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Gao Y, Kim H, Kitata RB, Lin TT, Swensen AC, Shi T, Liu T. Multiplexed quantitative proteomics in prostate cancer biomarker development. Adv Cancer Res 2024; 161:31-69. [PMID: 39032952 DOI: 10.1016/bs.acr.2024.04.003] [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: 07/23/2024]
Abstract
Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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2
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Benedetti E, Chetnik K, Flynn T, Barbieri CE, Scherr DS, Loda M, Krumsiek J. Plasma metabolomics profiling of 580 patients from an Early Detection Research Network prostate cancer cohort. Sci Data 2023; 10:830. [PMID: 38007532 PMCID: PMC10676366 DOI: 10.1038/s41597-023-02750-7] [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: 03/15/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
Prostate cancer is the second most common cancer in men and affects 1 in 9 men in the United States. Early screening for prostate cancer often involves monitoring levels of prostate-specific antigen (PSA) and performing digital rectal exams. However, a prostate biopsy is always required for definitive cancer diagnosis. The Early Detection Research Network (EDRN) is a consortium within the National Cancer Institute aimed at improving screening approaches and early detection of cancers. As part of this effort, the Weill Cornell EDRN Prostate Cancer has collected and biobanked specimens from men undergoing a prostate biopsy between 2008 and 2017. In this report, we describe blood metabolomics measurements for a subset of this population. The dataset includes detailed clinical and prospective records for 580 patients who underwent prostate biopsy, 287 of which were subsequentially diagnosed with prostate cancer, combined with profiling of 1,482 metabolites from plasma samples collected at the time of biopsy. We expect this dataset to provide a valuable resource for scientists investigating prostate cancer metabolism.
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Affiliation(s)
- Elisa Benedetti
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kelsey Chetnik
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Flynn
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Christopher E Barbieri
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Douglas S Scherr
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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3
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Li Z, Huang Y, Patil D, Rubin M, Sanda MG. Covariate-specific evaluation of continuous biomarker. Stat Med 2023; 42:953-969. [PMID: 36600184 PMCID: PMC10071998 DOI: 10.1002/sim.9652] [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: 03/07/2022] [Revised: 10/14/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
Diagnostic tests usually need to operate at a high sensitivity or specificity level in practice. Accordingly, specificity at the controlled sensitivity, or vice versa, is a clinically sensible performance metric for evaluating continuous biomarkers. Meanwhile, the performance of a biomarker may vary across sub-populations as defined by covariates, and covariate-specific evaluation can be informative. In this article, we develop a novel modeling and estimation method for covariate-specific specificity at a controlled sensitivity level. Unlike existing methods which typically adopt elaborate models of covariate effects over the entire biomarker distribution, our approach models covariate effects locally at a specific sensitivity level of interest. We also extend our proposed model to handle the whole continuum of sensitivities via dynamic regression and derive covariate-specific ROC curves. We provide the variance estimation through bootstrapping. The asymptotic properties are established. We conduct extensive simulation studies to evaluate the performance of our proposed methods in comparison with existing methods, and further illustrate the applications in two clinical studies for aggressive prostate cancer.
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Affiliation(s)
- Ziyi Li
- Department of Biostatistics, The University of Texas at MD Anderson Cancer Center, Houston, Texas, USA
| | - Yijian Huang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | | | - Mark Rubin
- Department for BioMedical Research, Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | - Martin G Sanda
- Department of Urology, Emory University, Atlanta, Georgia, USA
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4
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Wani S, Humaira, Farooq I, Ali S, Rehman MU, Arafah A. Proteomic profiling and its applications in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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5
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Detection of prostate cancer biomarkers via a SERS-based aptasensor. Biosens Bioelectron 2022; 216:114660. [DOI: 10.1016/j.bios.2022.114660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022]
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Li QK, Lih TSM, Wang Y, Hu Y, Höti N, Chan DW, Zhang H. Improving the detection of aggressive prostate cancer using immunohistochemical staining of protein marker panels. Am J Cancer Res 2022; 12:1323-1336. [PMID: 35411226 PMCID: PMC8984898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023] Open
Abstract
Prostate cancer (PCa) is a heterogeneous group of tumors, including non-aggressive (NAG) and aggressive (AG) cancer, with variable clinical outcomes. Clinically, in order to assess the aggressiveness of a PCa, a core needle biopsy of a tumor is usually obtained to evaluate the Gleason pattern and score of the tumor. However, it may be difficult to assign on a small biopsy sample using histology. Therefore, additional tool is needed to aid in the assessment. We studied the diagnostic utility of 12 protein markers to identify AG tumors using immunohistochemistry (IHC) and tumor tissue microarray (TMA), including 215 cores of PCa and 111 cores of tumor-matched normal adjacent tissue (NAT). Protein markers were evaluated for their potential utility as single or combined panels for identification of AG. Of 12 proteins, PSMA, phospho-EGFR, AR and P16 were over-expressed in AG. Galectin-3, DPP4 and MAN1B1 revealed stronger staining patterns in NAG. The sensitivity and specificity of individual marker varied widely. Based on AUC values of individual marker, we constructed two- and three-marker panels. In two-marker panels, especially in the panel of DPP4 and PSMA, the AUC value reached 0.83 (ranging from 0.76 to 0.83). In three-marker panels, containing both DPP4 and PSMA with either Galectin-3 or phospho-EGFR, the AUC value reached 0.86 (ranging from 0.83 to 0.86). The specificities at 95% sensitivity of three-marker panels were also significantly improved. In addition to Gleason score, our IHC panels provide a practical tool to assess the aggressiveness of PCa.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical InstitutionsBaltimore, MD 21287, USA
| | | | - Yuefan Wang
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical InstitutionsBaltimore, MD 21287, USA
- Department of Urology, Sidney Kimmel Cancer Center, Johns Hopkins Medical InstitutionsBaltimore, MD 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins UniversityBaltimore, MD 21287, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical InstitutionsBaltimore, MD 21287, USA
- Department of Urology, Sidney Kimmel Cancer Center, Johns Hopkins Medical InstitutionsBaltimore, MD 21287, USA
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Li QK, Chen J, Hu Y, Höti N, Lih TSM, Thomas SN, Chen L, Roy S, Meeker A, Shah P, Chen L, Bova GS, Zhang B, Zhang H. Proteomic characterization of primary and metastatic prostate cancer reveals reduced proteinase activity in aggressive tumors. Sci Rep 2021; 11:18936. [PMID: 34556748 PMCID: PMC8460832 DOI: 10.1038/s41598-021-98410-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022] Open
Abstract
Prostate cancer (PCa) is a heterogeneous group of tumors with variable clinical courses. In order to improve patient outcomes, it is critical to clinically separate aggressive PCa (AG) from non-aggressive PCa (NAG). Although recent genomic studies have identified a spectrum of molecular abnormalities associated with aggressive PCa, it is still challenging to separate AG from NAG. To better understand the functional consequences of PCa progression and the unique features of the AG subtype, we studied the proteomic signatures of primary AG, NAG and metastatic PCa. 39 PCa and 10 benign prostate controls in a discovery cohort and 57 PCa in a validation cohort were analyzed using a data-independent acquisition (DIA) SWATH-MS platform. Proteins with the highest variances (top 500 proteins) were annotated for the pathway enrichment analysis. Functional analysis of differentially expressed proteins in NAG and AG was performed. Data was further validated using a validation cohort; and was also compared with a TCGA mRNA expression dataset and confirmed by immunohistochemistry (IHC) using PCa tissue microarray (TMA). 4,415 proteins were identified in the tumor and benign control tissues, including 158 up-regulated and 116 down-regulated proteins in AG tumors. A functional analysis of tumor-associated proteins revealed reduced expressions of several proteinases, including dipeptidyl peptidase 4 (DPP4), carboxypeptidase E (CPE) and prostate specific antigen (KLK3) in AG and metastatic PCa. A targeted analysis further identified that the reduced expression of DPP4 was associated with the accumulation of DPP4 substrates and the reduced ratio of DPP4 cleaved peptide to intact substrate peptide. Findings were further validated using an independently-collected tumor cohort, correlated with a TCGA mRNA dataset, and confirmed by immunohistochemical stains of PCa tumor microarray (TMA). Our study is the first large-scale proteomics analysis of PCa tissue using a DIA SWATH-MS platform. It provides not only an interrogative proteomic signature of PCa subtypes, but also indicates the critical roles played by certain proteinases during tumor progression. The spectrum map and protein profile generated in the study can be used to investigate potential biological mechanisms involved in PCa and for the development of a clinical assay to distinguish aggressive from indolent PCa.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA.
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
| | - Jing Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Yingwei Hu
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Naseruddin Höti
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Tung-Shing Mamie Lih
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Stefani N Thomas
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Li Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Sujayita Roy
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Alan Meeker
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Punit Shah
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Lijun Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Bai Zhang
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Hui Zhang
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA.
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Urology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Johns Hopkins University, 400 N. Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21287, USA.
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Phua TJ. The Etiology and Pathophysiology Genesis of Benign Prostatic Hyperplasia and Prostate Cancer: A New Perspective. MEDICINES 2021; 8:medicines8060030. [PMID: 34208086 PMCID: PMC8230771 DOI: 10.3390/medicines8060030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022]
Abstract
Background: The etiology of benign prostatic hyperplasia and prostate cancer are unknown, with ageing being the greatness risk factor. Methods: This new perspective evaluates the available interdisciplinary evidence regarding prostate ageing in terms of the cell biology of regulation and homeostasis, which could explain the timeline of evolutionary cancer biology as degenerative, inflammatory and neoplasm progressions in these multifactorial and heterogeneous prostatic diseases. Results: This prostate ageing degeneration hypothesis encompasses the testosterone-vascular-inflamm-ageing triad, along with the cell biology regulation of amyloidosis and autophagy within an evolutionary tumorigenesis microenvironment. Conclusions: An understanding of these biological processes of prostate ageing can provide potential strategies for early prevention and could contribute to maintaining quality of life for the ageing individual along with substantial medical cost savings.
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Affiliation(s)
- Teow J Phua
- Molecular Medicine, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW 2305, Australia
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9
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Troyer D. Blood Test for Cancer: Are We There Yet? Eur Urol 2021; 79:772-773. [PMID: 33674181 DOI: 10.1016/j.eururo.2021.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Dean Troyer
- Microbiology and Molecular Cell Biology and Pathology, Eastern Virginia Medical School, Norfolk, VA, USA; Department of Pathology, UT Health San Antonio, San Antonio, TX, USA.
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10
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Bast RC, Srivastava S. The National Cancer Institute Early Detection Research Network: Two Decades of Progress. Cancer Epidemiol Biomarkers Prev 2020; 29:2396-2400. [PMID: 33262198 DOI: 10.1158/1055-9965.epi-20-1158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/25/2022] Open
Affiliation(s)
- Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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