1
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Dou Y, Zhou X, Liu X, Hou J. Exoproteome analysis of Pseudomonas aeruginosa response to high alkane stress. Arch Microbiol 2024; 206:51. [PMID: 38175208 DOI: 10.1007/s00203-023-03749-9] [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: 09/14/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Microbial biodegradation serves as an effective approach to treat oil pollution. However, the application of such methods for the degrading long-chain alkanes still encounters significant challenges. Comparative proteomics has extensively studied the intracellular proteins of bacteria that degrade short- and medium-chain alkanes, but the role and mechanism of extracellular proteins in many microorganism remain unclear. To enhance our understanding of the roles of extracellular proteins in the adaptation to long-chain alkanes, a label-free LC-MS/MS strategy was applied for the relative quantification of extracellular proteins of Pseudomonas aeruginosa SJTD-1-M (ProteomeXchange identifier PXD014638). 444 alkane-sentitive proteins were acquired and their cell localization analysis was performed using the Pseudomonas Genome Database. Among them, 111 proteins were found to be located in extracellular or Outer Membrane Vesicles (OMVs). The alkane-induced abundance of 11 extracellular or OMV target proteins was confirmed by parallel reaction monitoring (PRM). Furthermore, we observed that the expression levels of three proteins (Pra, PA2815, and FliC) were associated with the carbon chain length of the added alkane in the culture medium. The roles of these proteins in cell mobility, alkane emulsification, assimilation, and degradation were further discussed. OMVs were found to contain a number of enzymes involved in alkane metabolism, fatty acid beta-oxidation, and the TCA cycle, suggesting their potential as sites for facilitated alkane degradation. In this sense, this exoproteome analysis contributes to a better understanding of the role of extracellular proteins in the hydrocarbon treatment process.
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Affiliation(s)
- Yue Dou
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Xuefeng Zhou
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Xipeng Liu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Jingli Hou
- Instrumental Analysis Center of Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China.
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Zhang C, Sheng Y, Sun X, Wang Y. New insights for gynecological cancer therapies: from molecular mechanisms and clinical evidence to future directions. Cancer Metastasis Rev 2023; 42:891-925. [PMID: 37368179 PMCID: PMC10584725 DOI: 10.1007/s10555-023-10113-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 05/22/2023] [Indexed: 06/28/2023]
Abstract
Advanced and recurrent gynecological cancers lack effective treatment and have poor prognosis. Besides, there is urgent need for conservative treatment for fertility protection of young patients. Therefore, continued efforts are needed to further define underlying therapeutic targets and explore novel targeted strategies. Considerable advancements have been made with new insights into molecular mechanisms on cancer progression and breakthroughs in novel treatment strategies. Herein, we review the research that holds unique novelty and potential translational power to alter the current landscape of gynecological cancers and improve effective treatments. We outline the advent of promising therapies with their targeted biomolecules, including hormone receptor-targeted agents, inhibitors targeting epigenetic regulators, antiangiogenic agents, inhibitors of abnormal signaling pathways, poly (ADP-ribose) polymerase (PARP) inhibitors, agents targeting immune-suppressive regulators, and repurposed existing drugs. We particularly highlight clinical evidence and trace the ongoing clinical trials to investigate the translational value. Taken together, we conduct a thorough review on emerging agents for gynecological cancer treatment and further discuss their potential challenges and future opportunities.
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Affiliation(s)
- Chunxue Zhang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030 People’s Republic of China
- Shanghai Municipal Key Clinical Specialty, Female Tumor Reproductive Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Yaru Sheng
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030 People’s Republic of China
- Shanghai Municipal Key Clinical Specialty, Female Tumor Reproductive Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Xiao Sun
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030 People’s Republic of China
- Shanghai Municipal Key Clinical Specialty, Female Tumor Reproductive Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030 People’s Republic of China
- Shanghai Municipal Key Clinical Specialty, Female Tumor Reproductive Specialty, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
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3
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Miedema IHC, Huisman MC, Zwezerijnen GJC, Grempler R, Pitarch AP, Thiele A, Hesse R, Elgadi M, Peltzer A, Vugts DJ, van Dongen GAMS, de Gruijl TD, Menke-van der Houven van Oordt CW, Bahce I. 89Zr-immuno-PET using the anti-LAG-3 tracer [ 89Zr]Zr-BI 754111: demonstrating target specific binding in NSCLC and HNSCC. Eur J Nucl Med Mol Imaging 2023; 50:2068-2080. [PMID: 36859619 PMCID: PMC10199858 DOI: 10.1007/s00259-023-06164-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/18/2023] [Indexed: 03/03/2023]
Abstract
PURPOSE Although lymphocyte activation gene-3 (LAG-3) directed therapies demonstrate promising clinical anti-cancer activity, only a subset of patients seems to benefit and predictive biomarkers are lacking. Here, we explored the potential use of the anti-LAG-3 antibody tracer [89Zr]Zr-BI 754111 as a predictive imaging biomarker and investigated its target specific uptake as well as the correlation of its tumor uptake and the tumor immune infiltration. METHODS Patients with head and neck (N = 2) or lung cancer (N = 4) were included in an imaging substudy of a phase 1 trial with BI 754091 (anti-PD-1) and BI 754111 (anti-LAG-3). After baseline tumor biopsy and [18F]FDG-PET, patients were given 240 mg of BI 754091, followed 8 days later by administration of [89Zr]Zr-BI 754111 (37 MBq, 4 mg). PET scans were performed 2 h, 96 h, and 144 h post-injection. To investigate target specificity, a second tracer administration was given two weeks later, this time with pre-administration of 40 (N = 3) or 600 mg (N = 3) unlabeled BI 754111, followed by PET scans at 96 h and 144 h post-injection. Tumor immune cell infiltration was assessed by immunohistochemistry and RNA sequencing. RESULTS Tracer uptake in tumors was clearly visible at the 4-mg mass dose (tumor-to-plasma ratio 1.63 [IQR 0.37-2.89]) and could be saturated by increasing mass doses (44 mg: 0.67 [IQR 0.50-0.85]; 604 mg: 0.56 [IQR 0.42-0.75]), demonstrating target specificity. Tumor uptake correlated to immune cell-derived RNA signatures. CONCLUSIONS [89Zr]Zr-BI-754111 PET imaging shows favorable technical and biological characteristics for developing a potential predictive imaging biomarker for LAG-3-directed therapies. TRIAL REGISTRATION ClinicalTrials.gov , NCT03780725. Registered 19 December 2018.
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Affiliation(s)
- Iris H C Miedema
- Department of Medical Oncology, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Marc C Huisman
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Gerben J C Zwezerijnen
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Rolf Grempler
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Alejandro Perez Pitarch
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88400, Biberach and der Riss, Germany
| | - Andrea Thiele
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88400, Biberach and der Riss, Germany
| | - Raphael Hesse
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88400, Biberach and der Riss, Germany
| | - Mabrouk Elgadi
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Alexander Peltzer
- Department of Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88400, Biberach and der Riss, Germany
| | - Danielle J Vugts
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Guus A M S van Dongen
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Tanja D de Gruijl
- Department of Medical Oncology, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, De Boelelaan 1117, 1018 HV, Amsterdam, the Netherlands
| | - C Willemien Menke-van der Houven van Oordt
- Department of Medical Oncology, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.
| | - Idris Bahce
- Imaging and Biomarkers, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
- Department of Pulmonary Medicine, Amsterdam UMC location Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
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Wei D, Horton KL, Chen J, Dong L, Chen S, Abdul-Hadi K, Zhang TT, Casson CN, Shaw M, Shiraishi T, Wilkinson B, Ji C, Qian MG. Development of a Highly Sensitive Hybrid LC/MS Assay for the Quantitative Measurement of CTLA-4 in Human T Cells. Molecules 2023; 28:molecules28083311. [PMID: 37110545 PMCID: PMC10142971 DOI: 10.3390/molecules28083311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is a check point protein expressed on the surface of T cells and plays a central role in regulating the immune response. In recent years, CTLA-4 has become a popular target for cancer immunotherapy in which blocking CTLA-4 can restore T-cell function and enhance the immune response against cancer. Currently, there are many CTLA-4 inhibitors in a variety of modalities, including cell therapies, which are being developed in both preclinical and clinical stages to further harness the potential of the target for the treatment of certain types of cancer. In drug discovery research, measuring the level of CTLA-4 in T cells is important for drug discovery and development because it provides key information for quantitative assessment of the pharmacodynamics, efficacy, and safety of the CTLA-4-based therapies. However, to our best knowledge, there is still no report of a sensitive, specific, accurate, and reliable assay for CTLA-4 measurement. In this work, an LC/MS-based method was developed to measure CTLA-4 in human T cells. The assay demonstrated high specificity with an LLOQ of 5 copies of CTLA-4 per cell when using 2.5 million T cells for analysis. As shown in the work, the assay was successfully used to measure CTLA-4 levels in subtype T-cell samples from individual healthy subjects. The assay could be applied in supporting the studies of CTLA-4-based cancer therapies.
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Affiliation(s)
- Dong Wei
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Kristin L Horton
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - John Chen
- NovaBioAssays LLC, 52 Dragon Ct, Suite 3B, Woburn, MA 01801, USA
| | - Linlin Dong
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Susan Chen
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Kojo Abdul-Hadi
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Ting Ting Zhang
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Cierra N Casson
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Michael Shaw
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Tsubasa Shiraishi
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Brandon Wilkinson
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
| | - Chengjie Ji
- NovaBioAssays LLC, 52 Dragon Ct, Suite 3B, Woburn, MA 01801, USA
| | - Mark G Qian
- Takeda Pharmaceutical Company International Co., 35 Landsdowne Street, Cambridge, MA 02139, USA
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5
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Ackermann BL, Morrison RD, Hill S, Westfall MD, Butts BD, Soper MD, Fill JA, Schade AE, Liebler DC, Gruver AM. Targeted Quantitative Mass Spectrometry Analysis of Protein Biomarkers From Previously Stained Single Formalin-Fixed Paraffin-Embedded Tissue Sections. J Transl Med 2023; 103:100052. [PMID: 36870295 DOI: 10.1016/j.labinv.2022.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Formalin-fixed, paraffin-embedded tissues represent a majority of all biopsy specimens commonly analyzed by histologic or immunohistochemical staining with adhesive coverslips attached. Mass spectrometry (MS) has recently been used to precisely quantify proteins in samples consisting of multiple unstained formalin-fixed, paraffin-embedded sections. Here, we report an MS method to analyze proteins from a single coverslipped 4-μm section previously stained with hematoxylin and eosin, Masson trichrome, or 3,3'-diaminobenzidine-based immunohistochemical staining. We analyzed serial unstained and stained sections from non-small cell lung cancer specimens for proteins of varying abundance (PD-L1, RB1, CD73, and HLA-DRA). Coverslips were removed by soaking in xylene, and after tryptic digestion, peptides were analyzed by targeted high-resolution liquid chromatography with tandem MS with stable isotope-labeled peptide standards. The low-abundance proteins RB1 and PD-L1 were quantified in 31 and 35 of 50 total sections analyzed, respectively, whereas higher abundance CD73 and HLA-DRA were quantified in 49 and 50 sections, respectively. The inclusion of targeted β-actin measurement enabled normalization in samples where residual stain interfered with bulk protein quantitation by colorimetric assay. Measurement coefficient of variations for 5 replicate slides (hematoxylin and eosin stained vs unstained) from each block ranged from 3% to 18% for PD-L1, from 1% to 36% for RB1, 3% to 21% for CD73, and 4% to 29% for HLA-DRA. Collectively, these results demonstrate that targeted MS protein quantification can add a valuable data layer to clinical tissue specimens after assessment for standard pathology end points.
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Affiliation(s)
| | | | | | | | - Brent D Butts
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Michael D Soper
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jeff A Fill
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Andrew E Schade
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | - Aaron M Gruver
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana.
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6
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Stevenson VB, Klahn S, LeRoith T, Huckle WR. Canine melanoma: A review of diagnostics and comparative mechanisms of disease and immunotolerance in the era of the immunotherapies. Front Vet Sci 2023; 9:1046636. [PMID: 36686160 PMCID: PMC9853198 DOI: 10.3389/fvets.2022.1046636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Melanomas in humans and dogs are highly malignant and resistant to therapy. Since the first development of immunotherapies, interest in how the immune system interacts within the tumor microenvironment and plays a role in tumor development, progression, or remission has increased. Of major importance are tumor-infiltrating lymphocytes (TILs) where distribution and cell frequencies correlate with survival and therapeutic outcomes. Additionally, efforts have been made to identify subsets of TILs populations that can contribute to a tumor-promoting or tumor-inhibiting environment, such as the case with T regulatory cells versus CD8 T cells. Furthermore, cancerous cells have the capacity to express certain inhibitory checkpoint molecules, including CTLA-4, PD-L1, PD-L2, that can suppress the immune system, a property associated with poor prognosis, a high rate of recurrence, and metastasis. Comparative oncology brings insights to comprehend the mechanisms of tumorigenesis and immunotolerance in humans and dogs, contributing to the development of new therapeutic agents that can modulate the immune response against the tumor. Therapies that target signaling pathways such as mTOR and MEK/ERK that are upregulated in cancer, or immunotherapies with different approaches such as CAR-T cells engineered for specific tumor-associated antigens, DNA vaccines using human tyrosinase or CGSP-4 antigen, anti-PD-1 or -PD-L1 monoclonal antibodies that intercept their binding inhibiting the suppression of the T cells, and lymphokine-activated killer cells are already in development for treating canine tumors. This review provides concise and recent information about diagnosis, comparative mechanisms of tumor development and progression, and the current status of immunotherapies directed toward canine melanoma.
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Affiliation(s)
- Valentina B. Stevenson
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Shawna Klahn
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States,Small Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - William R. Huckle
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States,*Correspondence: William R. Huckle ✉
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VISTA, PDL-L1, and BRAF-A Review of New and Old Markers in the Prognosis of Melanoma. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58010074. [PMID: 35056382 PMCID: PMC8778318 DOI: 10.3390/medicina58010074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 12/26/2022]
Abstract
Melanoma is currently known as one of the most aggressive malignant tumors. The prognostic factors and particularities of this neoplasm are a persistent hot topic in the medical field. This review has multiple purposes. First, we aim to summarize the known data regarding the histological and immunohistochemical appearance of this versatile tumor and to look further into the analysis of several widely used prognostic markers, such as B-Raf proto-oncogene, serine/threonine kinase BRAF. The second purpose is to analyze the data on the new prognostic markers, V-domain Immunoglobulin Suppressor of T cell Activation (VISTA) and Programmed death-ligand 1 (PD-L1). VISTA is a novel target that is considered to be highly important in determining the invasive potential and treatment response of a melanoma, and there are currently only a limited number of studies describing its role. PD-L1 is a marker with whose importance has been revealed in multiple types of malignancies, but its exact role regarding melanoma remains under investigation. In conclusion, the gathered data highlights the importance of correlations between these markers toward providing patients with a better outcome.
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8
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Wang P, Tang L, Zhou B, Cheng L, Zhao RC, Zhang J. Analytical methods for the detection of PD-1/PD-L1 and other molecules related to immune checkpoints. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Yoon SJ, Lee CB, Chae SU, Jo SJ, Bae SK. The Comprehensive "Omics" Approach from Metabolomics to Advanced Omics for Development of Immune Checkpoint Inhibitors: Potential Strategies for Next Generation of Cancer Immunotherapy. Int J Mol Sci 2021; 22:6932. [PMID: 34203237 PMCID: PMC8268114 DOI: 10.3390/ijms22136932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022] Open
Abstract
In the past decade, immunotherapies have been emerging as an effective way to treat cancer. Among several categories of immunotherapies, immune checkpoint inhibitors (ICIs) are the most well-known and widely used options for cancer treatment. Although several studies continue, this treatment option has yet to be developed into a precise application in the clinical setting. Recently, omics as a high-throughput technique for understanding the genome, transcriptome, proteome, and metabolome has revolutionized medical research and led to integrative interpretation to advance our understanding of biological systems. Advanced omics techniques, such as multi-omics, single-cell omics, and typical omics approaches, have been adopted to investigate various cancer immunotherapies. In this review, we highlight metabolomic studies regarding the development of ICIs involved in the discovery of targets or mechanisms of action and assessment of clinical outcomes, including drug response and resistance and propose biomarkers. Furthermore, we also discuss the genomics, proteomics, and advanced omics studies providing insights and comprehensive or novel approaches for ICI development. The overview of ICI studies suggests potential strategies for the development of other cancer immunotherapies using omics techniques in future studies.
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Affiliation(s)
| | | | | | | | - Soo Kyung Bae
- College of Pharmacy and Integrated Research Institute of Pharmaceutical Sciences, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon 14662, Korea; (S.J.Y.); (C.B.L.); (S.U.C.); (S.J.J.)
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10
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Stevenson VB, Perry SN, Todd M, Huckle WR, LeRoith T. PD-1, PD-L1, and PD-L2 Gene Expression and Tumor Infiltrating Lymphocytes in Canine Melanoma. Vet Pathol 2021; 58:692-698. [PMID: 34169800 DOI: 10.1177/03009858211011939] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Melanoma in humans and dogs is considered highly immunogenic; however, the function of tumor-infiltrating lymphocytes (TILs) is often suppressed in the tumor microenvironment. In humans, current immunotherapies target checkpoint molecules (such as PD-L1, expressed by tumor cells), inhibiting their suppressive effect over TILs. The role of PD-L2, an alternative PD-1 ligand also overexpressed in malignant tumors and in patients with anti-PD-L1 resistance, remains poorly understood. In the current study, we evaluated the expression of checkpoint molecule mRNAs in canine melanoma and TILs. Analysis of checkpoint molecule gene expression was performed by RT-qPCR (real-time quantitative polymerase chain reaction) using total RNA isolated from formalin-fixed and paraffin-embedded melanomas (n = 22) and melanocytomas (n = 9) from the Virginia Tech Animal Laboratory Services archives. Analysis of checkpoint molecule expression revealed significantly higher levels of PDCD1 (PD-1) and CD274 (PD-L1) mRNAs and an upward trend in PDCD1LG2 (PD-L2) mRNA in melanomas relative to melanocytomas. Immunohistochemistry revealed markedly increased numbers of CD3+ T cells in the highest PD-1-expressing subgroup of melanomas compared to the lowest PD-1 expressors, whereas densities of IBA1+ cells (macrophages) were similar in both groups. CD79a+ cell numbers were low for both groups. As in human melanoma, overexpression of the PD-1/PD-L1/PD-L2 axis is a common feature of canine melanoma. High expression of PD-1 and PD-L1 correlates with increased numbers of CD3+ cells. Additionally, the high level of IBA1+ cells in melanomas with low PD-1 expression and low CD3+ cells levels suggest that the expression of checkpoint molecules is modulated by interactions between T cells and cancer cells rather than histiocytes.
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11
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Zhu Y, Zalaznick J, Sleczka B, Parrish K, Yang Z, Olah T, Shipkova P. Immunoaffinity microflow liquid chromatography/tandem mass spectrometry for the quantitation of PD1 and PD-L1 in human tumor tissues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8896. [PMID: 32666620 DOI: 10.1002/rcm.8896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE High tumor expression of programmed cell death protein (PD1) and programmed death-ligand 1 (PD-L1) is thought to be associated with positive clinical outcomes after treatment with anti-PD1 or anti-PD-L1 agents. Several sensitive methods based on immunohistochemistry, ligand binding assay (LBA), and liquid chromatography/mass spectrometry involving the measurement of PD1 and PD-L1 expression have been reported. Here, we expand on the characterization of different tumor types using a highly specific, sensitive, and robust immunoaffinity liquid chromatography/tandem mass spectrometry (IA-LC/MS/MS)-based method for the simultaneous quantitation of PD1 and PD-L1 in tumor tissues. METHODS Human tumor tissue samples were homogenized using a Precellys Evolution homogenizer. The samples were incubated with anti-PD1 and anti-PD-L1 capture polyclonal antibodies, which were bound to magnetic beads. Following enrichment, samples were digested with trypsin. A Waters iKEY HSS T3 1.8 um (150 μm × 100 mm) column with a gradient flow rate of 3 μL/min was used for chromatographic separation, and a Waters TQ-S triple quadrupole mass spectrometer was used for detection. Selected reaction monitoring (SRM) transitions with unit resolution for precursor/product ion masses were optimized for PD1 and PD-L1 surrogate peptides. RESULTS The surrogate peptides LAAFPEDR for PD1 and FTVTVPK for PD-L1 yielded the most intense SRM transitions at m/z 459.7 > 516.2 and m/z 396.2 > 543.3, respectively, and thus were selected for the quantitation of PD1 and PD-L1. The lower limit of quantitation for PD1 and PD-L1 was 0.062 ng/mL with an assay range up to 10 ng/mL. Using this method, human PD1 and PD-L1 were detected and quantified from four different types of tumor tissues. The data show that PD1 expression level was highly correlated with that of PD-L1 in all tumor tissues analyzed here. CONCLUSIONS A highly specific and sensitive immunoaffinity microflow LC/MS/MS method for the simultaneous quantification of PD1 and PD-L1 in tumor tissues was developed and implemented. This method combines the advantage of immuno-capture for analyte enrichment with the high specificity of detection of multiple surrogate peptides by LC/MS/MS. The quantification of PD1 and PD-L1 co-expression in tumor could help evaluate their role in assessing tumor type selection and patient stratification.
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Affiliation(s)
- Yongxin Zhu
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jacob Zalaznick
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Bogdan Sleczka
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Karen Parrish
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Zheng Yang
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Timothy Olah
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Petia Shipkova
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
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Zheng N, Taylor K, Gu H, Santockyte R, Wang XT, McCarty J, Adelakun O, Zhang YJ, Pillutla R, Zeng J. Antipeptide Immunocapture with In-Sample Calibration Curve Strategy for Sensitive and Robust LC-MS/MS Bioanalysis of Clinical Protein Biomarkers in Formalin-Fixed Paraffin-Embedded Tumor Tissues. Anal Chem 2020; 92:14713-14722. [PMID: 33047598 DOI: 10.1021/acs.analchem.0c03271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite huge promises, bioanalysis of protein biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for clinical applications is still very challenging. Here, we describe a sensitive and robust LC-MS/MS assay to quantify clinical protein biomarkers in FFPE tumor sections using automated antipeptide antibody immunocapture followed by in-sample calibration curve (ISCC) strategy with multiple isotopologue reaction monitoring (MIRM) technique. ISCC approach with MIRM of stable isotopically labeled (SIL) peptides eliminated the need for authentic matrices for external calibration curves, overcame the matrix effects, and validated the quantification range in each individual sample. Specifically, after deparaffinization, rehydration, antigen retrieval, and homogenization, the protein analytes in FFPE tumor tissues were spiked with a known concentration of one SIL peptide for each analyte, followed by trypsin digestion and antipeptide immunocapture enrichment prior to MIRM-ISCC-based LC-MS/MS analysis. This approach has been successfully used for sensitive quantification of programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) in 15 representative FFPE tumor samples from lung, colorectal, and head and neck cancer patients. Except for one sample, PD-L1 and PD-1 in all samples were quantifiable using this assay with concentrations of 27.85-798.43 (amol/μg protein) for PD-L1 and 16.96-129.89 (amol/μg protein) for PD-1. These results were generally in agreement with the immunohistochemistry (IHC) data but with some exceptions. This approach demonstrated the feasibility to quantify low abundant protein biomarkers in FFPE tissues with improved sensitivity, specificity, and robustness and showed great potential as an orthogonal analytical approach to IHC for clinical applications.
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Affiliation(s)
- Naiyu Zheng
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Kristin Taylor
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Huidong Gu
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rasa Santockyte
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xi-Tao Wang
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jean McCarty
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Olufemi Adelakun
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Yan J Zhang
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Renuka Pillutla
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jianing Zeng
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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13
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Van Gool A, Corrales F, Čolović M, Krstić D, Oliver-Martos B, Martínez-Cáceres E, Jakasa I, Gajski G, Brun V, Kyriacou K, Burzynska-Pedziwiatr I, Wozniak LA, Nierkens S, Pascual García C, Katrlik J, Bojic-Trbojevic Z, Vacek J, Llorente A, Antohe F, Suica V, Suarez G, t'Kindt R, Martin P, Penque D, Martins IL, Bodoki E, Iacob BC, Aydindogan E, Timur S, Allinson J, Sutton C, Luider T, Wittfooth S, Sammar M. Analytical techniques for multiplex analysis of protein biomarkers. Expert Rev Proteomics 2020; 17:257-273. [PMID: 32427033 DOI: 10.1080/14789450.2020.1763174] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research. AREAS COVERED We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses. EXPERT COMMENTARY The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.
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Affiliation(s)
- Alain Van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Fernado Corrales
- Functional Proteomics Laboratory, Centro Nacional De Biotecnología , Madrid, Spain
| | - Mirjana Čolović
- Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, University of Belgrade , Belgrade, Serbia
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade , Belgrade, Serbia
| | - Begona Oliver-Martos
- Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga , Malaga, Spain
| | - Eva Martínez-Cáceres
- Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona , Cerdanyola Del Vallès, Spain
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb , Zagreb, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health , Zagreb, Croatia
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE , Grenoble, France
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics , Nicosia, Cyprus
| | - Izabela Burzynska-Pedziwiatr
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Lucyna Alicja Wozniak
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Stephan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - César Pascual García
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST) , Belvaux, Luxembourg
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences , Bratislava, Slovakia
| | - Zanka Bojic-Trbojevic
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy - INEP, University of Belgrade , Belgrade, Serbia
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital , Oslo, Norway
| | - Felicia Antohe
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Viorel Suica
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Guillaume Suarez
- Center for Primary Care and Public Health (Unisanté), University of Lausanne , Lausanne, Switzerland
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC) , Kortrijk, Belgium
| | - Petra Martin
- Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James's Hospital , Dublin, Ireland
| | - Deborah Penque
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ines Lanca Martins
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ede Bodoki
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Bogdan-Cezar Iacob
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Eda Aydindogan
- Department of Chemistry, Graduate School of Sciences and Engineering, Koç University , Istanbul, Turkey
| | - Suna Timur
- Institute of Natural Sciences, Department of Biochemistry, Ege University , Izmir, Turkey
| | | | | | - Theo Luider
- Department of Neurology, Erasmus MC , Rotterdam, The Netherlands
| | | | - Marei Sammar
- Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College , Karmiel, Israel
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14
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Wuethrich A, Rajkumar AR, Shanmugasundaram KB, Reza KK, Dey S, Howard CB, Sina AAI, Trau M. Single droplet detection of immune checkpoints on a multiplexed electrohydrodynamic biosensor. Analyst 2019; 144:6914-6921. [PMID: 31657376 DOI: 10.1039/c9an01450k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Monitoring soluble immune checkpoints in circulating fluids has the potential for minimally-invasive diagnostics and personalised therapy in precision medicine. Yet, the sensitive detection of multiple immune checkpoints from small volumes of liquid biopsy samples is challenging. In this study, we develop a multiplexed immune checkpoint biosensor (MICB) for parallel detection of soluble immune checkpoints PD-1, PD-L1, and LAG-3. MICB integrates a microfluidic sandwich immunoassay using engineered single chain variable fragments and alternating current electrohydrodynamic in situ nanofluidic mixing for promoting biosensor-target interaction and reducing non-specific non-target binding. MICB provides advantages of simultaneous analysis of up to 28 samples in <2 h, requires as little as a single sample drop (i.e., 20 μL) per target immune checkpoint, and applies high-affinity yeast cell-derived single chain variable fragments as a cost-effective alternative to monoclonal antibodies. We investigate the assay performance of MICB and demonstrate its capability for accurate immune checkpoint detection in simulated patient serum samples at clinically-relevant levels. MICB provides a dynamic range of 5 to 200 pg mL-1 for PD-1 and PD-L1, and 50 to 1000 pg mL-1 for LAG-3 with a coefficient of variation <13.8%. Sensitive immune checkpoint detection was achieved with limits of detection values of 5 pg mL-1 for PD-1, 5 pg mL-1 for PD-L1, and 50 pg mL-1 for LAG-3. The multiplexing capability, sensitivity, and relative assay simplicity of MICB make it capable of serving as a bioanalytical tool for immune checkpoint therapy monitoring.
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Affiliation(s)
- Alain Wuethrich
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
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