1
|
Lee YB, Rhee HW. Spray-type modifications: an emerging paradigm in post-translational modifications. Trends Biochem Sci 2024; 49:208-223. [PMID: 38443288 DOI: 10.1016/j.tibs.2024.01.008] [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: 10/01/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/07/2024]
Abstract
A post-translational modification (PTM) occurs when a nucleophilic residue (e.g., lysine of a target protein) attacks electrophilic substrate molecules (e.g., acyl-AMP), involving writer enzymes or even occurring spontaneously. Traditionally, this phenomenon was thought to be sequence specific; however, recent research suggests that PTMs can also occur in a non-sequence-specific manner confined to a specific location in a cell. In this Opinion, we compile the accumulated evidence of spray-type PTMs and propose a mechanism for this phenomenon based on the exposure level of reactive electrophilic substrate molecules at the active site of the PTM writers. Overall, a spray-type PTM conceptual framework is useful for comprehending the promiscuous PTM writer events that cannot be adequately explained by the traditional concept of sequence-dependent PTM events.
Collapse
Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
2
|
Chen C, Chen M, Wen T, Anderson RA, Cryns VL. Regulation of NRF2 by Phosphoinositides and Small Heat Shock Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564194. [PMID: 37961303 PMCID: PMC10634847 DOI: 10.1101/2023.10.26.564194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Reactive oxygen species (ROS) are generated by aerobic metabolism, and their deleterious effects are buffered by the cellular antioxidant response, which prevents oxidative stress. The nuclear factor erythroid 2-related factor 2 (NRF2) is a master transcriptional regulator of the antioxidant response. Basal levels of NRF2 are kept low by ubiquitin-dependent degradation of NRF2 by E3 ligases, including the Kelch-like ECH-associated protein 1 (KEAP1). Here, we show that the stability and function of NRF2 is regulated by the type I phosphatidylinositol phosphate kinase g (PIPKIg), which binds NRF2 and transfers its product phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ) to NRF2. PtdIns(4,5)P 2 binding recruits the small heat shock protein HSP27 to the complex. Silencing PIPKIg or HSP27 destabilizes NRF2, reduces expression of its target gene HO-1, and sensitizes cells to oxidative stress. These data demonstrate an unexpected role of phosphoinositides and HSP27 in regulating NRF2 and point to PIPKIg and HSP27 as drug targets to destabilize NRF2 in cancer. In brief Phosphoinositides are coupled to NRF2 by PIPKIγ, and HSP27 is recruited and stabilizes NRF2, promoting stress-resistance.
Collapse
|
3
|
Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
Collapse
Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
| |
Collapse
|
4
|
Hmila I, Marnissi B, Kamali-Moghaddam M, Ghram A. Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus. Microbiol Spectr 2023; 11:e0208122. [PMID: 36651727 PMCID: PMC9927260 DOI: 10.1128/spectrum.02081-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus responsible for major health problems in the poultry industry. New virus strains continue to appear, causing large economic losses. To develop a rapid and accurate new quantitative assay for diagnosis of the virus without DNA extraction, we selected highly specific single-stranded DNA (ssDNA) aptamers with a high affinity to IBV, using the systematic evolution of ligands by exponential enrichment (SELEX) technology for aptamer screening, followed by high-throughput sequencing technology. Two of these aptamers, AptIBV5 and AptIBV2, were used to establish homogenous and solid-phase proximity ligation assays (PLAs). The developed assays were evaluated for their sensitivity and specificity using collected field samples and then compared to the newly developed sandwich enzyme-linked aptamer assay (ELAA) and reverse transcription-quantitative PCR (qRT-PCR), as the gold-standard method. The solid-phase PLA showed a lower limit of detection and a broader dynamic range than the two other assays. The developed technique may serve as an alternative assay for the diagnosis of IBV, with the potential to be extended to the detection of other important animal or human viruses. IMPORTANCE Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. To better monitor the emergence of this virus, the development of a rapid and highly sensitive diagnostic method should be implemented. For this, we generated aptamers with high affinity and specificity to the IBV in an ssDNA library. Using two high-affinity aptamers, we developed a sandwich ELAA and a very sensitive aptamer-based proximity ligation assay (PLA). The new assay showed high sensitivity and specificity and was used to detect IBV in farm samples. The PLA was compared to the newly developed sandwich ELAA and qRT-PCR, as the gold-standard technique.
Collapse
Affiliation(s)
- Issam Hmila
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Boutheina Marnissi
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
5
|
Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. MASS SPECTROMETRY REVIEWS 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [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: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
Collapse
Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
| |
Collapse
|
6
|
Liao C, Wang Q, An J, Chen J, Li X, Long Q, Xiao L, Guan X, Liu J. CD44 Glycosylation as a Therapeutic Target in Oncology. Front Oncol 2022; 12:883831. [PMID: 35936713 PMCID: PMC9351704 DOI: 10.3389/fonc.2022.883831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022] Open
Abstract
The interaction of non-kinase transmembrane glycoprotein CD44 with ligands including hyaluronic acid (HA) is closely related to the occurrence and development of tumors. Changes in CD44 glycosylation can regulate its binding to HA, Siglec-15, fibronectin, TM4SF5, PRG4, FGF2, collagen and podoplanin and activate or inhibit c-Src/STAT3/Twist1/Bmi1, PI3K/AKT/mTOR, ERK/NF-κB/NANOG and other signaling pathways, thereby having a profound impact on the tumor microenvironment and tumor cell fate. However, the glycosylation of CD44 is complex and largely unknown, and the current understanding of how CD44 glycosylation affects tumors is limited. These issues must be addressed before targeted CD44 glycosylation can be applied to treat human cancers.
Collapse
Affiliation(s)
- Chengcheng Liao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Jiaxing An
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jie Chen
- Department of Urology, The Third Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaolan Li
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Life Sciences Institute, Zunyi Medical University, Zunyi, China
| | - Qian Long
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Linlin Xiao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
| | - Xiaoyan Guan
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
| | - Jianguo Liu
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
- *Correspondence: Linlin Xiao, ; Xiaoyan Guan, ; Jianguo Liu,
| |
Collapse
|
7
|
Ultra-wide, attomolar-level limit detection of CD44 biomarker with a silanized optical fiber biosensor. Biosens Bioelectron 2022; 208:114217. [DOI: 10.1016/j.bios.2022.114217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
|
8
|
Xiao Y, Bi M, Guo H, Li M. Multi-omics approaches for biomarker discovery in early ovarian cancer diagnosis. EBioMedicine 2022; 79:104001. [PMID: 35439677 PMCID: PMC9035645 DOI: 10.1016/j.ebiom.2022.104001] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 12/03/2022] Open
Abstract
Ovarian cancer (OC) is a heterogeneous disease with the highest mortality rate and the poorest prognosis among gynecological malignancies. Because of the absence of specific early symptoms, most OC patients are often diagnosed at late stages. Thus, improved biomarkers of OC for use in research and clinical practice are urgently needed. The last decade has seen increasingly rapid advances in sequencing and biotechnological methodologies. Consequently, multiple omics technologies, including genomic/transcriptomic sequencings and proteomic/metabolomic mass spectra, have been widely applied to analyze tissue- and liquid-derived samples from OC patients. The integration of multi-omics data has increased our knowledge of the disease and identified valuable OC biomarkers. In this review, we summarize the recent advances and perspectives in the use of multi-omics technologies in OC research and highlight potential applications of multi-omics for identifying novel biomarkers and improving clinical assessments.
Collapse
Affiliation(s)
- Yinan Xiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing 10091, China
| | - Meiyu Bi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing 10091, China
| | - Hongyan Guo
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China
| | - Mo Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 10091, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing 10091, China.
| |
Collapse
|
9
|
Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue. Cancers (Basel) 2021; 14:cancers14010009. [PMID: 35008176 PMCID: PMC8750205 DOI: 10.3390/cancers14010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
In classical Hodgkin Lymphoma (cHL), immunoediting via protein signaling is key to evading tumor surveillance. We aimed to identify immune-related proteins that distinguish diagnostic cHL tissues (=diagnostic tumor lysates, n = 27) from control tissues (reactive lymph node lysates, n = 30). Further, we correlated our findings with the proteome plasma profile between cHL patients (n = 26) and healthy controls (n = 27). We used the proximity extension assay (PEA) with the OlinkTM multiplex Immuno-Oncology panel, consisting of 92 proteins. Univariate, multivariate-adjusted analysis and Benjamini–Hochberg’s false discovery testing (=Padj) were performed to detect significant discrepancies. Proteins distinguishing cHL cases from controls were more numerous in plasma (30 proteins) than tissue (17 proteins), all Padj < 0.05. Eight of the identified proteins in cHL tissue (PD-L1, IL-6, CCL17, CCL3, IL-13, MMP12, TNFRS4, and LAG3) were elevated in both cHL tissues and cHL plasma compared with control samples. Six proteins distinguishing cHL tissues from controls tissues were significantly correlated to PD-L1 expression in cHL tissue (IL-6, MCP-2, CCL3, CCL4, GZMB, and IFN-gamma, all p ≤0.05). In conclusion, this study introduces a distinguishing proteomic profile in cHL tissue and potential immune-related markers of pathophysiological relevance.
Collapse
|
10
|
Lin JC, Wang CC, Jiang RS, Wang WY, Liu SA. Application of proximity ligation assays to identify potential plasma biomarkers in oral cavity cancer patients: A case control study. Cancer Biomark 2021; 29:17-23. [PMID: 32568177 DOI: 10.3233/cbm-191195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Practical cancer biomarkers for oral cavity cancer are currently in limited use. OBJECTIVE We aimed to investigate the differences in soluble E-cadherin between patients with oral cavity cancer and matched healthy participants via Proximity Ligation Assay (PLA). METHODS Samples were taken from both patients diagnosed with oral cavity cancer, as well as non-cancerous participants. PLA was used to detect soluble E-cadherin and Cycle threshold (Ct) values derived from qPCR in order to calculate the number of starting amplicons. RESULTS In total, 74 patients with oral cavity cancer and 55 matched non-cancerous participants were included for final analysis. The Ct value of E-cadherin was found to be lower in oral cavity cancer patients when compared with that of the matched non-cancerous participants (20.72 ± 0.39 versus 21.27 ± 0.45, P< 0.001). Using a Ct value of 20.9 as a cut-off point, the sensitivity and specificity of discriminating patients with oral cavity cancer from the healthy controls was 63.5% and 87.3%, respectively. CONCLUSION Plasma soluble E-cadherin levels were significantly higher in patients with oral cavity cancer when compared with those from the matched non-cancerous participants.
Collapse
Affiliation(s)
- Jin-Ching Lin
- Department of Radiation Oncology, Changhua Christian Hospital, Changhua, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chen-Chi Wang
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Rong-San Jiang
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Wen-Yi Wang
- Department of Nursing, HungKuang University, Taichung, Taiwan
| | - Shih-An Liu
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan.,Center for Quality Management, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| |
Collapse
|
11
|
Marnissi B, Khalfaoui K, Ebai T, Marques Souza de Oliveira F, Ghram A, Kamali-Moghaddam M, Hmila I. Accurate detection of Newcastle disease virus using proximity-dependent DNA aptamer ligation assays. FEBS Open Bio 2021; 11:1122-1131. [PMID: 33595202 PMCID: PMC8016122 DOI: 10.1002/2211-5463.13117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/28/2021] [Accepted: 02/15/2021] [Indexed: 11/20/2022] Open
Abstract
Detecting viral antigens at low concentrations in field samples can be crucial for early veterinary diagnostics. Proximity ligation assays (PLAs) in both solution and solid‐phase formats are widely used for high‐performance protein detection in medical research. However, the affinity reagents used, which are mainly poly‐ and monoclonal antibodies, play an important role in the performance of PLAs. Here, we have established the first homogeneous and solid‐phase proximity‐dependent DNA aptamer ligation assays for rapid and accurate detection of Newcastle disease virus (NDV). NDV is detected by a pair of extended DNA aptamers that, upon binding in proximity to proteins on the envelope of the virus, are joined by enzymatic ligation to form a unique amplicon that can be sensitively detected using real‐time PCR. The sensitivity, specificity, and reproducibility of the assays were validated using 40 farm samples. The results demonstrated that the developed homogeneous and solid‐phase PLAs, which use NDV‐selective DNA aptamers, are more sensitive than the sandwich enzymatic‐linked aptamer assay (ELAA), and have a comparable sensitivity to real‐time reverse transcription PCR (rRT‐PCR) as the gold standard detection method. In addition, the solid‐phase PLA was shown to have a greater dynamic range with improved lower limit of detection, upper‐ and lower limit of quantification, and minimal detectable dose as compared with those of ELAA and rRT‐PCR. The specificity of PLA is shown to be concordant with rRT‐PCR.
Collapse
Affiliation(s)
- Boutheina Marnissi
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Khouloud Khalfaoui
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Tonge Ebai
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Issam Hmila
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
12
|
Proximity ligation assay: an ultrasensitive method for protein quantification and its applications in pathogen detection. Appl Microbiol Biotechnol 2021; 105:923-935. [PMID: 33427935 DOI: 10.1007/s00253-020-11049-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/27/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023]
Abstract
It is of great significance to establish sensitive and accurate pathogen detection methods, considering the continuous emergence or re-emergence of infectious diseases seriously influences the safety of human and animals. Proximity ligation assay (PLA) is developed for the sensitive protein detection and also can be used for the detection of pathogens. PLA employs aptamer or monoclonal/polyclonal antibody-nucleic acid complexes as proximity probes. When the paired proximity probes bind to the same target protein or protein complex, they will be adjacent to each other and form an amplifiable DNA sequence through ligation. Combining the specificity of enzyme-linked immunosorbent assay (ELISA) and sensitivity of polymerase chain reaction (PCR), PLA transforms the detection of protein into the detection of DNA nucleic acid sequence. Therefore, as an ultrasensitive protein assay, PLA has great potential for quantification, localization of protein, and clinical diagnostics. In this review, we summarize the basic principles of PLA and its applications in pathogen detection. KEY POINTS: • Different forms of proximity ligation assay are introduced. • Applications of proximity ligation assay in pathogen detection are summarized. • Proximity ligation assay is an ultrasensitive method to quantify protein and pathogen.
Collapse
|
13
|
Byrnes SA, Huynh T, Chang TC, Anderson CE, McDermott JJ, Oncina CI, Weigl BH, Nichols KP. Wash-Free, Digital Immunoassay in Polydisperse Droplets. Anal Chem 2020; 92:3535-3543. [DOI: 10.1021/acs.analchem.9b02526] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samantha A. Byrnes
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Toan Huynh
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Tim C. Chang
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Caitlin E. Anderson
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - James J. McDermott
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Ciela I. Oncina
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Bernhard H. Weigl
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Kevin P. Nichols
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| |
Collapse
|
14
|
Moreira IB, Pinto F, Gomes C, Campos D, Reis CA. Impact of Truncated O-glycans in Gastric-Cancer-Associated CD44v9 Detection. Cells 2020; 9:cells9020264. [PMID: 31973075 PMCID: PMC7072479 DOI: 10.3390/cells9020264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023] Open
Abstract
CD44 variant isoforms are often upregulated in cancer and associated with increased aggressive tumor phenotypes. The CD44v9 is one of the major protein splice variant isoforms expressed in human gastrointestinal cancer cells. Immunodetection of CD44 isoforms like CD44v9 in tumor tissue is almost exclusively performed by using specific monoclonal antibodies. However, the structural variability conferred by both the alternative splicing and CD44 protein glycosylation is disregarded. In the present work, we have evaluated the role of O-glycosylation using glycoengineered gastric cancer models in the detection of CD44v9 by monoclonal antibodies. We demonstrated, using different technical approaches, that the presence of immature O-glycan structures, such as Tn and STn, enhance CD44v9 protein detection. These findings can have significant implications in clinical applications mainly at the detection and targeting of this cancer-related CD44v9 isoform and highlight the utmost importance of considering glycan structures in cancer biomarker detection and in therapy targeting.
Collapse
Affiliation(s)
- Inês B. Moreira
- I3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (I.B.M.); (F.P.); (C.G.)
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Filipe Pinto
- I3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (I.B.M.); (F.P.); (C.G.)
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Catarina Gomes
- I3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (I.B.M.); (F.P.); (C.G.)
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Diana Campos
- I3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (I.B.M.); (F.P.); (C.G.)
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Correspondence: (D.C.); (C.A.R.)
| | - Celso A. Reis
- I3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (I.B.M.); (F.P.); (C.G.)
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence: (D.C.); (C.A.R.)
| |
Collapse
|
15
|
Altered glycosylation of glycodelin in endometrial carcinoma. J Transl Med 2020; 100:1014-1025. [PMID: 32205858 PMCID: PMC7312397 DOI: 10.1038/s41374-020-0411-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 01/14/2023] Open
Abstract
Glycodelin is a major glycoprotein expressed in reproductive tissues, like secretory and decidualized endometrium. It has several reproduction related functions that are dependent on specific glycosylation, but it has also been found to drive differentiation of endometrial carcinoma cells toward a less malignant phenotype. Here we aimed to elucidate whether the glycosylation and function of glycodelin is altered in endometrial carcinoma as compared with a normal endometrium. We carried out glycan structure analysis of glycodelin expressed in HEC-1B human endometrial carcinoma cells (HEC-1B Gd) by mass spectrometry glycomics strategies. Glycans of HEC-1B Gd were found to comprise a typical mixture of high-mannose, hybrid, and complex-type N-glycans, often containing undecorated LacNAc (Galβ1-4GlcNAc) antennae. However, several differences, as compared with previously reported glycan structures of normal human decidualized endometrium-derived glycodelin isoform, glycodelin-A (GdA), were also found. These included a lower level of sialylation and more abundant poly-LacNAc antennae, some of which are fucosylated. This allowed us to select lectins that showed different binding to these classes of glycodelin. Despite the differences in glycosylation between HEC-1B Gd and GdA, both showed similar inhibitory activity on trophoblast cell invasion and peripheral blood mononuclear cell proliferation. For the detection of cancer associated glycodelin, we established a novel in situ proximity-ligation based histochemical staining method using a specific glycodelin antibody and UEAI lectin. We found that the UEAI reactive glycodelin was abundant in endometrial carcinoma, but virtually absent in normal endometrial tissue even when glycodelin was strongly expressed. In conclusion, we established a histochemical staining method for the detection of endometrial carcinoma-associated glycodelin and showed that this specific glycodelin is exclusively expressed in cancer, not in normal endometrium. Similar methods can be used for studies of other glycoproteins.
Collapse
|
16
|
Dovgan I, Koniev O, Kolodych S, Wagner A. Antibody-Oligonucleotide Conjugates as Therapeutic, Imaging, and Detection Agents. Bioconjug Chem 2019; 30:2483-2501. [PMID: 31339691 DOI: 10.1021/acs.bioconjchem.9b00306] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibody-oligonucleotide conjugates (AOCs) are a novel class of synthetic chimeric biomolecules that has been continually gaining traction in different fields of modern biotechnology. This is mainly due to the unique combination of the properties of their two constituents, exceptional targeting abilities and antibody biodistribution profiles, in addition to an extensive scope of oligonucleotide functional and structural roles. Combining these two classes of biomolecules in one chimeric construct has therefore become an important milestone in the development of numerous biotechnological applications, including imaging (DNA-PAINT), detection (PLA, PEA), and therapeutics (targeted siRNA/antisense delivery). Numerous synthetic approaches have been developed to access AOCs ranging from stochastic chemical bioconjugation to site-specific conjugation with reactive handles, introduced into antibody sequences through protein engineering. This Review gives a general overview of the current status of AOC applications with a specific emphasis on the synthetic methods used for their preparation. The reported synthetic techniques are discussed in terms of their practical aspects and limitations. The importance of the development of novel methods for the facile generation of AOCs possessing a defined constitution is highlighted as a priority in AOC research to ensure the advance of their new applications.
Collapse
Affiliation(s)
- Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
| | - Oleksandr Koniev
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Sergii Kolodych
- Syndivia SAS , 650 Boulevard Gonthier d'Andernach , 67400 Illkirch-Graffenstaden , France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis , University of Strasbourg , 74 Route du Rhin , 67400 Illkirch-Graffenstaden , France
| |
Collapse
|
17
|
Mereiter S, Martins ÁM, Gomes C, Balmaña M, Macedo JA, Polom K, Roviello F, Magalhães A, Reis CA. O‐glycan truncation enhances cancer‐related functions of
CD
44 in gastric cancer. FEBS Lett 2019; 593:1675-1689. [DOI: 10.1002/1873-3468.13432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Stefan Mereiter
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Álvaro M. Martins
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Catarina Gomes
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Meritxell Balmaña
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Joana A. Macedo
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Karol Polom
- Department of Surgical Oncology Medical University of Gdansk Poland
- General Surgery and Surgical Oncology Department University of Siena Italy
| | - Franco Roviello
- General Surgery and Surgical Oncology Department University of Siena Italy
| | - Ana Magalhães
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
| | - Celso A. Reis
- I3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto Portugal
- IPATIMUP – Institute of Molecular Pathology and Immunology University of Porto Portugal
- Faculty of Medicine University of Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar University of Porto Portugal
| |
Collapse
|