1
|
Zhen K, Hou W, Bai L, Wang M, Yue Z, Xu Z, Xiong D, Gao L, Ying W. An effective urobilin clearance strategy based on paramagnetic beads facilitates microscale proteomic analysis of urine. Analyst 2024; 149:3625-3635. [PMID: 38775334 DOI: 10.1039/d4an00312h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Urine provides an ideal source for disease biomarker discovery. High-adhesion contaminants such as urobilin, which are difficult to remove from urine, can severely interfere with urinary proteomic analysis. Here, we aimed to establish a strategy based on single-pot, solid-phase-enhanced sample preparation (SP3) technology to prepare samples for urinary proteomics analysis that almost completely eliminates the impact of urobilin. A systematic evaluation of the effects of two urinary protein precipitation methods, two types of protein lysis buffers, and different ratios of magnetic digestion beads on the identification and quantification of the microscale urinary proteome was conducted. Our results indicate that methanol-chloroform precipitation, coupled with efficient lysis facilitated by urea, and subsequent enzymatic digestion using a mix of hydrophilic and hydrophobic magnetic beads offers the best performance. Further applying this strategy to the urine of patients with benign prostatic hyperplasia, prostate cancer and healthy individuals, combined with a narrow window of data-independent acquisition, FGFR4, MYLK, ORM2, GOLM1, SPP1, CD55, CSF1, DLD and TIMP3 were identified as potential biomarkers to discriminate benign prostatic hyperplasia and prostate cancer patients.
Collapse
Affiliation(s)
- Kemiao Zhen
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Wenhao Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Lu Bai
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Mingchao Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zhan Yue
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zanxin Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Deyun Xiong
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Li Gao
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| |
Collapse
|
2
|
Khoo A, Govindarajan M, Qiu Z, Liu LY, Ignatchenko V, Waas M, Macklin A, Keszei A, Neu S, Main BP, Yang L, Lance RS, Downes MR, Semmes OJ, Vesprini D, Liu SK, Nyalwidhe JO, Boutros PC, Kislinger T. Prostate cancer reshapes the secreted and extracellular vesicle urinary proteomes. Nat Commun 2024; 15:5069. [PMID: 38871730 PMCID: PMC11176296 DOI: 10.1038/s41467-024-49424-5] [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: 08/24/2023] [Accepted: 05/31/2024] [Indexed: 06/15/2024] Open
Abstract
Urine is a complex biofluid that reflects both overall physiologic state and the state of the genitourinary tissues through which it passes. It contains both secreted proteins and proteins encapsulated in tissue-derived extracellular vesicles (EVs). To understand the population variability and clinical utility of urine, we quantified the secreted and EV proteomes from 190 men, including a subset with prostate cancer. We demonstrate that a simple protocol enriches prostatic proteins in urine. Secreted and EV proteins arise from different subcellular compartments. Urinary EVs are faithful surrogates of tissue proteomes, but secreted proteins in urine or cell line EVs are not. The urinary proteome is longitudinally stable over several years. It can accurately and non-invasively distinguish malignant from benign prostatic lesions and can risk-stratify prostate tumors. This resource quantifies the complexity of the urinary proteome and reveals the synergistic value of secreted and EV proteomes for translational and biomarker studies.
Collapse
Affiliation(s)
- Amanda Khoo
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Meinusha Govindarajan
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Zhuyu Qiu
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Lydia Y Liu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Matthew Waas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Alexander Keszei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Sarah Neu
- Division of Surgery, Urology, Sunnybrook Health Sciences Centre, Toronto, ON, M4N 3M5, Canada
| | - Brian P Main
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | - Lifang Yang
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | | | - Michelle R Downes
- Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, M4N 3M5, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - O John Semmes
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | - Danny Vesprini
- Department of Radiation Oncology, University of Toronto, Toronto, ON, M5T 1P5, Canada
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, M5T 1P5, Canada
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Julius O Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, 23507, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, 90095, USA.
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada.
| |
Collapse
|
3
|
Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. The dynamic impact of location and resection on the glioma CSF proteome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307463. [PMID: 38798641 PMCID: PMC11118641 DOI: 10.1101/2024.05.15.24307463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples, including anatomical location and post-surgical changes, remains unknown. To that end, pre- versus post-resection intracranial CSF samples were obtained at early (1-16 days; n=20) or delayed (86-153 days; n=11) timepoints for patients with glioma. Paired lumbar-versus-intracranial glioma CSF samples were also obtained (n=14). Using aptamer-based proteomics, we identify significant differences in the CSF proteome between lumbar, subarachnoid, and ventricular CSF. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome. Proteomic data are provided with individual clinical annotations as a resource for the field. One Sentence Summary Glioma cerebrospinal fluid (CSF) accessed intra-operatively and longitudinally via devices can reveal impacts of treatment and anatomical location.
Collapse
|
4
|
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] [Grants] [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.
Collapse
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.
| |
Collapse
|
5
|
Li H, Sui T, Chen X, Gu Y, Luo X, Liu Y, He Q. Screening and identification of serum exosomal protein ZNF587B in liquid biopsy for ovarian cancer diagnosis. Am J Cancer Res 2024; 14:1904-1913. [PMID: 38726286 PMCID: PMC11076262 DOI: 10.62347/rbtm1834] [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: 01/23/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
Addressing the critical challenge of early ovarian cancer (OC) detection, our study focuses on identifying novel biomarkers by analyzing preoperative peripheral blood exosomes from high-grade serous ovarian cancer (HGSC) patients and healthy controls. Utilizing high-performance liquid chromatography-mass spectrometry-based quantitative proteomics, we isolated and analyzed peripheral blood exosomes to identify differentially expressed proteins (DEPs). This comprehensive analysis, supported by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) database assessments, revealed 28 proteins with decreased abundance and 33 with increased abundance in HGSC patients compared to controls. Notably, Zinc Finger Protein 587B (ZNF587B) exhibited a significant reduction in abundance, confirmed by decreased mRNA and protein levels in HGSC and normal ovarian tissues, consistent with omes exosomal protein expression levels. Immunohistochemical staining further confirmed reduced ZNF587B protein levels in HGSC tissues. The significant correlation between ZNF587B expression levels and tumor stage underscores its potential as a valuable biomarker for early liquid biopsy screening of OC. Our findings suggest ZNF587B plays a crucial role in early HGSC detection, highlighting the importance of further research to validate its clinical utility and improve ovarian cancer patient outcomes.
Collapse
Affiliation(s)
- Hu Li
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| | - Tiantian Sui
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| | - Xiaoxiao Chen
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| | - Yanqiong Gu
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| | - Xuezhen Luo
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan UniversityShanghai 200011, China
| | - Yiyao Liu
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghai 201204, China
| |
Collapse
|
6
|
Lu S, Yang J, Gu Y, He D, Wu H, Sun W, Xu D, Li C, Guo C. Advances in Machine Learning Processing of Big Data from Disease Diagnosis Sensors. ACS Sens 2024; 9:1134-1148. [PMID: 38363978 DOI: 10.1021/acssensors.3c02670] [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: 02/18/2024]
Abstract
Exploring accurate, noninvasive, and inexpensive disease diagnostic sensors is a critical task in the fields of chemistry, biology, and medicine. The complexity of biological systems and the explosive growth of biomarker data have driven machine learning to become a powerful tool for mining and processing big data from disease diagnosis sensors. With the development of bioinformatics and artificial intelligence (AI), machine learning models formed by data mining have been able to guide more sensitive and accurate molecular computing. This review presents an overview of big data collection approaches and fundamental machine learning algorithms and discusses recent advances in machine learning and molecular computational disease diagnostic sensors. More specifically, we highlight existing modular workflows and key opportunities and challenges for machine learning to achieve disease diagnosis through big data mining.
Collapse
Affiliation(s)
- Shasha Lu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Jianyu Yang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Yu Gu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Dongyuan He
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Haocheng Wu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Wei Sun
- College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158, China
| | - Dong Xu
- Department of Diagnostic Ultrasound Imaging & Interventional Therapy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Changming Li
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Chunxian Guo
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| |
Collapse
|
7
|
Wenk D, Zuo C, Kislinger T, Sepiashvili L. Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers. Clin Proteomics 2024; 21:6. [PMID: 38287260 PMCID: PMC10826105 DOI: 10.1186/s12014-024-09452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological matrices with numerous advantages that make it attractive for clinical applications in oncology. The use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodologies has allowed laboratories to overcome challenges associated with immunoassays that are more widely used for tumor marker measurements. Yet, clinical implementation of targeted proteomics methodologies has so far been limited to a few cancer markers. This is due to numerous challenges associated with paucity of robust validation studies of new biomarkers and the labor-intensive and operationally complex nature of LC-MS/MS workflows. The purpose of this review is to provide an overview of targeted proteomics applications in cancer, workflows used in targeted proteomics, and requirements for clinical validation and implementation of targeted proteomics assays. We will also discuss advantages and challenges of targeted MS-based proteomics assays for clinical cancer biomarker analysis and highlight some recent developments that will positively contribute to the implementation of this technique into clinical laboratories.
Collapse
Affiliation(s)
- Deborah Wenk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charlotte Zuo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Research Tower, Room 9-807, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Lusia Sepiashvili
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Ave, Rm 3606, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Sickkids Research Institute, Toronto, ON, Canada.
| |
Collapse
|
8
|
Shin D, Lee J, Kim Y, Park J, Shin D, Song Y, Joo EJ, Roh S, Lee KY, Oh S, Ahn YM, Rhee SJ, Kim Y. Evaluation of a Nondepleted Plasma Multiprotein-Based Model for Discriminating Psychiatric Disorders Using Multiple Reaction Monitoring-Mass Spectrometry: Proof-of-Concept Study. J Proteome Res 2024; 23:329-343. [PMID: 38063806 DOI: 10.1021/acs.jproteome.3c00580] [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: 01/06/2024]
Abstract
Psychiatric evaluation relies on subjective symptoms and behavioral observation, which sometimes leads to misdiagnosis. Despite previous efforts to utilize plasma proteins as objective markers, the depletion method is time-consuming. Therefore, this study aimed to enhance previous quantification methods and construct objective discriminative models for major psychiatric disorders using nondepleted plasma. Multiple reaction monitoring-mass spectrometry (MRM-MS) assays for quantifying 453 peptides in nondepleted plasma from 132 individuals [35 major depressive disorder (MDD), 47 bipolar disorder (BD), 23 schizophrenia (SCZ) patients, and 27 healthy controls (HC)] were developed. Pairwise discriminative models for MDD, BD, and SCZ, and a discriminative model between patients and HC were constructed by machine learning approaches. In addition, the proteins from nondepleted plasma-based discriminative models were compared with previously developed depleted plasma-based discriminative models. Discriminative models for MDD versus BD, BD versus SCZ, MDD versus SCZ, and patients versus HC were constructed with 11 to 13 proteins and showed reasonable performances (AUROC = 0.890-0.955). Most of the shared proteins between nondepleted and depleted plasma models had consistent directions of expression levels and were associated with neural signaling, inflammatory, and lipid metabolism pathways. These results suggest that multiprotein markers from nondepleted plasma have a potential role in psychiatric evaluation.
Collapse
Affiliation(s)
- Dongyoon Shin
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam 13520, Republic of Korea
| | - Jihyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yeongshin Kim
- Department of Life Science, General Graduate School, CHA University, Seongnam 13488, Republic of Korea
| | - Junho Park
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam 13520, Republic of Korea
- Department of Life Science, General Graduate School, CHA University, Seongnam 13488, Republic of Korea
| | - Daun Shin
- Department of Psychiatry, Korea University Anam Hospital, Seoul 02841, Republic of Korea
| | - Yoojin Song
- Department of Psychiatry, Kangwon National University Hospital, Chuncheon 24289, Republic of Korea
| | - Eun-Jeong Joo
- Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Republic of Korea
- Department of Psychiatry, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu 11759, Republic of Korea
| | - Sungwon Roh
- Department of Psychiatry, Hanyang University Hospital and Hanyang University College of Medicine, Seoul 04763, Republic of Korea
| | - Kyu Young Lee
- Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Republic of Korea
- Department of Psychiatry, Nowon Eulji University Hospital, Seoul 01830, Republic of Korea
| | - Sanghoon Oh
- Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Republic of Korea
- Department of Psychiatry, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu 11759, Republic of Korea
| | - Yong Min Ahn
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Sang Jin Rhee
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam 13520, Republic of Korea
- Department of Life Science, General Graduate School, CHA University, Seongnam 13488, Republic of Korea
| |
Collapse
|
9
|
Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
Collapse
Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
10
|
Shi M, Li X, Li M, Si Y. Attention-based generative adversarial networks improve prognostic outcome prediction of cancer from multimodal data. Brief Bioinform 2023; 24:bbad329. [PMID: 37756592 DOI: 10.1093/bib/bbad329] [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: 02/20/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The prediction of prognostic outcome is critical for the development of efficient cancer therapeutics and potential personalized medicine. However, due to the heterogeneity and diversity of multimodal data of cancer, data integration and feature selection remain a challenge for prognostic outcome prediction. We proposed a deep learning method with generative adversarial network based on sequential channel-spatial attention modules (CSAM-GAN), a multimodal data integration and feature selection approach, for accomplishing prognostic stratification tasks in cancer. Sequential channel-spatial attention modules equipped with an encoder-decoder are applied for the input features of multimodal data to accurately refine selected features. A discriminator network was proposed to make the generator and discriminator learning in an adversarial way to accurately describe the complex heterogeneous information of multiple modal data. We conducted extensive experiments with various feature selection and classification methods and confirmed that the CSAM-GAN via the multilayer deep neural network (DNN) classifier outperformed these baseline methods on two different multimodal data sets with miRNA expression, mRNA expression and histopathological image data: lower-grade glioma and kidney renal clear cell carcinoma. The CSAM-GAN via the multilayer DNN classifier bridges the gap between heterogenous multimodal data and prognostic outcome prediction.
Collapse
Affiliation(s)
- Mingguang Shi
- School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xuefeng Li
- School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Mingna Li
- School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yichong Si
- School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China
| |
Collapse
|
11
|
Froń A, Semianiuk A, Lazuk U, Ptaszkowski K, Siennicka A, Lemiński A, Krajewski W, Szydełko T, Małkiewicz B. Artificial Intelligence in Urooncology: What We Have and What We Expect. Cancers (Basel) 2023; 15:4282. [PMID: 37686558 PMCID: PMC10486651 DOI: 10.3390/cancers15174282] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION Artificial intelligence is transforming healthcare by driving innovation, automation, and optimization across various fields of medicine. The aim of this study was to determine whether artificial intelligence (AI) techniques can be used in the diagnosis, treatment planning, and monitoring of urological cancers. METHODOLOGY We conducted a thorough search for original and review articles published until 31 May 2022 in the PUBMED/Scopus database. Our search included several terms related to AI and urooncology. Articles were selected with the consensus of all authors. RESULTS Several types of AI can be used in the medical field. The most common forms of AI are machine learning (ML), deep learning (DL), neural networks (NNs), natural language processing (NLP) systems, and computer vision. AI can improve various domains related to the management of urologic cancers, such as imaging, grading, and nodal staging. AI can also help identify appropriate diagnoses, treatment options, and even biomarkers. In the majority of these instances, AI is as accurate as or sometimes even superior to medical doctors. CONCLUSIONS AI techniques have the potential to revolutionize the diagnosis, treatment, and monitoring of urologic cancers. The use of AI in urooncology care is expected to increase in the future, leading to improved patient outcomes and better overall management of these tumors.
Collapse
Affiliation(s)
- Anita Froń
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| | - Alina Semianiuk
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| | - Uladzimir Lazuk
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| | - Kuba Ptaszkowski
- Department of Physiotherapy, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Agnieszka Siennicka
- Department of Physiology and Pathophysiology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Artur Lemiński
- Department of Urology and Urological Oncology, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Wojciech Krajewski
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| | - Tomasz Szydełko
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| | - Bartosz Małkiewicz
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (A.S.); (U.L.); (W.K.); (T.S.)
| |
Collapse
|
12
|
Khoo A, Govindarajan M, Qiu Z, Liu LY, Ignatchenko V, Waas M, Macklin A, Keszei A, Main BP, Yang L, Lance RS, Downes MR, Semmes OJ, Vesprini D, Liu SK, Nyalwidhe JO, Boutros PC, Kislinger T. Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550214. [PMID: 37546794 PMCID: PMC10402038 DOI: 10.1101/2023.07.23.550214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Urine is a complex biofluid that reflects both overall physiologic state and the state of the genitourinary tissues through which it passes. It contains both secreted proteins and proteins encapsulated in tissue-derived extracellular vesicles (EVs). To understand the population variability and clinical utility of urine, we quantified the secreted and EV proteomes from 190 men, including a subset with prostate cancer. We demonstrate that a simple protocol enriches prostatic proteins in urine. Secreted and EV proteins arise from different subcellular compartments. Urinary EVs are faithful surrogates of tissue proteomes, but secreted proteins in urine or cell line EVs are not. The urinary proteome is longitudinally stable over several years. It can accurately and non-invasively distinguish malignant from benign prostatic lesions, and can risk-stratify prostate tumors. This resource quantifies the complexity of the urinary proteome, and reveals the synergistic value of secreted and EV proteomes for translational and biomarker studies.
Collapse
|
13
|
Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
Collapse
|
14
|
Prestagiacomo LE, Tradigo G, Aracri F, Gabriele C, Rota MA, Alba S, Cuda G, Damiano R, Veltri P, Gaspari M. Data-Independent Acquisition Mass Spectrometry of EPS-Urine Coupled to Machine Learning: A Predictive Model for Prostate Cancer. ACS OMEGA 2023; 8:6244-6252. [PMID: 36844540 PMCID: PMC9948177 DOI: 10.1021/acsomega.2c05487] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/06/2022] [Indexed: 06/18/2023]
Abstract
Prostate cancer (PCa) is annually the most frequently diagnosed cancer in the male population. To date, the diagnostic path for PCa detection includes the dosage of serum prostate-specific antigen (PSA) and the digital rectal exam (DRE). However, PSA-based screening has insufficient specificity and sensitivity; besides, it cannot discriminate between the aggressive and indolent types of PCa. For this reason, the improvement of new clinical approaches and the discovery of new biomarkers are necessary. In this work, expressed prostatic secretion (EPS)-urine samples from PCa patients and benign prostatic hyperplasia (BPH) patients were analyzed with the aim of detecting differentially expressed proteins between the two analyzed groups. To map the urinary proteome, EPS-urine samples were analyzed by data-independent acquisition (DIA), a high-sensitivity method particularly suitable for detecting proteins at low abundance. Overall, in our analysis, 2615 proteins were identified in 133 EPS-urine specimens obtaining the highest proteomic coverage for this type of sample; of these 2615 proteins, 1670 were consistently identified across the entire data set. The matrix containing the quantified proteins in each patient was integrated with clinical parameters such as the PSA level and gland size, and the complete matrix was analyzed by machine learning algorithms (by exploiting 90% of samples for training/testing using a 10-fold cross-validation approach, and 10% of samples for validation). The best predictive model was based on the following components: semaphorin-7A (sema7A), secreted protein acidic and rich in cysteine (SPARC), FT ratio, and prostate gland size. The classifier could predict disease conditions (BPH, PCa) correctly in 83% of samples in the validation set. Data are available via ProteomeXchange with the identifier PXD035942.
Collapse
Affiliation(s)
- Licia E. Prestagiacomo
- Research
Centre for Advanced Biochemistry and Molecular Biology, Department
of Experimental and Clinical Medicine, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | | | - Federica Aracri
- Department
of Surgical and Medical Sciences, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Caterina Gabriele
- Research
Centre for Advanced Biochemistry and Molecular Biology, Department
of Experimental and Clinical Medicine, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | | | | | - Giovanni Cuda
- Research
Centre for Advanced Biochemistry and Molecular Biology, Department
of Experimental and Clinical Medicine, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Rocco Damiano
- Department
of Experimental and Clinical Medicine, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Pierangelo Veltri
- Department
of Surgical and Medical Sciences, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Marco Gaspari
- Research
Centre for Advanced Biochemistry and Molecular Biology, Department
of Experimental and Clinical Medicine, Magna
Graecia University of Catanzaro, 88100 Catanzaro, Italy
| |
Collapse
|
15
|
Chisholm J, Haas-Neill S, Margetts P, Al-Nedawi K. Characterization of proteins, mRNAs, and miRNAs of circulating extracellular vesicles from prostate cancer patients compared to healthy subjects. Front Oncol 2022; 12:895555. [PMID: 36568159 PMCID: PMC9776661 DOI: 10.3389/fonc.2022.895555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PC) is the fifth leading cause of death in men globally. Measurement of the blood PSA level is still considered the gold-standard biomarker test for PC despite its high rate of delivering false positives and negatives that result in an inappropriate medical response, including overtreatment. We collected extracellular vesicles (EVs) from the blood plasma of PC patients with organ-confined, extracapsular-invading, and seminal vesicle-invading tumors and from healthy subjects. We examined the protein, mRNA, and miRNA content of these EVs using mass spectrometry (MS), a human PC PCR array, and a miScript miRNA PCR array, respectively. The proteomic analysis showed distinct groups of proteins that are differently expressed in each group of patients, as well as in healthy subjects. Samples from healthy subjects and each tumor type were used for both mRNA and miRNA arrays. The mRNA analysis showed distinct groups of mRNAs that were overexpressed in healthy or in one of the three tumor types but not in the EVs of the other groups. The miRNA analysis showed distinct groups of miRNAs as well. The fold of regulation in the expression of the identified mRNA and miRNA of each stage of the disease from healthy subjects showed that various mRNAs and miRNAs could discriminate the disease stage. Overall, our data suggest many molecular marker candidates for distinguishing between healthy subjects and PC patients using the cargo of circulating vesicles, as well as markers to discriminate between the different tumor types. Once verified, these markers might have a diagnostic value for PC.
Collapse
|
16
|
Kasahara K, Narumi R, Nagayama S, Masuda K, Esaki T, Obama K, Tomonaga T, Sakai Y, Shimizu Y, Adachi J. A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer. Cancer Med 2022; 12:7616-7626. [PMID: 36394150 PMCID: PMC10067095 DOI: 10.1002/cam4.5442] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The pathogenesis of cancers depends on the molecular background of each individual patient. Therefore, verifying as many biomarkers as possible and clarifying their relationships with each disease status would be very valuable. We performed a large-scale targeted proteomics analysis of plasma extracellular vesicles (EVs) that may affect tumor progression and/or therapeutic resistance. EXPERIMENTAL DESIGN Plasma EVs from 59 were collected patients with colorectal cancer (CRC) and 59 healthy controls (HC) in cohort 1, and 150 patients with CRC in cohort 2 for the large-scale targeted proteomics analysis of 457 proteins as candidate CRC markers. The Mann-Whitney-Wilcoxon test and random forest model were applied in cohort 1 to select promising markers. Consensus clustering was applied to classify patients with CRC in cohort 2. The Kaplan-Meier method and Cox regression analysis were performed to identify potential molecular factors contributing to the overall survival (OS) of patients. RESULTS In the analysis of cohort 1, 99 proteins were associated with CRC. The analysis of cohort 2 revealed two clusters showing significant differences in OS (p = 0.017). Twelve proteins, including alpha-1-acid glycoprotein 1 (ORM1), were suggested to be associated with the identified CRC subtypes, and ORM1 was shown to significantly contribute to OS, suggesting that ORM1 might be one of the factors closely related to the OS. CONCLUSIONS The study identified two novel subtypes of CRC, which exhibit differences in OS, as well as important biomarker proteins that are closely related to the identified subtypes. Liquid biopsy assessment with targeted proteomics analysis was proposed to be crucial for predicting the CRC prognosis.
Collapse
Affiliation(s)
- Keiko Kasahara
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Ryohei Narumi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Satoshi Nagayama
- Department of Gastroenterological SurgeryGastroenterological Center, Cancer Institute Hospital, Japanese Foundation for Cancer ResearchTokyoJapan
- Department of SurgeryUji‐Tokusyukai Medical CenterKyotoJapan
| | - Keiko Masuda
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Tsuyoshi Esaki
- The Center for Data Science Education and ResearchShiga UniversityShigaJapan
| | - Kazutaka Obama
- Department of SurgeryKyoto University Graduate School of MedicineKyotoJapan
| | - Takeshi Tomonaga
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| | | | - Yoshihiro Shimizu
- Laboratory for Cell‐Free Protein SynthesisRIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Jun Adachi
- Laboratory of Proteome ResearchNational Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Proteomics for Drug DiscoveryCenter for Drug Design Research, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
- Laboratory of Clinical and Analytical ChemistryCollaborative Research Center for Health and Medicine, National Institute of Biomedical Innovation, Health and NutritionOsakaJapan
| |
Collapse
|
17
|
Wang R, Qin Z, Luo H, Pan M, Liu M, Yang P, Shi T. Prognostic value of PNN in prostate cancer and its correlation with therapeutic significance. Front Genet 2022; 13:1056224. [PMID: 36468018 PMCID: PMC9708726 DOI: 10.3389/fgene.2022.1056224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 10/11/2023] Open
Abstract
Prostate cancer (PCa) is the most common malignancy. New biomarkers are in demand to facilitate the management. The role of the pinin protein (encoded by PNN gene) in PCa has not been thoroughly explored yet. Using The Cancer Genome Atlas (TCGA-PCa) dataset validated with Gene Expression Omnibus (GEO) and protein expression data retrieved from the Human Protein Atlas, the prognostic and diagnostic values of PNN were studied. Highly co-expressed genes with PNN (HCEG) were constructed for pathway enrichment analysis and drug prediction. A prognostic signature based on methylation status using HCEG was constructed. Gene set enrichment analysis (GSEA) and the TISIDB database were utilised to analyse the associations between PNN and tumour-infiltrating immune cells. The upregulated PNN expression in PCa at both transcription and protein levels suggests its potential as an independent prognostic factor of PCa. Analyses of the PNN's co-expression network indicated that PNN plays a role in RNA splicing and spliceosomes. The prognostic methylation signature demonstrated good performance for progression-free survival. Finally, our results showed that the PNN gene was involved in splicing-related pathways in PCa and identified as a potential biomarker for PCa.
Collapse
Affiliation(s)
- Ruisong Wang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
- Changde Research Centre for Artificial Intelligence and Biomedicine, Changde, China
- Affiliated Hospital of Hunan University of Arts and Science (the Maternal and Child Health Hospital), Changde, Hunan, China
| | - Ziyi Qin
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Huiling Luo
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Meisen Pan
- Affiliated Hospital of Hunan University of Arts and Science (the Maternal and Child Health Hospital), Changde, Hunan, China
- Medical College, Hunan University of Arts and Science, Changde, Hunan, China
| | - Mingyao Liu
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
- Changde Research Centre for Artificial Intelligence and Biomedicine, Changde, China
| | - Pinhong Yang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
- Changde Research Centre for Artificial Intelligence and Biomedicine, Changde, China
- Hunan Provincial Ley Laboratory for Molecular Immunity Techonology of Aquatic Animal Diseases, Changde, China
| | - Tieliu Shi
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
- Changde Research Centre for Artificial Intelligence and Biomedicine, Changde, China
| |
Collapse
|
18
|
Artificial Intelligence for Clinical Diagnosis and Treatment of Prostate Cancer. Cancers (Basel) 2022; 14:cancers14225595. [PMID: 36428686 PMCID: PMC9688370 DOI: 10.3390/cancers14225595] [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: 09/09/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
As medical science and technology progress towards the era of "big data", a multi-dimensional dataset pertaining to medical diagnosis and treatment is becoming accessible for mathematical modelling. However, these datasets are frequently inconsistent, noisy, and often characterized by a significant degree of redundancy. Thus, extensive data processing is widely advised to clean the dataset before feeding it into the mathematical model. In this context, Artificial intelligence (AI) techniques, including machine learning (ML) and deep learning (DL) algorithms based on artificial neural networks (ANNs) and their types, are being used to produce a precise and cross-sectional illustration of clinical data. For prostate cancer patients, datasets derived from the prostate-specific antigen (PSA), MRI-guided biopsies, genetic biomarkers, and the Gleason grading are primarily used for diagnosis, risk stratification, and patient monitoring. However, recording diagnoses and further stratifying risks based on such diagnostic data frequently involves much subjectivity. Thus, implementing an AI algorithm on a PC's diagnostic data can reduce the subjectivity of the process and assist in decision making. In addition, AI is used to cut down the processing time and help with early detection, which provides a superior outcome in critical cases of prostate cancer. Furthermore, this also facilitates offering the service at a lower cost by reducing the amount of human labor. Herein, the prime objective of this review is to provide a deep analysis encompassing the existing AI algorithms that are being deployed in the field of prostate cancer (PC) for diagnosis and treatment. Based on the available literature, AI-powered technology has the potential for extensive growth and penetration in PC diagnosis and treatment to ease and expedite the existing medical process.
Collapse
|
19
|
Del Campo M, Peeters CFW, Johnson ECB, Vermunt L, Hok-A-Hin YS, van Nee M, Chen-Plotkin A, Irwin DJ, Hu WT, Lah JJ, Seyfried NT, Dammer EB, Herradon G, Meeter LH, van Swieten J, Alcolea D, Lleó A, Levey AI, Lemstra AW, Pijnenburg YAL, Visser PJ, Tijms BM, van der Flier WM, Teunissen CE. CSF proteome profiling across the Alzheimer's disease spectrum reflects the multifactorial nature of the disease and identifies specific biomarker panels. NATURE AGING 2022; 2:1040-1053. [PMID: 37118088 PMCID: PMC10292920 DOI: 10.1038/s43587-022-00300-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/28/2022] [Indexed: 04/30/2023]
Abstract
Development of disease-modifying therapies against Alzheimer's disease (AD) requires biomarkers reflecting the diverse pathological pathways specific for AD. We measured 665 proteins in 797 cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment with abnormal amyloid (MCI(Aβ+): n = 50), AD-dementia (n = 230), non-AD dementias (n = 322) and cognitively unimpaired controls (n = 195) using proximity ligation-based immunoassays. Here we identified >100 CSF proteins dysregulated in MCI(Aβ+) or AD compared to controls or non-AD dementias. Proteins dysregulated in MCI(Aβ+) were primarily related to protein catabolism, energy metabolism and oxidative stress, whereas those specifically dysregulated in AD dementia were related to cell remodeling, vascular function and immune system. Classification modeling unveiled biomarker panels discriminating clinical groups with high accuracies (area under the curve (AUC): 0.85-0.99), which were translated into custom multiplex assays and validated in external and independent cohorts (AUC: 0.8-0.99). Overall, this study provides novel pathophysiological leads delineating the multifactorial nature of AD and potential biomarker tools for diagnostic settings or clinical trials.
Collapse
Affiliation(s)
- Marta Del Campo
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands.
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain.
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain.
| | - Carel F W Peeters
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Mathematical & Statistical Methods group (Biometris), Wageningen University & Research, Wageningen, The Netherlands
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Lisa Vermunt
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Yanaika S Hok-A-Hin
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Mirrelijn van Nee
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - William T Hu
- Rutgers-RWJ Medical School, Institute for Health, Health Care Policy, and Aging Research, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Gonzalo Herradon
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Lieke H Meeter
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John van Swieten
- Department of Neurology and Alzheimer Center, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniel Alcolea
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University, Atlanta, GA, USA
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Pieter J Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Department of Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, Amsterdam, The Netherlands
| |
Collapse
|
20
|
Desaire H, Go EP, Hua D. Advances, obstacles, and opportunities for machine learning in proteomics. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101069. [PMID: 36381226 PMCID: PMC9648337 DOI: 10.1016/j.xcrp.2022.101069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated.
Collapse
Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
21
|
Urinary marker panels for aggressive prostate cancer detection. Sci Rep 2022; 12:14837. [PMID: 36050450 PMCID: PMC9437030 DOI: 10.1038/s41598-022-19134-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Majority of patients with indolent prostate cancer (PCa) can be managed with active surveillance. Therefore, finding biomarkers for classifying patients between indolent and aggressive PCa is essential. In this study, we investigated urinary marker panels composed of urinary glycopeptides and/or urinary prostate-specific antigen (PSA) for their clinical utility in distinguishing non-aggressive (Grade Group 1) from aggressive (Grade Group ≥ 2) PCa. Urinary glycopeptides acquired via data-independent acquisition mass spectrometry (DIA-MS) were quantitatively analyzed, where prostatic acid phosphatase (ACPP), clusterin (CLU), alpha-1-acid glycoprotein 1 (ORM1), and CD antigen 97 (CD97) were selected to be evaluated in various combinations with and without urinary PSA. Targeted parallel reaction monitoring (PRM) assays of the glycopeptides from urinary ACPP and CLU were investigated along with urinary PSA for the ability of aggressive PCa detection. The multi-urinary marker panels, combined via logistic regression, were statistically evaluated using bootstrap resampling and validated by an independent cohort. Majority of the multi-urinary marker panels (e.g., a panel consisted of ACPP, CLU, and Urinary PSA) achieved area under the curve (AUC) ranged from 0.70 to 0.85. Thus, multi-marker panels investigated in this study showed clinically meaningful results on aggressive PCa detection to separate Grade Group 1 from Grade Group 2 and above warranting further evaluation in clinical setting in future.
Collapse
|
22
|
Noninvasive urinary protein signatures associated with colorectal cancer diagnosis and metastasis. Nat Commun 2022; 13:2757. [PMID: 35589723 PMCID: PMC9119985 DOI: 10.1038/s41467-022-30391-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/25/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, imaging, fecal immunochemical tests (FITs) and serum carcinoembryonic antigen (CEA) tests are not adequate for the early detection and evaluation of metastasis and recurrence in colorectal cancer (CRC). To comprehensively identify and validate more accurate noninvasive biomarkers in urine, we implement a staged discovery-verification-validation pipeline in 657 urine and 993 tissue samples from healthy controls and CRC patients with a distinct metastatic risk. The generated diagnostic signature combined with the FIT test reveals a significantly increased sensitivity (+21.2% in the training set, +43.7% in the validation set) compared to FIT alone. Moreover, the generated metastatic signature for risk stratification correctly predicts over 50% of CEA-negative metastatic patients. The tissue validation shows that elevated urinary protein biomarkers reflect their alterations in tissue. Here, we show promising urinary protein signatures and provide potential interventional targets to reliably detect CRC, although further multi-center external validation is needed to generalize the findings. More sensitive and specific non-invasive biomarkers are desired for early detection of cancer. Here, the authors show a protein signature in the urine that increases sensitivity for colorectal cancer detection when combined with fecal immunochemical tests and corrects diagnosis in some fecal immunochemical tests-negative patients.
Collapse
|
23
|
Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
Collapse
Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
| |
Collapse
|
24
|
Ding Z, Wang N, Ji N, Chen ZS. Proteomics technologies for cancer liquid biopsies. Mol Cancer 2022; 21:53. [PMID: 35168611 PMCID: PMC8845389 DOI: 10.1186/s12943-022-01526-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/31/2022] [Indexed: 02/07/2023] Open
Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
Collapse
Affiliation(s)
- Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Gangxing 3rd Rd, High-Tech and Innovation Zone, Bldg. 2, Rm. 2201, Jinan City, Shandong Province 250101 P. R. China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Gangxing 3rd Rd, High-Tech and Innovation Zone, Bldg. 2, Rm. 2201, Jinan City, Shandong Province 250101 P. R. China
| | - Ning Ji
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Institute for Biotechnology, St. John’s University, 8000 Utopia Parkway, Queens, New York, 11439 USA
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060 China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Institute for Biotechnology, St. John’s University, 8000 Utopia Parkway, Queens, New York, 11439 USA
| |
Collapse
|
25
|
Correll VL, Otto JJ, Risi CM, Main BP, Boutros PC, Kislinger T, Galkin VE, Nyalwidhe JO, Semmes OJ, Yang L. Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis. J Extracell Vesicles 2022; 11:e12184. [PMID: 35119778 PMCID: PMC8815402 DOI: 10.1002/jev2.12184] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/22/2021] [Accepted: 12/22/2021] [Indexed: 01/23/2023] Open
Abstract
The isolation and subsequent molecular analysis of extracellular vesicles (EVs) derived from patient samples is a widely used strategy to understand vesicle biology and to facilitate biomarker discovery. Expressed prostatic secretions in urine are a tumor proximal fluid that has received significant attention as a source of potential prostate cancer (PCa) biomarkers for use in liquid biopsy protocols. Standard EV isolation methods like differential ultracentrifugation (dUC) co-isolate protein contaminants that mask lower-abundance proteins in typical mass spectrometry (MS) protocols. Further complicating the analysis of expressed prostatic secretions, uromodulin, also known as Tamm-Horsfall protein (THP), is present at high concentrations in urine. THP can form polymers that entrap EVs during purification, reducing yield. Disruption of THP polymer networks with dithiothreitol (DTT) can release trapped EVs, but smaller THP fibres co-isolate with EVs during subsequent ultracentrifugation. To resolve these challenges, we describe here a dUC method that incorporates THP polymer reduction and alkaline washing to improve EV isolation and deplete both THP and other common protein contaminants. When applied to human expressed prostatic secretions in urine, we achieved relative enrichment of known prostate and prostate cancer-associated EV-resident proteins. Our approach provides a promising strategy for global proteomic analyses of urinary EVs.
Collapse
Affiliation(s)
- Vanessa L. Correll
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Joseph J. Otto
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Cristina M. Risi
- Department of Physiological SciencesEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Brian P. Main
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Paul C. Boutros
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Department of Pharmacology and ToxicologyUniversity of TorontoTorontoCanada
- Department of Human GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- Department of UrologyUniversity of CaliforniaLos AngelesCaliforniaUSA
- Institute for Precision HealthUniversity of CaliforniaLos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer CenterUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Thomas Kislinger
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoCanada
| | - Vitold E. Galkin
- Department of Physiological SciencesEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Julius O. Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - O. John Semmes
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVirginiaUSA
| | - Lifang Yang
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVirginiaUSA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVirginiaUSA
| |
Collapse
|
26
|
Mikolajewicz N, Khan S, Trifoi M, Skakdoub A, Ignatchenko V, Mansouri S, Zuccato J, Zacharia BE, Glantz M, Zadeh G, Moffat J, Kislinger T, Mansouri A. Leveraging the CSF proteome toward minimally-invasive diagnostics surveillance of brain malignancies. Neurooncol Adv 2022; 4:vdac161. [PMID: 36382110 PMCID: PMC9639356 DOI: 10.1093/noajnl/vdac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background Diagnosis and prognostication of intra-axial brain tumors hinges on invasive brain sampling, which carries risk of morbidity. Minimally-invasive sampling of proximal fluids, also known as liquid biopsy, can mitigate this risk. Our objective was to identify diagnostic and prognostic cerebrospinal fluid (CSF) proteomic signatures in glioblastoma (GBM), brain metastases (BM), and primary central nervous system lymphoma (CNSL). Methods CSF samples were retrospectively retrieved from the Penn State Neuroscience Biorepository and profiled using shotgun proteomics. Proteomic signatures were identified using machine learning classifiers and survival analyses. Results Using 30 µL CSF volumes, we recovered 755 unique proteins across 73 samples. Proteomic-based classifiers identified malignancy with area under the receiver operating characteristic (AUROC) of 0.94 and distinguished between tumor entities with AUROC ≥0.95. More clinically relevant triplex classifiers, comprised of just three proteins, distinguished between tumor entities with AUROC of 0.75-0.89. Novel biomarkers were identified, including GAP43, TFF3 and CACNA2D2, and characterized using single cell RNA sequencing. Survival analyses validated previously implicated prognostic signatures, including blood-brain barrier disruption. Conclusions Reliable classification of intra-axial malignancies using low CSF volumes is feasible, allowing for longitudinal tumor surveillance.
Collapse
Affiliation(s)
- Nicholas Mikolajewicz
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mara Trifoi
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Anna Skakdoub
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | | | - Sheila Mansouri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Brad E Zacharia
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Michael Glantz
- Department of Neurosurgery, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Jason Moffat
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Thomas Kislinger, PhD, Department of Medical Biophysics, University of Toronto, MaRS Centre, 101 College Street, Room 9-807, Toronto, Ontario, M5G 1L8, Canada ()
| | - Alireza Mansouri
- Corresponding Authors: Alireza Mansouri, MD, MSc, Department of Neurosurgery, Penn State Health, 30 Hope Drive Suite 1200, Hershey, PA, 17011, USA ()
| |
Collapse
|
27
|
Khoo A, Liu LY, Nyalwidhe JO, Semmes OJ, Vesprini D, Downes MR, Boutros PC, Liu SK, Kislinger T. Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry. Nat Rev Urol 2021; 18:707-724. [PMID: 34453155 PMCID: PMC8639658 DOI: 10.1038/s41585-021-00500-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
Prostate cancer is the second most frequently diagnosed non-skin cancer in men worldwide. Patient outcomes are remarkably heterogeneous and the best existing clinical prognostic tools such as International Society of Urological Pathology Grade Group, pretreatment serum PSA concentration and T-category, do not accurately predict disease outcome for individual patients. Thus, patients newly diagnosed with prostate cancer are often overtreated or undertreated, reducing quality of life and increasing disease-specific mortality. Biomarkers that can improve the risk stratification of these patients are, therefore, urgently needed. The ideal biomarker in this setting will be non-invasive and affordable, enabling longitudinal evaluation of disease status. Prostatic secretions, urine and blood can be sources of biomarker discovery, validation and clinical implementation, and mass spectrometry can be used to detect and quantify proteins in these fluids. Protein biomarkers currently in use for diagnosis, prognosis and relapse-monitoring of localized prostate cancer in fluids remain centred around PSA and its variants, and opportunities exist for clinically validating novel and complimentary candidate protein biomarkers and deploying them into the clinic.
Collapse
Affiliation(s)
- Amanda Khoo
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Lydia Y Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julius O Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - O John Semmes
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Danny Vesprini
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Canada
| | - Michelle R Downes
- Division of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Vector Institute for Artificial Intelligence, Toronto, Canada.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, Canada.
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Canada.
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
| |
Collapse
|
28
|
Dell'Olio F. Multiplexed Liquid Biopsy and Tumor Imaging Using Surface-Enhanced Raman Scattering. BIOSENSORS 2021; 11:449. [PMID: 34821665 PMCID: PMC8615571 DOI: 10.3390/bios11110449] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
The recent improvements in diagnosis enabled by advances in liquid biopsy and oncological imaging significantly better cancer care. Both these complementary approaches, which are used for early tumor detection, characterization, and monitoring, can benefit from applying techniques based on surface-enhanced Raman scattering (SERS). With a detection sensitivity at the single-molecule level, SERS spectroscopy is widely used in cell and molecular biology, and its capability for the in vitro detection of several types of cancer biomarkers is well established. In the last few years, several intriguing SERS applications have emerged, including in vivo imaging for tumor targeting and the monitoring of drug release. In this paper, selected recent developments and trends in SERS applications in the field of liquid biopsy and tumor imaging are critically reviewed, with a special emphasis on results that demonstrate the clinical utility of SERS.
Collapse
Affiliation(s)
- Francesco Dell'Olio
- Department of Electrical and Information Engineering, Polytechnic University of Bari, 70125 Bari, Italy
| |
Collapse
|
29
|
Blaschke CRK, Hartig JP, Grimsley G, Liu L, Semmes OJ, Wu JD, Ippolito JE, Hughes-Halbert C, Nyalwidhe JO, Drake RR. Direct N-Glycosylation Profiling of Urine and Prostatic Fluid Glycoproteins and Extracellular Vesicles. Front Chem 2021; 9:734280. [PMID: 34646811 PMCID: PMC8503230 DOI: 10.3389/fchem.2021.734280] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/10/2021] [Indexed: 12/19/2022] Open
Abstract
Expressed prostatic secretions (EPS), also called post digital rectal exam urines, are proximal fluids of the prostate that are widely used for diagnostic and prognostic assays for prostate cancer. These fluids contain an abundant number of glycoproteins and extracellular vesicles secreted by the prostate gland, and the ability to detect changes in their N-glycans composition as a reflection of disease state represents potential new biomarker candidates. Methods to characterize these N-glycan constituents directly from clinical samples in a timely manner and with minimal sample processing requirements are not currently available. In this report, an approach is described to directly profile the N-glycan constituents of EPS urine samples, prostatic fluids and urine using imaging mass spectrometry for detection. An amine reactive slide is used to immobilize glycoproteins from a few microliters of spotted samples, followed by peptide N-glycosidase digestion. Over 100 N-glycan compositions can be detected with this method, and it works with urine, urine EPS, prostatic fluids, and urine EPS-derived extracellular vesicles. A comparison of the N-glycans detected from the fluids with tissue N-glycans from prostate cancer tissues was done, indicating a subset of N-glycans present in fluids derived from the gland lumens. The developed N-glycan profiling is amenable to analysis of larger clinical cohorts and adaptable to other biofluids.
Collapse
Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Jordan P Hartig
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Grace Grimsley
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Liping Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Jennifer D Wu
- Departments of Urology and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Joseph E Ippolito
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Chanita Hughes-Halbert
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States.,The Leroy T. Canoles Jr., Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States.,Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
30
|
Miles HN, Delafield DG, Li L. Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research. RSC Chem Biol 2021; 4:1050-1072. [PMID: 34430874 PMCID: PMC8341969 DOI: 10.1039/d1cb00039j] [Citation(s) in RCA: 4] [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: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Innovations in medical technology and dedicated focus from the scientific community have inspired numerous treatment strategies for benign and invasive cancers. While these improvements often lend themselves to more positive prognoses and greater patient longevity, means for early detection and severity stratification have failed to keep pace. Detection and validation of cancer-specific biomarkers hinges on the ability to identify subtype-specific phenotypic and proteomic alterations and the systematic screening of diverse patient groups. For this reason, clinical and scientific research settings rely on high throughput and high sensitivity mass spectrometry methods to discover and quantify unique molecular perturbations in cancer patients. Discussed within is an overview of quantitative proteomics strategies and a summary of recent applications that enable revealing potential biomarkers and treatment targets in prostate, ovarian, breast, and pancreatic cancer in a high throughput manner.
Collapse
Affiliation(s)
- Hannah N. Miles
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
| | | | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
- Department of Chemistry, University of Wisconsin-MadisonMadisonWI53706USA
| |
Collapse
|
31
|
Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BJM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc 2021; 16:3737-3760. [PMID: 34244696 PMCID: PMC8830262 DOI: 10.1038/s41596-021-00566-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
Collapse
Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Astrid M Suchy-Dicey
- Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
32
|
Dong M, Lih TSM, Höti N, Chen SY, Ponce S, Partin A, Zhang H. Development of Parallel Reaction Monitoring Assays for the Detection of Aggressive Prostate Cancer Using Urinary Glycoproteins. J Proteome Res 2021; 20:3590-3599. [PMID: 34106707 DOI: 10.1021/acs.jproteome.1c00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, we have found that two urinary glycoproteins, prostatic acid phosphatase (ACPP) and clusterin (CLU), combined with serum prostate-specific antigen (PSA) can serve as a three-signature panel for detecting aggressive prostate cancer (PCa) based on a quantitative glycoproteomic study. To facilitate the translation of candidates into clinically applicable tests, robust and accurate targeted parallel reaction monitoring (PRM) assays that can be widely adopted in multiple labs were developed in this study. The developed PRM assays for the urinary glycopeptides, FLN*ESYK from ACPP and EDALN*ETR from CLU, demonstrated good repeatability and a sufficient working range covering three to four orders of magnitude, and their performance in differentiating aggressive PCa was assessed by the quantitative analysis of urine specimens collected from 69 nonaggressive (Gleason score = 6) and 73 aggressive (Gleason ≥ 8) PCa patients. When ACPP combined with CLU, the discrimination power was improved from an area under a curve (AUC) of 0.66 to 0.78. By combining ACPP, CLU, and serum PSA to form a three-signature panel, the AUC was further improved to 0.83 (sensitivity: 84.9%, specificity: 66.7%). Since the serum PSA test alone had an AUC of 0.68, our results demonstrated that the new urinary glycopeptide PRM assays can serve as an adjunct to the serum PSA test to achieve better predictive power toward aggressive PCa. In summary, our developed PRM assays for urinary glycopeptides were successfully applied to clinical PCa urine samples with a promising performance in aggressive PCa detection.
Collapse
Affiliation(s)
- Mingming Dong
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States
| | - Tung-Shing Mamie Lih
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States
| | - Naseruddin Höti
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States
| | - Shao-Yung Chen
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sean Ponce
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alan Partin
- The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland 21287, United States
| | - Hui Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, Maryland 21231, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
33
|
Li S, Xu J, Qian J, Gao X. Engineering extracellular vesicles for cancer therapy: recent advances and challenges in clinical translation. Biomater Sci 2021; 8:6978-6991. [PMID: 33155579 DOI: 10.1039/d0bm01385d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular vesicles (EVs) are receiving increasing attention in recent years in the field of cancer treatment. EVs contain specific contents closely related to their donor cells, such as miRNAs, proteins and dsDNAs. As endogenous vesicles, EVs naturally have the characteristics of low toxicity and low immunogenicity and can stably pass through the circulatory system to reach the recipient cells, which make them good carriers to deliver therapeutic agents such as nucleic acid sequences and chemotherapeutics. In many preclinical studies and clinical trials, EVs have demonstrated their unlimited advantages in the field of cancer therapy. However, there are still some challenges that restrict their clinical application, such as yield, heterogeneity, safety, and specificity. In this review, we will focus on the latest breakthrough of EVs in the field of cancer treatment and discuss the challenges in the clinical translation of EVs.
Collapse
Affiliation(s)
- Sha Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Shanghai 200032, China.
| | | | | | | |
Collapse
|
34
|
Liu YR, Yang NJ, Zhao ML, Tang ZS, Duan JA, Zhou R, Chen L, Sun J, Song ZX, Hu JH, Shi XB. Hypericum perforatum L. Regulates Glutathione Redox Stress and Normalizes Ggt1/Anpep Signaling to Alleviate OVX-Induced Kidney Dysfunction. Front Pharmacol 2021; 12:628651. [PMID: 33981220 PMCID: PMC8109178 DOI: 10.3389/fphar.2021.628651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/19/2021] [Indexed: 11/28/2022] Open
Abstract
Menopause and associated renal complications are linked to systemic redox stress, and the causal factors remain unclear. As the role of Hypericum perforatum L. (HPL) in menopause-induced kidney disease therapy is still ambiguous, we aim to explore the effects of HPL on systemic redox stress under ovariectomy (OVX)-induced kidney dysfunction conditions. Here, using combined proteomic and metabolomic approaches, we constructed a multi-scaled “HPL-disease-gene-metabolite” network to generate a therapeutic “big picture” that indicated an important link between glutathione redox stress and kidney impairment. HPL exhibited the potential to maintain cellular redox homeostasis by inhibiting gamma-glutamyltransferase 1 (Ggt1) overexpression, along with promoting the efflux of accumulated toxic amino acids and their metabolites. Moreover, HPL restored alanyl-aminopeptidase (Anpep) expression and metabolite shifts, promoting antioxidative metabolite processing, and recovery. These findings provide a comprehensive description of OVX-induced glutathione redox stress at multiple levels and support HPL therapy as an effective modulator in renal tissues to locally influence the glutathione metabolism pathway and subsequent redox homeostasis.
Collapse
Affiliation(s)
- Yan-Ru Liu
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Ning-Juan Yang
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Meng-Li Zhao
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhi-Shu Tang
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jin-Ao Duan
- Key Laboratory for High Technology Research of TCM Formulae and Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rui Zhou
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Lin Chen
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jing Sun
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhong-Xing Song
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jin-Hang Hu
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xin-Bo Shi
- Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research, Shaanxi Collaborative Innovation Center Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, China
| |
Collapse
|
35
|
Zhang YH, Li Z, Zeng T, Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One 2021; 16:e0250032. [PMID: 33886611 PMCID: PMC8062050 DOI: 10.1371/journal.pone.0250032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Pregnancy is a complicated and long procedure during one or more offspring development inside a woman. A short period of oxygen shortage after birth is quite normal for most babies and does not threaten their health. However, if babies have to suffer from a long period of oxygen shortage, then this condition is an indication of pathological fetal intolerance, which probably causes their death. The identification of the pathological fetal intolerance from the physical oxygen shortage is one of the important clinical problems in obstetrics for a long time. The clinical syndromes typically manifest five symptoms that indicate that the baby may suffer from fetal intolerance. At present, liquid biopsy combined with high-throughput sequencing or mass spectrum techniques provides a quick approach to detect real-time alteration in the peripheral blood at multiple levels with the rapid development of molecule sequencing technologies. Gene methylation is functionally correlated with gene expression; thus, the combination of gene methylation and expression information would help in screening out the key regulators for the pathogenesis of fetal intolerance. We combined gene methylation and expression features together and screened out the optimal features, including gene expression or methylation signatures, for fetal intolerance prediction for the first time. In addition, we applied various computational methods to construct a comprehensive computational pipeline to identify the potential biomarkers for fetal intolerance dependent on the liquid biopsy samples. We set up qualitative and quantitative computational models for the prediction for fetal intolerance during pregnancy. Moreover, we provided a new prospective for the detailed pathological mechanism of fetal intolerance. This work can provide a solid foundation for further experimental research and contribute to the application of liquid biopsy in antenatal care.
Collapse
Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Margarita Gamarra
- Department of Computational Science and Electronic, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Romany F. Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga, Egypt
| | - José Escorcia-Gutierrez
- Electronic and Telecommunicacions Program, Universidad Autónoma del Caribe, Barranquilla, Colombia
- * E-mail: (JEG); (TH); (YDC)
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| |
Collapse
|
36
|
Kim H, Park S, Jeong IG, Song SH, Jeong Y, Kim CS, Lee KH. Noninvasive Precision Screening of Prostate Cancer by Urinary Multimarker Sensor and Artificial Intelligence Analysis. ACS NANO 2021; 15:4054-4065. [PMID: 33296173 DOI: 10.1021/acsnano.0c06946] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Screening for prostate cancer relies on the serum prostate-specific antigen test, which provides a high rate of false positives (80%). This results in a large number of unnecessary biopsies and subsequent overtreatment. Considering the frequency of the test, there is a critical unmet need of precision screening for prostate cancer. Here, we introduced a urinary multimarker biosensor with a capacity to learn to achieve this goal. The correlation of clinical state with the sensing signals from urinary multimarkers was analyzed by two common machine learning algorithms. As the number of biomarkers was increased, both algorithms provided a monotonic increase in screening performance. Under the best combination of biomarkers, the machine learning algorithms screened prostate cancer patients with more than 99% accuracy using 76 urine specimens. Urinary multimarker biosensor leveraged by machine learning analysis can be an important strategy of precision screening for cancers using a drop of bodily fluid.
Collapse
Affiliation(s)
- Hojun Kim
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungwook Park
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - In Gab Jeong
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sang Hoon Song
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Youngdo Jeong
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Choung-Soo Kim
- Department of Urology, Asan Medical Center (AMC), University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Kwan Hyi Lee
- Biomaterials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
37
|
Van Booven DJ, Kuchakulla M, Pai R, Frech FS, Ramasahayam R, Reddy P, Parmar M, Ramasamy R, Arora H. A Systematic Review of Artificial Intelligence in Prostate Cancer. Res Rep Urol 2021; 13:31-39. [PMID: 33520879 PMCID: PMC7837533 DOI: 10.2147/rru.s268596] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
The diagnosis and management of prostate cancer involves the interpretation of data from multiple modalities to aid in decision making. Tools like PSA levels, MRI guided biopsies, genomic biomarkers, and Gleason grading are used to diagnose, risk stratify, and then monitor patients during respective follow-ups. Nevertheless, diagnosis tracking and subsequent risk stratification often lend itself to significant subjectivity. Artificial intelligence (AI) can allow clinicians to recognize difficult relationships and manage enormous data sets, which is a task that is both extraordinarily difficult and time consuming for humans. By using AI algorithms and reducing the level of subjectivity, it is possible to use fewer resources while improving the overall efficiency and accuracy in prostate cancer diagnosis and management. Thus, this systematic review focuses on analyzing advancements in AI-based artificial neural networks (ANN) and their current role in prostate cancer diagnosis and management.
Collapse
Affiliation(s)
- Derek J Van Booven
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Manish Kuchakulla
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Raghav Pai
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Fabio S Frech
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Reshna Ramasahayam
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Pritika Reddy
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Madhumita Parmar
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ranjith Ramasamy
- Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA.,The Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Himanshu Arora
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.,Department of Urology, Miller School of Medicine, University of Miami, Miami, FL, USA.,The Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| |
Collapse
|
38
|
Breast Cancer-Derived Microvesicles Are the Source of Functional Metabolic Enzymes as Potential Targets for Cancer Therapy. Biomedicines 2021; 9:biomedicines9020107. [PMID: 33499132 PMCID: PMC7910888 DOI: 10.3390/biomedicines9020107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/10/2021] [Accepted: 01/18/2021] [Indexed: 11/17/2022] Open
Abstract
Membrane-derived extracellular vesicles, referred to as microvesicles (MVs), have been proposed to participate in several cancer diseases. In this study, MV fractions were isolated by differential ultracentrifugation from a metastatic breast cancer (BC) cell line MDA-MB-231 and a non-cancerous breast cell line MCF10A, then analyzed by nano-liquid chromatography coupled to tandem mass spectrometry. A total of 1519 MV proteins were identified from both cell lines. The data obtained were compared to previously analyzed proteins from small extracellular vesicles (sEVs), revealing 1272 proteins present in both MVs and sEVs derived from the MDA-MB-231 cell line. Among the 89 proteins unique to MDA-MB-231 MVs, three enzymes: ornithine aminotransferase (OAT), transaldolase (TALDO1) and bleomycin hydrolase (BLMH) were previously proposed as cancer therapy targets. These proteins were enzymatically validated in cells, sEVs, and MVs derived from both cell lines. The specific activity of OAT and TALDO1 was significantly higher in MDA-MB-231-derived MVs than in MCF10A MVs. BLMH was highly expressed in MDA-MB-231-derived MVs, compared to MCF10A MVs. This study shows that MVs carry functional metabolic enzymes and provides a framework for future studies of their biological role in BC and potential in therapeutic applications.
Collapse
|
39
|
Dell'Olio F, Su J, Huser T, Sottile V, Cortés-Hernández LE, Alix-Panabières C. Photonic technologies for liquid biopsies: recent advances and open research challenges. LASER & PHOTONICS REVIEWS 2021; 15:2000255. [PMID: 35360260 PMCID: PMC8966629 DOI: 10.1002/lpor.202000255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 05/15/2023]
Abstract
The recent development of sophisticated techniques capable of detecting extremely low concentrations of circulating tumor biomarkers in accessible body fluids, such as blood or urine, could contribute to a paradigm shift in cancer diagnosis and treatment. By applying such techniques, clinicians can carry out liquid biopsies, providing information on tumor presence, evolution, and response to therapy. The implementation of biosensing platforms for liquid biopsies is particularly complex because this application domain demands high selectivity/specificity and challenging limit-of-detection (LoD) values. The interest in photonics as an enabling technology for liquid biopsies is growing owing to the well-known advantages of photonic biosensors over competing technologies in terms of compactness, immunity to external disturbance, and ultra-high spatial resolution. Some encouraging experimental results in the field of photonic devices and systems for liquid biopsy have already been achieved by using fluorescent labels and label-free techniques and by exploiting super-resolution microscopy, surface plasmon resonance, surface-enhanced Raman scattering, and whispering gallery mode resonators. This paper critically reviews the current state-of-the-art, starting from the requirements imposed by the detection of the most common circulating biomarkers. Open research challenges are considered together with competing technologies, and the most promising paths of improvement are discussed for future applications.
Collapse
Affiliation(s)
- Francesco Dell'Olio
- Department of Electrical and Information Engineering, Polytechnic University of Bari, 70125, Italy
| | - Judith Su
- Department of Biomedical Engineering, College of Optical Sciences, and BIO5 Institute, University of Arizona, 85721, USA
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Germany
| | - Virginie Sottile
- Department of Molecular Medicine, University of Pavia, 27100, Italy
| | | | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Center of Montpellier, 34093 CEDEX 5, France
| |
Collapse
|
40
|
Yang WY, Feng LF, Meng X, Chen R, Xu WH, Hou J, Xu T, Zhang L. Liquid biopsy in head and neck squamous cell carcinoma: circulating tumor cells, circulating tumor DNA, and exosomes. Expert Rev Mol Diagn 2020; 20:1213-1227. [PMID: 33232189 DOI: 10.1080/14737159.2020.1855977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Introduction: Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide. Due to a lack of reliable markers, HNSCC patients are usually diagnosed at a late stage, which will lead to a worse outcome. Therefore, it is critical to improve the clinical management of cancer patients. Nowadays, the development of liquid biopsy enables a minimally invasive manner to extract molecular information from HNSCCs. Thus, this review aims to outline the clinical value of liquid biopsy in early detection, real-time monitoring, and prognostic evaluation of HNSCC. Areas covered: This comprehensive review focused on the characteristics as well as clinical applications of three liquid biopsy markers (CTCs, ctDNA, and exosomes) in HNSCC. What is more, it is promising to incorporate machine learning and 3D organoid models in the liquid biopsy of HNSCC. Expert opinion: Liquid biopsy provides a noninvasive technique to reflect the inter and intra-lesional heterogeneity through the detection of tumor cells or materials released from the primary and secondary tumors. Recently, some evolving technologies have the potential to combine with liquid biopsy to improve clinical management of HNSCC patients.
Collapse
Affiliation(s)
- Wen-Ying Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Lin-Fei Feng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University , Hefei, 230032, China
| | - Xiang Meng
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Ran Chen
- School of Stomatology, Anhui Medical University , Hefei, 230032, China
| | - Wen-Hua Xu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China
| | - Jun Hou
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University , Hefei, 230032, China
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University , Hefei, 230032, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University , Hefei, 230032, China
| | - Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. Of Oral Diseases Research of Anhui Province , Hefei, 230032, China.,Periodontal Department, Anhui Stomatology Hospital affiliated to Anhui Medical University , Hefei, 230032, China
| |
Collapse
|
41
|
Liss MA, Leach RJ, Sanda MG, Semmes OJ. Prostate Cancer Biomarker Development: National Cancer Institute's Early Detection Research Network Prostate Cancer Collaborative Group Review. Cancer Epidemiol Biomarkers Prev 2020; 29:2454-2462. [PMID: 33093161 PMCID: PMC7710596 DOI: 10.1158/1055-9965.epi-20-1104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer remains the most common non-skin cancer and second leading cause of death among men in the United States. Although progress has been made in diagnosis and risk assessment, many clinical questions remain regarding early identification of prostate cancer and management. The early detection of aggressive disease continues to provide high curative rates if diagnosed in a localized state. Unfortunately, prostate cancer displays significant heterogeneity within the prostate organ and between individual patients making detection and treatment strategies complex. Although prostate cancer is common among men, the majority will not die from prostate cancer, introducing the issue of overtreatment as a major concern in clinical management of the disease. The focus of the future is to identify those at highest risk for aggressive prostate cancer and to develop prevention and screening strategies, as well as discerning the difference in malignant potential of diagnosed tumors. The Prostate Cancer Research Group of the National Cancer Institute's Early Detection Research Network has contributed to the progress in addressing these concerns. This summary is an overview of the activities of the group.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
Collapse
Affiliation(s)
- Michael A Liss
- Department of Urology, University of Texas Health San Antonio, San Antonio, Texas
| | - Robin J Leach
- Department of Urology, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Martin G Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia
| | - Oliver J Semmes
- The Leroy T. Canoles Jr. Cancer Research Center, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia.
| |
Collapse
|
42
|
Möginger U, Marcussen N, Jensen ON. Histo-molecular differentiation of renal cancer subtypes by mass spectrometry imaging and rapid proteome profiling of formalin-fixed paraffin-embedded tumor tissue sections. Oncotarget 2020; 11:3998-4015. [PMID: 33216824 PMCID: PMC7646834 DOI: 10.18632/oncotarget.27787] [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: 05/09/2020] [Accepted: 10/10/2020] [Indexed: 12/24/2022] Open
Abstract
Pathology differentiation of renal cancer types is challenging due to tissue similarities or overlapping histological features of various tumor (sub) types. As assessment is often manually conducted outcomes can be prone to human error and therefore require high-level expertise and experience. Mass spectrometry can provide detailed histo-molecular information on tissue and is becoming increasingly popular in clinical settings. Spatially resolving technologies such as mass spectrometry imaging and quantitative microproteomics profiling in combination with machine learning approaches provide promising tools for automated tumor classification of clinical tissue sections. In this proof of concept study we used MALDI-MS imaging (MSI) and rapid LC-MS/MS-based microproteomics technologies (15 min/sample) to analyze formalin-fixed paraffin embedded (FFPE) tissue sections and classify renal oncocytoma (RO, n = 11), clear cell renal cell carcinoma (ccRCC, n = 12) and chromophobe renal cell carcinoma (ChRCC, n = 5). Both methods were able to distinguish ccRCC, RO and ChRCC in cross-validation experiments. MSI correctly classified 87% of the patients whereas the rapid LC-MS/MS-based microproteomics approach correctly classified 100% of the patients. This strategy involving MSI and rapid proteome profiling by LC-MS/MS reveals molecular features of tumor sections and enables cancer subtype classification. Mass spectrometry provides a promising complementary approach to current pathological technologies for precise digitized diagnosis of diseases.
Collapse
Affiliation(s)
- Uwe Möginger
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Present address: Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, Bagsværd, Denmark
| | - Niels Marcussen
- Institute for Pathology, Odense University Hospital, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
43
|
Otto JJ, Correll VL, Engstroem HA, Hitefield NL, Main BP, Albracht B, Johnson‐Pais T, Yang LF, Liss M, Boutros PC, Kislinger T, Leach RJ, Semmes OJ, Nyalwidhe JO. Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination. Proteomics Clin Appl 2020; 14:e2000012. [PMID: 32614141 PMCID: PMC7674190 DOI: 10.1002/prca.202000012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 06/08/2020] [Indexed: 01/03/2023]
Abstract
PURPOSE The rs17632542 single nucleotide polymorphism (SNP) results in lower serum prostate specific antigen (PSA) levels which may further mitigate against its clinical utility as a prostate cancer biomarker. Post-digital rectal exam (post-DRE) urine is a minimally invasive fluid that is currently utilized in prostate cancer diagnosis. To detect and quantitate the variant protein in urine. EXPERIMENTAL DESIGN Fifty-three post-DRE urines from rs17632542 genotyped individuals processed and analyzed by liquid chromatography/mass spectrometry (LC-MS) in a double-blinded randomized study. The ability to distinguish between homozygous wild-type, heterozygous, or homozygous variant is examined before unblinding. RESULTS Stable-isotope labeled peptides are used in the detection and quantitation of three peptides of interest in each sample using parallel reaction monitoring (PRM). Using these data, groupings are predicted using hierarchical clustering in R. Accuracy of the predictions show 100% concordance across the 53 samples, including individuals homozygous and heterozygous for the SNP. CONCLUSIONS AND CLINICAL RELEVANCE The study demonstrates that MS based peptide variant quantitation in urine could be useful in determining patient genotype expression. This assay provides a tool to evaluate the utility of PSA variant (rs17632542) in parallel with current and forthcoming urine biomarker panels.
Collapse
Affiliation(s)
- Joseph J. Otto
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Vanessa L. Correll
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Hampus A. Engstroem
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Naomi L. Hitefield
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Brian P. Main
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Brenna Albracht
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Teresa Johnson‐Pais
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Li Fang Yang
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Michael Liss
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
- Mays Cancer Center at UT Health San Antonio/MD AndersonSan AntonioTX78229USA
| | - Paul C. Boutros
- Departments of Human Genetics and UrologyJonsson Comprehensive Cancer CenterInstitute for Precision Health University of California Los AngelesLos AngelesCA90095USA
- University of TorontoDepartment of Medical BiophysicsTorontoON M5G 1L7Canada
| | - Thomas Kislinger
- University of TorontoDepartment of Medical BiophysicsTorontoON M5G 1L7Canada
| | - Robin J. Leach
- Department of UrologyThe University of Texas Health San AntonioSan AntonioTX78229USA
- Department of Cell Systems and AnatomyThe University of Texas Health San AntonioSan AntonioTX78229USA
| | - Oliver J. Semmes
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| | - Julius O. Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research CenterEastern Virginia Medical SchoolNorfolkVA23507USA
- Department of Microbiology and Molecular Cell BiologyEastern Virginia Medical SchoolNorfolkVA23507USA
| |
Collapse
|
44
|
Dong M, Lih TM, Chen SY, Cho KC, Eguez RV, Höti N, Zhou Y, Yang W, Mangold L, Chan DW, Zhang Z, Sokoll LJ, Partin A, Zhang H. Urinary glycoproteins associated with aggressive prostate cancer. Am J Cancer Res 2020; 10:11892-11907. [PMID: 33204318 PMCID: PMC7667684 DOI: 10.7150/thno.47066] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background: There is an urgent need for the detection of aggressive prostate cancer. Glycoproteins play essential roles in cancer development, while urine is a noninvasive and easily obtainable biological fluid that contains secretory glycoproteins from the urogenital system. Therefore, here we aimed to identify urinary glycoproteins that are capable of differentiating aggressive from non-aggressive prostate cancer. Methods: Quantitative mass spectrometry data of glycopeptides from a discovery cohort comprised of 74 aggressive (Gleason score ≥8) and 68 non-aggressive (Gleason score = 6) prostate cancer urine specimens were acquired via a data independent acquisition approach. The glycopeptides showing distinct expression profiles in aggressive relative to non-aggressive prostate cancer were further evaluated for their performance in distinguishing the two groups either individually or in combination with others using repeated 5-fold cross validation with logistic regression to build predictive models. Predictive models showing good performance from the discovery cohort were further evaluated using a validation cohort. Results: Among the 20 candidate glycoproteins, urinary ACPP outperformed the other candidates. Urinary ACPP can also serve as an adjunct to serum PSA to further improve the discrimination power for aggressive prostate cancer (AUC= 0.82, 95% confidence interval 0.75 to 0.89). A three-signature panel including urinary ACPP, urinary CLU, and serum PSA displayed the ability to distinguish aggressive prostate cancer from non-aggressive prostate cancer with an AUC of 0.86 (95% confidence interval 0.8 to 0.92). Another three-signature panel containing urinary ACPP, urinary LOX, and serum PSA also demonstrated its ability in recognizing aggressive prostate cancer (AUC=0.82, 95% confidence interval 0.75 to 0.9). Moreover, consistent performance was observed from each panel when evaluated using a validation cohort. Conclusion: We have identified glycopeptides of urinary glycoproteins associated with aggressive prostate cancer using a quantitative mass spectrometry-based glycoproteomic approach and demonstrated their potential to serve as noninvasive urinary glycoprotein biomarkers worthy of further validation by a multi-center study.
Collapse
|
45
|
Das T, Andrieux G, Ahmed M, Chakraborty S. Integration of Online Omics-Data Resources for Cancer Research. Front Genet 2020; 11:578345. [PMID: 33193699 PMCID: PMC7645150 DOI: 10.3389/fgene.2020.578345] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
The manifestations of cancerous phenotypes necessitate alterations at different levels of information-flow from genome to proteome. The molecular alterations at different information processing levels serve as the basis for the cancer phenotype to emerge. To understand the underlying mechanisms that drive the acquisition of cancer hallmarks it is required to interrogate cancer cells using multiple levels of information flow represented by different omics - such as genomics, epigenomics, transcriptomics, and proteomics. The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to integrate the omics-data in a biologically meaningful manner. The plethora of cancer-specific online omics-data resources, if able to be integrated efficiently and systematically, may facilitate the generation of new biological insights for cancer research. In this review, we provide a comprehensive overview of the online single- and multi-omics resources that are dedicated to cancer. We catalog various online omics-data resources such as The Cancer Genome Atlas (TCGA) along with various TCGA-associated data portals and tools for multi-omics analysis and visualization, the International Cancer Genome Consortium (ICGC), Catalogue of Somatic Mutations in Cancer (COSMIC), The Pathology Atlas, Gene Expression Omnibus (GEO), and PRoteomics IDEntifications (PRIDE). By comparing the strengths and limitations of the respective online resources, we aim to highlight the current biological and technological challenges and possible strategies to overcome these challenges. We outline the available schemes for the integration of the multi-omics dimensions for stratifying cancer patients and biomarker prediction based on the integrated molecular-signatures of cancer. Finally, we propose the multi-omics driven systems-biology approaches to realize the potential of precision onco-medicine as the future of cancer research. We believe this systematic review will encourage scientists and clinicians worldwide to utilize the online resources to explore and integrate the available omics datasets that may provide a window of opportunity to generate new biological insights and contribute to the advancement of the field of cancer research.
Collapse
Affiliation(s)
- Tonmoy Das
- Molecular Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Geoffroy Andrieux
- Medical Center - University of Freiburg, Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Freiburg, Freiburg, Germany
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sajib Chakraborty
- Molecular Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
46
|
Frantzi M, Gomez-Gomez E, Mischak H. Noninvasive biomarkers to guide intervention: toward personalized patient management in prostate cancer. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1804866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maria Frantzi
- Department of Biomarker Research, Mosaiques Diagnostics GmbH, Hannover, Germany
| | | | - Harald Mischak
- Department of Biomarker Research, Mosaiques Diagnostics GmbH, Hannover, Germany
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
- Maimonides Institute of Biomedical Research of Cordoba (IMIBIC), University of Cordoba, Cordoba, Spain
| |
Collapse
|
47
|
Jeon J, Olkhov-Mitsel E, Xie H, Yao CQ, Zhao F, Jahangiri S, Cuizon C, Scarcello S, Jeyapala R, Watson JD, Fraser M, Ray J, Commisso K, Loblaw A, Fleshner NE, Bristow RG, Downes M, Vesprini D, Liu S, Bapat B, Boutros PC. Temporal Stability and Prognostic Biomarker Potential of the Prostate Cancer Urine miRNA Transcriptome. J Natl Cancer Inst 2020; 112:247-255. [PMID: 31161221 DOI: 10.1093/jnci/djz112] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/01/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development of noninvasive tests for the early detection of aggressive prostate tumors is a major unmet clinical need. miRNAs are promising noninvasive biomarkers: they play essential roles in tumorigenesis, are stable under diverse analytical conditions, and can be detected in body fluids. METHODS We measured the longitudinal stability of 673 miRNAs by collecting serial urine samples from 10 patients with localized prostate cancer. We then measured temporally stable miRNAs in an independent training cohort (n = 99) and created a biomarker predictive of Gleason grade using machine-learning techniques. Finally, we validated this biomarker in an independent validation cohort (n = 40). RESULTS We found that each individual has a specific urine miRNA fingerprint. These fingerprints are temporally stable and associated with specific biological functions. We identified seven miRNAs that were stable over time within individual patients and integrated them with machine-learning techniques to create a novel biomarker for prostate cancer that overcomes interindividual variability. Our urine biomarker robustly identified high-risk patients and achieved similar accuracy as tissue-based prognostic markers (area under the receiver operating characteristic = 0.72, 95% confidence interval = 0.69 to 0.76 in the training cohort, and area under the receiver operating characteristic curve = 0.74, 95% confidence interval = 0.55 to 0.92 in the validation cohort). CONCLUSIONS These data highlight the importance of quantifying intra- and intertumoral heterogeneity in biomarker development. This noninvasive biomarker may usefully supplement invasive or expensive radiologic- and tissue-based assays.
Collapse
Affiliation(s)
- Jouhyun Jeon
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Honglei Xie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fang Zhao
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Sahar Jahangiri
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Carmelle Cuizon
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Seville Scarcello
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Renu Jeyapala
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jessica Ray
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Kristina Commisso
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Andrew Loblaw
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Neil E Fleshner
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | | | - Danny Vesprini
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada
| | - Stanley Liu
- Sunnybrook Research Institute and Department of Radiation Oncology, Sunnybrook-Odette Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Bharati Bapat
- Lunenfeld-Tannenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA.,Department of Urology, University of California, Los Angeles, Los Angeles, CA.,Broad Stem Cell Research Centre, University of California, Los Angeles, Los Angeles, CA.,Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA
| |
Collapse
|
48
|
Exploration of Circulating Tumour Cell (CTC) Biology: A Paradigm Shift in Liquid Biopsy. Indian J Clin Biochem 2020; 36:131-142. [PMID: 33867703 PMCID: PMC7994460 DOI: 10.1007/s12291-020-00923-4] [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: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 01/07/2023]
Abstract
Circulating tumour cells (CTCs), are disseminated tumour cells found in the blood in solid tumour malignancies. Identification of CTCs act as emerging tools in the field of the Liquid Biopsy. Majority of the studies focused on detection and enumeration of CTCs due to technological challenges those results from the rarity of CTCs in the blood. Enumeration of CTCs has already proven their value as prognostic as well as predictive biomarkers for disease prognosis. However, recent advances in technology permitted to study the molecular and functional features of CTCs and these features have the potential to change the diagnostic, prognostic and predictive landscape in oncology. In this review, we summarize the paradigm shift in the field of liquid biopsy-based cancer diagnostics using CTC isolation and detection. We have discussed recent advances in the technologies for molecular characterization of CTCs which have aided a shift from CTC enumeration to an in-depth analysis of the CTC genome, transcriptomes, proteins, epigenomes along with various functional features. Finally, as a prognosticating strategy, the potentials of CTCs as a tool of liquid biopsy to predict micrometastasis, monitor prognosis and how to use them as an additional tool for cancer staging has been discussed.
Collapse
|
49
|
Daouk R, Bahmad HF, Saleh E, Monzer A, Ballout F, Kadara H, Abou-Kheir W. Genome-wide gene expression analysis of a murine model of prostate cancer progression: Deciphering the roles of IL-6 and p38 MAPK as potential therapeutic targets. PLoS One 2020; 15:e0237442. [PMID: 32790767 PMCID: PMC7425932 DOI: 10.1371/journal.pone.0237442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the most commonly diagnosed cancer and the second leading cause of cancer-related deaths among adult males globally. The poor prognosis of PCa is largely due to late diagnosis of the disease when it has already progressed to an advanced stage marked by androgen-independence, thus necessitating new strategies for early detection and treatment. We construe that these direly needed advances are limited by our poor understanding of early events in the progression of PCa and that would thus represent ideal targets for early intervention. To begin to fill this void, we interrogated molecular "oncophenotypes" that embody the transition of PCa from an androgen-dependent (AD) to-independent (AI) state. METHODS To accomplish this aim, we used our previously established AD and AI murine PCa cell lines, PLum-AD and PLum-AI, respectively, which recapitulate primary and progressive PCa morphologically and molecularly. We statistically surveyed global gene expressions in these cell lines by microarray analysis. Differential profiles were functionally interrogated by pathways, gene set enrichment and topological gene network analyses. RESULTS Gene expression analysis of PLum-AD and PLum-AI transcriptomes (n = 3 each), revealed 723 differentially expressed genes (392 upregulated and 331 downregulated) in PLum-AI compared to PLum-AD cells. Gene set analysis demonstrated enrichment of biological functions and pathways in PLum-AI cells that are central to tumor aggressiveness including cell migration and invasion facilitated by epithelial-to-mesenchymal transition (EMT). Further analysis demonstrated that the p38 mitogen-activated protein kinase (MAPK) was predicted to be significantly activated in the PLum-AI cells, whereas gene sets previously associated with favorable response to the p38 inhibitor SB203580 were attenuated (i.e., inversely enriched) in the PLum-AI cells, suggesting that these aggressive cells may be therapeutically vulnerable to p38 inhibition. Gene set and gene-network analysis also alluded to activation of other signaling networks particularly those associated with enhanced EMT, inflammation and immune function/response including, but not limited to Tnf, IL-6, Mmp 2, Ctgf, and Ptges. Accordingly, we chose SB203580 and IL-6 to validate their effect on PLum-AD and PLum-AI. Some of the common genes identified in the gene-network analysis were validated at the molecular and functional level. Additionally, the vulnerability to SB203580 and the effect of IL-6 were also validated on the stem/progenitor cell population using the sphere formation assay. CONCLUSIONS In summary, our study highlights pathways associated with an augmented malignant phenotype in AI cells and presents new high-potential targets to constrain the aggressive malignancy seen in the castration-resistant PCa.
Collapse
Affiliation(s)
- Reem Daouk
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hisham F. Bahmad
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL, United States of America
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States of America
| | - Eman Saleh
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Alissar Monzer
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Farah Ballout
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
50
|
Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteomics 2020; 17:17. [PMID: 32489335 PMCID: PMC7247207 DOI: 10.1186/s12014-020-09283-w] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
Collapse
Affiliation(s)
- Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| |
Collapse
|