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Crawford AJ, Forjaz A, Bons J, Bhorkar I, Roy T, Schell D, Queiroga V, Ren K, Kramer D, Huang W, Russo GC, Lee MH, Wu PH, Shih IM, Wang TL, Atkinson MA, Schilling B, Kiemen AL, Wirtz D. Combined assembloid modeling and 3D whole-organ mapping captures the microanatomy and function of the human fallopian tube. SCIENCE ADVANCES 2024; 10:eadp6285. [PMID: 39331707 PMCID: PMC11430475 DOI: 10.1126/sciadv.adp6285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024]
Abstract
The fallopian tubes play key roles in processes from pregnancy to ovarian cancer where three-dimensional (3D) cellular and extracellular interactions are important to their pathophysiology. Here, we develop a 3D multicompartment assembloid model of the fallopian tube that molecularly, functionally, and architecturally resembles the organ. Global label-free proteomics, innovative assays capturing physiological functions of the fallopian tube (i.e., oocyte transport), and whole-organ single-cell resolution mapping are used to validate these assembloids through a multifaceted platform with direct comparisons to fallopian tube tissue. These techniques converge at a unique combination of assembloid parameters with the highest similarity to the reference fallopian tube. This work establishes (i) an optimized model of the human fallopian tubes for in vitro studies of their pathophysiology and (ii) an iterative platform for customized 3D in vitro models of human organs that are molecularly, functionally, and microanatomically accurate by combining tunable assembloid and tissue mapping methods.
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Affiliation(s)
- Ashleigh J Crawford
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - André Forjaz
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Isha Bhorkar
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Triya Roy
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - David Schell
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vasco Queiroga
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kehan Ren
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Donald Kramer
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biotechnology, Johns Hopkins Advanced Academic Programs, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Wilson Huang
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gabriella C Russo
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Meng-Horng Lee
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pei-Hsun Wu
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tian-Li Wang
- Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mark A Atkinson
- Departments of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL 32610, USA
- Departments of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL 32610, USA
| | | | - Ashley L Kiemen
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Functional Anatomy and Evolution, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Denis Wirtz
- Johns Hopkins Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Lee J, Park JE, Lee D, Seo N, An HJ. Advancements in protein glycosylation biomarkers for ovarian cancer through mass spectrometry-based approaches. Expert Rev Mol Diagn 2024; 24:249-258. [PMID: 38112537 DOI: 10.1080/14737159.2023.2297933] [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: 08/17/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Ovarian cancer, characterized by metastasis and reduced 5-year survival rates, stands as a substantial factor in the mortality of gynecological malignancies worldwide. The challenge of delayed diagnosis originates from vague early symptoms and the absence of efficient screening and diagnostic biomarkers for early cancer detection. Recent studies have explored the intricate interplay between ovarian cancer and protein glycosylation, unveiling the potential significance of glycosylation-oriented biomarkers. AREAS COVERED This review examines the progress in glycosylation biomarker research, with particular emphasis on advances driven by mass spectrometry-based technologies. We document milestones achieved, discuss encountered limitations, and also highlight potential areas for future research and development of protein glycosylation biomarkers for ovarian cancer. EXPERT OPINION The association of glycosylation in ovarian cancer is well known, but current research lacks desired sensitivity and specificity for early detection. Notably, investigations into protein-specific and site-specific glycoproteomics have the potential to significantly enhance our understanding of ovarian cancer and facilitate the identification of glycosylation-based biomarkers. Furthermore, the integration of advanced mass spectrometry techniques with AI-driven analysis and glycome databases holds the promise for revolutionizing biomarker discovery for ovarian cancer, ultimately transforming diagnosis and improving patient outcomes.
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Affiliation(s)
- Jua Lee
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Ji Eun Park
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Daum Lee
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
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3
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Wolf J, Franco JA, Yip R, Dabaja MZ, Velez G, Liu F, Bassuk AG, Mruthyunjaya P, Dufour A, Mahajan VB. Liquid Biopsy Proteomics in Ophthalmology. J Proteome Res 2024; 23:511-522. [PMID: 38171013 PMCID: PMC10845144 DOI: 10.1021/acs.jproteome.3c00756] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.
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Affiliation(s)
- Julian Wolf
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Joel A. Franco
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Rui Yip
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Mohamed Ziad Dabaja
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gabriel Velez
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Fei Liu
- Department
of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexander G. Bassuk
- Department
of Pediatrics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Prithvi Mruthyunjaya
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Antoine Dufour
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Vinit B. Mahajan
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
- Veterans
Affairs Palo Alto Health Care System, Palo Alto, California 94304, United States
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Wang Y, Douville C, Chien YW, Wang BG, Chen CL, Pinto A, Smith SA, Drapkin R, Chui MH, Numan T, Vang R, Papadopoulos N, Wang TL, Shih IM. Aneuploidy Landscape in Precursors of Ovarian Cancer. Clin Cancer Res 2024; 30:600-615. [PMID: 38048050 DOI: 10.1158/1078-0432.ccr-23-0932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/21/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
PURPOSE Serous tubal intraepithelial carcinoma (STIC) is now recognized as the main precursor of ovarian high-grade serous carcinoma (HGSC). Other potential tubal lesions include p53 signatures and tubal intraepithelial lesions. We aimed to investigate the extent and pattern of aneuploidy in these epithelial lesions and HGSC to define the features that characterize stages of tumor initiation and progression. EXPERIMENTAL DESIGN We applied RealSeqS to compare genome-wide aneuploidy patterns among the precursors, HGSC (cases, n = 85), and histologically unremarkable fallopian tube epithelium (HU-FTE; control, n = 65). On the basis of a discovery set (n = 67), we developed an aneuploidy-based algorithm, REAL-FAST (Repetitive Element AneupLoidy Sequencing Fallopian Tube Aneuploidy in STIC), to correlate the molecular data with pathology diagnoses. We validated the result in an independent validation set (n = 83) to determine its performance. We correlated the molecularly defined precursor subgroups with proliferative activity and histology. RESULTS We found that nearly all p53 signatures lost the entire Chr17, offering a "two-hit" mechanism involving both TP53 and BRCA1 in BRCA1 germline mutation carriers. Proliferatively active STICs harbor gains of 19q12 (CCNE1), 19q13.2, 8q24 (MYC), or 8q arm, whereas proliferatively dormant STICs show 22q loss. REAL-FAST classified HU-FTE and STICs into 5 clusters and identified a STIC subgroup harboring unique aneuploidy that is associated with increased proliferation and discohesive growth. On the basis of a validation set, REAL-FAST showed 95.8% sensitivity and 97.1% specificity in detecting STIC/HGSC. CONCLUSIONS Morphologically similar STICs are molecularly distinct. The REAL-FAST assay identifies a potentially "aggressive" STIC subgroup harboring unique DNA aneuploidy that is associated with increased cellular proliferation and discohesive growth. REAL-FAST offers a highly reproducible adjunct technique to assist the diagnosis of STIC lesions.
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Affiliation(s)
- Yeh Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yen-Wei Chien
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Brant G Wang
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia
- School of Medicine Inova Campus, University of Virginia, Falls Church, Virginia
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - Chi-Long Chen
- Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Andre Pinto
- University of Miami Sylvester Comprehensive Cancer Center, Miami, Florida
| | - Saron Ann Smith
- Cascade Pathology Services, Legacy Health System, Portland, Oregon
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology and Basser Center for BRCA, University of Pennsylvania, Philadelphia, Pennsylvania
| | - M Herman Chui
- Department of Pathology and Laboratory Medicine, Sloan-Kettering Cancer Center, New York, New York
| | - Tricia Numan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Pathology, Sibley Memorial Hospital, Washington, DC
| | - Russell Vang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
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Jordan HA, Thomas SN. Novel proteomic technologies to address gaps in pre-clinical ovarian cancer biomarker discovery efforts. Expert Rev Proteomics 2023; 20:439-450. [PMID: 38116719 DOI: 10.1080/14789450.2023.2295861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION An estimated 20,000 women in the United States will receive a diagnosis of ovarian cancer in 2023. Late-stage diagnosis is associated with poor prognosis. There is a need for novel diagnostic biomarkers for ovarian cancer to improve early-stage detection and novel prognostic biomarkers to improve patient treatment. AREAS COVERED This review provides an overview of the clinicopathological features of ovarian cancer and the currently available biomarkers and treatment options. Two affinity-based platforms using proximity extension assays (Olink) and DNA aptamers (SomaLogic) are described in the context of highly reproducible and sensitive multiplexed assays for biomarker discovery. Recent developments in ion mobility spectrometry are presented as novel techniques to apply to the biomarker discovery pipeline. Examples are provided of how these aforementioned methods are being applied to biomarker discovery efforts in various diseases, including ovarian cancer. EXPERT OPINION Translating novel ovarian cancer biomarkers from candidates in the discovery phase to bona fide biomarkers with regulatory approval will have significant benefits for patients. Multiplexed affinity-based assay platforms and novel mass spectrometry methods are capable of quantifying low abundance proteins to aid biomarker discovery efforts by enabling the robust analytical interrogation of the ovarian cancer proteome.
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Affiliation(s)
- Helen A Jordan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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Wang Y, Huang P, Wang BG, Murdock T, Cope L, Hsu FC, Wang TL, Shih IM. Spatial Transcriptomic Analysis of Ovarian Cancer Precursors Reveals Reactivation of IGFBP2 during Pathogenesis. Cancer Res 2022; 82:4528-4541. [PMID: 36206311 PMCID: PMC9808976 DOI: 10.1158/0008-5472.can-22-1620] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 01/24/2023]
Abstract
Elucidating the earliest pathogenic steps in cancer development is fundamental to improving its early detection and prevention. Ovarian high-grade serous carcinoma (HGSC), a highly aggressive cancer, mostly originates from the fallopian tube epithelium through a precursor stage, serous tubal intraepithelial carcinoma (STIC). In this study, we performed spatial transcriptomic analysis to compare STICs, carcinoma, and their matched normal fallopian tube epithelium. Several differentially expressed genes in STICs and carcinomas were involved in cancer metabolism and detected in a larger independent transcriptomic dataset of ovarian HGSCs. Among these, insulin-like growth factor binding protein-2 (IGFBP2) was found to undergo DNA hypomethylation and to be increased at the protein level in STICs. Pyrosequencing revealed an association of IGFBP2 expression with the methylation state of its proximal enhancer, and 5-azacytidine treatment increased IGFBP2 expression. In postmenopausal fallopian tubes, where most STICs are detected, IGFBP2 immunoreactivity was detected in all 38 proliferatively active STICs but was undetectable in morphologically normal tubal epithelia, including those with TP53 mutations. In premenopausal fallopian tubes, IGFBP2 expression was limited to the secretory epithelium at the proliferative phase, and estradiol treatment increased IGFBP2 expression levels. IGFBP2 knockdown suppressed the growth of IGFBP2-expressing tubal epithelial cells via inactivation of the AKT pathway. Taken together, demethylation of the proximal enhancer of IGFBP2 drives tumor development by maintaining the increased IGFBP2 required for proliferation in an otherwise estrogen-deprived, proliferation-quiescent, and postmenopausal tubal microenvironment. SIGNIFICANCE Molecular studies of the earliest precursor lesions of ovarian cancer reveal a role of IGFBP2 in propelling tumor initiation, providing new insights into ovarian cancer development.
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Affiliation(s)
- Yeh Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peng Huang
- Biostatistics Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brant G. Wang
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia
| | - Tricia Murdock
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leslie Cope
- Biostatistics Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fang-Chi Hsu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Gynecology and Obstetrics and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Gynecology and Obstetrics and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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León-Letelier RA, Katayama H, Hanash S. Mining the Immunopeptidome for Antigenic Peptides in Cancer. Cancers (Basel) 2022; 14:4968. [PMID: 36291752 PMCID: PMC9599891 DOI: 10.3390/cancers14204968] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Although harnessing the immune system for cancer therapy has shown success, response to immunotherapy has been limited. The immunopeptidome of cancer cells presents an opportunity to discover novel antigens for immunotherapy applications. These neoantigens bind to MHC class I and class II molecules. Remarkably, the immunopeptidome encompasses protein post-translation modifications (PTMs) that may not be evident from genome or transcriptome profiling. A case in point is citrullination, which has been demonstrated to induce a strong immune response. In this review, we cover how the immunopeptidome, with a special focus on PTMs, can be utilized to identify cancer-specific antigens for immunotherapeutic applications.
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Affiliation(s)
| | | | - Sam Hanash
- Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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Circulating and non-circulating proteins and nucleic acids as biomarkers and therapeutic molecules in ovarian cancer. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tao M, Wu X. The role of patient-derived ovarian cancer organoids in the study of PARP inhibitors sensitivity and resistance: from genomic analysis to functional testing. J Exp Clin Cancer Res 2021; 40:338. [PMID: 34702316 PMCID: PMC8547054 DOI: 10.1186/s13046-021-02139-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/12/2021] [Indexed: 12/23/2022] Open
Abstract
Epithelial ovarian cancer (EOC) harbors distinct genetic features such as homologous recombination repair (HRR) deficiency, and therefore may respond to poly ADP-ribose polymerase inhibitors (PARPi). Over the past few years, PARPi have been added to the standard of care for EOC patients in both front-line and recurrent settings. Next-generation sequencing (NGS) genomic analysis provides key information, allowing for the prediction of PARPi response in patients who are PARPi naïve. However, there are indeed some limitations in NGS analyses. A subset of patients can benefit from PARPi, despite the failed detection of the predictive biomarkers such as BRCA1/2 mutations or HRR deficiency. Moreover, in the recurrent setting, the sequencing of initial tumor does not allow for the detection of reversions or secondary mutations restoring proficient HRR and thus leading to PARPi resistance. Therefore, it becomes crucial to better screen patients who will likely benefit from PARPi treatment, especially those with prior receipt of maintenance PARPi therapy. Recently, patient-derived organoids (PDOs) have been regarded as a reliable preclinical platform with clonal heterogeneity and genetic features of original tumors. PDOs are found feasible for functional testing and interrogation of biomarkers for predicting response to PARPi in EOC. Hence, we review the strengths and limitations of various predictive biomarkers and highlight the role of patient-derived ovarian cancer organoids as functional assays in the study of PARPi response. It was found that a combination of NGS and functional assays using PDOs could enhance the efficient screening of EOC patients suitable for PARPi, thus prolonging their survival time.
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Affiliation(s)
- Mengyu Tao
- Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Gynecology Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai, 200127, People's Republic of China
- Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, People's Republic of China
| | - Xia Wu
- Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Gynecology Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai, 200127, People's Republic of China.
- Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, People's Republic of China.
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10
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Su KM, Gao HW, Chang CM, Lu KH, Yu MH, Lin YH, Liu LC, Chang CC, Li YF, Chang CC. Synergistic AHR Binding Pathway with EMT Effects on Serous Ovarian Tumors Recognized by Multidisciplinary Integrated Analysis. Biomedicines 2021; 9:866. [PMID: 34440070 PMCID: PMC8389648 DOI: 10.3390/biomedicines9080866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelial ovarian cancers (EOCs) are fatal and obstinate among gynecological malignancies in advanced stage or relapsed status, with serous carcinomas accounting for the vast majority. Unlike EOCs, borderline ovarian tumors (BOTs), including serous BOTs, maintain a semimalignant appearance. Using gene ontology (GO)-based integrative analysis, we analyzed gene set databases of serous BOTs and serous ovarian carcinomas for dysregulated GO terms and pathways and identified multiple differentially expressed genes (DEGs) in various aspects. The SRC (SRC proto-oncogene, non-receptor tyrosine kinase) gene and dysfunctional aryl hydrocarbon receptor (AHR) binding pathway consistently influenced progression-free survival and overall survival, and immunohistochemical staining revealed elevated expression of related biomarkers (SRC, ARNT, and TBP) in serous BOT and ovarian carcinoma samples. Epithelial-mesenchymal transition (EMT) is important during tumorigenesis, and we confirmed the SNAI2 (Snail family transcriptional repressor 2, SLUG) gene showing significantly high performance by immunohistochemistry. During serous ovarian tumor formation, activated AHR in the cytoplasm could cooperate with SRC, enter cell nuclei, bind to AHR nuclear translocator (ARNT) together with TATA-Box Binding Protein (TBP), and act on DNA to initiate AHR-responsive genes to cause tumor or cancer initiation. Additionally, SNAI2 in the tumor microenvironment can facilitate EMT accompanied by tumorigenesis. Although it has not been possible to classify serous BOTs and serous ovarian carcinomas as the same EOC subtype, the key determinants of relevant DEGs (SRC, ARNT, TBP, and SNAI2) found here had a crucial role in the pathogenetic mechanism of both tumor types, implying gradual evolutionary tendencies from serous BOTs to ovarian carcinomas. In the future, targeted therapy could focus on these revealed targets together with precise detection to improve therapeutic effects and patient survival rates.
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Affiliation(s)
- Kuo-Min Su
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Hong-Wei Gao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Chia-Ming Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Kai-Hsi Lu
- Department of Medical Research and Education, Cheng-Hsin General Hospital, Taipei 112, Taiwan;
| | - Mu-Hsien Yu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Yi-Hsin Lin
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Li-Chun Liu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
- Division of Obstetrics and Gynecology, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei 105, Taiwan
| | - Chia-Ching Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
| | - Yao-Feng Li
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Cheng-Chang Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan; (K.-M.S.); (M.-H.Y.)
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan; (Y.-H.L.); (L.-C.L.); (C.-C.C.)
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11
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Kagiwada H, Kiboku T, Matsuo H, Kitazawa M, Fukui K, Horimoto K. Assessing the activation/inhibition of tyrosine kinase-related pathways with a newly developed platform. Proteomics 2021; 21:e2000251. [PMID: 34151541 DOI: 10.1002/pmic.202000251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/21/2022]
Abstract
The phosphorylation of cellular proteins plays a crucial role in the transduction of various signals from outside the cell into the nucleus. The signals are transduced by phosphorylation chain reactions within multiple pathways; however, determining which pathways are responsible for each defined signal has proven challenging. To estimate the activity of each pathway, we developed a phosphorylation array platform comprising a protein array with 1200 proteins belonging to 376 signalling pathways and an analytical method to estimate pathway activity based on the phosphorylation levels of proteins. The performance of our system was assessed by reconstructing kinase-substrate relationships, as well as by estimating pathway activity upon epidermal growth factor (EGF) stimulation and the pharmacological inhibition of epidermal growth factor receptor (EGFR). As a result, kinase-substrate relationships were reliably reconstructed based on the precise measurement of phosphorylation levels of constituent proteins on the array. Furthermore, the pathway activities associated with EGF stimulation and EGFR inhibition were successfully traced through the related pathways from the outer membrane to the nucleus along a time course. Thus, our phosphorylation array system can effectively assess the activity of specific signalling pathways that are perturbed by extracellular stimuli, such as various drugs.
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Affiliation(s)
- Harumi Kagiwada
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Kotu-ku, Tokyo, Japan
| | | | | | | | - Kazuhiko Fukui
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Kotu-ku, Tokyo, Japan
| | - Katsuhisa Horimoto
- Socium Inc., Tokyo, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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12
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Mukherjee S, Sundfeldt K, Borrebaeck CAK, Jakobsson ME. Comprehending the Proteomic Landscape of Ovarian Cancer: A Road to the Discovery of Disease Biomarkers. Proteomes 2021; 9:25. [PMID: 34070600 PMCID: PMC8163166 DOI: 10.3390/proteomes9020025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022] Open
Abstract
Despite recent technological advancements allowing the characterization of cancers at a molecular level along with biomarkers for cancer diagnosis, the management of ovarian cancers (OC) remains challenging. Proteins assume functions encoded by the genome and the complete set of proteins, termed the proteome, reflects the health state. Comprehending the circulatory proteomic profiles for OC subtypes, therefore, has the potential to reveal biomarkers with clinical utility concerning early diagnosis or to predict response to specific therapies. Furthermore, characterization of the proteomic landscape of tumor-derived tissue, cell lines, and PDX models has led to the molecular stratification of patient groups, with implications for personalized therapy and management of drug resistance. Here, we review single and multiple marker panels that have been identified through proteomic investigations of patient sera, effusions, and other biospecimens. We discuss their clinical utility and implementation into clinical practice.
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Affiliation(s)
- Shuvolina Mukherjee
- Department of Immunotechnology, Lund University, 22100 Lund, Sweden; (S.M.); (C.A.K.B.)
| | - Karin Sundfeldt
- Sahlgrenska Center for Cancer Research, Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Carl A. K. Borrebaeck
- Department of Immunotechnology, Lund University, 22100 Lund, Sweden; (S.M.); (C.A.K.B.)
| | - Magnus E. Jakobsson
- Department of Immunotechnology, Lund University, 22100 Lund, Sweden; (S.M.); (C.A.K.B.)
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13
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Bradbury M, Borràs E, Pérez-Benavente A, Gil-Moreno A, Santamaria A, Sabidó E. Proteomic Studies on the Management of High-Grade Serous Ovarian Cancer Patients: A Mini-Review. Cancers (Basel) 2021; 13:cancers13092067. [PMID: 33922979 PMCID: PMC8123279 DOI: 10.3390/cancers13092067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 01/23/2023] Open
Abstract
High-grade serous ovarian cancer (HGSC) remains the most common and deadly subtype of ovarian cancer. It is characterized by its late diagnosis and frequent relapse despite standardized treatment with cytoreductive surgery and platinum-based chemotherapy. The past decade has seen significant advances in the clinical management and molecular understanding of HGSC following the publication of the Cancer Genome Atlas (TCGA) researchers and the introduction of targeted therapies with anti-angiogenic drugs and poly(ADP-ribose) polymerase inhibitors in specific subgroups of patients. We provide a comprehensive review of HGSC, focusing on the most important molecular advances aimed at providing a better understanding of the disease and its response to treatment. We emphasize the role that proteomic technologies are now playing in these two aspects of the disease, through the identification of proteins and their post-translational modifications in ovarian cancer tumors. Finally, we highlight how the integration of proteomics with genomics, exemplified by the work performed by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), can guide the development of new biomarkers and therapeutic targets.
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Affiliation(s)
- Melissa Bradbury
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain; (M.B.); (E.B.)
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.P.-B.); (A.G.-M.)
- Gynecologic Oncology Unit, Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Eva Borràs
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain; (M.B.); (E.B.)
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Assumpció Pérez-Benavente
- Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.P.-B.); (A.G.-M.)
- Gynecologic Oncology Unit, Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.P.-B.); (A.G.-M.)
- Gynecologic Oncology Unit, Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBERONC), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Anna Santamaria
- Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.P.-B.); (A.G.-M.)
- Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Correspondence: (A.S.); (E.S.)
| | - Eduard Sabidó
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain; (M.B.); (E.B.)
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
- Correspondence: (A.S.); (E.S.)
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14
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Ahn HS, Yeom J, Yu J, Kwon YI, Kim JH, Kim K. Convergence of Plasma Metabolomics and Proteomics Analysis to Discover Signatures of High-Grade Serous Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12113447. [PMID: 33228226 PMCID: PMC7709037 DOI: 10.3390/cancers12113447] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary In-time diagnosing ovarian cancer, intractable cancer that has no symptoms can increase the survival of women. The aim of this study was to discover biomarkers from liquid biopsy samples using multi-omics approach, metabolomics and proteomics for the diagnosis of ovarian cancer. To verify our biomarker candidates, we conducted comparative analysis with other previous published studies. Despite the limitations of non-invasive samples, our findings are able to discover emerging properties through the interplay between metabolites and proteins and mechanism-based biomarkers through integrated protein and metabolite analysis. Abstract The 5-year survival rate in the early and late stages of ovarian cancer differs by 63%. In addition, a liquid biopsy is necessary because there are no symptoms in the early stage and tissue collection is difficult without using invasive methods. Therefore, there is a need for biomarkers to achieve this goal. In this study, we found blood-based metabolite or protein biomarker candidates for the diagnosis of ovarian cancer in the 20 clinical samples (10 ovarian cancer patients and 10 healthy control subjects). Plasma metabolites and proteins were measured and quantified using mass spectrometry in ovarian cancer patients and control groups. We identified the differential abundant biomolecules (34 metabolites and 197 proteins) and statistically integrated molecules of different dimensions to better understand ovarian cancer signal transduction and to identify novel biological mechanisms. In addition, the biomarker reliability was verified through comparison with existing research results. Integrated analysis of metabolome and proteome identified emerging properties difficult to grasp with the single omics approach, more reliably interpreted the cancer signaling pathway, and explored new drug targets. Especially, through this analysis, proteins (PPCS, PMP2, and TUBB) and metabolites (L-carnitine and PC-O (30:0)) related to the carnitine system involved in cancer plasticity were identified.
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Affiliation(s)
- Hee-Sung Ahn
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
| | - Jeonghun Yeom
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea;
| | - Jiyoung Yu
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
| | | | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06237, Korea
- Correspondence: (J.-H.K.); (K.K.); Tel.: +82-2-2019-3436 (J.-H.K.); +82-2-1688-7575 (K.K.)
| | - Kyunggon Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea;
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea
- Clinical Proteomics Core Laboratory, Convergence Medicine Research Center, Asan Medical Center, Seoul 05505, Korea
- Bio-Medical Institute of Technology, Asan Medical Center, Seoul 05505, Korea
- Correspondence: (J.-H.K.); (K.K.); Tel.: +82-2-2019-3436 (J.-H.K.); +82-2-1688-7575 (K.K.)
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15
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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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16
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019; 18:4098-4107. [PMID: 31430157 PMCID: PMC6898754 DOI: 10.1021/acs.jproteome.9b00434] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Room 425, Building #114, 50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, South Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Siqi Liu
- BGI Group-Shenzhen, Yantian District, Shenzhen 518083, China
| | - Stephen Pennington
- School of Medicine, University College Dublin, Conway Institute Belfield, Dublin 4, Ireland
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive and 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road, North Ryde, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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17
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Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol 2019; 16:150-159. [PMID: 31768034 PMCID: PMC6982592 DOI: 10.1038/s41589-019-0404-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022]
Abstract
Covalent probes serve as valuable tools for global investigation of protein function and ligand binding capacity. Despite efforts to expand coverage of residues available for chemical proteomics (e.g. cysteine and lysine), a large fraction of the proteome remains inaccessible with current activity-based probes. Here, we introduce sulfur-triazole exchange (SuTEx) chemistry as a tunable platform for developing covalent probes with broad applications for chemical proteomics. We show modifications to the triazole leaving group can furnish sulfonyl probes with ~5-fold enhanced chemoselectivity for tyrosines over other nucleophilic amino acids to investigate, for the first time, more than 10,000 tyrosine sites in lysates and live cells. We discover that tyrosines with enhanced nucleophilicity are enriched in enzymatic, protein-protein interaction, and nucleotide recognition domains. We apply SuTEx as a chemical phosphoproteomics strategy to monitor activation of phosphotyrosine sites. Collectively, we describe SuTEx as a biocompatible chemistry for chemical biology investigations of the human proteome.
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18
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Matrine inhibits the development and progression of ovarian cancer by repressing cancer associated phosphorylation signaling pathways. Cell Death Dis 2019; 10:770. [PMID: 31601793 PMCID: PMC6787190 DOI: 10.1038/s41419-019-2013-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy with late detection and acquired chemoresistance. Advanced understanding of the pathophysiology and novel treatment strategies are urgently required. A growing body of proteomic investigations suggest that phosphorylation has a pivotal role in the regulation of ovarian cancer associated signaling pathways. Matrine has been extensively studied for its potent anti-tumor activities. However, its effect on ovarian cancer cells and underlying molecular mechanisms remain unclear. Herein we showed that matrine treatment inhibited the development and progression of ovarian cancer cells by regulating proliferation, apoptosis, autophagy, invasion and angiogenesis. Matrine treatment retarded the cancer associated signaling transduction by decreasing the phosphorylation levels of ERK1/2, MEK1/2, PI3K, Akt, mTOR, FAK, RhoA, VEGFR2, and Tie2 in vitro and in vivo. Moreover, matrine showed excellent antitumor effect on chemoresistant ovarian cancer cells. No obvious toxic side effects were observed in matrine-administrated mice. As the natural agent, matrine has the potential to be the targeting drug against ovarian cancer cells with the advantages of overcoming the chemotherapy resistance and decreasing the toxic side effects.
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19
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Qi H, Wang F, Tao SC. Proteome microarray technology and application: higher, wider, and deeper. Expert Rev Proteomics 2019; 16:815-827. [PMID: 31469014 DOI: 10.1080/14789450.2019.1662303] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Introduction: Protein microarray is a powerful tool for both biological study and clinical research. The most useful features of protein microarrays are their miniaturized size (low reagent and sample consumption), high sensitivity and their capability for parallel/high-throughput analysis. The major focus of this review is functional proteome microarray. Areas covered: For proteome microarray, this review will discuss some recently constructed proteome microarrays and new concepts that have been used for constructing proteome microarrays and data interpretation in past few years, such as PAGES, M-NAPPA strategy, VirD technology, and the first protein microarray database. this review will summarize recent proteomic scale applications and address the limitations and future directions of proteome microarray technology. Expert opinion: Proteome microarray is a powerful tool for basic biological and clinical research. It is expected to see improvements in the currently used proteome microarrays and the construction of more proteome microarrays for other species by using traditional strategies or novel concepts. It is anticipated that the maximum number of features on a single microarray and the number of possible applications will be increased, and the information that can be obtained from proteome microarray experiments will more in-depth in the future.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
| | - Fei Wang
- School of Pharmacy, Shanghai Jiao Tong University , Shanghai , China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai , China
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20
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Li N, Qian S, Li B, Zhan X. Quantitative analysis of the human ovarian carcinoma mitochondrial phosphoproteome. Aging (Albany NY) 2019; 11:6449-6468. [PMID: 31442208 PMCID: PMC6738437 DOI: 10.18632/aging.102199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/10/2019] [Indexed: 05/02/2023]
Abstract
To investigate the existence and their potential biological roles of mitochondrial phosphoproteins (mtPPs) in human ovarian carcinoma (OC), mitochondria purified from OC and control tissues were analyzed with TiO2 enrichment-based iTRAQ quantitative proteomics. Totally 67 mtPPs with 124 phosphorylation sites were identified, which of them included 48 differential mtPPs (mtDPPs). Eighteen mtPPs were reported previously in OCs, and they were consistent in this study compared to previous literature. GO analysis revealed those mtPPs were involved in multiple cellular processes. PPI network indicated that those mtPPs were correlated mutually, and some mtPPs acted as hub molecules, such as EIF2S2, RPLP0, RPLP2, CFL1, MYH10, HSP90, HSPD1, PSMA3, TMX1, VDAC2, VDAC3, TOMM22, and TOMM20. Totally 32 mtPP-pathway systems (p<0.05) were enriched and clustered into 15 groups, including mitophagy, apoptosis, deubiquitination, signaling by VEGF, RHO-GTPase effectors, mitochondrial protein import, translation initiation, RNA transport, cellular responses to stress, and c-MYC transcriptional activation. Totally 29 mtPPs contained a certain protein domains. Upstream regulation analysis showed that TP53, TGFB1, dexamethasone, and thapsigargin might act as inhibitors, and L-dopa and forskolin might act as activators. This study provided novel insights into mitochondrial protein phosphorylations and their potential roles in OC pathogenesis and offered new biomarker resource for OCs.
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Affiliation(s)
- Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Shehua Qian
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Biao Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
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