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Reed TJ, Tyl MD, Tadych A, Troyanskaya OG, Cristea IM. Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts. Nat Methods 2024; 21:488-500. [PMID: 38361019 PMCID: PMC11249048 DOI: 10.1038/s41592-024-02179-9] [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: 04/06/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024]
Abstract
Protein-protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global PPIs in dynamic contexts. Tapioca predicts de novo interactions by integrating mass spectrometry interactome data from thermal/ion denaturation or cofractionation workflows with protein properties and tissue-specific functional networks. Focusing on the thermal proximity coaggregation method, we improved the experimental workflow. Finely tuned thermal denaturation afforded increased throughput, while cell lysis optimization enhanced protein detection from different subcellular compartments. The Tapioca workflow was next leveraged to investigate viral infection dynamics. Temporal PPIs were characterized during the reactivation from latency of the oncogenic Kaposi's sarcoma-associated herpesvirus. Together with functional assays, NUCKS was identified as a proviral hub protein, and a broader role was uncovered by integrating PPI networks from alpha- and betaherpesvirus infections. Altogether, Tapioca provides a web-accessible platform for predicting PPIs in dynamic contexts.
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Affiliation(s)
- Tavis J Reed
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew D Tyl
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Flatiron Institute, Simons Foundation, New York City, NY, USA.
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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2
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Liang T, Chen H, Liu L, Zheng Y, Ma Z, Min L, Zhang J, Wu L, Ma J, Liu Z, Zhang Q, Luo K, Hu D, Ji T, Yu X. Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis. Mol Cell Proteomics 2024; 23:100729. [PMID: 38309569 PMCID: PMC10933552 DOI: 10.1016/j.mcpro.2024.100729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/27/2023] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
Diagnosing, predicting disease outcome, and identifying effective treatment targets for virus-related cancers are lacking. Protein biomarkers have the potential to bridge the gap between prevention and treatment for these types of cancers. While it has been shown that certain antibodies against EBV proteins could be used to detect nasopharyngeal carcinoma (NPC), antibodies targeting are solely a tiny part of the about 80 proteins expressed by the EBV genome. Furthermore, it remains unclear what role other viruses play in NPC since many diseases are the result of multiple viral infections. For the first time, this study measured both IgA and IgG antibody responses against 646 viral proteins from 23 viruses in patients with NPC and control subjects using nucleic acid programmable protein arrays. Candidate seromarkers were then validated by ELISA using 1665 serum samples from three clinical cohorts. We demonstrated that the levels of five candidate seromarkers (EBV-BLLF3-IgA, EBV-BLRF2-IgA, EBV-BLRF2-IgG, EBV-BDLF1-IgA, EBV-BDLF1-IgG) in NPC patients were significantly elevated than controls. Additional examination revealed that NPC could be successfully diagnosed by combining the clinical biomarker EBNA1-IgA with the five anti-EBV antibodies. The sensitivity of the six-antibody signature at 95% specificity to diagnose NPC was comparable to the current clinically-approved biomarker combination, VCA-IgA, and EBNA1-IgA. However, the recombinant antigens of the five antibodies are easier to produce and standardize compared to the native viral VCA proteins. This suggests the potential replacement of the traditional VCA-IgA assay with the 5-antibodies combination to screen and diagnose NPC. Additionally, we investigated the prognostic significance of these seromarkers titers in NPC. We showed that NPC patients with elevated BLLF3-IgA and BDLF1-IgA titers in their serum exhibited significantly poorer disease-free survival, suggesting the potential of these two seromarkers as prognostic indicators of NPC. These findings will help develop serological tests to detect and treat NPC in the future.
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Affiliation(s)
- Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Hao Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Lei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhaoen Ma
- Otolaryngological department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Min
- Department of Laboratory Medicine, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jiahui Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Lianfu Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Zexian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Kai Luo
- Department of Laboratory Medicine, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Di Hu
- ProteomicsEra Medical Co., Ltd., Beijing, China
| | - Tianxing Ji
- Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
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3
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Carlton LH, McGregor R, Moreland NJ. Human antibody profiling technologies for autoimmune disease. Immunol Res 2023; 71:516-527. [PMID: 36690876 PMCID: PMC9870766 DOI: 10.1007/s12026-023-09362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery.
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Affiliation(s)
- Lauren H Carlton
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| | - Reuben McGregor
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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4
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Abstract
The protein array is a powerful platform to study humoral responses to infectious agents using small sample volumes [<3 μL]. Its success can be largely attributed to the development of new strategies for high-throughput cloning and expression, and improved manufacturing techniques for the construction of arrays. Here, we describe a method to hybridize protein arrays with malaria patients' sera in order to identify seroreactive antigens, some of which may have a high potential of conferring protection from severe forms of malaria.
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5
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Zhao T, Zhou Y, Wang Q, Yi X, Ge S, He H, Xue S, Du B, Ge J, Dong J, Qu L, Wang L, Zhou W. QPCT regulation by CTCF leads to sunitinib resistance in renal cell carcinoma by promoting angiogenesis. Int J Oncol 2021; 59:48. [PMID: 34036385 PMCID: PMC8208629 DOI: 10.3892/ijo.2021.5228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Sunitinib is widely used as a first‑line treatment for advanced renal cell carcinoma (RCC). However, a number of patients with RCC who receive sunitinib develop drug resistance; and the biological mechanisms involved in resistance to sunitinib remain unclear. It has previously been suggested that the protein glutaminyl‑peptide cyclotransferase (QPCT) is closely related to sunitinib resistance in RCC. Thus, in the present study, in order to further examine the molecular mechanisms responsible for sunitinib resistance in RCC, sunitinib‑non‑responsive and ‑responsive RCC tissue and plasma samples were collected and additional experiments were performed in order to elucidate the molecular mechanisms responsible for sunitinib resistance in RCC. The upstream and downstream regulatory mechanisms of QPCT were also evaluated. On the whole, the data from the present study suggest that QPCT, CCCTC‑binding factor (CTCF) and phosphatidylinositol‑4,5‑bisphosphate 3‑kinase catalytic subunit alpha (PIK3CA) may be used as targets for predicting, reversing and treating sunitinib‑resistant RCC.
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Affiliation(s)
- Tangliang Zhao
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Yulin Zhou
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
- Department of Urology, Xuzhou Central Hospital, Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Qingyun Wang
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Xiaoming Yi
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Silun Ge
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Haowei He
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Song Xue
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Bowen Du
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Jingping Ge
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Jie Dong
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Le Qu
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Wenquan Zhou
- Department of Urology, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, P.R. China
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6
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Detection of Posttranslational Modification Autoantibodies Using Peptide Microarray. Methods Mol Biol 2021. [PMID: 34115354 DOI: 10.1007/978-1-0716-1562-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Autoantibodies are humoral antibodies against self-proteins and play vital roles in maintaining the homeostasis. Autoantibodies can also target posttranslational modifications (PTMs) of proteins and the identification of new PTM autoantibodies is important to identify biomarkers for the early diagnosis of cancer and autoimmune diseases. In this chapter, we describe a method to detect PTM autoantibodies using citrullinated peptide microarray as an example. This method can be used to screen serum autoantibodies for different human diseases.
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7
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Tracking the Antibody Immunome in Sporadic Colorectal Cancer by Using Antigen Self-Assembled Protein Arrays. Cancers (Basel) 2021; 13:cancers13112718. [PMID: 34072782 PMCID: PMC8198956 DOI: 10.3390/cancers13112718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Immunome in Sporadic Colorectal Cancer as source for biomarkers. Hence, a self-assembled protein array has been designed and developed to perform a serum screening to determined specific immune response against tumor antigens proteins as potential diagnostics biomarker panel. Abstract Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.
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8
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Weng S, Wang M, Zhao Y, Ying W, Qian X. Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition. J Proteomics 2021; 238:104152. [PMID: 33609755 DOI: 10.1016/j.jprot.2021.104152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/21/2021] [Accepted: 02/08/2021] [Indexed: 12/27/2022]
Abstract
Proteomics is increasingly used for exploring disease biomarkers and therapeutic targets. The data-independent acquisition (DIA) method collects all peptide signals in a sample, and provides a convenient way to archive disease-related molecular features for further exploration. In this study, we first established a high-coverage human hepatocellular carcinoma (HCC) spectral library containing 9393 protein groups, 119,903 peptides. Furthermore, we optimised the DIA method with respect to four key parameters: settings for mass spectrometry acquisition, gradient length, amount of sample loading, and length of analytical column. More than 6000 proteins from HepG2 cells could be stably quantified using the optimised one-shot DIA approach with a 2 h gradient time. One-shot DIA identified a similar number of proteins as did multi-fraction data-dependent acquisition (DDA) from the same group of HCC samples, but at a quarter of the total acquisition time. DIA data could recapture the classification results obtained from DDA data, thus paving the way for large-scale, multi-centre proteomics analysis of clinical samples. SIGNIFICANCE: The organ-specific spectral library for HCC and the optimised 2 h DIA approach met the urgent demands for large-scale quantitative proteomics analysis of HCC clinical samples. Compared with multi-fraction-DDA, the optimised one-shot DIA could reach a similar identification while consuming shorter acquisition time, thus making it possible to analyse thousands of clinical samples.
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Affiliation(s)
- Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yingyi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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9
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Poulsen TBG, Karamehmedovic A, Aboo C, Jørgensen MM, Yu X, Fang X, Blackburn JM, Nielsen CH, Kragstrup TW, Stensballe A. Protein array-based companion diagnostics in precision medicine. Expert Rev Mol Diagn 2020; 20:1183-1198. [PMID: 33315478 DOI: 10.1080/14737159.2020.1857734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The development of companion diagnostics (CDx) will increase efficacy and cost-benefit markedly, compared to the currently prevailing trial-and-error approach for treatment. Recent improvements in high-throughput protein technology have resulted in large amounts of predictive biomarkers that are potentially useful components of future CDx assays. Current high multiplex protein arrays are suitable for discovery-based approaches, while low-density and more simple arrays are suitable for use in point-of-care facilities. AREA COVERED This review discusses the technical platforms available for protein array focused CDx, explains the technical details of the platforms and provide examples of clinical use, ranging from multiplex arrays to low-density clinically applicable arrays. We thereafter highlight recent predictive biomarkers within different disease areas, such as oncology and autoimmune diseases. Lastly, we discuss some of the challenges connected to the implementation of CDx assays as point-of-care tests. EXPERT OPINION Recent advances in the field of protein arrays have enabled high-density arrays permitting large biomarker discovery studies, which are beneficial for future CDx assays. The density of protein arrays range from a single protein to proteome-wide arrays, allowing the discovery of protein signatures that may correlate with drug response. Protein arrays will undoubtedly play a key role in future CDx assays.
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Affiliation(s)
- Thomas B G Poulsen
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Azra Karamehmedovic
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Christopher Aboo
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital , Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University , Aalborg, Denmark
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics , Beijing, China
| | - Xiangdong Fang
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , China
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa.,Sengenics Corporation Pte Ltd , Singapore
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet , Copenhagen, Denmark
| | - Tue W Kragstrup
- Department of Biomedicine, Aarhus University , Aarhus, Denmark.,Department of Rheumatology, Aarhus University Hospital , Aarhus, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark
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10
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Antibody Printing Technologies. Methods Mol Biol 2020. [PMID: 33237416 DOI: 10.1007/978-1-0716-1064-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.
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11
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Rauf F, Anderson KS, LaBaer J. Autoantibodies in Early Detection of Breast Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:2475-2485. [PMID: 32994341 PMCID: PMC7710604 DOI: 10.1158/1055-9965.epi-20-0331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
In spite of the progress made in treatment and early diagnosis, breast cancer remains a major public health issue worldwide. Although modern image-based screening modalities have significantly improved early diagnosis, around 15% to 20% of breast cancers still go undetected. In underdeveloped countries, lack of resources and cost concerns prevent implementing mammography for routine screening. Noninvasive, low-cost, blood-based markers for early breast cancer diagnosis would be an invaluable alternative that would complement mammography screening. Tumor-specific autoantibodies are excellent biosensors that could be exploited to monitor disease-specific changes years before disease onset. Although clinically informative autoantibody markers for early breast cancer screening have yet to emerge, progress has been made in the development of tools to discover and validate promising autoantibody signatures. This review focuses on the current progress toward the development of autoantibody-based early screening markers for breast cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Femina Rauf
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Karen S Anderson
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Joshua LaBaer
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona.
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12
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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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13
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Proteomic Technologies for Deciphering Local and Global Protein Interactions. Trends Biochem Sci 2020; 45:454-455. [DOI: 10.1016/j.tibs.2020.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 01/12/2023]
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14
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Köhler T, Heida T, Hoefgen S, Weigel N, Valiante V, Thiele J. Cell-free protein synthesis and in situ immobilization of deGFP-MatB in polymer microgels for malonate-to-malonyl CoA conversion. RSC Adv 2020; 10:40588-40596. [PMID: 35520868 PMCID: PMC9057574 DOI: 10.1039/d0ra06702d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
We describe a bottom-up approach towards functional enzymes utilizing microgels as carriers for genetic information that enable cell-free protein synthesis, in situ immobilization, and utilization of functional deGFP-MatB.
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Affiliation(s)
- Tony Köhler
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Thomas Heida
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Sandra Hoefgen
- Biobricks of Microbial Natural Product Syntheses
- Department of Molecular and Applied Microbiology
- Leibniz Institute for Natural Product Research and Infection Biology
- 07745 Jena
- Germany
| | - Niclas Weigel
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Vito Valiante
- Biobricks of Microbial Natural Product Syntheses
- Department of Molecular and Applied Microbiology
- Leibniz Institute for Natural Product Research and Infection Biology
- 07745 Jena
- Germany
| | - Julian Thiele
- Institute of Physical Chemistry and Polymer Physics
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
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15
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Zhao T, Bao Y, Gan X, Wang J, Chen Q, Dai Z, Liu B, Wang A, Sun S, Yang F, Wang L. DNA methylation-regulated QPCT promotes sunitinib resistance by increasing HRAS stability in renal cell carcinoma. Theranostics 2019; 9:6175-6190. [PMID: 31534544 PMCID: PMC6735520 DOI: 10.7150/thno.35572] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/26/2019] [Indexed: 01/04/2023] Open
Abstract
Rationale: Although sunitinib has been shown to improve the survival rate of advanced renal cell carcinoma (RCC) patients, poor drug response is a major challenge that reduces patient benefit. It is important to elucidate the underlying mechanism so that the therapeutic response to sunitinib can be restored. Methods: We used an Illumina HumanMethylation 850K microarray to find methylation-differentiated CpG sites between sunitinib-nonresponsive and -responsive RCC tissues and Sequenom MassARRAY methylation analysis to verify the methylation chip results. We verified glutaminyl peptide cyclotransferase (QPCT) expression in sunitinib-nonresponsive and -responsive RCC tissues via qRT-PCR, western blot and immunohistochemical assays. Then, cell counting kit 8 (CCK-8), plate colony formation and flow cytometric assays were used to verify the function of QPCT in RCC sunitinib resistance after QPCT intervention or overexpression. Chromatin immunoprecipitation (ChIP) was performed to clarify the upstream regulatory mechanism of QPCT. A human proteome microarray assay was used to identify downstream proteins that interact with QPCT, and co-immunoprecipitation (co-IP) and confocal laser microscopy were used to verify the protein chip results. Results: We found that the degree of methylation in the QPCT promoter region was significantly different between sunitinib-nonresponsive and -responsive RCC tissues. In the sunitinib-nonresponsive tissues, the degree of methylation in the QPCT promoter region was significantly reduced, and the expression of QPCT was upregulated, which correlated with a clinically poor response to sunitinib. A knockdown of QPCT conferred sunitinib sensitivity traits to RCC cells, whereas an overexpression of QPCT restored sunitinib resistance in RCC cells. Mechanistically, reducing the methylation degree of the QPCT promoter region by 5-aza-2'-deoxycytidine (decitabine) in RCC cells could increase the expression of QPCT and NF-κB (p65) bound to the QPCT promoter region, positively regulating its expression, while the hypermethylation in the QPCT promoter region could inhibit the binding of NF-κB (p65). QPCT could bind to HRAS and attenuate the ubiquitination of HRAS, thus increasing its stability and leading to the activation of the ERK pathway in RCC cells. Conclusion: QPCT may be a novel predictor of the response to sunitinib therapy in RCC patients and a potential therapeutic target.
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Affiliation(s)
- Tangliang Zhao
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yi Bao
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Xinxin Gan
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Jie Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Qiong Chen
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Zhihui Dai
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Bing Liu
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Shuhan Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
- Shanghai Key Laboratory of Cell Engineering, Second Military Medical University, Shanghai 200433, China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
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16
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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17
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Nevenzal H, Noach-Hirsh M, Skornik-Bustan O, Brio L, Barbiro-Michaely E, Glick Y, Avrahami D, Lahmi R, Tzur A, Gerber D. A high-throughput integrated microfluidics method enables tyrosine autophosphorylation discovery. Commun Biol 2019; 2:42. [PMID: 30729180 PMCID: PMC6353932 DOI: 10.1038/s42003-019-0286-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 12/21/2018] [Indexed: 01/22/2023] Open
Abstract
Autophosphorylation of receptor and non-receptor tyrosine kinases is a common molecular switch with broad implications for pathogeneses and therapy of cancer and other human diseases. Technologies for large-scale discovery and analysis of autophosphorylation are limited by the inherent difficulty to distinguish between phosphorylation and autophosphorylation in vivo and by the complexity associated with functional assays of receptors kinases in vitro. Here, we report a method for the direct detection and analysis of tyrosine autophosphorylation using integrated microfluidics and freshly synthesized protein arrays. We demonstrate the efficacy of our platform in detecting autophosphorylation activity of soluble and transmembrane tyrosine kinases, and the dependency of in vitro autophosphorylation assays on membranes. Our method, Integrated Microfluidics for Autophosphorylation Discovery (IMAD), is high-throughput, requires low reaction volumes and can be applied in basic and translational research settings. To our knowledge, it is the first demonstration of posttranslational modification analysis of membrane protein arrays.
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Affiliation(s)
- Hadas Nevenzal
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Meirav Noach-Hirsh
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Or Skornik-Bustan
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Lev Brio
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Efrat Barbiro-Michaely
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Yair Glick
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Dorit Avrahami
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Roxane Lahmi
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Amit Tzur
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
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18
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Kamuyu G, Tuju J, Kimathi R, Mwai K, Mburu J, Kibinge N, Chong Kwan M, Hawkings S, Yaa R, Chepsat E, Njunge JM, Chege T, Guleid F, Rosenkranz M, Kariuki CK, Frank R, Kinyanjui SM, Murungi LM, Bejon P, Färnert A, Tetteh KKA, Beeson JG, Conway DJ, Marsh K, Rayner JC, Osier FHA. KILchip v1.0: A Novel Plasmodium falciparum Merozoite Protein Microarray to Facilitate Malaria Vaccine Candidate Prioritization. Front Immunol 2018; 9:2866. [PMID: 30619257 PMCID: PMC6298441 DOI: 10.3389/fimmu.2018.02866] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
Passive transfer studies in humans clearly demonstrated the protective role of IgG antibodies against malaria. Identifying the precise parasite antigens that mediate immunity is essential for vaccine design, but has proved difficult. Completion of the Plasmodium falciparum genome revealed thousands of potential vaccine candidates, but a significant bottleneck remains in their validation and prioritization for further evaluation in clinical trials. Focusing initially on the Plasmodium falciparum merozoite proteome, we used peer-reviewed publications, multiple proteomic and bioinformatic approaches, to select and prioritize potential immune targets. We expressed 109 P. falciparum recombinant proteins, the majority of which were obtained using a mammalian expression system that has been shown to produce biologically functional extracellular proteins, and used them to create KILchip v1.0: a novel protein microarray to facilitate high-throughput multiplexed antibody detection from individual samples. The microarray assay was highly specific; antibodies against P. falciparum proteins were detected exclusively in sera from malaria-exposed but not malaria-naïve individuals. The intensity of antibody reactivity varied as expected from strong to weak across well-studied antigens such as AMA1 and RH5 (Kruskal–Wallis H test for trend: p < 0.0001). The inter-assay and intra-assay variability was minimal, with reproducible results obtained in re-assays using the same chip over a duration of 3 months. Antibodies quantified using the multiplexed format in KILchip v1.0 were highly correlated with those measured in the gold-standard monoplex ELISA [median (range) Spearman's R of 0.84 (0.65–0.95)]. KILchip v1.0 is a robust, scalable and adaptable protein microarray that has broad applicability to studies of naturally acquired immunity against malaria by providing a standardized tool for the detection of antibody correlates of protection. It will facilitate rapid high-throughput validation and prioritization of potential Plasmodium falciparum merozoite-stage antigens paving the way for urgently needed clinical trials for the next generation of malaria vaccines.
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Affiliation(s)
- Gathoni Kamuyu
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - James Tuju
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Biochemistry, Pwani University, Kilifi, Kenya
| | - Rinter Kimathi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Kennedy Mwai
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - James Mburu
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Nelson Kibinge
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Marisa Chong Kwan
- Arrayjet, Innovative Microarray Solutions, Edinburgh, United Kingdom
| | - Sam Hawkings
- Arrayjet, Innovative Microarray Solutions, Edinburgh, United Kingdom
| | - Reuben Yaa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Emily Chepsat
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - James M Njunge
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Timothy Chege
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Fatuma Guleid
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Micha Rosenkranz
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christopher K Kariuki
- Department of Tropical and Infectious Diseases, Institute of Primate Research, Nairobi, Kenya.,Cellular and Molecular Immunology, Vrije Universiteit Brussels, Brussels, Belgium
| | - Roland Frank
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Samson M Kinyanjui
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Biochemistry, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Linda M Murungi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Kevin K A Tetteh
- Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - James G Beeson
- Burnet Institute, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,African Academy of Sciences, Nairobi, Kenya
| | - Julian C Rayner
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Faith H A Osier
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.,Department of Biochemistry, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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19
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Abstract
INTRODUCTION Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method. Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.
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Affiliation(s)
- Xiaobo Yu
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Brianne Petritis
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Hu Duan
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Danke Xu
- c State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , China
| | - Joshua LaBaer
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
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20
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Yu X, Song L, Petritis B, Bian X, Wang H, Viloria J, Park J, Bui H, Li H, Wang J, Liu L, Yang L, Duan H, McMurray DN, Achkar JM, Magee M, Qiu J, LaBaer J. Multiplexed Nucleic Acid Programmable Protein Arrays. Theranostics 2017; 7:4057-4070. [PMID: 29109798 PMCID: PMC5667425 DOI: 10.7150/thno.20151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022] Open
Abstract
Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays. Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot. Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA. Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.
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Affiliation(s)
- Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Lusheng Song
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Brianne Petritis
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaofang Bian
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Haoyu Wang
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jennifer Viloria
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jin Park
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hoang Bui
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Han Li
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jie Wang
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Liuhui Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Hu Duan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - David N. McMurray
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Jacqueline M. Achkar
- Department of Medicine, Albert Einstein College of Medicine, NY 10461, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mitch Magee
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ji Qiu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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21
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Song L, Wallstrom G, Yu X, Hopper M, Van Duine J, Steel J, Park J, Wiktor P, Kahn P, Brunner A, Wilson D, Jenny-Avital ER, Qiu J, Labaer J, Magee DM, Achkar JM. Identification of Antibody Targets for Tuberculosis Serology using High-Density Nucleic Acid Programmable Protein Arrays. Mol Cell Proteomics 2017; 16:S277-S289. [PMID: 28223349 DOI: 10.1074/mcp.m116.065953] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/17/2017] [Indexed: 12/11/2022] Open
Abstract
Better and more diverse biomarkers for the development of simple point-of-care tests for active tuberculosis (TB), a clinically heterogeneous disease, are urgently needed. We generated a proteomic Mycobacterium tuberculosis (Mtb) High-Density Nucleic Acid Programmable Protein Array (HD-NAPPA) that used a novel multiplexed strategy for expedited high-throughput screening for antibody responses to the Mtb proteome. We screened sera from HIV uninfected and coinfected TB patients and controls (n = 120) from the US and South Africa (SA) using the multiplex HD-NAPPA for discovery, followed by deconvolution and validation through single protein HD-NAPPA with biologically independent samples (n = 124). We verified the top proteins with enzyme-linked immunosorbent assays (ELISA) using the original screening and validation samples (n = 244) and heretofore untested samples (n = 41). We identified 8 proteins with TB biomarker value; four (Rv0054, Rv0831c, Rv2031c and Rv0222) of these were previously identified in serology studies, and four (Rv0948c, Rv2853, Rv3405c, Rv3544c) were not known to elicit antibody responses. Using ELISA data, we created classifiers that could discriminate patients' TB status according to geography (US or SA) and HIV (HIV- or HIV+) status. With ROC curve analysis under cross validation, the classifiers performed with an AUC for US/HIV- at 0.807; US/HIV+ at 0.782; SA/HIV- at 0.868; and SA/HIV+ at 0.723. With this study we demonstrate a new platform for biomarker/antibody screening and delineate its utility to identify previously unknown immunoreactive proteins.
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Affiliation(s)
- Lusheng Song
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Garrick Wallstrom
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Xiaobo Yu
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Marika Hopper
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jennifer Van Duine
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jason Steel
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Jin Park
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Peter Wiktor
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287.,¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Peter Kahn
- ¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Al Brunner
- ¶Engineering Arts LLC, Tempe, Arizona 85287
| | - Douglas Wilson
- ‖Department of Internal Medicine, Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Ji Qiu
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - Joshua Labaer
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287
| | - D Mitchell Magee
- From the ‡The Virginia G Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona, 85287;
| | - Jacqueline M Achkar
- **Departments of Medicine and .,‡‡Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
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22
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Tagit O, Hildebrandt N. Fluorescence Sensing of Circulating Diagnostic Biomarkers Using Molecular Probes and Nanoparticles. ACS Sens 2017; 2:31-45. [PMID: 28722447 DOI: 10.1021/acssensors.6b00625] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interplay of photonics, nanotechnology, and biochemistry has significantly improved the identification and characterization of multiple types of biomarkers by optical biosensors. Great achievements in fluorescence-based technologies have been realized, for example, by the advancement of multiplexing techniques or the introduction of nanoparticles to biochemical and clinical research. This review presents a concise overview of recent advances in fluorescence sensing techniques for the detection of circulating disease biomarkers. Detection principles of representative approaches, including fluorescence detection using molecular fluorophores, quantum dots, and metallic and silica nanoparticles, are explained and illustrated by pertinent examples from the recent literature. Advanced detection technologies and material development play a major role in modern biosensing and consistently provide significant improvements toward robust, sensitive, and versatile platforms for early detection of circulating diagnostic biomarkers.
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Affiliation(s)
- Oya Tagit
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
- Department
of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Niko Hildebrandt
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
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23
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Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X. AAgAtlas 1.0: a human autoantigen database. Nucleic Acids Res 2016; 45:D769-D776. [PMID: 27924021 PMCID: PMC5210642 DOI: 10.1093/nar/gkw946] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 09/22/2016] [Accepted: 10/11/2016] [Indexed: 12/25/2022] Open
Abstract
Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sentences from PubMed using the keywords of either ‘autoantigen’ or ‘autoantibody’ or their lexical variants, which were further refined to 25 520 abstracts, 43 253 sentences and 3984 candidates by our bio-entity recognizer based on the Protein Ontology. Finally, we identified 1126 genes as human autoantigens and 1071 related human diseases, with which we constructed a human autoantigen database (AAgAtlas database 1.0). The database provides a user-friendly interface to conveniently browse, retrieve and download human autoantigens as well as their associated diseases. The database is freely accessible at http://biokb.ncpsb.org/aagatlas/. We believe this database will be a valuable resource to track and understand human autoantigens as well as to investigate their functions in basic and translational research.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Liuhui Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ping Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Henning Hermjakob
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China .,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China
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24
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Lakhanpal A, Brahn E. Biosimilars in rheumatic diseases: structural and functional variability that may impact clinical and regulatory decisions. Clin Rheumatol 2016; 35:2869-2875. [PMID: 27714482 DOI: 10.1007/s10067-016-3430-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 12/19/2022]
Abstract
Biologics as therapeutic interventions for human disease represent both a distinctly modern novelty and an echo of ancient, or at least old, medical practice. The similarity lies in the sense that in both the synthetic effort occurs in living organisms (an extract of a plant, animal tissue, or a cell culture) while the difference is apparent in the bioengineering required in modern methods and the corresponding flexibility to customize the therapeutic product. Although the concept of looking to living systems as a source of medically useful compounds either for research or for actual patient care has never vanished, the development of biochemistry and advances in medicinal chemistry made production by total synthesis the standard for a safe, reliable, and commercial drug production at sufficient scale. In this interval was where much of the modern apparatus for approving medical therapies came to be developed, and as such, the most proper extension of the regulatory regime to modern biologics is not entirely obvious. In particular, the notion of generics for off-patent conventional pharmaceuticals and their role in the marketplace with respect to increasing the accessibility of treatment is not congruent with the relationship between what are known as biosimilars and off-patent originating biologics. In this article, we review elements of the scientific basis for challenges in the production, use, and regulation of biosimilars. In light of these advances, we propose suggestions to modify constraints on biosimilar regulations in the interest of patient care and access to therapies.
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Affiliation(s)
- Amit Lakhanpal
- David Geffen UCLA School of Medicine, Los Angeles, CA, 90095, USA
| | - Ernest Brahn
- Division of Rheumatology, David Geffen UCLA School of Medicine, 1000 Veteran Ave., Room 32-59, Los Angeles, CA, 90095-1670, USA.
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