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Anurogo D, Liu CL, Chang YC, Chang YH, Qiu JT. Discovery of differentially expressed proteins for CAR-T therapy of ovarian cancers with a bioinformatics analysis. Aging (Albany NY) 2024; 16:11409-11433. [PMID: 39033780 PMCID: PMC11315388 DOI: 10.18632/aging.206024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/07/2024] [Indexed: 07/23/2024]
Abstract
Target antigens are crucial for developing chimeric antigen receptor (CAR)-T cells, but their application to ovarian cancers is limited. This study aimed to identify potential genes as CAR-T-cell antigen candidates for ovarian cancers. A differential gene expression analysis was performed on ovarian cancer samples from four datasets obtained from the GEO datasets. Functional annotation, pathway analysis, protein localization, and gene expression analysis were conducted using various datasets and tools. An oncogenicity analysis and network analysis were also performed. In total, 153 differentially expressed genes were identified in ovarian cancer samples, with 60 differentially expressed genes expressing plasma membrane proteins suitable for CAR-T-cell antigens. Among them, 21 plasma membrane proteins were predicted to be oncogenes in ovarian cancers, with nine proteins playing crucial roles in the network. Key genes identified in the oncogenic pathways of ovarian cancers included MUC1, CXCR4, EPCAM, RACGAP1, UBE2C, PRAME, SORT1, JUP, and CLDN3, suggesting them as recommended antigens for CAR-T-cell therapy for ovarian cancers. This study sheds light on potential targets for immunotherapy in ovarian cancers.
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Affiliation(s)
- Dito Anurogo
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Makassar, Makassar 90221, Indonesia
| | - Chao-Lien Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Chu Chang
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Hsiang Chang
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - J. Timothy Qiu
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
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Jo A, Green A, Medina JE, Iyer S, Ohman AW, McCarthy ET, Reinhardt F, Gerton T, Demehin D, Mishra R, Kolin DL, Zheng H, Cheon J, Crum CP, Weinberg RA, Rueda BR, Castro CM, Dinulescu DM, Lee H. Inaugurating High-Throughput Profiling of Extracellular Vesicles for Earlier Ovarian Cancer Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301930. [PMID: 37485618 PMCID: PMC10520636 DOI: 10.1002/advs.202301930] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/13/2023] [Indexed: 07/25/2023]
Abstract
Detecting early cancer through liquid biopsy is challenging due to the lack of specific biomarkers for early lesions and potentially low levels of these markers. The current study systematically develops an extracellular-vesicle (EV)-based test for early detection, specifically focusing on high-grade serous ovarian carcinoma (HGSOC). The marker selection is based on emerging insights into HGSOC pathogenesis, notably that it arises from precursor lesions within the fallopian tube. This work thus establishes murine fallopian tube (mFT) cells with oncogenic mutations and performs proteomic analyses on mFT-derived EVs. The identified markers are then evaluated with an orthotopic HGSOC animal model. In serially-drawn blood of tumor-bearing mice, mFT-EV markers increase with tumor initiation, supporting their potential use in early cancer detection. A pilot clinical study (n = 51) further narrows EV markers to five candidates, EpCAM, CD24, VCAN, HE4, and TNC. The combined expression of these markers distinguishes HGSOC from non-cancer with 89% sensitivity and 93% specificity. The same markers are also effective in classifying three groups (non-cancer, early-stage HGSOC, and late-stage HGSOC). The developed approach, for the first time inaugurated in fallopian tube-derived EVs, could be a minimally invasive tool to monitor women at high risk of ovarian cancer for timely intervention.
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Affiliation(s)
- Ala Jo
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Center for NanomedicineInstitute for Basic ScienceSeoul03722Republic of Korea
| | - Allen Green
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Jamie E. Medina
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Sonia Iyer
- Whitehead InstituteMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Anders W. Ohman
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Eric T. McCarthy
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Ferenc Reinhardt
- Whitehead InstituteMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Thomas Gerton
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Daniel Demehin
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Ranjan Mishra
- Whitehead InstituteMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - David L. Kolin
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Hui Zheng
- Biostatistics CenterMassachusetts General HospitalBostonMA02114USA
| | - Jinwoo Cheon
- Center for NanomedicineInstitute for Basic ScienceSeoul03722Republic of Korea
| | - Christopher P. Crum
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Robert A. Weinberg
- Whitehead InstituteMassachusetts Institute of TechnologyCambridgeMA02142USA
| | - Bo R. Rueda
- Division of Gynecologic OncologyDepartment of Obstetrics and GynecologyMassachusetts General HospitalBostonMA02114USA
| | - Cesar M. Castro
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Cancer CenterMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Daniela M. Dinulescu
- Division of Women's and Perinatal PathologyDepartment of PathologyBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Hakho Lee
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Center for NanomedicineInstitute for Basic ScienceSeoul03722Republic of Korea
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3
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Jo A, Green A, Medina JE, Iyer S, Ohman AW, McCarthy ET, Reinhardt F, Gerton T, Demehin D, Mishra R, Kolin DL, Zheng H, Crum CP, Weinberg RA, Rueda BR, Castro CM, Dinulescu DM, Lee H. Profiling extracellular vesicles in circulation enables the early detection of ovarian cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524549. [PMID: 36711872 PMCID: PMC9882285 DOI: 10.1101/2023.01.19.524549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ovarian cancer is a heterogeneous group of tumors in both cell type and natural history. While outcomes are generally favorable when detected early, the most common subtype, high-grade serous carcinoma (HGSOC), typically presents at an advanced stage and portends less favorable prognoses. Its aggressive nature has thwarted early detection efforts through conventional detection methods such as serum CA125 and ultrasound screening and thus inspired the investigation of novel biomarkers. Here, we report the systematic development of an extracellular-vesicle (EV)-based test to detect early-stage HGSOC. Our study is based on emerging insights into HGSOC biology, notably that it arises from precursor lesions within the fallopian tube before traveling to ovarian and/or peritoneal surfaces. To identify HGSOC marker candidates, we established murine fallopian tube (mFT) cells with oncogenic mutations in Brca1/2, Tp53 , and Pten genes, and performed proteomic analyses on mFT EVs. The identified markers were then evaluated with an orthotopic HGSOC animal model. In serially-drawn blood samples of tumor-bearing mice, mFT-EV markers increased with tumor initiation, supporting their potential use in early cancer detection. A pilot human clinical study ( n = 51) further narrowed EV markers to five candidates, EpCAM, CD24, VCAN, HE4, and TNC. Combined expression of these markers achieved high OvCa diagnostic accuracy (cancer vs. non-cancer) with a sensitivity of 0.89 and specificity of 0.93. The same five markers were also effective in a three-group classification: non-cancer, early-stage (I & II) HGSOC, and late-stage (III & IV) HGSOC. In particular, they differentiated early-stage HGSOC from the rest with a specificity of 0.91. Minimally invasive and repeatable, this EV-based testing could be a versatile and serial tool for informing patient care and monitoring women at high risk for ovarian cancer.
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Dowling P, Ohlendieck K. DIGE Analysis of Immunodepleted Plasma. Methods Mol Biol 2023; 2596:363-375. [PMID: 36378451 DOI: 10.1007/978-1-0716-2831-7_25] [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] [Indexed: 06/16/2023]
Abstract
This chapter focuses on upstream immunodepletion of high-abundance proteins from plasma samples and subsequent analysis by fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed ten orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low-abundance proteins by 2D-DIGE analysis. To increase the detection, quantification, and identification of medium-low-abundance proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed. From the literature, it is clear that the performance of abundant protein depletion with immunodepletion columns has been successful in broadening the coverage of the biofluid proteome and facilitating the identification of disease-specific biomarkers. The task for a successful biomarker strategy involves the combination of a reproducible and robust fractionation method, coupled with a highly accurate quantitative method, a task that is exemplified by combining both immunodepletion and 2D-DIGE together to discover significant proteins associated with the disease phenotype.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Dowling P. DIGE Saturation Labeling for Scarce Amounts of Protein from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue. Methods Mol Biol 2023; 2596:113-118. [PMID: 36378435 DOI: 10.1007/978-1-0716-2831-7_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] [Indexed: 06/16/2023]
Abstract
In this chapter, we describe the utility of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) as a proteomics platform for the global detection of expressed proteins in formalin-fixed paraffin-embedded (FFPE) tissues and its use for biomarker discovery/identification of proteins that may contribute to cancer development and progression. Formalin fixation and paraffin embedding of tissue is the standard processing methodology practiced in pathology laboratories worldwide, resulting in a highly stable form of tissue that is easily stored due to its inherent stability at room temperature. Consequently, FFPE tissues represent an attractive reservoir of clinical material for conducting retrospective protein biomarker analysis. A limitation for proteomics research in this type of clinical sample is the amount of viable protein that can be obtained from fixed tissues. Tissue biopsies are precious samples that can generally be acquired in very small amounts due to the invasive nature of the sample collection, mainly during surgery or biopsy. Subsequently, the amount of extracted protein can be, in many cases, very limited. The saturation 2D-DIGE technology has emerged as a useful method for protein analysis where only scarce amounts of protein are available. This approach can be adapted successfully to label low-level protein isolated from FFPE tissue.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Zapata-García JA, Riveros-Magaña AR, Ortiz-Lazareno PC, Hernández-Flores G, Jave-Suárez LF, Aguilar-Lemarroy A. Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene. Diagnostics (Basel) 2022; 12:diagnostics12112788. [PMID: 36428851 PMCID: PMC9689318 DOI: 10.3390/diagnostics12112788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) in children or adults is characterized by structural and numeric aberrations in chromosomes; these anomalies strongly correlate with prognosis and clinical outcome. Therefore, this work aimed to identify the genes present in chromosomal gain regions found more frequently in patients with acute lymphoblastic leukemia (ALL) and ALL-derived cell lines using comparative genomic hybridization (CGH). In addition, validation of the genes found in these regions was performed utilizing RNAseq from JURKAT, CEM, and SUP-B15 cell lines, as well as expression microarrays derived from a MILE study. Chromosomes with common gain zones that were maintained in six or more samples were 14, 17, and 22, in which a total of 22 genes were identified. From them, NT5C3B, CNP, ACLY, and GNB1L maintained overexpression at the mRNA level in the cell lines and in patients with ALL. It is noteworthy that SALL2 showed very high expression in T-ALL, while JUP was highly expressed in B-ALL lineages. Interestingly, the latter correlated with worse survival in patients. This provided evidence that the measurement of these genes has high potential for clinical utility; however, their expressions should first be evaluated with a sensitive test in a more significant number of patients.
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Affiliation(s)
- Jessica Alejandra Zapata-García
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Alma Rocío Riveros-Magaña
- Centro Universitario del Sur, Universidad de Guadalajara, Ciudad Guzmán C.P. 49000, Mexico
- Hospital General Zona 9, Ciudad Guzmán C.P. 49000, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Georgina Hernández-Flores
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Luis Felipe Jave-Suárez
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Adriana Aguilar-Lemarroy
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
- Correspondence: ; Tel.: +52-331-520-7625
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Neville MC, Webb PG, Baumgartner HK, Bitler BG. Claudin-4 localization in epithelial ovarian cancer. Heliyon 2022; 8:e10862. [PMID: 36237976 PMCID: PMC9552118 DOI: 10.1016/j.heliyon.2022.e10862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/06/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Claudin-4, a protein with the structure of classic claudins most often found in cell-cell junctions, is frequently overexpressed in epithelial cancers where its localization has not been studied. In this study we aimed to find out where this membrane protein is localized in an ovarian tumor model, OVCAR3 cells, that express high levels of the protein. Immunohistochemical studies showed claudin-4 staining in a perinuclear region, at most plasma membranes and in cytoplasmic puncta. Native claudin-4 did not overlap with phosphorylated claudin-4, which was partially located in focal adhesions. Using claudin-4 BioID technology we confirmed that large amounts of claudin-4 are localized to the Golgi compartment, including in dispersed Golgi in cells where claudin-4 is partially knocked down and in dividing cells. Claudin-4 appears to be present in the vicinity of several types of cell-cell junctions, but there is no evidence that it forms tight junctions in these tumor cells. Both claudin-4, the Golgi marker GM130, and the plasma membrane receptor Notch2 were found in dispersed Golgi in dividing cells. This definition of the cellular architecture of claudin-4 should provide a framework for better understanding of the function of claudin-4 in tumor cells and its molecular interactions.
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Affiliation(s)
- Margaret C. Neville
- Departments of Obstetrics and Gynecology and Physiology and Biophysics, University of Colorado School of Medicine, Aurora, CO, 80845, USA
- Corresponding author.
| | - Patricia G. Webb
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, 80845, USA
| | - Heidi K. Baumgartner
- University of Colorado Anschutz Medical Campus, 2700 E. 19th Ave., Aurora, CO, 80045, USA
| | - Benjamin G. Bitler
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, University of Colorado Denver Anschutz Medical Campus, Mail Stop 8613, 12700 E. 19 Ave., Aurora, CO, 80045, USA
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