1
|
Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
Collapse
Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
| |
Collapse
|
2
|
Gasparri R, Sedda G, Noberini R, Bonaldi T, Spaggiari L. Clinical Application of Mass Spectrometry-Based Proteomics in Lung Cancer Early Diagnosis. Proteomics Clin Appl 2020; 14:e1900138. [PMID: 32418314 DOI: 10.1002/prca.201900138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/06/2020] [Indexed: 12/18/2022]
Abstract
The current knowledge on proteomic biomarker analysis for the early diagnosis of lung cancer is summarized, underlining the diversity among the results and the current interest in translating research results into clinical practice. A MEDLINE/PubMed literature search to retrieve all the papers published in the last 10 years is performed. Proteomics studies on lung cancer have gathered evidence on the potential role of biomarkers in early diagnosis. Although promising, none of them have proved to be sufficiently reliable to achieve validation. Future research should evolve toward a multipanel analysis of proteins, considering the possibility that individual biomarkers might not be specific enough to diagnose lung cancer, but could be related to oncological conditions.
Collapse
Affiliation(s)
- Roberto Gasparri
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Giulia Sedda
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Lorenzo Spaggiari
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono, Milan, 7 - 20122, Italy
| |
Collapse
|
3
|
Sun Y, Zhang J, Guo F, Zhao W, Zhan Y, Liu C, Fan Y, Wang J. Identification of Apolipoprotein C-I Peptides as a Potential Biomarker and its Biological Roles in Breast Cancer. Med Sci Monit 2016; 22:1152-60. [PMID: 27052600 PMCID: PMC4827518 DOI: 10.12659/msm.896531] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Breast cancer (BC) is one of the most common cancers and is among the main causes of death in females around the world. Although several serum biomarkers have been identified for breast cancer, due to lack of adequate sensitivity and specificity they do not adequately distinguish BC from confounding conditions. New approaches are urgently needed to improve BC detection and treatment. Material/Methods Eighty serum samples from 20 healthy individuals and 60 patients with BC (22 triple-negative breast cancer, TNBC; 38 non-triple-negative breast cancer, NTNBC) were included. Protein profiling of serum samples was analyzed using surface-enhanced laser desorption/ionization time-of-flight mass spectroscopy (SELDI-TOF-MS). Candidate biomarkers were purified by SDS-PAGE electrophoresis and identified by MALDI-TOF/TOF. Results The candidate biomarker positioned at 6447.9 m/z was significantly decreased in BC patients. Moreover, the expression intensity of the candidate biomarker was weaker in the TNBC and pre-surgery group compared with the NTNBC and post-surgery group. We ultimately identified the biomarker as apolipoprotein C-I (ApoC-I). Furthermore, we found that ApoC-I peptides inhibited proliferation of human breast cancer cells in vitro and suppressed tumor growth in vivo. Conclusions These results suggest that ApoC-I peptides may be a potential diagnostic biomarker and therapeutic approach for BC.
Collapse
Affiliation(s)
- Yadong Sun
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Junjie Zhang
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Fei Guo
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Wei Zhao
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Yuxiao Zhan
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Chenyu Liu
- Department of Breast, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Yuxia Fan
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Jiaxiang Wang
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| |
Collapse
|
4
|
Zhang HW, Zhou P, Wang KZ, Liu JB, Huang YS, Tu YT, Deng ZH, Zhu XD, Hang YL. Platelet proteomics in diagnostic differentiation of primary immune thrombocytopenia using SELDI-TOF-MS. Clin Chim Acta 2016; 455:75-9. [DOI: 10.1016/j.cca.2016.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 01/17/2016] [Accepted: 01/26/2016] [Indexed: 12/30/2022]
|
5
|
Amin A, Bukhari S, Mokhdomi TA, Anjum N, Wafai AH, Wani Z, Manzoor S, Koul AM, Amin B, Ain QU, Qazi H, Tyub S, Lone GN, Qadri RA. Comparative proteomics and global genome-wide expression data implicate role of ARMC8 in lung cancer. Asian Pac J Cancer Prev 2016; 16:3691-6. [PMID: 25987023 DOI: 10.7314/apjcp.2015.16.9.3691] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards. MATERIALS AND METHODS In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS. RESULTS Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways. CONCLUSIONS The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.
Collapse
Affiliation(s)
- Asif Amin
- Department of Biotechnology, University of Kashmir, Srinagar India E-mail :
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Tracing the voyage of SELDI-TOF MS in cancer biomarker discovery and its current depreciation trend – need for resurrection? Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
7
|
Yang RH, Tian RF, Ren QL, Chui HY, Guo ST, Zhang XD, Song X. Serum protein profiles of patients with lung cancer of different histological types. Asia Pac J Clin Oncol 2015; 12:70-6. [PMID: 26668125 DOI: 10.1111/ajco.12441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 06/27/2015] [Accepted: 10/11/2015] [Indexed: 12/24/2022]
Abstract
AIMS To compare serum protein expression profiles between lung cancer patients and healthy individuals, and to examine whether there are differences in serum protein expression profiles among patients with lung cancers of different histological types and whether the characteristic expression of serum proteins may assist in differential diagnosis of various subtypes of lung cancers. METHODS Blood samples were collected from 123 lung cancer patients before commencement of treatment who attended Shanxi Cancer Hospital, China, between 2008 and 2013. Blood samples from 60 healthy individuals were also collected in the same period. Serum protein expression profiles were analyzed using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. The differences in the serum protein spectrums of lung cancer patients with different histological subtypes were analyzed by one-way Analysis of Variance and receiver operating characteristic curves. RESULTS A cluster of 48 protein mass-to-change ratio (M/Z) peaks was differentially expressed between sera of lung cancer patients and healthy individuals. The M/Z 1205, 4673, 1429 and 4279 peaks were differentially expressed among patients with lung squamous cell carcinomas, adenocarcinomas and small-cell lung carcinomas. CONCLUSION These results reinforce the notion that profiling of serum proteins may be of diagnostic value in lung cancer, and suggest that the differences in serum protein profiles may be useful in differential diagnosis of lung cancers of varying histological subtypes.
Collapse
Affiliation(s)
| | - Rui Fen Tian
- Pulmonary Oncology, Shanxi Cancer Hospital and Institute, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, China
| | - Qiao Li Ren
- Pulmonary Oncology, Shanxi Cancer Hospital and Institute, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, China
| | - Hong Ying Chui
- Pulmonary Oncology, Shanxi Cancer Hospital and Institute, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, China
| | | | - Xu Dong Zhang
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Xia Song
- Pulmonary Oncology, Shanxi Cancer Hospital and Institute, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan, China
| |
Collapse
|
8
|
Santini AC, Giovane G, Auletta A, Di Carlo A, Fiorelli A, Cito L, Astarita C, Giordano A, Alfano R, Feola A, Di Domenico M. Translational Research and Plasma Proteomic in Cancer. J Cell Biochem 2015; 117:828-35. [PMID: 26479787 DOI: 10.1002/jcb.25413] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/16/2015] [Indexed: 12/14/2022]
Abstract
Proteomics is a recent field of research in molecular biology that can help in the fight against cancer through the search for biomarkers that can detect this disease in the early stages of its development. Proteomic is a speedily growing technology, also thanks to the development of even more sensitive and fast mass spectrometry analysis. Although this technique is the most widespread for the discovery of new cancer biomarkers, it still suffers of a poor sensitivity and insufficient reproducibility, essentially due to the tumor heterogeneity. Common technical shortcomings include limitations in the sensitivity of detecting low abundant biomarkers and possible systematic biases in the observed data. Current research attempts are trying to develop high-resolution proteomic instrumentation for high-throughput monitoring of protein changes that occur in cancer. In this review, we describe the basic features of the proteomic tools which have proven to be useful in cancer research, showing their advantages and disadvantages. The application of these proteomic tools could provide early biomarkers detection in various cancer types and could improve the understanding the mechanisms of tumor growth and dissemination.
Collapse
Affiliation(s)
- Annamaria Chiara Santini
- Department of Morphopathology, Thoracic Surgery Unit, Second University of Naples, Naples, Italy
| | - Giancarlo Giovane
- Department of Experimental Medicine, Section of Hygiene, Occupational Medicine and Forensic Medicine, Second University of Naples, Naples, Italy
| | - Adelaide Auletta
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Angelina Di Carlo
- Department of Medico-Surgical Sciences and Biotechnologies, "Sapienza" University of Rome, Rome, Italy
| | - Alfonso Fiorelli
- Department of Morphopathology, Thoracic Surgery Unit, Second University of Naples, Naples, Italy
| | - Letizia Cito
- Oncology Research Center of Mercogliano (CROM), Istituto Nazionale Tumori "Fodazione G. Pascale" - IRCCS, Naples, Italy
| | - Carlo Astarita
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, Pennsylvania
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, Pennsylvania.,Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Roberto Alfano
- Department of Anesthesiological, Surgical and Emergency Sciences. Second University of Naples, Naples, Italy
| | - Antonia Feola
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Marina Di Domenico
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, Pennsylvania
| |
Collapse
|
9
|
SUN LIPING, LI LI, LI ZHAO, HONG SHUHUI, YANG QIFENG, QU XUN, KONG BEIHUA. Alterations in the serum proteome profile during the development of ovarian cancer. Int J Oncol 2014; 45:2495-501. [DOI: 10.3892/ijo.2014.2675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/11/2014] [Indexed: 11/06/2022] Open
|
10
|
Mesri M. Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med 2014; 2014:238045. [PMID: 26556407 PMCID: PMC4590950 DOI: 10.1155/2014/238045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
Collapse
Affiliation(s)
- Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
11
|
Rodrigo MAM, Zitka O, Krizkova S, Moulick A, Adam V, Kizek R. MALDI-TOF MS as evolving cancer diagnostic tool: a review. J Pharm Biomed Anal 2014; 95:245-55. [PMID: 24699369 DOI: 10.1016/j.jpba.2014.03.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 02/09/2023]
Abstract
Recent developments in mass spectrometry have introduced clinical proteomics to the forefront of diseases diagnosis, offering reliable, robust and efficient analytical method for biomarker discovery and monitoring. MALDI-TOF is a powerful tool for surveying proteins and peptides comprising the realm for clinical analysis. MALDI-TOF has the potential to revolutionize cancer diagnostics by facilitating biomarker discovery, enabling tissue imaging and quantifying biomarker levels. Healthy (control) and cancerous tissues can be analyzed on the basis of mass spectrometry (MALDI-TOF) imaging to identify cancer-specific changes that may prove to be clinically useful. We review MALDI-TOF profiling techniques as tools for detection of cancer biomarkers in various cancers. We mainly discuss recent advances including period from 2011 to 2013.
Collapse
Affiliation(s)
- Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic.
| |
Collapse
|