies have used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to search for blood-based proteins that are related to the presence of breast cancer. We review the biomarkers discovered or targeted measured by these methods and discuss the strengths and weaknesses of these studies. We highlight two proteins that were most often related to breast cancer: C3a des-arginine anaphylatoxin (C3adesArg) (molecular weight: 8,938 Da) and fragments of inter-alpha trypsin inhibitor heavy chain H4 (ITIH4). In addition, we elaborate on three important methodological aspects related to these studies: protein identification, specificity of the markers, and disease heterogeneity. Finally, we propose some points to be addressed in future studies. These include the use of other analytical measurement techniques, need of protein identification, the importance of identical sample handling protocols for cases and controls, and the stratification of the results according to molecular subtypes and stages of breast cancer. Ultimately this may lead to the discovery of new and valid breast cancer specific biomarkers.
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Hodgkinson VC, ELFadl D, Agarwal V, Garimella V, Russell C, Long ED, Fox JN, McManus PL, Mahapatra TK, Kneeshaw PJ, Drew PJ, Lind MJ, Cawkwell L. Proteomic identification of predictive biomarkers of resistance to neoadjuvant chemotherapy in luminal breast cancer: a possible role for 14-3-3 theta/tau and tBID? J Proteomics 2011; 75:1276-83. [PMID: 22115752 DOI: 10.1016/j.jprot.2011.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/27/2011] [Accepted: 11/03/2011] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Chemotherapy resistance is a major obstacle in effective neoadjuvant treatment for estrogen receptor-positive breast cancer. The ability to predict tumour response would allow chemotherapy administration to be directed towards only those patients who would benefit, thus maximising treatment efficiency. We aimed to identify putative protein biomarkers associated with chemotherapy resistance, using fresh tumour samples with antibody microarray analysis and then to perform pilot clinical validation experiments. MATERIALS AND METHODS Chemotherapy resistant and chemotherapy sensitive tumour samples were collected from breast cancer patients who had received anthracycline based neoadjuvant therapy consisting of epirubicin with cyclophosphamide followed by docetaxel. A total of 5 comparative proteomics experiments were performed using invasive ductal carcinomas which demonstrated estrogen receptor positivity (luminal subtype). Protein expression was compared between chemotherapy resistant and chemotherapy sensitive tumour samples using the Panorama XPRESS Profiler725 antibody microarray containing 725 antibodies from a wide variety of cell signalling and apoptosis pathways. A pilot series of archival samples was used for clinical validation of putative predictive biomarkers. RESULTS AbMA analysis revealed 38 differentially expressed proteins which demonstrated at least 1.8 fold difference in expression in chemotherapy resistant tumours and 7 of these proteins (Zyxin, 14-3-3 theta/tau, tBID, Pinin, Bcl-xL, RIP and MyD88) were found in at least 2 experiments. Clinical validation in a pilot series of archival samples revealed 14-3-3 theta/tau and tBID to be significantly associated with chemotherapy resistance. CONCLUSIONS For the first time, antibody microarrays have been used to identify proteins associated with chemotherapy resistance using fresh breast cancer tissue. We propose a potential role for 14-3-3 theta/tau and tBID as predictive biomarkers of neoadjuvant chemotherapy resistance in breast cancer. Further validation in a larger sample series is now required.
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Affiliation(s)
- Victoria C Hodgkinson
- Cancer Biology Proteomics Group, Postgraduate Medical Institute of the University of Hull, Hull, UK
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Repeatedly identified differentially expressed proteins (RIDEPs) from antibody microarray proteomic analysis. J Proteomics 2011; 74:698-703. [DOI: 10.1016/j.jprot.2011.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/19/2011] [Accepted: 02/14/2011] [Indexed: 02/08/2023]
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Exploring the immunoproteome for ovarian cancer biomarker discovery. Int J Mol Sci 2011; 12:410-28. [PMID: 21339995 PMCID: PMC3039961 DOI: 10.3390/ijms12010410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 01/12/2011] [Indexed: 01/09/2023] Open
Abstract
Most scientific efforts towards early detection of ovarian cancer are commonly focused on the discovery of tumour-associated antigens (TAA). Autologous antibodies against TAA, however, may serve as more sensitive diagnostic markers. They circulate in the blood before TAA and are usually more abundant than the TAAs themselves as a result of amplification through the humoral immune response. Accumulating evidence also suggests that a humoral response already exists during malignant transformation when aberrant gene expression is translated into premalignant cellular changes. This article reviews the current knowledge about autoantibodies against TAA in ovarian cancer and presents current immunoproteomic approaches for their detection.
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Down-regulation of CD3zeta is a breast cancer biomarker associated with immune suppression. Cell Biol Int 2011; 35:165-9. [DOI: 10.1042/cbi20100346] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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37
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Zhang GL, DeLuca DS, Brusic V. Database resources for proteomics-based analysis of cancer. Methods Mol Biol 2011; 723:349-64. [PMID: 21370076 DOI: 10.1007/978-1-61779-043-0_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biological/bioinformatics databases are essential for medical and biological studies. They integrate and organize biologically related information in a structured format and provide researchers with easy access to a variety of relevant data. This review presents an overview of publicly available databases relevant to proteomics studies in cancer research. They include gene/protein expression databases, gene mutation and single nucleotide polymorphisms databases, tumor antigen databases, protein-protein interaction, and biological pathway databases. Automated information retrieval from these databases enables efficient large-scale proteomics data analysis.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Gerstner AOH. Early detection in head and neck cancer - current state and future perspectives. GMS CURRENT TOPICS IN OTORHINOLARYNGOLOGY, HEAD AND NECK SURGERY 2010; 7:Doc06. [PMID: 22073093 PMCID: PMC3199835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Survival and quality of life in head and neck cancer are directly linked to the size of the primary tumor at first detection. In order to achieve substantial gain at these issues, both, primary prevention and secondary prevention, which is early detection of malignant lesions at a small size, have to be improved. So far, there is not only a lack in the necessary infrastructure not only in Germany, but rather worldwide, but additionally the techniques developed so far for early detection have a significance and specificity too low as to warrant safe implementation for screening programs. However, the advancements recently achieved in endoscopy and in quantitative analysis of hypocellular specimens open new perspectives for secondary prevention. Chromoendoscopy and narrow band imaging (NBI) pinpoint suspicious lesions more easily, confocal endomicroscopy and optical coherence tomography obtain optical sections through those lesions, and hyperspectral imaging classifies lesions according to characteristic spectral signatures. These techniques therefore obtain optical biopsies. Once a "bloody" biopsy has been taken, the plethora of parameters that can be quantified objectively has been increased and could be the basis for an objective and quantitative classification of epithelial lesions (multiparametric cytometry, quantitative histology). Finally, cytomics and proteomics approaches, and lab-on-the-chip technology might help to identify patients at high-risk. Sensitivity and specificity of these approaches have to be validated, yet, and some techniques have to be adapted for the specific conditions for early detection of head and neck cancer. On this background it has to be stated that it is still a long way to go until a population based screening for head and neck cancer is available. The recent results of screening for cancer of the prostate and breast highlight the difficulties implemented in such a task.
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Abstract
Advances in the generation and interpretation of proteomics data have spurred a transition from focusing on protein identification to functional analysis. Here we review recent proteomics results that have elucidated new aspects of the roles and regulation of signal transduction pathways in cancer using the epidermal growth factor receptor (EGFR), ERK and breakpoint cluster region (BCR)-ABL1 networks as examples. The emerging theme is to understand cancer signalling as networks of multiprotein machines which process information in a highly dynamic environment that is shaped by changing protein interactions and post-translational modifications (PTMs). Cancerous genetic mutations derange these protein networks in complex ways that are tractable by proteomics.
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Affiliation(s)
- Walter Kolch
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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40
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Hodgkinson VC, Eagle GL, Drew PJ, Lind MJ, Cawkwell L. Biomarkers of chemotherapy resistance in breast cancer identified by proteomics: current status. Cancer Lett 2010; 294:13-24. [PMID: 20176436 DOI: 10.1016/j.canlet.2010.01.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/26/2010] [Accepted: 01/29/2010] [Indexed: 11/26/2022]
Abstract
This review describes and discusses the advantages and limitations of proteomic approaches in the identification of biomarkers associated with chemotherapy resistance. Both gel-based (two-dimensional polyacrylamide gel electrophoresis) and gel-free (shotgun and quantitative) mass spectrometry approaches are discussed. Non-mass spectrometry approaches including antibody microarray platforms are described as complementary proteomic strategies. Methods for technical confirmation and clinical validation of putative biomarkers are presented. Use of this proteomic toolbox in the quest for biomarkers of chemotherapy resistance in breast cancer is reviewed. Technical aspects of sample selection, acquisition, storage and analysis are discussed and putative biomarkers identified through proteomic approaches are presented.
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Affiliation(s)
- Victoria C Hodgkinson
- Cancer Biology Proteomics Group, Postgraduate Medical Institute of the University of Hull, Hull, UK
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41
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Lavigne D, Guerrier L, Gueguen V, Michel JB, Boschetti E, Meilhac O, Letourneur D. Culture of human cells and synthesis of extracellular matrix on materials compatible with direct analysis by mass spectrometry. Analyst 2010; 135:503-11. [PMID: 20174702 DOI: 10.1039/b914539g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The extracellular matrix (ECM) is a complex three-dimensional network of macromolecules synthesized by cells and is essential for the structure and the function of a tissue. The aim of our approach was to propose a surface allowing cell culture and subsequent analysis of ECM produced by cells directly on materials compatible with Surface Enhanced Laser Desorption Ionization-Time Of Flight (SELDI-TOF) mass spectrometry on a 96-well format. Surfaces were made of aluminium and spots of 2 mm in diameter were covered with specific chemical groups (silica, C(6) and C(12) alkyl groups, carboxyl, quaternary amine, or nitrilotriacetic acid groups). We found that among the chemically modified aluminium spots, only silica groups allowed the culture of human vascular cells. The wettability was an essential parameter for cell culture on the surfaces. Indeed, cells could only be cultured on surfaces presenting a moderate wettability with water contact angles of ca. 60 degrees. Then, by treatment of confluent cells with detergents (Triton X100 and deoxycholate), we were able to obtain ECM on the surfaces that were subsequently analyzed using a mass spectrometer, which is currently impossible with any type of cell culture system. As an example, the analysis of ECM from human vascular smooth muscle cells (hVSMCs) and human umbilical vein endothelial cells (HUVECs) appeared to be reproducible and evidenced different ECM patterns from the two cell types. Applications based on these materials can be proposed for biomarker discovery or characterization of cells for biomedical/diagnostic purposes.
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Affiliation(s)
- Damien Lavigne
- Inserm U698, Cardiovascular Bio-engineering, X. Bichat Hospital, University Paris 7, Paris, F-75018, France
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Sanchez-Carbayo M. Antibody array-based technologies for cancer protein profiling and functional proteomic analyses using serum and tissue specimens. Tumour Biol 2010; 31:103-12. [DOI: 10.1007/s13277-009-0014-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 12/22/2009] [Indexed: 10/19/2022] Open
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Tainsky MA. Genomic and proteomic biomarkers for cancer: a multitude of opportunities. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1796:176-93. [PMID: 19406210 PMCID: PMC2752479 DOI: 10.1016/j.bbcan.2009.04.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/14/2009] [Accepted: 04/21/2009] [Indexed: 02/06/2023]
Abstract
Biomarkers are molecular indicators of a biological status, and as biochemical species can be assayed to evaluate the presence of cancer and therapeutic interventions. Through a variety of mechanisms cancer cells provide the biomarker material for their own detection. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Biomarkers have potential both as diagnostic indicators and monitors of the effectiveness of clinical interventions. Biomarkers are also able to stratify cancer patients to the most appropriate treatment. Effective biomarkers for the early detection of cancer should provide a patient with a better outcome which in turn will translate into more efficient delivery of healthcare. Technologies for the early detection of cancer have resulted in reductions in disease-associated mortalities from cancers that are otherwise deadly if allowed to progress. Such screening technologies have proven that early detection will decrease the morbidity and mortality from cancer. An emerging theme in biomarker research is the expectation that panels of biomarker analytes rather than single markers will be needed to have sufficient sensitivity and specificity for the presymptomatic detection of cancer. Biomarkers may provide prognostic information of disease enabling interventions using targeted therapeutic agents as well as course-corrections in cancer treatment. Novel genomic, proteomic and metabolomic technologies are being used to discover and validate tumor biomarkers individually and in panels.
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Affiliation(s)
- Michael A Tainsky
- Program in Molecular Biology and Genetics, Barbara Ann Karmanos Cancer Institute, Department of Pathology, Wayne State University School of Medicine, USA.
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44
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Mas VR, Fisher RA, Archer KJ, Maluf DG. Proteomics and liver fibrosis: identifying markers of fibrogenesis. Expert Rev Proteomics 2009; 6:421-31. [PMID: 19681677 DOI: 10.1586/epr.09.59] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chronic hepatic disease damages the liver and the resulting wound-healing process might lead to liver fibrosis and subsequent cirrhosis development. Fibrosis is the excessive deposition of extracellular matrix (ECM) in the tissue as consequence of chronic liver damage. The fibrotic response triggers almost all of the complications of end-stage liver disease, including portal hypertension, ascites, encephalopathy, synthetic dysfunction and impaired metabolic capacity. Thus, efforts to understand and attenuate fibrosis have direct clinical implications. Reliable, accurate, disease-specific, noninvasive biomarkers of fibrosis and fibrogenesis in order to prevent or minimize the impact of the chronic liver disease progression are a critical need. This review aims to provide an overview of the possibilities that proteome technology can offer to the knowledge, diagnosis and prognosis of liver fibrosis.
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Affiliation(s)
- Valeria R Mas
- Transplant Molecular Laboratory, Transplant Division, Department of Surgery, Molecular Medicine Research Building, Virginia Commonwealth University, 1220 E. Broad Street, Richmond, VA 23298, USA.
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45
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Guedj N, Zhan Q, Perigny M, Rautou PE, Degos F, Belghiti J, Farges O, Bedossa P, Paradis V. Comparative protein expression profiles of hilar and peripheral hepatic cholangiocarcinomas. J Hepatol 2009; 51:93-101. [PMID: 19446907 DOI: 10.1016/j.jhep.2009.03.017] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 01/23/2009] [Accepted: 03/05/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND/AIMS Hepatic cholangiocarcinomas are tumors with poor prognosis and with increasing incidence worldwide. The aim of the study was to compare morphological features and protein profiles of hilar and peripheral cholangiocarcinomas. METHODS Clinicopathological data were collected from 111 cholangiocarcinomas (59 peripheral and 52 hilar). Protein expression, assessed on tissue samples using tissue microarray and protein array technologies, was compared between both types of tumors and with extrahepatic cholangiocarcinoma and hepatocholangiocarcinoma. RESULTS Hilar cholangiocarcinomas were smaller in size (mean: 2.7 vs. 8 cm, p<0.001), were more often well differentiated adenocarcinomas (65% vs. 36% well differentiated, p<0.01) and carried out stronger perineural invasion (83% vs. 42%, p<0.001) than peripheral cholangiocarcinomas. Regarding protein expression, hilar cholangiocarcinomas more often expressed MUC5AC (62% vs. 22%, p<0.0001), Akt2 (54% vs. 27%, p<0.001), CK8 (98% vs. 81%, p<0.005) and annexin II (92% vs. 66%, p<0.001). Interestingly, VEGF A expression was more frequently encountered in peripheral cholangiocarcinoma (69% vs. 25%, p<0.0001) and correlated with increased vascular density. Using protein array antibody, we identified filamin A as significantly overexpressed (>2-fold) in peripheral cholangiocarcinomas. CONCLUSIONS Our results show that hilar and peripheral cholangiocarcinomas display specific protein profiles, especially regarding VEGF expression. This suggests a potential benefit for anti-angiogenic therapies in peripheral hepatic CCs.
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Affiliation(s)
- Nathalie Guedj
- Department of Pathology, Beaujon Hospital, 100 boulevard du Général Leclerc, 92118 Clichy, France
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46
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Proteomics: New technologies and clinical applications. Eur J Cancer 2008; 44:2737-41. [DOI: 10.1016/j.ejca.2008.09.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 09/23/2008] [Indexed: 12/26/2022]
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47
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Wilson S, Mazzatti DJ. Current status and future prospects in the search for protein biomarkers of immunosenescence. Expert Rev Proteomics 2008; 5:561-9. [PMID: 18761467 DOI: 10.1586/14789450.5.4.561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Complex adaptations including changes in cellular redox status, the production of high levels of pro-inflammatory cytokines and alterations in immunity occur as the result of aging of the immune system (immunosenescence). These events are thought to underlie the progression of chronic degenerative diseases of aging, such as atherosclerosis, Type 2 diabetes and Alzheimer's disease. It is envisaged that identifying early biomarkers of immune aging would aid in identifying individuals at risk of age-related disease and would allow the discovery of novel intervention strategies. Proteomics has emerged as a rapidly expanding and innovative field, investigating protein expression, interaction and function at a global level. Several proteomic strategies, including use of mass spectrometry and non-mass spectrometry-based detection systems (including secondary antibody labeling with fluorescent tags) may be particularly advantageous in identifying biomarkers of immune health. Application of these approaches may identify factors that both contribute to (and define) age-dependent deregulation of the immune system.
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Affiliation(s)
- Steve Wilson
- Unilever Corporate Research, Colworth Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
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Jain KK. Innovations, challenges and future prospects of oncoproteomics. Mol Oncol 2008; 2:153-60. [PMID: 19383334 PMCID: PMC5527761 DOI: 10.1016/j.molonc.2008.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Revised: 05/08/2008] [Accepted: 05/20/2008] [Indexed: 12/13/2022] Open
Abstract
Oncoproteomics is playing an increasingly important role in the diagnosis and management of cancer as well as in the development of personalized treatment of cancer. Innovative proteomic technologies relevant to cancer are described briefly, which are helping in the understanding of mechanism of drug resistance in cancer and will provide some leads to improve the management. Most important of these are nanoproteomics, i.e. application of nanobiotechnology to proteomics is playing an important role in nanooncology. Examples of some cancers will be given to point out the challenges and future prospects of oncoproteomics including those involving translation of technologies from the bench to the bedside.
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Affiliation(s)
- Kewal K Jain
- Jain PharmaBiotech, Bläsiring 7, CH-4057 Basel, Switzerland.
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Ghosh G, Bachas LG, Anderson KW. Biosensor incorporating cell barrier architectures on ion selective electrodes for early screening of cancer. Anal Bioanal Chem 2008; 391:2783-91. [PMID: 18537028 DOI: 10.1007/s00216-008-2192-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/14/2008] [Accepted: 05/16/2008] [Indexed: 01/09/2023]
Abstract
Angiogenesis occurs during the early phase of cancer. Recruitment of new blood vessels by existing cancer cells leads to the release of higher concentrations of cytokines as compared to cells in healthy individuals. Some of the common cytokines observed at higher concentrations, such as vascular endothelial growth factor, basic fibroblast growth factor, hepatocyte growth factor and tumor necrosis factor-alpha, are also known to induce increased permeability across an endothelial cell monolayer. A whole-cell-based biosensor has been developed that can detect the presence of small quantities of the abovementioned cytokines individually and in different combinations. It was observed that the biosensor could differentiate between the cytokine concentrations observed in the sera of healthy individuals and cancer patients. The biosensor was also evaluated by exposing it to actual serum. These results demonstrated that the sensor can distinguish between healthy individuals and cancer patients and that the corresponding biosensor responses correlate with the stages of cancer.
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Affiliation(s)
- Gargi Ghosh
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
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50
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Abstract
Ovarian cancer is associated with an overall mortality of 75%, but can be cured in up to 90% of cases if diagnosed while still limited to the ovaries. Given the low prevalence of ovarian cancer in the general population, an effective screening strategy must not only have a high sensitivity for early-stage disease (>75%), but must also have a very high specificity (99.6%) to prompt no more than ten operations for each case of ovarian cancer diagnosed (positive predictive value [PPV] of 10%). Attempts to develop an effective screening strategy for ovarian cancer have utilized ultrasonography and serum tumor markers. Transvaginal sonography (TVS) and the serum marker CA125 have received the most attention to date. Used individually on a single occasion, neither of these approaches provides an adequate PPV and the cost of annual TVS is significant. Recent clinical trials have focused on serial monitoring of CA125 and the sequential use of a rising CA125 to prompt TVS in a limited number of women screened. Sequential monitoring of CA125 has significantly improved specificity of the assay in women over 50 years of age. The limited sensitivity of CA125 has, however, prompted a search for multiple serum markers that, in combination, would detect more than 90% of early-stage disease. Recent developments in genomic and proteomic research have identified a number of candidate biomarkers. Platforms have been developed that can assay more than 50 analytes in a few hundred microliters of serum. Panels of biomarkers have been discovered with high sensitivity and specificity for early-stage disease, but these require prospective validation. Several biomarkers have also been detected in urine, raising the possibility of a less expensive, more convenient screening test. Imaging techniques have been improved and mathematical methods developed that, in aggregate, promise to provide an effective screening strategy for ovarian cancer. In this review, we will assess the current status and describe future directions in ovarian cancer screening.
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Affiliation(s)
- Partha M Das
- University of Texas, MD Anderson Cancer Center, Department of Experimental Therapeutics, Houston, TX, USA Tel.: +1 713 792 3790; Fax: +1 713 792 7864
| | - Robert C Bast
- University of Texas, MD Anderson Cancer Center, Box 355, 1515 Holcombe Boulevard Houston, TX 77030, USA Tel.: +1 713 792 7743; Fax: +1 713 792 7864
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