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Zou M, Zhou H, Gu L, Zhang J, Fang L. Therapeutic Target Identification and Drug Discovery Driven by Chemical Proteomics. BIOLOGY 2024; 13:555. [PMID: 39194493 DOI: 10.3390/biology13080555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/07/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity into the pharmacodynamics and toxicological mechanisms of small-molecule drugs, assisting in the elucidation of drug off-target effects and resistance mechanisms. Consequently, innovative methods to study small-molecule targets have proliferated in recent years, with chemical proteomics standing out as a vanguard development in chemical biology in the post-genomic age. Chemical proteomics can non-selectively identify unknown targets of compounds within complex biological matrices, with both probe and non-probe modalities enabling effective target identification. This review attempts to summarize methods and illustrative examples of small-molecule target identification via chemical proteomics. It delves deeply into the interactions between small molecules and human biology to provide pivotal directions and strategies for the discovery and comprehension of novel pharmaceuticals, as well as to improve the evaluation of drug safety.
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Affiliation(s)
- Mingjie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Haiyuan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Letian Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
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Su J, Yang L, Sun Z, Zhan X. Personalized Drug Therapy: Innovative Concept Guided With Proteoformics. Mol Cell Proteomics 2024; 23:100737. [PMID: 38354979 PMCID: PMC10950891 DOI: 10.1016/j.mcpro.2024.100737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Personalized medicine can reduce adverse effects, enhance drug efficacy, and optimize treatment outcomes, which represents the essence of personalized medicine in the pharmacy field. Protein drugs are crucial in the field of personalized drug therapy and are currently the mainstay, which possess higher target specificity and biological activity than small-molecule chemical drugs, making them efficient in regulating disease-related biological processes, and have significant potential in the development of personalized drugs. Currently, protein drugs are designed and developed for specific protein targets based on patient-specific protein data. However, due to the rapid development of two-dimensional gel electrophoresis and mass spectrometry, it is now widely recognized that a canonical protein actually includes multiple proteoforms, and the differences between these proteoforms will result in varying responses to drugs. The variation in the effects of different proteoforms can be significant and the impact can even alter the intended benefit of a drug, potentially making it harmful instead of lifesaving. As a result, we propose that protein drugs should shift from being targeted through the lens of protein (proteomics) to being targeted through the lens of proteoform (proteoformics). This will enable the development of personalized protein drugs that are better equipped to meet patients' specific needs and disease characteristics. With further development in the field of proteoformics, individualized drug therapy, especially personalized protein drugs aimed at proteoforms as a drug target, will improve the understanding of disease mechanisms, discovery of new drug targets and signaling pathways, provide a theoretical basis for the development of new drugs, aid doctors in conducting health risk assessments and making more cost-effective targeted prevention strategies conducted by artificial intelligence/machine learning, promote technological innovation, and provide more convenient treatment tailored to individualized patient profile, which will benefit the affected individuals and society at large.
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Affiliation(s)
- Junwen Su
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Lamei Yang
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ziran Sun
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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Sun J, Xu M, Ru J, James-Bott A, Xiong D, Wang X, Cribbs AP. Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications. Eur J Med Chem 2023; 257:115500. [PMID: 37262996 DOI: 10.1016/j.ejmech.2023.115500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Small molecules have been providing medical breakthroughs for human diseases for more than a century. Recently, identifying small molecule inhibitors that target microRNAs (miRNAs) has gained importance, despite the challenges posed by labour-intensive screening experiments and the significant efforts required for medicinal chemistry optimization. Numerous experimentally-verified cases have demonstrated the potential of miRNA-targeted small molecule inhibitors for disease treatment. This new approach is grounded in their posttranscriptional regulation of the expression of disease-associated genes. Reversing dysregulated gene expression using this mechanism may help control dysfunctional pathways. Furthermore, the ongoing improvement of algorithms has allowed for the integration of computational strategies built on top of laboratory-based data, facilitating a more precise and rational design and discovery of lead compounds. To complement the use of extensive pharmacogenomics data in prioritising potential drugs, our previous work introduced a computational approach based on only molecular sequences. Moreover, various computational tools for predicting molecular interactions in biological networks using similarity-based inference techniques have been accumulated in established studies. However, there are a limited number of comprehensive reviews covering both computational and experimental drug discovery processes. In this review, we outline a cohesive overview of both biological and computational applications in miRNA-targeted drug discovery, along with their disease implications and clinical significance. Finally, utilizing drug-target interaction (DTIs) data from DrugBank, we showcase the effectiveness of deep learning for obtaining the physicochemical characterization of DTIs.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Miaoer Xu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Jinlong Ru
- Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, 85354, Germany
| | - Anna James-Bott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Dodd-O J, Acevedo-Jake AM, Azizogli AR, Mulligan VK, Kumar VA. How to Design Peptides. Methods Mol Biol 2023; 2597:187-216. [PMID: 36374423 DOI: 10.1007/978-1-0716-2835-5_15] [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] [Indexed: 11/16/2022]
Abstract
Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes. Shorter proteins, or peptides, can offer combinatorial synergies with dendrimer, polymer, or other peptide carriers for enhanced local signaling, which larger proteins may sterically hinder. Here, we present a generalized method for designing a novel peptide. We first show how to create a script protocol that can be used to iteratively optimize and screen novel peptide sequences for binding a target protein. We present a step-by-step introduction to utilizing file repositories, data bases, and the Rosetta software suite. RosettaScripts, an .xml interface that allows for sequential functions to be performed, is used to order the functions for repeatable performance. These strategies may lead to more groups venturing into computational design, which may result in synergies from artificial intelligence/machine learning (AI/ML) to phage display and screening. Importantly, the beginner is expected to be able to design their first peptide ligand and begin their journey in peptide drug discovery. Generally, these peptides potentially could be used to interact with any enzyme or receptor, for example, in the study of chemokines and their interactions with glycosoaminoglycans and their receptors.
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Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, USA
| | - Amanda M Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, USA
| | | | | | - Vivek A Kumar
- York Center for Environmental Engineering and Science, New Jersey Institute of Technology, Newark, NJ, USA.
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Fedorov II, Lineva VI, Tarasova IA, Gorshkov MV. Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:983-994. [PMID: 36180990 DOI: 10.1134/s0006297922090103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment. At the same time, recent developments in high-resolution mass spectrometry have provided the technology for searching the drug targets across the whole cell proteomes. This review provides a concise description of the main objectives and problems of mass spectrometry-based chemical proteomics, the methods and approaches to their solution, and examples of implementation of these methods in biomedical research.
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Affiliation(s)
- Ivan I Fedorov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Victoria I Lineva
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
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Luan H, He Y, Zhang T, Su Y, Zhou L. The identification of liver metastasis- and prognosis-associated genes in pancreatic ductal adenocarcinoma. BMC Cancer 2022; 22:463. [PMID: 35477379 PMCID: PMC9047343 DOI: 10.1186/s12885-022-09577-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is an often fatal malignancy with an extremely low survival rate. Liver metastasis, which causes high mortality, is the most common recurring metastasis for PDAC. However, the mechanisms underlying this liver metastasis and associated candidate biomarkers are unknown. METHODS We performed mRNA profiling comparisons in 8 primary tumors (T) and 12 liver metastases (M) samples using the Gene Expression Omnibus (GEO) database. After determining differentially expressed genes (DEG), gene ontology (GO), pathway enrichment and protein-protein interaction (PPI) network analyses were performed to determine DEG functions. Then, Cytoscape was used to screen out significant hub genes, after which their clinical relevance was investigated using The Cancer Genome Atlas (TCGA) resources. Furthermore, prognosis-associated gene expression was validated using Oncomine and TCGA database. Lastly, associations between prognosis-associated genes, immune cells and immunological checkpoint genes were evaluated using the Tumor Immune Estimation Resource (TIMER). RESULTS In total, 102 genes were related to liver metastasis and predominantly involved in cell migration, motility, and adhesion. Using Cytoscape, this number was narrowed down to 16 hub genes. Elevated mRNA expression levels for two of these genes, SPARC (P = 0.019) and TPM1 (P = 0.037) were significantly correlated with poor disease prognosis. For the remaining 14, expression was not related to overall patient survival. SPARC had higher expression in patients with metastatic PDAC than those with non-metastatic PDAC in TCGA dataset. SPARC and TPM1 levels were also positively correlated with the immune infiltration of specific cell types. Additionally, both genes exhibited strong co-expression associations with immune checkpoint genes. CONCLUSIONS Combined, we suggest SPARC has high potential as biomarker to predict liver metastasis during PDAC. Additionally, both SPARC and TPM1 appeared to recruit and regulate immune-infiltrating cells during these pathophysiological processes.
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Affiliation(s)
- Hong Luan
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, People's Republic of China
| | - Ye He
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, People's Republic of China
| | - Tuo Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, People's Republic of China
| | - Yanna Su
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, People's Republic of China
| | - Liping Zhou
- Department of Post Graduation Training, The First Affiliated Hospital of China Medical University, No. 155, Nanjingbei Street, Heping District, Shenyang, Liaoning Province, 110001, People's Republic of China.
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Han J, Rong Y, Gao X. Multiomic analysis of the function of SPOCK1 across cancers: an integrated bioinformatics approach. J Int Med Res 2021; 49:300060520962659. [PMID: 34156309 PMCID: PMC8236807 DOI: 10.1177/0300060520962659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective To investigate SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 (SPOCK1) gene expression across The Cancer Genome Atlas (TCGA) cancers, both in cancer versus normal tissues and in different stages across the cancer types. Methods This integrated bioinformatics study used data from several bioinformatics databases (Cancer Cell Line Encyclopedia, Genotype-Tissue Expression, TCGA, Tumor Immune Estimation Resource [TIMER]) to define the expression pattern of the SPOCK1 gene. A survival analysis was undertaken across the cancers. The search tool for retrieval of interacting genes (STRING) database was used to identify proteins that interacted with SPOCK1. Gene Set Enrichment Analysis was conducted to determine pathway enrichment. The TIMER database was used to explore the correlation between SPOCK1 and immune cell infiltration. Results This multiomic analysis showed that the SPOCK1 gene was expressed differently between normal tissues and tumours in several cancers and that it was involved in cancer progression. The overexpression of the SPOCK1 gene was associated with poor clinical outcomes. Analysis of gene expression and tumour-infiltrating immune cells showed that SPOCK1 correlated with several immune cells across cancers. Conclusions This research showed that SPOCK1 might serve as a new target for several cancer therapies in the future.
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Affiliation(s)
- Jie Han
- Department of Hepatology, Qilu Hospital, Shandong University, Shandong, China
| | - Yihui Rong
- Infection Disease Center of Peking University International Hospital, Beijing, China
| | - Xudong Gao
- Infection Disease Center of Peking University International Hospital, Beijing, China
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Hou MX, Gao YL, Liu JX, Dai LY, Kong XZ, Shang J. Network analysis based on low-rank method for mining information on integrated data of multi-cancers. Comput Biol Chem 2018; 78:468-473. [PMID: 30563751 DOI: 10.1016/j.compbiolchem.2018.11.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 02/01/2023]
Abstract
The noise problem of cancer sequencing data has been a problem that can't be ignored. Utilizing considerable way to reduce noise of these cancer data is an important issue in the analysis of gene co-expression network. In this paper, we apply a sparse and low-rank method which is Robust Principal Component Analysis (RPCA) to solve the noise problem for integrated data of multi-cancers from The Cancer Genome Atlas (TCGA). And then we build the gene co-expression network based on the integrated data after noise reduction. Finally, we perform nodes and pathways mining on the denoising networks. Experiments in this paper show that after denoising by RPCA, the gene expression data tend to be orderly and neat than before, and the constructed networks contain more pathway enrichment information than unprocessed data. Moreover, learning from the betweenness centrality of the nodes in the network, we find some abnormally expressed genes and pathways proven that are associated with many cancers from the denoised network. The experimental results indicate that our method is reasonable and effective, and we also find some candidate suspicious genes that may be linked to multi-cancers.
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Affiliation(s)
- Mi-Xiao Hou
- School of Information Science and Engineering, Qufu Normal University, Rizhao, China
| | - Ying-Lian Gao
- Library of Qufu Normal University, Qufu Normal University, Rizhao, China
| | - Jin-Xing Liu
- School of Information Science and Engineering, Qufu Normal University, Rizhao, China; Co-Innovation Center for Information Supply & Assurance Technology, Anhui University, Hefei, China.
| | - Ling-Yun Dai
- School of Information Science and Engineering, Qufu Normal University, Rizhao, China
| | - Xiang-Zhen Kong
- School of Information Science and Engineering, Qufu Normal University, Rizhao, China
| | - Junliang Shang
- School of Information Science and Engineering, Qufu Normal University, Rizhao, China
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Adrianzen Herrera D, Ashai N, Perez-Soler R, Cheng H. Nanoparticle albumin bound-paclitaxel for treatment of advanced non-small cell lung cancer: an evaluation of the clinical evidence. Expert Opin Pharmacother 2018; 20:95-102. [DOI: 10.1080/14656566.2018.1546290] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Diego Adrianzen Herrera
- Department of Medical Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
| | - Nadia Ashai
- Department of Medical Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
| | - Roman Perez-Soler
- Department of Medical Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
| | - Haiying Cheng
- Department of Medical Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
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Diagnostic role of circulating extracellular matrix-related proteins in non-small cell lung cancer. BMC Cancer 2018; 18:899. [PMID: 30227835 PMCID: PMC6145327 DOI: 10.1186/s12885-018-4772-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/23/2018] [Indexed: 12/16/2022] Open
Abstract
Background Interactions between cancer cells and the surrounding microenvironment are crucial determinants of cancer progression. During this process, bi-directional communication among tumor cells and cancer associated fibroblasts (CAF) regulate extracellular matrix (ECM) deposition and remodeling. As a result of this dynamic process, soluble ECM proteins can be released into the bloodstream and may represent novel circulating biomarkers useful for cancer diagnosis. The aim of the present study was to measure the levels of three circulating ECM related proteins (COL11A1, COL10A1 and SPARC) in plasma samples of lung cancer patients and in healthy heavy-smokers controls and test whether such measurements have diagnostic or prognostic value. Methods Gene expression profiling of lung fibroblasts isolated from paired normal and cancer tissue of NSCLC patients was performed by gene expression microarrays. The prioritization of the candidates for the study of circulating proteins in plasma was based on the most differentially expressed genes in cancer associated fibroblasts. Soluble ECM proteins were assessed by western blot in the conditioned medium of lung fibroblasts and by ELISA assays in plasma samples. Results Plasma samples from lung cancer patients and healthy heavy-smokers controls were tested for levels of COL11A1 and COL10A1 (n = 57 each) and SPARC (n = 90 each). Higher plasma levels of COL10A1 were detected in patients (p ≤ 0.001), a difference that was driven specifically by females (p < 0.001). No difference in COL11A1 levels between patients and controls was found. SPARC levels were also higher in plasma patients than controls (p < 0.001) with good performance in discriminating the two groups (AUC = 0.744). No significant association was observed between plasma proteins levels and clinicopathological features or survival. Conclusion Soluble factors related to proficient tumor-stroma cross-talk are detectable in plasma of primary lung cancer patients and may represent a valuable complementary diagnostic tool to discriminate lung cancer patients from healthy heavy-smokers individuals as shown for the SPARC protein. Electronic supplementary material The online version of this article (10.1186/s12885-018-4772-0) contains supplementary material, which is available to authorized users.
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Zhao P, Wang Y, Wu A, Rao Y, Huang Y. Roles of Albumin-Binding Proteins in Cancer Progression and Biomimetic Targeted Drug Delivery. Chembiochem 2018; 19:1796-1805. [PMID: 29920893 DOI: 10.1002/cbic.201800201] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Indexed: 12/18/2022]
Abstract
Nutrient transporters have attracted significant attention for their promising application in biomimetic delivery. Due to the active consumption of nutrients, cancer cells generally overexpress nutrient transporters to meet their increased need for energy and materials. For example, albumin-binding proteins (ABPs) are highly overexpressed in malignant cells, stromal cells, and tumor vessel endothelial cells responsible for albumin uptake. ABP (e.g., SPARC) is a promising target for tumor-specific drug delivery, and albumin has been widely used as a biomimetic delivery carrier. Apart from the transportation function, ABPs are closely associated with neoplasia, invasion, and metastasis. Herein, a summary of the roles of ABP in cancer progression and the application of albumin-based biomimetic tumor-targeted delivery through the ABP pathway is presented.
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Affiliation(s)
- Pengfei Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, P.R. China.,Zhejiang Academy of Medical Science, 182 Tianmushan Road, Hangzhou, 310013, P.R. China
| | - Yonghui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, P.R. China
| | - Aihua Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, P.R. China
| | - Yuefeng Rao
- The First Affiliated Hospital of the College of Medicine, Zhejiang University, Hangzhou, 310003, P.R. China
| | - Yongzhuo Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
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Innovative methods for biomarker discovery in the evaluation and development of cancer precision therapies. Cancer Metastasis Rev 2018; 37:125-145. [PMID: 29392535 DOI: 10.1007/s10555-017-9710-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The discovery of biomarkers able to detect cancer at an early stage, to evaluate its aggressiveness, and to predict the response to therapy remains a major challenge in clinical oncology and precision medicine. In this review, we summarize recent achievements in the discovery and development of cancer biomarkers. We also highlight emerging innovative methods in biomarker discovery and provide insights into the challenges faced in their evaluation and validation.
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Kremer L, Schultz-Fademrecht C, Baumann M, Habenberger P, Choidas A, Klebl B, Kordes S, Schöler HR, Sterneckert J, Ziegler S, Schneider G, Waldmann H. Discovery of a Novel Inhibitor of the Hedgehog Signaling Pathway through Cell-based Compound Discovery and Target Prediction. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lea Kremer
- Abteilung für Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Germany
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Germany
| | | | - Matthias Baumann
- Lead Discovery Center GmbH; Otto-Hahn-Straße 15 44227 Dortmund Germany
| | - Peter Habenberger
- Lead Discovery Center GmbH; Otto-Hahn-Straße 15 44227 Dortmund Germany
| | - Axel Choidas
- Lead Discovery Center GmbH; Otto-Hahn-Straße 15 44227 Dortmund Germany
| | - Bert Klebl
- Lead Discovery Center GmbH; Otto-Hahn-Straße 15 44227 Dortmund Germany
| | - Susanne Kordes
- Lead Discovery Center GmbH; Otto-Hahn-Straße 15 44227 Dortmund Germany
- Abteilung Zell- und Entwicklungsbiologie; Max-Planck-Institut für Molekulare Biomedizin; Röntgenstraße 20 48149 Münster Germany
| | - Hans R. Schöler
- Abteilung Zell- und Entwicklungsbiologie; Max-Planck-Institut für Molekulare Biomedizin; Röntgenstraße 20 48149 Münster Germany
| | - Jared Sterneckert
- Abteilung Zell- und Entwicklungsbiologie; Max-Planck-Institut für Molekulare Biomedizin; Röntgenstraße 20 48149 Münster Germany
- DFG-Center for Regenerative Therapies; Cluster of Excellence; Technische Universität Dresden; Fetscherstr. 105 01307 Dresden Germany
| | - Slava Ziegler
- Abteilung für Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Gisbert Schneider
- Institut für Pharmazeutische Wissenschaften; Departement Chemie und Angewandte Biowissenschaften; ETH Zürich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Herbert Waldmann
- Abteilung für Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Germany
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Germany
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15
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Kremer L, Schultz-Fademrecht C, Baumann M, Habenberger P, Choidas A, Klebl B, Kordes S, Schöler HR, Sterneckert J, Ziegler S, Schneider G, Waldmann H. Discovery of a Novel Inhibitor of the Hedgehog Signaling Pathway through Cell-based Compound Discovery and Target Prediction. Angew Chem Int Ed Engl 2017; 56:13021-13025. [PMID: 28833911 DOI: 10.1002/anie.201707394] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Indexed: 01/20/2023]
Abstract
Cell-based assays enable monitoring of small-molecule bioactivity in a target-agnostic manner and help uncover new biological mechanisms. Subsequent identification and validation of the small-molecule targets, typically employing proteomics techniques, is very challenging and limited, in particular if the targets are membrane proteins. Herein, we demonstrate that the combination of cell-based bioactive-compound discovery with cheminformatic target prediction may provide an efficient approach to accelerate the process and render target identification and validation more efficient. Using a cell-based assay, we identified the pyrazolo-imidazole smoothib as a new inhibitor of hedgehog (Hh) signaling and an antagonist of the protein smoothened (SMO) with a novel chemotype. Smoothib targets the heptahelical bundle of SMO, prevents its ciliary localization, reduces the expression of Hh target genes, and suppresses the growth of Ptch+/- medulloblastoma cells.
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Affiliation(s)
- Lea Kremer
- Abteilung für Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | | | - Matthias Baumann
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany
| | - Peter Habenberger
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany
| | - Axel Choidas
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany
| | - Susanne Kordes
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227, Dortmund, Germany.,Abteilung Zell- und Entwicklungsbiologie, Max-Planck-Institut für Molekulare Biomedizin, Röntgenstraße 20, 48149, Münster, Germany
| | - Hans R Schöler
- Abteilung Zell- und Entwicklungsbiologie, Max-Planck-Institut für Molekulare Biomedizin, Röntgenstraße 20, 48149, Münster, Germany
| | - Jared Sterneckert
- Abteilung Zell- und Entwicklungsbiologie, Max-Planck-Institut für Molekulare Biomedizin, Röntgenstraße 20, 48149, Münster, Germany.,DFG-Center for Regenerative Therapies, Cluster of Excellence, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Slava Ziegler
- Abteilung für Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Gisbert Schneider
- Institut für Pharmazeutische Wissenschaften, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Herbert Waldmann
- Abteilung für Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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16
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Edwards RL, Odom John AR. Muddled mechanisms: recent progress towards antimalarial target identification. F1000Res 2016; 5:2514. [PMID: 27803804 PMCID: PMC5070598 DOI: 10.12688/f1000research.9477.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 01/06/2023] Open
Abstract
In the past decade, malaria rates have plummeted as a result of aggressive infection control measures and the adoption of artemisinin-based combination therapies (ACTs). However, a potential crisis looms ahead. Treatment failures to standard antimalarial regimens have been reported in Southeast Asia, and devastating consequences are expected if resistance spreads to the African continent. To prevent a potential public health emergency, the antimalarial arsenal must contain therapeutics with novel mechanisms of action (MOA). An impressive number of high-throughput screening (HTS) campaigns have since been launched, identifying thousands of compounds with activity against one of the causative agents of malaria,
Plasmodium falciparum. Now begins the difficult task of target identification, for which studies are often tedious, labor intensive, and difficult to interpret. In this review, we highlight approaches that have been instrumental in tackling the challenges of target assignment and elucidation of the MOA for hit compounds. Studies that apply these innovative techniques to antimalarial target identification are described, as well as the impact of the data in the field.
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Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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17
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Liu Z, Chen X. Simple bioconjugate chemistry serves great clinical advances: albumin as a versatile platform for diagnosis and precision therapy. Chem Soc Rev 2016; 45:1432-56. [PMID: 26771036 PMCID: PMC5227548 DOI: 10.1039/c5cs00158g] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Albumin is the most abundant circulating protein in plasma and has recently emerged as a versatile protein carrier for drug targeting and for improving the pharmacokinetic profile of peptide or protein based drugs. Three drug delivery technologies related to albumin have been developed, which include the coupling of low-molecular weight drugs to exogenous or endogenous albumin, conjugating bioactive proteins by albumin fusion technology (AFT), and encapsulation of drugs into albumin nanoparticles. This review article starts with a brief introduction of human serum albumin (HSA), and then summarizes the mainstream chemical strategies of developing HSA binding molecules for coupling with drug molecules. Moreover, we also concisely condense the recent progress of the most important clinical applications of HSA-binding platforms, and specify the current challenges that need to be met for a bright future of HSA-binding.
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Affiliation(s)
- Zhibo Liu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Kao SC, Kirschner MB, Cooper WA, Tran T, Burgers S, Wright C, Korse T, van den Broek D, Edelman J, Vallely M, McCaughan B, Pavlakis N, Clarke S, Molloy MP, van Zandwijk N, Reid G. A proteomics-based approach identifies secreted protein acidic and rich in cysteine as a prognostic biomarker in malignant pleural mesothelioma. Br J Cancer 2016; 114:524-31. [PMID: 26889976 PMCID: PMC4782201 DOI: 10.1038/bjc.2015.470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/19/2015] [Indexed: 12/29/2022] Open
Abstract
Background: We aimed to identify prognostic blood biomarkers using proteomics-based approaches in malignant pleural mesothelioma (MPM). Methods: Plasma samples from 12 MPM patients were used for exploratory mass spectrometry and ELISA analyses. The significance of secreted protein acidic and rich in cysteine (SPARC) was examined in sera from a Dutch series (n=97). To determine the source of the circulating SPARC, we investigated SPARC expression in MPM tumours and healthy controls, as well as the expression and secretion from cell lines and xenografts. Results: Secreted protein acidic and rich in cysteine was identified as a putative prognostic marker in plasma. Validation in the Dutch series showed that the median survival was higher in patients with low SPARC compared with those with high SPARC (19.0 vs 8.8 months; P=0.01). In multivariate analyses, serum SPARC remained as an independent predictor (HR 1.55; P=0.05). In MPM tumour samples, SPARC was present in the tumour cells and stromal fibroblasts. Cellular SPARC expression was higher in 5 out of 7 cell lines compared with two immortalized mesothelial lines. Neither cell lines nor xenograft tumours secreted detectable SPARC. Conclusions: Low circulating SPARC was associated with favourable prognosis. Secreted protein acidic and rich in cysteine was present in both tumour cells and stromal fibroblasts; and our in vitro and in vivo experiments suggest that stromal fibroblasts are a potential source of circulating SPARC.
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Affiliation(s)
- Steven C Kao
- Asbestos Diseases Research Institute, PO Box 3628, Rhodes, Sydney, NSW2139, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW 2050, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michaela B Kirschner
- Asbestos Diseases Research Institute, PO Box 3628, Rhodes, Sydney, NSW2139, Australia
| | - Wendy A Cooper
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia.,University of Western Sydney, Sydney, NSW 2150, Australia
| | - Thang Tran
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Sjaak Burgers
- Division of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Casey Wright
- Asbestos Diseases Research Institute, PO Box 3628, Rhodes, Sydney, NSW2139, Australia
| | - Tiny Korse
- Division of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Daan van den Broek
- Division of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - James Edelman
- Department of Cardiothoracic Surgery, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Michael Vallely
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Department of Cardiothoracic Surgery, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia.,Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Brian McCaughan
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Cardiothoracic Surgeons, RPAH Medical Centre, Sydney, NSW 2050, Australia
| | - Nick Pavlakis
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Stephen Clarke
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Nico van Zandwijk
- Asbestos Diseases Research Institute, PO Box 3628, Rhodes, Sydney, NSW2139, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Glen Reid
- Asbestos Diseases Research Institute, PO Box 3628, Rhodes, Sydney, NSW2139, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
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20
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Acosta-Martin AE, Lane L. Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics 2014; 11:269-84. [PMID: 24720436 DOI: 10.1586/14789450.2014.900446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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