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Whitham D, Bruno P, Haaker N, Arcaro KF, Pentecost BT, Darie CC. Deciphering a proteomic signature for the early detection of breast cancer from breast milk: the role of quantitative proteomics. Expert Rev Proteomics 2024; 21:81-98. [PMID: 38376826 DOI: 10.1080/14789450.2024.2320158] [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: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Breast cancer is one of the most prevalent cancers among women in the United States. Current research regarding breast milk has been focused on the composition and its role in infant growth and development. There is little information about the proteins, immune cells, and epithelial cells present in breast milk which can be indicative of the emergence of BC cells and tumors. AREAS COVERED We summarize all breast milk studies previously done in our group using proteomics. These studies include 1D-PAGE and 2D-PAGE analysis of breast milk samples, which include within woman and across woman comparisons to identify dysregulated proteins in breast milk and the roles of these proteins in both the development of BC and its diagnosis. Our projected outlook for the use of milk for cancer detection is also discussed. EXPERT OPINION Analyzing the samples by multiple methods allows one to interrogate a set of samples with various biochemical methods that complement each other, thus providing a more comprehensive proteome. Complementing methods like 1D-PAGE, 2D-PAGE, in-solution digestion and proteomics analysis with PTM-omics, peptidomics, degradomics, or interactomics will provide a better understanding of the dysregulated proteins, but also the modifications or interactions between these proteins.
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Affiliation(s)
- Danielle Whitham
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Pathea Bruno
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Norman Haaker
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Brian T Pentecost
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Costel C Darie
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
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Neagu AN, Whitham D, Seymour L, Haaker N, Pelkey I, Darie CC. Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype. Proteomes 2023; 11:proteomes11020013. [PMID: 37092454 PMCID: PMC10123686 DOI: 10.3390/proteomes11020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Invasive ductal carcinoma (IDC) is the most common histological subtype of malignant breast cancer (BC), and accounts for 70–80% of all invasive BCs. IDC demonstrates great heterogeneity in clinical and histopathological characteristics, prognoses, treatment strategies, gene expressions, and proteomic profiles. Significant proteomic determinants of the progression from intraductal pre-invasive malignant lesions of the breast, which characterize a ductal carcinoma in situ (DCIS), to IDC, are still poorly identified, validated, and clinically applied. In the era of “6P” medicine, it remains a great challenge to determine which patients should be over-treated versus which need to be actively monitored without aggressive treatment. The major difficulties for designating DCIS to IDC progression may be solved by understanding the integrated genomic, transcriptomic, and proteomic bases of invasion. In this review, we showed that multiple proteomics-based techniques, such as LC–MS/MS, MALDI-ToF MS, SELDI-ToF-MS, MALDI-ToF/ToF MS, MALDI-MSI or MasSpec Pen, applied to in-tissue, off-tissue, BC cell lines and liquid biopsies, improve the diagnosis of IDC, as well as its prognosis and treatment monitoring. Classic proteomics strategies that allow the identification of dysregulated protein expressions, biological processes, and interrelated pathway analyses based on aberrant protein–protein interaction (PPI) networks have been improved to perform non-invasive/minimally invasive biomarker detection of early-stage IDC. Thus, in modern surgical oncology, highly sensitive, rapid, and accurate MS-based detection has been coupled with “proteome point sampling” methods that allow for proteomic profiling by in vivo “proteome point characterization”, or by minimal tissue removal, for ex vivo accurate differentiation and delimitation of IDC. For the detection of low-molecular-weight proteins and protein fragments in bodily fluids, LC–MS/MS and MALDI-MS techniques may be coupled to enrich and capture methods which allow for the identification of early-stage IDC protein biomarkers that were previously invisible for MS-based techniques. Moreover, the detection and characterization of protein isoforms, including posttranslational modifications of proteins (PTMs), is also essential to emphasize specific molecular mechanisms, and to assure the early-stage detection of IDC of the breast.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd. No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Norman Haaker
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Isabella Pelkey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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Cancer proteomics: Application of case studies in diverse cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Usman M, Ilyas A, Syed B, Hashim Z, Ahmed A, Zarina S. Serum HSP90-Alpha and Oral Squamous Cell Carcinoma : A Prospective Biomarker. Protein Pept Lett 2021; 28:1157-1163. [PMID: 34137356 DOI: 10.2174/0929866528666210616112539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022]
Abstract
AIM Current study aims to perform differential protein expression analysis of serum samples from Oral squamous cell carcinoma (OSCC) patients and healthy controls in search of potential diagnostic and/or prognostic biomarker(s). OBJECTIVE OSCC is diagnosed late, resulting in poor survival and high mortality. Identification of non-invasive prognostic biomarker is of utmost importance for early diagnosis and proper management of the disease; hence we used proteomic approach to identify potential biomarkers from serum. METHODS Serum samples (OSCC n=45 and control n=30) were depleted and proteins were separated using 2-D gel electrophoresis followed by identification by mass spectrometric analysis. Gene expression analysis of identified proteins in malignant and normal tissue was also performed to complement proteomics studies. RESULTS Among differentially expressed proteins, a noteworthy observation was up regulation of Heat shock protein alpha (HSP90α) from serum of oral cancer patients. We also observed elevated levels of Haptoglobin (HP) along with down regulation of Type II keratin cytoskeletal 1(KRT1) and serum Albumin (ALB) in oral cancer patients. Gene expression studies of identified proteins in malignant and normal tissue revealed a similar pattern with the exception of KRT1. We believe that elevated levels of serum HSP90 alpha might be used as a potential biomarker. CONCLUSION Our findings suggest the contribution of HSP90 alpha and other identified proteins in oral pathology as pro/anti apoptotic modulators, thus they are being considered as predictive biomarkers.
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Affiliation(s)
- Muhammad Usman
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi 75270, Pakistan
| | - Amber Ilyas
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi 75270, Pakistan
| | - Basir Syed
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, Orange, CA 92866, United States
| | - Zehra Hashim
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi 75270, Pakistan
| | - Aftab Ahmed
- Department of Biomedical and Pharmaceutical Sciences, Chapman University, Orange, CA 92866, United States
| | - Shamshad Zarina
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi 75270, Pakistan
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Abstract
Haptoglobin (Hp) is a blood plasma glycoprotein that binds free hemoglobin (Hb) and plays a critical role in tissue protection and the prevention of oxidative damage. In addition, it has a number of regulatory functions. Haptoglobin is an acute phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. Only in humans, the Hp gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of Hp, homozygous Hp1-1 and Hp2-2, and heterozygous Hp2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual's predisposition to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting of the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the Hp β-chain has become the main direction in the study of pathological processes, including malignant neoplasms. Many studies are focused on the identification of PTM and changes in the level of the α2-chain of this protein in pathology. These characteristics of Hp indicate the possibility of the existence of this protein as different proteoforms, probably with different functions. This review is devoted to the description of the structural and functional diversity of Hp and its potential use as a biomarker of various pathologies.
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Affiliation(s)
- S N Naryzhny
- Institute of Biomedical Chemistry, Moscow, Russia; Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
| | - O K Legina
- Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
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Naryzny SN, Legina OK. Haptoglobin as a Biomarker. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES B, BIOMEDICAL CHEMISTRY 2021; 15:184-198. [PMID: 34422226 PMCID: PMC8365284 DOI: 10.1134/s1990750821030069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Haptoglobin (Hp) is a glycoprotein that binds free hemoglobin (Hb) in plasma and plays a critical role in tissue protection and prevention of oxidative damage. Besides, it has some regulatory functions. Haptoglobin is an acute-phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. The human Нр gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of haptoglobin: homozygous Нр1-1 and Нр2-2, and heterozygous Нр2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual predisposition of a person to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting off the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the β-chain of Hp has become the main direction in the study of pathological processes, including malignant neoplasms. These characteristics indicate the possibility of the existence of Hp in the form of a multitude of proteoforms, probably performing different functions. This review is devoted to the description of the structural and functional diversity and the potential use of Hp as a biomarker of various pathologies.
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Affiliation(s)
- S. N. Naryzny
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia ,St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
| | - O. K. Legina
- St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
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Huang J, Wang Q, Hu Y, Qi Z, Lin Z, Ying W, Zhou M. Proteomic Profiling for Serum Biomarkers in Mice Exposed to Ionizing Radiation. Dose Response 2019; 17:1559325819894794. [PMID: 31853238 PMCID: PMC6909274 DOI: 10.1177/1559325819894794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
In response to large-scale radiological incidents, rapid, accurate, and early triage biodosimeters are urgently required. In this study, we investigated candidate radiation-responsive biomarkers using proteomics approaches in mouse models. A total of 452 dysregulated proteins were identified in the serum samples of mice exposed to 0, 2, 5.5, 7, and 8 Gy at 6, 24, and 72 hours postirradiation. Ninety-eight proteins, including 46 at 6 hours, 36 at 24 hours, and 36 at 72 hours, were identified as radiation-responsive proteins (RRPs). Gene Ontology analysis showed the RRPs were involved in proteolysis, extracellular space, hydrolase activity, and carbohydrate binding. Kyoto Encyclopedia of Genes and Genome enrichment showed the RRPs were regulated in "the pentose phosphate pathway," "the proteasome," and "AGE-RAGE signaling in diabetic complications." There were 3 proteins changed and overlapped at all the 3 time points, 8 proteins changed at 6 and 24 hours, 4 proteins changed at 24 and 72hours, and 2 proteins changed at both 6 and 72 hours. Of these proteins, ORM2, HP, SAA1, SAA2, MBL2, COL1A1, and APCS were identified as candidate biomarkers for biodosimeter-based diagnosis through Pearson correlation analysis.
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Affiliation(s)
- Jinfeng Huang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Yingchun Hu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhenhua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Zhongwu Lin
- Science Research Management Department of the Academy of Military Sciences, Beijing, People’s Republic of China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, People’s Republic of China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
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Zhang Y, Zhao Z, Li S, Dong L, Li Y, Mao Y, Liang Y, Tao Y, Ma J. Inhibition of miR‑214 attenuates the migration and invasion of triple‑negative breast cancer cells. Mol Med Rep 2019; 19:4035-4042. [PMID: 30942417 PMCID: PMC6471216 DOI: 10.3892/mmr.2019.10112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022] Open
Abstract
Triple‑negative breast cancer (TNBC) is a subtype of breast cancer. MicroRNA (miR)‑214 is closely associated with controlling the development of tumor cells; therefore, in the present study, the target gene and effects of miR‑214 on TNBC cells were explored. Luciferase activity was examined by luciferase reporter assay. The viability, invasion and migration of MDA‑MB‑231 TNBC cells were measured using Cell Counting kit‑8, Transwell and wound‑healing assays, respectively. The expression levels of various factors were determined using reverse transcription‑quantitative polymerase chain reaction and western blotting. The results demonstrated that the expression levels of miR‑214 were higher and the levels of α1‑antitrypsin (α1‑AT) were lower in TNBC tissues compared with in normal tissues. Subsequently, α1‑AT was revealed to be a target of miR‑214. Furthermore, inhibition of miR‑214 decreased cell viability, invasion and migration, enhanced the expression of E‑cadherin and tissue inhibitor of metalloproteinases‑2, and reduced the expression of metastatic tumour antigen 1 and matrix metalloproteinase‑2. Inhibition of miR‑214 also significantly downregulated the phosphorylation of protein kinase B (Akt) and mammalian target of rapamycin (mTOR), and markedly downregulated that of phosphoinositide 3‑kinase (PI3K); however, the expression levels of total PI3K, Akt and mTOR remained stable in all groups. Taken together, these findings indicated that α1‑AT may be a target of miR‑214. Downregulation of miR‑214 markedly suppressed the viability, migration and invasion of MDA‑MB‑231 cells, and inhibited the PI3K/Akt/mTOR pathway. These findings suggested that miR‑214 targeting α1‑AT may be a potential mechanism underlying TNBC development.
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Affiliation(s)
- Yi Zhang
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Zhijing Zhao
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Siqi Li
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Liying Dong
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Yan Li
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Ying Mao
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Ying Liang
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Yun Tao
- Clinical Skill Center, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Junfeng Ma
- Thyroid-Breast Surgery Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
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Nasr R, Salim Hammoud M, Nassar F, Mukherji D, Shamseddine A, Temraz S. Inflammatory Markers and MicroRNAs: The Backstage Actors Influencing Prognosis in Colorectal Cancer Patients. Int J Mol Sci 2018; 19:E1867. [PMID: 29949857 PMCID: PMC6073730 DOI: 10.3390/ijms19071867] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/17/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) remains a deadly disease, afflicting the lives of millions worldwide. The prognosis of CRC patients is best predicted by surgical resection and pathological analysis of specimens. Emerging evidence has attributed a significant role to inflammatory markers and microRNAs (miRNAs) in the prognosis and survival of CRC patients. AIM Here, we review the literature on inflammatory markers and miRNAs with an established role on survival rates, response to systemic chemotherapy, and other clinic-pathological parameters in CRC patients. RESULTS Our literature review revealed a critical role of inflammatory markers—specifically, the acute-phase proteins, inflammatory cytokines, and blood cell ratios—on prognostic outcomes in CRC patients. MiRNAs, on the other hand, were useful in predicting prognosis and clinical response and accordingly stratifying CRC patients for optimal drug selection. CONCLUSION These biomarkers are easily measured in routine blood exams and can be used in adjunct to the tumor-node-metastasis (TNM) staging system to identify high-risk patients and those who are more likely to benefit from chemotherapy and other targeted therapies. However, more prospective studies are needed for the validation of these discussed prognostic and predictive biomarkers.
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Affiliation(s)
- Rihab Nasr
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
| | - Miza Salim Hammoud
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
| | - Farah Nassar
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
| | - Deborah Mukherji
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
| | - Ali Shamseddine
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
| | - Sally Temraz
- Department of Internal Medicine, American University of Beirut Medical Center, Riad El Solh, Beirut 110 72020, Lebanon.
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Pang WW, Abdul-Rahman PS, Wan-Ibrahim WI, Hashim OH. Can the Acute-Phase Reactant Proteins be Used as Cancer Biomarkers? Int J Biol Markers 2018; 25:1-11. [DOI: 10.1177/172460081002500101] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The association between the acute-phase reactant proteins (APRPs) and cancer has long been established. There have been numerous reports correlating altered levels of various APRPs with different types of cancers. However, researchers are often quick to dismiss the use of these APRPs as potential biomarkers for the diagnosis and monitoring of cancer because alterations in APRP concentrations are observed in a wide range of diseases. Recent progress in proteomics studies which profiled the serum proteins of cancer patients and those of normal individuals indicated that the altered APRP expressions were different for distinct types, subtypes, and even stages of cancer. Interestingly, these data are in agreement with those observed earlier using immunochemical and biochemical assays. In view of this compelling association of different patterns of APRPs with various types of cancers and in an apparent shift of paradigm, we present in this review some indications that APRP fingerprinting may be used as complementary cancer biomarkers.
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Affiliation(s)
- Wei Wei Pang
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
| | - Puteri Shafinaz Abdul-Rahman
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
| | - Wan Izlina Wan-Ibrahim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
| | - Onn Haji Hashim
- University of Malaya Centre for Proteomics Research, University of Malaya, Kuala Lumpur - Malaysia
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur - Malaysia
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Araújo JE, López-Fernández H, Diniz MS, Baltazar PM, Pinheiro LC, da Silva FC, Carrascal M, Videira P, Santos HM, Capelo JL. Dithiothreitol-based protein equalization technology to unravel biomarkers for bladder cancer. Talanta 2017; 180:36-46. [PMID: 29332824 DOI: 10.1016/j.talanta.2017.11.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 12/16/2022]
Abstract
This study aimed to assess the benefits of dithiothreitol (DTT)-based sample treatment for protein equalization to assess potential biomarkers for bladder cancer. The proteome of plasma samples of patients with bladder carcinoma, patients with lower urinary tract symptoms (LUTS) and healthy volunteers, was equalized with dithiothreitol (DTT) and compared. The equalized proteomes were interrogated using two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry. Six proteins, namely serum albumin, gelsolin, fibrinogen gamma chain, Ig alpha-1 chain C region, Ig alpha-2 chain C region and haptoglobin, were found dysregulated in at least 70% of bladder cancer patients when compared with a pool of healthy individuals. One protein, serum albumin, was found overexpressed in 70% of the patients when the equalized proteome of the healthy pool was compared with the equalized proteome of the LUTS patients. The pathways modified by the proteins differentially expressed were analyzed using Cytoscape. The method here presented is fast, cheap, of easy application and it matches the analytical minimalism rules as outlined by Halls. Orthogonal validation was done using western-blot. Overall, DTT-based protein equalization is a promising methodology in bladder cancer research.
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Affiliation(s)
- J E Araújo
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - H López-Fernández
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; SING Research Group, Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain; Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
| | - M S Diniz
- Biotox Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro M Baltazar
- Serviço de Urologia, Centro Hospital de Lisboa Central, Lisboa, Portugal; Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Luís Campos Pinheiro
- Serviço de Urologia, Centro Hospital de Lisboa Central, Lisboa, Portugal; Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Fernando Calais da Silva
- Serviço de Urologia, Centro Hospital de Lisboa Central, Lisboa, Portugal; Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Mylène Carrascal
- Glycoimmunology Group, UCIBIO, Departamento Ciências da Vida, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Videira
- Glycoimmunology Group, UCIBIO, Departamento Ciências da Vida, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - H M Santos
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - J L Capelo
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculdade de Ciência e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal.
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Proteome Profiling of Urinary Exosomes Identifies Alpha 1-Antitrypsin and H2B1K as Diagnostic and Prognostic Biomarkers for Urothelial Carcinoma. Sci Rep 2016; 6:34446. [PMID: 27686150 PMCID: PMC5043375 DOI: 10.1038/srep34446] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/14/2016] [Indexed: 11/09/2022] Open
Abstract
MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96.9%) and m/z 5947 (fragmented peptide of histone H2B1K sensitivity, 62.0%; specificity, 92.3%) were identified as UC diagnosis exosome biomarkers. UC patients with detectable histone H2B1K showed 2.29- and 3.11-fold increased risks of recurrence and progression, respectively, compared with those with nondetectable histone H2B1K. Verification results of IHC staining revealed significantly higher expression of alpha 1-antitrypsin (p = 0.038) and H2B1K (p = 0.005) in UC tissues than in normal tissues. The expression of alpha 1-antitrypsin and H2B1K in UC tissues was significantly correlated with UC grades (p < 0.05). Urinary exosome proteins alpha 1-antitrypsin and histone H2B1K, which are identified through MALDI-TOF analysis, could facilitate rapid diagnosis and prognosis of UC.
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Possibilities and limitations of 2DE-based analyses for identifying low-abundant tumor markers in human serum and plasma. Proteomics 2016; 16:2519-2532. [DOI: 10.1002/pmic.201600154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/24/2016] [Accepted: 06/29/2016] [Indexed: 11/07/2022]
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Sun L, Hu S, Yu L, Guo C, Sun L, Yang Z, Qi J, Ran Y. Serum haptoglobin as a novel molecular biomarker predicting colorectal cancer hepatic metastasis. Int J Cancer 2016; 138:2724-31. [PMID: 26756179 DOI: 10.1002/ijc.29993] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/16/2015] [Indexed: 12/24/2022]
Abstract
Early detection of liver metastasis is important for improving colorectal cancer (CRC) patient survival. Our previous studies showed haptoglobin was highly expressed in primary CRC tissues, especially in heterochronous metastatic cases. Here, we assessed the potential of serum haptoglobin (sHP) as a biomarker for early detection of CRC liver metastasis by evaluating the sHP in 475 CRC patients and 152 healthy volunteers. In the training set (250 cases), sHP level in CRC-M1 (1773.18 ± 690.25 ng/mL) were significantly increased as compared to in CRC-M0 (1544.37 ± 1497.65 ng/mL) or healthy (917.76 ± 571.59 ng/mL). And the high sHP level was correlated with poor survival. Logistic regression analysis revealed that sHP, serum carcinoembryonic antigen (sCEA) and serum carbohydrate antigen 19.9 (sCA19.9) level were the significant parameters for detecting liver metastasis. In leave-one-out-cross-validation, these three markers resulted in 89.1% sensitivity and 85.8% specificity for hepatic metastasis detection. In an independent test set (225 cases), receiver operating characteristic curve analysis of sHP in CRC liver metastasis showed an area under the curve of 0.735, with a sensitivity of 87.2% and a specificity of 59.9%. Combination of sHP, sCEA and sCA19.9 improved diagnostic accuracy to 0.880, with a sensitivity of 88.5% and a specificity of 87.8%. Silencing of HP by specific shRNA significantly inhibited the LOVO and SW620 cell invasion, and suppressed xenograft tumor invasive growth. In summary, these results demonstrate that sHP is associated with poor prognosis of CRC patients and that HP promotes colorectal cancer cell invasion. sHP combining with sCA19.9 and sCEA may be used as accurate predictors of CRC liver metastasis.
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Affiliation(s)
- Lichao Sun
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Shusheng Hu
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Long Yu
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Chunguang Guo
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Lixin Sun
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Zhihua Yang
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Jun Qi
- Clinical Laboratory, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Yuliang Ran
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Beijing, People's Republic of China
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Abstract
Lung cancer is the most frequently occurring cancer in the world and continually leads in mortality among cancers. The overall 5-year survival rate for lung cancer has risen only 4% (from 12% to 16%) over the past 4 decades, and late diagnosis is a major obstacle in improving lung cancer prognosis. Survival of patients undergoing lung resection is greater than 80%, suggesting that early detection and diagnosis of cancers before they become inoperable and lethal will greatly improve mortality. Lung cancer biomarkers can be used for screening, detection, diagnosis, prognosis, prediction, stratification, therapy response monitoring, and so on. This review focuses on noninvasive diagnostic and prognostic biomarkers. For that purpose, our discussion in this review will focus on biological fluid-based biomarkers. The body fluids include blood (serum or plasma), sputum, saliva, BAL, pleural effusion, and VOC. Since it is rich in different cellular and molecular elements and is one of the most convenient and routine clinical procedures, serum or plasma is the main source for the development and validation of many noninvasive biomarkers. In terms of molecular aspects, the most widely validated ones are proteins, some of which are used in the clinical sector, though in limited accessory purposes. We will also discuss the lung cancer (protein) biomarkers in clinical trials and currently in the validation phase with hundreds of samples. After proteins, we will discuss microRNAs, methylated DNA, and circulating tumor cells, which are being vigorously developed and validated as potential lung cancer biomarkers. The main aim of this review is to provide researchers and clinicians with an understanding of the potential noninvasive lung cancer biomarkers in biological fluids that have recently been discovered.
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Fan S, Xu Y, Li X, Tie L, Pan Y, Li X. Opposite angiogenic outcome of curcumin against ischemia and Lewis lung cancer models: in silico, in vitro and in vivo studies. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1742-54. [PMID: 24970744 DOI: 10.1016/j.bbadis.2014.06.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/30/2014] [Accepted: 06/17/2014] [Indexed: 11/30/2022]
Abstract
The aim of this study was to investigate the angiogenic effects of curcumin on an ischemia and lung cancer model. To induce ischemia combined with lung cancer models, unilateral femoral arteries of C57BL/6 mice were disconnected on one side of the mouse and Lewis lung carcinoma (LLC) cells were xenografted on the opposite side. Angiogenic effects and underlying mechanisms associated with curcumin were investigated. Molecular target(s), signaling cascades and binding affinities were detected by Western blot, two-dimensional gel electrophoresis (2-DE), computer simulations and surface plasmon resonance (SPR) techniques. Curcumin promoted post-ischemic blood recirculation and suppressed lung cancer progression in inbred C57BL/6 mice via regulation of the HIF1α/mTOR/VEGF/VEGFR cascade oppositely. Inflammatory stimulation induced by neutrophil elastase (NE) promoted angiogenesis in lung cancer tissues, but these changes were reversed by curcumin through directly reducing NE secretion and stimulating α1-antitrypsin (α1-AT) and insulin receptor substrate-1 (IRS-1) production. Meanwhile, curcumin dose-dependently influenced endothelial cells (EC) tube formation and chicken embryo chorioallantoic membrane (CAM) neovascularization. Curcumin had opposite effects on blood vessel regeneration under physiological and pathological angiogenesis, which was effected through negative or positive regulation of the HIF1α/mTOR/VEGF/VEGFR cascade. Curcumin had the promise as a new treatment modality for both ischemic conditions and lung cancer simultaneously in the clinic.
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Affiliation(s)
- Shengjun Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
| | - Yan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
| | - Xin Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
| | - Lu Tie
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
| | - Yan Pan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
| | - Xuejun Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China.
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Abstract
AbstractLung cancer is one of the most common cancers in terms of both incidence and mortality.The major reasons for the increasing number of deaths from lung cancer are late detection and lack of effective therapies. To improve our understanding of lung cancer biology, there is urgent need for blood-based, non-invasive molecular tests to assist in its detection in a cost-effective manner at an early stage when curative interventions are still possible. Recent advances in proteomic technology have provided extensive, high throughput analytical tools for identification, characterization and functional studies of proteomes. Changes in protein expression patterns in response to stimuli can serve as indicators or biomarkers of biological and pathological processes as well as physiological and pharmacological responses to drug treatment, thus aiding in early diagnosis and prognosis of disease. However, only a few biomarkers have been approved by the FDA to date for screening and diagnostic purposes. This review provides a brief overview of currently available proteomic techniques, their applications and limitations and the current state of knowledge about important serum biomarkers in lung cancer and their potential value as prognostic and diagnostic tools.
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Analysis of trypsin inhibition activity in human plasma proteins after separation by non-denaturing two-dimensional electrophoresis. Clin Chim Acta 2013; 425:48-53. [DOI: 10.1016/j.cca.2013.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/24/2013] [Accepted: 07/02/2013] [Indexed: 11/22/2022]
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Miyake M, Ross S, Lawton A, Chang M, Dai Y, Mengual L, Alcaraz A, Giacoia EG, Goodison S, Rosser CJ. Investigation of CCL18 and A1AT as potential urinary biomarkers for bladder cancer detection. BMC Urol 2013; 13:42. [PMID: 24011266 PMCID: PMC3846766 DOI: 10.1186/1471-2490-13-42] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In this study, we further investigated the association of two biomarkers, CCL18 and A1AT, with bladder cancer (BCa) and evaluated the influence of potentially confounding factors in an experimental model. METHODS In a cohort of 308 subjects (102 with BCa), urinary concentrations of CCL18 and A1AT were assessed by enzyme-linked immunosorbent assay (ELISA). In an experimental model, benign or cancerous cells, in addition to blood, were added to urines from healthy controls and analyzed by ELISA. Lastly, immunohistochemical staining for CCL18 and A1AT in human bladder tumors was performed. RESULTS Median urinary protein concentrations of CCL18 (52.84 pg/ml vs. 11.13 pg/ml, p < 0.0001) and A1AT (606.4 ng/ml vs. 120.0 ng/ml, p < 0.0001) were significantly elevated in BCa subjects compared to controls. Furthermore, the addition of whole blood to pooled normal urine resulted in a significant increase in both CCL18 and A1AT. IHC staining of bladder tumors revealed CCL18 immunoreactivity in inflammatory cells only, and there was no significant increase in these immunoreactive cells within benign and cancerous tissue and no association with BCa grade nor stage was noted. A1AT immunoreactivity was observed in the cytoplasm of epithelia cells and intensity of immunostaining increased with tumor grade, but not tumor stage. CONCLUSIONS Further development of A1AT as a diagnostic biomarker for BCa is warranted.
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Affiliation(s)
- Makito Miyake
- Cancer Research Institute, Orlando Health, Orlando, FL 32827, USA
| | - Shanti Ross
- Cancer Research Institute, Orlando Health, Orlando, FL 32827, USA
| | - Adrienne Lawton
- Department of Pathology, Orlando Health, Orlando, FL 32806, USA
| | - Myron Chang
- Department of Biostatistics, University of Florida, Gainesville, FL 32601, USA
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville, FL 32601, USA
| | - Lourdes Mengual
- Laboratory and Department of Urology, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratory and Department of Urology, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | | | - Steve Goodison
- Cancer Research Institute, Orlando Health, Orlando, FL 32827, USA
- Nonagen Bioscience Corporation, Orlando, FL 32827, USA
| | - Charles J Rosser
- Cancer Research Institute, Orlando Health, Orlando, FL 32827, USA
- Nonagen Bioscience Corporation, Orlando, FL 32827, USA
- Section of Urologic Oncology, 1400 S. Orange Ave., Orlando, FL 32806, USA
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Gu J, Ding JY, Lu CL, Lin ZW, Chu YW, Zhao GY, Guo J, Ge D. Overexpression of CD88 predicts poor prognosis in non-small-cell lung cancer. Lung Cancer 2013; 81:259-65. [DOI: 10.1016/j.lungcan.2013.04.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 04/12/2013] [Accepted: 04/23/2013] [Indexed: 01/08/2023]
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21
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Barbosa EB, Vidotto A, Polachini GM, Henrique T, Marqui ABTD, Tajara EH. Proteomics: methodologies and applications to the study of human diseases. Rev Assoc Med Bras (1992) 2013. [PMID: 22735231 DOI: 10.1590/s0104-42302012000300019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteomic approach has allowed large-scale studies of protein expression in different tissues and body fluids in discrete conditions and/or time points. Recent advances of methodologies in this field have opened new opportunities to obtain relevant information on normal and abnormal processes occurring in the human body. In the current report, the main proteomics techniques and their application to human disease study are reviewed.
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22
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Indovina P, Marcelli E, Pentimalli F, Tanganelli P, Tarro G, Giordano A. Mass spectrometry-based proteomics: the road to lung cancer biomarker discovery. MASS SPECTROMETRY REVIEWS 2013; 32:129-142. [PMID: 22829143 DOI: 10.1002/mas.21355] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 06/01/2023]
Abstract
Lung cancer is the leading cause of cancer death in men and women in Western nations, and is among the deadliest cancers with a 5-year survival rate of 15%. The high mortality caused by lung cancer is attributable to a late-stage diagnosis and the lack of effective treatments. So, it is crucial to identify new biomarkers that could function not only to detect lung cancer at an early stage but also to shed light on the molecular mechanisms that underlie cancer development and serve as the basis for the development of novel therapeutic strategies. Considering that DNA-based biomarkers for lung cancer showed inadequate sensitivity, specificity, and reproducibility, proteomics could represent a better tool for the identification of useful biomarkers and therapeutic targets for this cancer type. Among the proteomics technologies, the most powerful tool is mass spectrometry. In this review, we describe studies that use mass spectrometry-based proteomics technologies to analyze tumor proteins and peptides, which might represent new diagnostic, prognostic, and predictive markers for lung cancer. We focus in particular on those findings that hold promise to impact significantly on the clinical management of this disease.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers/blood
- Biomarkers/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/metabolism
- Chromatography, High Pressure Liquid
- Glycosylation/drug effects
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/diagnosis
- Lung Neoplasms/drug therapy
- Lung Neoplasms/metabolism
- Pleural Effusion, Malignant/blood
- Pleural Effusion, Malignant/drug therapy
- Pleural Effusion, Malignant/metabolism
- Prognosis
- Protein Processing, Post-Translational/drug effects
- Proteomics/methods
- Saliva/chemistry
- Saliva/drug effects
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Paola Indovina
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
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23
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Jaros JAJ, Guest PC, Bahn S, Martins-de-Souza D. Affinity depletion of plasma and serum for mass spectrometry-based proteome analysis. Methods Mol Biol 2013; 1002:1-11. [PMID: 23625390 DOI: 10.1007/978-1-62703-360-2_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein biomarker discovery in blood plasma and serum is severely hampered by the vast dynamic range of the proteome. With protein concentrations spanning 12 orders of magnitude, conventional mass spectrometric analysis allows for detection of only a few low-abundance proteins. Prior depletion of high-abundant proteins from the sample can increase analytical depth considerably and has become a widely used practice. We describe in detail an affinity depletion method that selectively removes 14 of the most abundant proteins in plasma and serum.
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24
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Jaros JA, Martins-de-Souza D, Rahmoune H, Rothermundt M, Leweke FM, Guest PC, Bahn S. Protein phosphorylation patterns in serum from schizophrenia patients and healthy controls. J Proteomics 2012; 76 Spec No.:43-55. [DOI: 10.1016/j.jprot.2012.05.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 01/10/2023]
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25
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López-Árias E, Aguilar-Lemarroy A, Felipe Jave-Suárez L, Morgan-Villela G, Mariscal-Ramírez I, Martínez-Velázquez M, Alvarez AH, Gutiérrez-Ortega A, Hernández-Gutiérrez R. Alpha 1-antitrypsin: a novel tumor-associated antigen identified in patients with early-stage breast cancer. Electrophoresis 2012; 33:2130-7. [PMID: 22821488 DOI: 10.1002/elps.201100491] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Several studies have demonstrated that sera from patients with cancer contain antibodies that recognize a unique group of autologous antigens called tumor-associated antigens (TAA). In the current study, we employed an immunoproteomic approach, combining 2DE, Western blot, and MALDI-MS to identify TAA in the sera of patients diagnosed with infiltrating ductal or in situ carcinoma breast cancer. Sera obtained from 25 newly diagnosed patients with stage II breast cancer and 20 healthy volunteers was evaluated for the presence of novel TAA. Alpha 1-antitrypsin (A1AT) antibodies were detected in 24 of 25 patients with breast cancer (96%) and in 2 of 20 controls (10%). Sensitivity of detection of autoantibodies against A1AT in patients with breast cancer was 96%. Our preliminary results suggest that A1AT and autoantibodies against alpha 1 antitrypsin may be useful serum biomarkers for early-stage breast cancer screening and diagnosis.
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Affiliation(s)
- Eneida López-Árias
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C.-CIATEJ, Guadalajara, México
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26
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Opstal-van Winden AWJ, Rodenburg W, Pennings JLA, van Oostrom CTM, Beijnen JH, Peeters PH, van Gils CH, de Vries A. A bead-based multiplexed immunoassay to evaluate breast cancer biomarkers for early detection in pre-diagnostic serum. Int J Mol Sci 2012. [PMID: 23202969 PMCID: PMC3497343 DOI: 10.3390/ijms131013587] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF)) can predict early stage breast cancer in samples collected before clinical diagnosis (phase III samples). We performed a nested case-control study within the Prospect-EPIC (European Prospective Investigation into Cancer and nutrition) cohort. We examined to what extent the biomarker panel could discriminate between 68 women diagnosed with breast cancer up to three years after enrollment and 68 matched healthy controls (all 56-64 years at baseline). Using a quantitative bead-based multiplexed assay, we determined protein concentrations in serum samples collected at enrollment. Principal Component Analysis (PCA) and Random Forest (RF) analysis revealed that on the basis of all ten proteins, early cases could not be separated from controls. When we combined serum protein concentrations and subject characteristics related to breast cancer risk in the RF analysis, this did not result in classification accuracy scores that could correctly classify the samples (sensitivity: 50%, specificity: 50%). Our findings indicate that this panel of selected tumor markers cannot be used for diagnosis of early breast cancer.
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Affiliation(s)
- Annemieke W. J. Opstal-van Winden
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands; E-Mails: (A.W.J.O.-W.); (P.H.M.P.)
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute and Slotervaart Hospital, Louwesweg 6, 1066 EC Amsterdam, The Netherlands; E-Mail:
| | - Wendy Rodenburg
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), A. van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; E-Mails: (W.R.); (J.L.A.P.); (C.T.M.O.); (A.V.)
| | - Jeroen L. A. Pennings
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), A. van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; E-Mails: (W.R.); (J.L.A.P.); (C.T.M.O.); (A.V.)
| | - Conny T. M. van Oostrom
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), A. van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; E-Mails: (W.R.); (J.L.A.P.); (C.T.M.O.); (A.V.)
| | - Jos H. Beijnen
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute and Slotervaart Hospital, Louwesweg 6, 1066 EC Amsterdam, The Netherlands; E-Mail:
- Department of Pharmaceutical Sciences, Division of Biomedical Analysis, Section of Drug Toxicology, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
| | - Petra H.M. Peeters
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands; E-Mails: (A.W.J.O.-W.); (P.H.M.P.)
- Department of Epidemiology, Public Health and Primary Care, Faculty of Medicine, Imperial College, Norfolk Place, London W2 1PG, UK
| | - Carla H. van Gils
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands; E-Mails: (A.W.J.O.-W.); (P.H.M.P.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +31-88-7553014; Fax: +31-88-7555485
| | - Annemieke de Vries
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), A. van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; E-Mails: (W.R.); (J.L.A.P.); (C.T.M.O.); (A.V.)
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Urquidi V, Goodison S, Ross S, Chang M, Dai Y, Rosser CJ. Diagnostic potential of urinary α1-antitrypsin and apolipoprotein E in the detection of bladder cancer. J Urol 2012; 188:2377-83. [PMID: 23088986 DOI: 10.1016/j.juro.2012.07.094] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Indexed: 11/28/2022]
Abstract
PURPOSE The ability to reliably diagnose bladder cancer in voided urine samples would be a major advance. Using high throughput technologies, we identified a panel of bladder cancer associated biomarkers with potential clinical usefulness. In this study we tested 4 potential biomarkers for the noninvasive detection of bladder cancer. MATERIALS AND METHODS We examined voided urine specimens from 124 patients, including 63 newly diagnosed with bladder cancer and 61 controls. Concentrations of proteins were assessed by enzyme-linked immunosorbent assay, including α1-antitrypsin, apolipoprotein E, osteopontin and pentraxin 3. Data were compared to the results of urinary cytology and the BTA Trak® enzyme-linked immunosorbent assay based bladder cancer detection assay. We used the AUC of ROC curves to compare the usefulness of each biomarker to detect bladder cancer. RESULTS Urinary levels of α1-antitrypsin, apolipoprotein E and bladder tumor antigen were significantly increased in subjects with bladder cancer. α1-Antitrypsin (AUC 0.9087, 95% CI 0.8555-0.9619) and apolipoprotein E (AUC 0.8987, 95% CI 0.8449-0.9525) were the most accurate biomarkers. The combination of α1-antitrypsin and apolipoprotein E (AUC 0.9399) achieved 91% sensitivity, 89% specificity, and a positive and negative predictive value of 89% and 90%, respectively. Multivariate regression analysis highlighted only apolipoprotein E as an independent predictor of bladder cancer (OR 24.9, 95% CI 4.22-146.7, p = 0.0004). CONCLUSIONS Alone or in combination, α1-antitrypsin and apolipoprotein E show promise for the noninvasive detection of bladder cancer (OR 24.9, 95% CI 4.22-146.7, p = 0.0004). Larger, prospective studies including more low grade, low stage tumors are needed to confirm these results.
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Affiliation(s)
- Virginia Urquidi
- Cancer Research Institute, MD Anderson Cancer Center Orlando, Orlando, Florida 32806, USA
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28
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Wu W, Juan WC, Liang CRMY, Yeoh KG, So J, Chung MCM. S100A9, GIF and AAT as potential combinatorial biomarkers in gastric cancer diagnosis and prognosis. Proteomics Clin Appl 2012; 6:152-62. [PMID: 22532451 DOI: 10.1002/prca.201100050] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE We have mined the gastric fluid proteome for potential gastric cancer (GC) biomarkers that may enhance disease detection and facilitate prognostic monitoring. EXPERIMENTAL DESIGN In biomarker discovery, a total of 12 patient gastric fluid samples (stages I, III, IV and gastritis) were analysed by 2DE for expression changes that correlated with GC status or disease progression. Gastric fluid proteins showing differential expression with GC were identified by MALDI-TOF/TOF MS as putative biomarkers. Levels of these potential biomarker candidates were independently validated by Western blotting in further 60 gastritis and GC patients. A targeted approach that recruits biomarker candidates for panel consideration was adopted to test if two or more biomarkers in combination improved diagnostic power. RESULTS From the 15 differentially regulated proteins identified, expression levels of S100A9, GIF and AAT in the gastric fluid clearly correlated with GC status. S100A9/AAT (AUC = 0.81) and S100A9/GIF (AUC = 0.92) were revealed as promising biomarker pairs for early GC diagnosis and disease monitoring, respectively. CONCLUSION AND CLINICAL RELEVANCE Early diagnosis, accurate staging and constant disease monitoring remain the prerequisites for effective treatment against GC. As current biomarkers like CA19-9 and carcinoembryonic antigen (CEA) lack sensitivity and specificity, there is a pressing need for novel GC detection and monitoring methods. To this end, S100A9, GIF and AAT from the gastric fluid may significantly augment existing methods of GC detection and monitoring, and eliminate the need for invasive tissue biopsies.
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Affiliation(s)
- Wei Wu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Muraoka S, Kume H, Watanabe S, Adachi J, Kuwano M, Sato M, Kawasaki N, Kodera Y, Ishitobi M, Inaji H, Miyamoto Y, Kato K, Tomonaga T. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res 2012; 11:4201-10. [PMID: 22716024 DOI: 10.1021/pr300322q] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since LC-MS-based quantitative proteomics has become increasingly applied to a wide range of biological applications over the past decade, numerous studies have performed relative and/or absolute abundance determinations across large sets of proteins. In this study, we discovered prognostic biomarker candidates from limited breast cancer tissue samples using discovery-through-verification strategy combining iTRAQ method followed by selected reaction monitoring/multiple reaction monitoring analysis (SRM/MRM). We identified and quantified 5122 proteins with high confidence in 18 patient tissue samples (pooled high-risk (n=9) or low-risk (n=9)). A total of 2480 proteins (48.4%) of them were annotated as membrane proteins, 16.1% were plasma membrane and 6.6% were extracellular space proteins by Gene Ontology analysis. Forty-nine proteins with >2-fold differences in two groups were chosen for further analysis and verified in 16 individual tissue samples (high-risk (n=9) or low-risk (n=7)) using SRM/MRM. Twenty-three proteins were differentially expressed among two groups of which MFAP4 and GP2 were further confirmed by Western blotting in 17 tissue samples (high-risk (n=9) or low-risk (n=8)) and Immunohistochemistry (IHC) in 24 tissue samples (high-risk (n=12) or low-risk (n=12)). These results indicate that the combination of iTRAQ and SRM/MRM proteomics will be a powerful tool for identification and verification of candidate protein biomarkers.
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Affiliation(s)
- Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Ibaraki, Japan
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Semaan SM, Wang X, Marshall AG, Sang QXA. Identification of Potential Glycoprotein Biomarkers in Estrogen Receptor Positive (ER+) and Negative (ER-) Human Breast Cancer Tissues by LC-LTQ/FT-ICR Mass Spectrometry. J Cancer 2012; 3:269-84. [PMID: 22773931 PMCID: PMC3390597 DOI: 10.7150/jca.4592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/20/2012] [Indexed: 01/02/2023] Open
Abstract
Breast cancer is the second most fatal cancer in American women. To increase the life expectancy of patients with breast cancer new diagnostic and prognostic biomarkers and drug targets must be identified. A change in the glycosylation on a glycoprotein often causes a change in the function of that glycoprotein; such a phenomenon is correlated with cancerous transformation. Thus, glycoproteins in human breast cancer estrogen receptor positive (ER+) tissues and those in the more advanced stage of breast cancer, estrogen receptor negative (ER-) tissues, were compared. Glycoproteins showing differences in glycosylation were examined by 2-dimensional gel electrophoresis with double staining (glyco- and total protein staining) and identified by reversed-phase nano-liquid chromatography coupled with a hybrid linear quadrupole ion trap/ Fourier transform ion cyclotron resonance mass spectrometer. Among the identified glycosylated proteins are alpha 1 acid glycoprotein, alpha-1-antitrypsin, calmodulin, and superoxide dismutase mitochondrial precursor that were further verified by Western blotting for both ER+ and ER- human breast tissues. Results show the presence of a possible glycosylation difference in alpha-1-antitrypsin, a potential tumor-derived biomarker for breast cancer progression, which was expressed highest in the ER- samples.
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Affiliation(s)
- Suzan M Semaan
- 1. Department of Chemistry and Biochemistry and Institute of Molecular Biophysics
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Barbosa EB, Vidotto A, Polachini GM, Henrique T, de Marqui ABT, Helena Tajara E. Proteomics: methodologies and applications to the study of human diseases. Rev Assoc Med Bras (1992) 2012. [DOI: 10.1016/s0104-4230(12)70209-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Yao L, Lao W, Zhang Y, Tang X, Hu X, He C, Hu X, Xu LX. Identification of EFEMP2 as a Serum Biomarker for the Early Detection of Colorectal Cancer with Lectin Affinity Capture Assisted Secretome Analysis of Cultured Fresh Tissues. J Proteome Res 2012; 11:3281-94. [PMID: 22506683 DOI: 10.1021/pr300020p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Weifeng Lao
- Biomedical Research Center and
Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw
Hospital, Zhejiang University, Hangzhou,
China
| | | | | | - Xiaotong Hu
- Biomedical Research Center and
Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw
Hospital, Zhejiang University, Hangzhou,
China
| | - Chao He
- Biomedical Research Center and
Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw
Hospital, Zhejiang University, Hangzhou,
China
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Kazuno S, Fujimura T, Arai T, Ueno T, Nagao K, Fujime M, Murayama K. Multi-sequential surface plasmon resonance analysis of haptoglobin–lectin complex in sera of patients with malignant and benign prostate diseases. Anal Biochem 2011; 419:241-9. [DOI: 10.1016/j.ab.2011.08.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/29/2022]
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Lee HJ, Kim YT, Park PJ, Shin YS, Kang KN, Kim Y, Kim CW. A novel detection method of non-small cell lung cancer using multiplexed bead-based serum biomarker profiling. J Thorac Cardiovasc Surg 2011; 143:421-7. [PMID: 22104668 DOI: 10.1016/j.jtcvs.2011.10.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 08/23/2011] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
Abstract
OBJECTIVES Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality. Development of an early diagnosis method may improve survivals. We aimed to develop a new diagnostic model for NSCLC using serum biomarkers. METHODS We set up a patient group diagnosed with NSCLC (n = 122) and a healthy control group (n = 225). Thirty serum analytes were selected on the basis of previous studies and a literature search. An antibody-bead array of 30 markers was constructed using the Luminex bead array platform (Luminex Inc, Austin, Tex) and was analyzed. Each marker was ranked by importance using the random forest method and then selected. Using selected markers, multivariate classification algorithms were constructed and were validated by application to independent validation cohort of 21 NSCLC and 28 control subjects. RESULTS There was no difference in demographics between patients and the control population except for age (64.8 ± 10.0 for patients vs 53.0 ± 7.6 years for the control group). Among the 30 serum proteins, 23 showed a difference between the 2 groups (12 increased and 11 decreased in the patient group). We found the highest accuracy of multivariate classification algorithms when using the 5 highest-ranked biomarkers (A1AT, CYFRA 21-1, IGF-1, RANTES, AFP). When we applied the algorithms on a validation cohort, each method recognized the patients from the controls with high accuracy (89.8% with random forest, 91.8% with support vector machine, 88.2% with linear discriminant analysis, and 90.5% with logistic regression). CONCLUSIONS We confirmed that a new diagnostic method using 5 serum biomarkers profiling constructed by multivariate classification algorithms could distinguish NSCLC from healthy controls with high accuracy.
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Affiliation(s)
- Hyun Joo Lee
- Department of Molecular Oncology, Cancer Research Institute, Seoul National University Graduate School of Medicine, Seoul, Korea
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Kozmin YP, Manoilov AV, Serebryakova MV, Mirgorodskaya OA. A direct introduction of 18O isotopes into peptides and proteins for quantitative mass spectroscopy analysis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:793-806. [DOI: 10.1134/s1068162011060094] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dowling P, Clarke C, Hennessy K, Torralbo-Lopez B, Ballot J, Crown J, Kiernan I, O'Byrne KJ, Kennedy MJ, Lynch V, Clynes M. Analysis of acute-phase proteins, AHSG, C3, CLI, HP and SAA, reveals distinctive expression patterns associated with breast, colorectal and lung cancer. Int J Cancer 2011; 131:911-23. [DOI: 10.1002/ijc.26462] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/31/2011] [Indexed: 11/05/2022]
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Baldini C, Giusti L, Ciregia F, Da Valle Y, Giacomelli C, Donadio E, Ferro F, Galimberti S, Donati V, Bazzichi L, Bombardieri S, Lucacchini A. Correspondence between salivary proteomic pattern and clinical course in primary Sjögren syndrome and non-Hodgkin's lymphoma: a case report. J Transl Med 2011; 9:188. [PMID: 22047044 PMCID: PMC3223154 DOI: 10.1186/1479-5876-9-188] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/02/2011] [Indexed: 12/26/2022] Open
Abstract
Background In the last years human proteomic has represented a promising tool to promote the communication between basic and clinical science. Methods To explore the correspondence between salivary proteomic profile and clinical response, herein, we used a proteomic approach to analyse the whole saliva of a patient with primary Sjögren's Syndrome (pSS) and non-Hodgkin's-MALT type parotid lymphoma before, during and after a standard treatment with cyclophosphamide (CTX) and rituximab (RTX). To identify any discriminatory therapeutic salivary biomarker patient's whole saliva was collected at the baseline, after the fourth infusion of rituximab, and on remission and analysed combining two-dimensional electrophoresis (2DE) and MALDI-TOF/TOF mass spectrometry. Results Proteomic results obtained from the comparison of salivary samples indicated several qualitative and quantitative modifications in the salivary expression of putative albumin, immunoglobulin J chain, Ig kappa chain C region, alpha-1-antitrypsin, haptoglobin and Ig alpha-1 chain C region. Conclusion This study suggests that clinical and functional changes of the salivary glands driven by autoimmune and lymphoproliferative processes might be reflected in patients' whole saliva proteins, shedding new light on the potential usefulness of salivary proteomic analysis in the identification of prognostic and therapeutic biomarkers for patients with pSS and non Hodgkin's lymphomas.
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Affiliation(s)
- Chiara Baldini
- Department of Internal Medicine, Rheumatology Unit, University of Pisa, Pisa, Italy
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Lung cancer proteomics: recent advances in biomarker discovery. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:726869. [PMID: 22229091 PMCID: PMC3196861 DOI: 10.1155/2011/726869] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/16/2011] [Indexed: 12/21/2022]
Abstract
Lung cancer is the most common cause of cancer death in both men and women in Western countries, with a 5-year survival rate of 15%, which is among the lowest of all cancers. The high mortality from lung cancer is due not only to the late stage diagnosis but also to the lack of effective treatments even for patients diagnosed with stage I lung cancer. Therefore, there is an urgent need to identify new markers for early diagnosis and prognosis that could serve to open novel therapeutic avenues. Proteomics can represent an important tool for the identification of biomarkers and therapeutic targets for lung cancer since DNA-based biomarkers did not prove to have adequate sensitivity, specificity, and reproducibility. In this paper we will describe studies focused on the identification of new diagnostic, prognostic, and predictive markers for lung cancer, using proteomics technologies.
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Yang N, Feng S, Shedden K, Xie X, Liu Y, Rosser CJ, Lubman DM, Goodison S. Urinary glycoprotein biomarker discovery for bladder cancer detection using LC/MS-MS and label-free quantification. Clin Cancer Res 2011; 17:3349-59. [PMID: 21459797 DOI: 10.1158/1078-0432.ccr-10-3121] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Cancers of the urinary bladder are the fifth most commonly diagnosed malignancy in the United States. Early clinical diagnosis of bladder cancer remains a major challenge, and the development of noninvasive methods for detection and surveillance is desirable for both patients and health care providers. APPROACH To identify urinary proteins with potential clinical utility, we enriched and profiled the glycoprotein component of urine samples by using a dual-lectin affinity chromatography and liquid chromatography/tandem mass spectrometry platform. RESULTS From a primary sample set obtained from 54 cancer patients and 46 controls, a total of 265 distinct glycoproteins were identified with high confidence, and changes in glycoprotein abundance between groups were quantified by a label-free spectral counting method. Validation of candidate biomarker alpha-1-antitrypsin (A1AT) for disease association was done on an independent set of 70 samples (35 cancer cases) by using an ELISA. Increased levels of urinary A1AT glycoprotein were indicative of the presence of bladder cancer (P < 0.0001) and augmented voided urine cytology results. A1AT detection classified bladder cancer patients with a sensitivity of 74% and specificity of 80%. SUMMARY The described strategy can enable higher resolution profiling of the proteome in biological fluids by reducing complexity. Application of glycoprotein enrichment provided novel candidates for further investigation as biomarkers for the noninvasive detection of bladder cancer.
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Affiliation(s)
- Na Yang
- Department of Surgery, University of Michigan Medical Center, University of Michigan, Ann Arbor, Michigan, USA
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Prospective highlights of serum glycoproteins in spontaneous tolerance after orthotopic liver transplantation. Clin Chim Acta 2011; 412:604-13. [DOI: 10.1016/j.cca.2010.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 02/07/2023]
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Kang SM, Sung HJ, Ahn JM, Park JY, Lee SY, Park CS, Cho JY. The Haptoglobin β chain as a supportive biomarker for human lung cancers. MOLECULAR BIOSYSTEMS 2011; 7:1167-75. [PMID: 21253648 DOI: 10.1039/c0mb00242a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Haptoglobin (Hp) is produced as an acute phase reactant during inflammation, infection, malignant diseases, and several cancers. In proteomics analysis using human blood samples, the Hp peptide levels were about 3-fold higher in lung cancer patients versus normal individuals. This study is aimed at analyzing the elevation of which chain of Hp is closely related to lung cancers and can be a serum biomarker for lung cancers. In Western blot (WB) analysis, we found that the Hp β chain can be a better diagnostic biomarker for lung cancers. In the result of the Hp β chain ELISA developed by us, the concentrations of the Hp β chain in the sera increased about 4-fold in 190 lung adenocarcinoma patients versus 190 healthy controls (8.0 ± 3.8 μg ml(-1)vs. 1.9 ± 1.2 μg ml(-1)). ELISA data showed that the serum levels of the Hp β chain in breast cancer (1.5 ± 0.5 μg ml(-1)) and hepatocellular carcinoma (HCC) (1.4 ± 1.0 μg ml(-1)) patients remained similar to those of healthy controls. Compared to lung adenocarcinoma, the Hp β chain levels in the plasma of patients with other respiratory diseases such as tuberculosis (TBC), idiopathic pulmonary fibrosis (IPF) and bronchial asthma (BA) were closer to those of healthy controls. Our data suggest that an increase of the Hp β chain can be a potential serum biomarker for lung cancers.
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Affiliation(s)
- Sung-Min Kang
- Department of Biochemistry, School of Dentistry and Brain Korea 21, Kyungpook National University, and ProtAnBio, Dongin-dong 2 Ga 101, Daegu 700-422, South Korea
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Rodenburg W, Pennings JLA, van Oostrom CTM, Roodbergen M, Kuiper RV, Luijten M, de Vries A. Identification of breast cancer biomarkers in transgenic mouse models: A proteomics approach. Proteomics Clin Appl 2010; 4:603-12. [PMID: 21137078 DOI: 10.1002/prca.200900175] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/26/2009] [Accepted: 12/08/2009] [Indexed: 01/30/2023]
Abstract
PURPOSE Transgenic mouse models for cancer circumvent many challenges that hamper human studies aimed at biomarker discovery. Lower biological variances among mice combined with controllable factors such as food uptake and health status may enable the detection of more subtle protein expression differences. This is envisioned to result in the identification of biomarkers better discriminating cancer cases from controls. EXPERIMENTAL DESIGN The current study used two innovative mouse models for breast-cancer to identify new serum biomarkers. Multi-analyte profiling technique was used to analyze 70 proteins in individual serum samples of non-tumor and mammary tumor-bearing Tg.NK (MMTV/c-neu) mice. RESULTS A small set of proteins fully differentiated tumor samples from controls. These comprised osteopontin, interleukin-18, cystatin C and CD40 antigen. Comparison of protein expression in another breast-cancer mouse model, the humanized p53.R270H mice, showed common discriminatory expression of osteopontin. However, other biomarkers showed distinct expression in the two different breast-cancer models, indicating that different mammary tumor sub-types with respect to molecular and estrogen receptor status reveal divergent serum biomarker sets. CONCLUSIONS AND CLINICAL RELEVANCE The current study supports the concept that serum proteins can discriminate mammary tumor cases from controls, and yielded interesting biomarkers that need further testing and validation in human studies.
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Affiliation(s)
- Wendy Rodenburg
- Laboratory for Health Protection Research, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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A unique proteolytic fragment of alpha1-antitrypsin is elevated in ductal fluid of breast cancer patient. Breast Cancer Res Treat 2009; 123:73-86. [PMID: 19902353 DOI: 10.1007/s10549-009-0625-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 10/28/2009] [Indexed: 10/20/2022]
Abstract
By comparison of mass spectra from a small cohort of nipple aspiration fluids (NAF), we previously discovered a panel of five candidate breast cancer biomarkers among them an unidentified 4.7 kD peptide BF5. The purposes of the present study were to verify the presence of BF5 in an independent cohort; to determine the protein identity of BF5; and to provide insight into the biology of BF5 production and elevation in tumor-associated NAF. We prospectively collected bilaterally matched NAF from patients with unilateral Stage I/II breast cancer (IBC-31), ductal carcinoma in situ (DCIS-6), atypical ductal hyperplasia (ADH-5), and presumed healthy women who came to routine mammography and had a normal exam (31). Following the consolidation of its cancer-associated expression on SELDI-mass spectrometry, BF5 was isolated by gel electrophoresis and sequenced by tandem mass spectrometry. BF5 was elevated in 15-25% of women with IBC, DCIS, or ADH vs. 0% of controls. This elevation was restricted to the affected breasts. BF5 was identified as 41/42-aa C-terminal peptide of alpha1-antitrypsin (AAT), the principle inhibitor of serine protease neutrophile elastase. The full length AAT showed a consistent expression pattern as C-41/42, and C-41/42 can be generated in vitro by MMP-7 cleavage. In conclusion, elevated C-41/42 is likely the result of elevated AAT synthesis, and the activity of specific MMPs present within the tumor. As other C-terminal fragments of AAT are reported to function as tumor-derived suppressors to the host immune-system, elevated C-41/42 may also be predictive of a poor outcome.
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