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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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Integrated Proteomics Based on 2D Gel Electrophoresis and Mass Spectrometry with Validations: Identification of a Biomarker Compendium for Oral Submucous Fibrosis—An Indian Study. J Pers Med 2022; 12:jpm12020208. [PMID: 35207696 PMCID: PMC8878868 DOI: 10.3390/jpm12020208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Oral Submucous Fibrosis (OSMF) is a chronic debilitating disease more frequently found in the South East Asian population. This disease poses a public health priority, as it is grouped under oral potentially malignant disorders, with malignant transformation rates of around 7 to 13%. Hence, early identification of high-risk OSMF patients is of the utmost importance to prevent malignant transformation. Proteomic expression profiling is a promising method for identifying differentially expressed proteins for disease prognosis and risk stratification in OSMF. In this study, overexpressed proteins in OSMF, OSMF transformed into oral squamous cell carcinoma (OSCC) and normal tissues were evaluated by proteomic analysis using two-dimensional electrophoresis (2DE) and mass spectrometry, which revealed 23 upregulated proteins. Validation was done using immunohistochemistry for three secretory proteins, namely 14-3-3ε (n = 130), carbonic anhydrase 1 (CA 1) (n = 125) and heat shock protein 70 (HSP 70) (n = 117), which showed significant overexpression in OSMF, OSCC compared to normal. The present study is the first of its kind in India to the best of our knowledge, assessing the altered expression of proteins in OSMF and OSMF which has undergone malignant transformation, obtaining a better knowledge of the molecular pathways involved in the disease progression. The current study shows that the biomarkers studied can be potentially useful for risk stratification of OSMF to OSCC serving as novel targets for therapeutic intervention. Clinical validation of the targets can further pave way for precision medicine to improve the quality of life in OSMF patients.
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Neagu AN, Whitham D, Buonanno E, Jenkins A, Alexa-Stratulat T, Tamba BI, Darie CC. Proteomics and its applications in breast cancer. Am J Cancer Res 2021; 11:4006-4049. [PMID: 34659875 PMCID: PMC8493401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023] Open
Abstract
Breast cancer is an individually unique, multi-faceted and chameleonic disease, an eternal challenge for the new era of high-integrated precision diagnostic and personalized oncomedicine. Besides traditional single-omics fields (such as genomics, epigenomics, transcriptomics and metabolomics) and multi-omics contributions (proteogenomics, proteotranscriptomics or reproductomics), several new "-omics" approaches and exciting proteomics subfields are contributing to basic and advanced understanding of these "multiple diseases termed breast cancer": phenomics/cellomics, connectomics and interactomics, secretomics, matrisomics, exosomics, angiomics, chaperomics and epichaperomics, phosphoproteomics, ubiquitinomics, metalloproteomics, terminomics, degradomics and metadegradomics, adhesomics, stressomics, microbiomics, immunomics, salivaomics, materiomics and other biomics. Throughout the extremely complex neoplastic process, a Breast Cancer Cell Continuum Concept (BCCCC) has been modeled in this review as a spatio-temporal and holistic approach, as long as the breast cancer represents a complex cascade comprising successively integrated populations of heterogeneous tumor and cancer-associated cells, that reflect the carcinoma's progression from a "driving mutation" and formation of the breast primary tumor, toward the distant secondary tumors in different tissues and organs, via circulating tumor cell populations. This BCCCC is widely sustained by a Breast Cancer Proteomic Continuum Concept (BCPCC), where each phenotype of neoplastic and tumor-associated cells is characterized by a changing and adaptive proteomic profile detected in solid and liquid minimal invasive biopsies by complex proteomics approaches. Such a profile is created, beginning with the proteomic landscape of different neoplastic cell populations and cancer-associated cells, followed by subsequent analysis of protein biomarkers involved in epithelial-mesenchymal transition and intravasation, circulating tumor cell proteomics, and, finally, by protein biomarkers that highlight the extravasation and distant metastatic invasion. Proteomics technologies are producing important data in breast cancer diagnostic, prognostic, and predictive biomarkers discovery and validation, are detecting genetic aberrations at the proteome level, describing functional and regulatory pathways and emphasizing specific protein and peptide profiles in human tissues, biological fluids, cell lines and animal models. Also, proteomics can identify different breast cancer subtypes and specific protein and proteoform expression, can assess the efficacy of cancer therapies at cellular and tissular level and can even identify new therapeutic target proteins in clinical studies.
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Affiliation(s)
- Anca-Narcisa Neagu
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IașiCarol I bvd. No. 22, Iași 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Emma Buonanno
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Avalon Jenkins
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Teodora Alexa-Stratulat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and PharmacyIndependenței bvd. No. 16-18, Iași 700021, Romania
| | - Bogdan Ionel Tamba
- Advanced Center for Research and Development in Experimental Medicine (CEMEX), “Grigore T. Popa” University of Medicine and PharmacyMihail Kogălniceanu Street No. 9-13, Iași 700454, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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Cong Y, Cui Y, Wang S, Jiang L, Cao J, Zhu S, Birkin E, Lane J, Ruge F, Jiang WG, Qiao G. Calcium-Binding Protein S100P Promotes Tumor Progression but Enhances Chemosensitivity in Breast Cancer. Front Oncol 2020; 10:566302. [PMID: 33042844 PMCID: PMC7522638 DOI: 10.3389/fonc.2020.566302] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/24/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Chemoresistance remains one of the obstacles to overcome in the treatment of breast cancer. S100 calcium-binding protein P (S100P) has been observed to be overexpressed in several cancers and has been associated with drug resistance, metastasis, and prognosis. However, the role of S100P in chemoresistance in breast cancer has not been thoroughly determined. METHODS Immunohistochemistry was used to evaluate the expression level of S100P protein in 22 pairs (pre-chemo and post-chemo) of breast cancer tissue from patients who underwent neoadjuvant chemotherapy. The influence of S100P on the biological behavior and chemosensitivity of breast cancer cells was then investigated. RESULTS The protein level of S100P in breast cancer tissue was significantly higher than in benign fibroadenoma (p < 0.001). The S100P expression level was shown to be decreased by 46.55% after neoadjuvant chemotherapy (p = 0.015). Subgroup analysis revealed that S100P reduction (57.58%) was mainly observed in the HER2+ tumors (p = 0.027). Our in vitro experiments showed that the knockdown of S100P suppressed the proliferation, adhesion, migrative and invasive abilities of T47D and SK-BR-3 breast cancer cells. We further demonstrated that this knockdown increased the chemoresistance to paclitaxel and cisplatin in SK-BR-3 cells. We found S100P exerted its function by upregulating NF-κB, CCND1 and Vimentin, but downregulating E-cadherin. CONCLUSION S100P promotes the aggressive properties of breast cancer cells and may be considered as a promising therapeutic target. Moreover, S100P can be used to predict the therapeutic effect of chemotherapy in HER2+ breast cancer patients.
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Affiliation(s)
- Yizi Cong
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yuxin Cui
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Suxia Wang
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Lei Jiang
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Jianqiao Cao
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Shiguang Zhu
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Emily Birkin
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jane Lane
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Fiona Ruge
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Wen G. Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Guangdong Qiao
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
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Getzenberg RH. CANCER BIOMARKERS. Cancer 2019. [DOI: 10.1002/9781119645214.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Zhao R, Zhang R, Tang T, Feng X, Li J, Liu Y, Zhu R, Wang G, Li K, Zhou W, Yang Y, Wang Y, Ba Y, Zhang J, Liu Y, Zhou F. TriZ-a rotation-tolerant image feature and its application in endoscope-based disease diagnosis. Comput Biol Med 2018; 99:182-190. [PMID: 29936284 DOI: 10.1016/j.compbiomed.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
Abstract
Endoscopy is becoming one of the widely-used technologies to screen the gastric diseases, and it heavily relies on the experiences of the clinical endoscopists. The location, shape, and size are the typical patterns for the endoscopists to make the diagnosis decisions. The contrasting texture patterns also suggest the potential lesions. This study designed a novel rotation-tolerant image feature, TriZ, and demonstrated the effectiveness on both the rotation invariance and the lesion detection of three gastric lesion types, i.e., gastric polyp, gastric ulcer, and gastritis. TriZ achieved 87.0% in the four-class classification problem of the three gastric lesion types and the healthy controls, averaged over the twenty random runs of 10-fold cross-validations. Due to that biomedical imaging technologies may capture the lesion sites from different angles, the symmetric image feature extraction algorithm TriZ may facilitate the biomedical image based disease diagnosis modeling. Compared with the 378,434 features of the HOG algorithm, TriZ achieved a better accuracy using only 126 image features.
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Affiliation(s)
- Ruixue Zhao
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Ruochi Zhang
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Tongyu Tang
- First Hospital, Jilin University, Changchun, Jilin, 130012, China
| | - Xin Feng
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Jialiang Li
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yue Liu
- College of Communication Engineering, Jilin University, Changchun, Jilin, 130012, China
| | - Renxiang Zhu
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Guangze Wang
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Kangning Li
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Wenyang Zhou
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Yunfei Yang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yuzhao Wang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yuanjie Ba
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Jiaojiao Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yang Liu
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.
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Gajbhiye A, Dabhi R, Taunk K, Jagadeeshaprasad MG, RoyChoudhury S, Mane A, Bayatigeri S, Chaudhury K, Santra MK, Rapole S. Multipronged quantitative proteomics reveals serum proteome alterations in breast cancer intrinsic subtypes. J Proteomics 2017; 163:1-13. [DOI: 10.1016/j.jprot.2017.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/29/2022]
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8
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Singh A, Sharma RK, Chagtoo M, Agarwal G, George N, Sinha N, Godbole MM. 1H NMR Metabolomics Reveals Association of High Expression of Inositol 1, 4, 5 Trisphosphate Receptor and Metabolites in Breast Cancer Patients. PLoS One 2017; 12:e0169330. [PMID: 28072864 PMCID: PMC5225010 DOI: 10.1371/journal.pone.0169330] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
1H NMR is used to detect alterations in metabolites and their linkage to metabolic processes in a number of pathological conditions including breast cancer. Inositol 1, 4, 5 trisphosphate (IP3R) receptor is an intracellular calcium channel known to regulate metabolism and cellular bioenergetics. Its expression is up regulated in a number of cancers. However, its linkage to metabolism in disease conditions has not been evaluated. This study was designed to determine the association if any, of these metabolites with altered expression of IP3R in breast cancer. We used 1H NMR to identify metabolites in the serum of breast cancer patients (n = 27) and performed Real-time Polymerase Chain Reaction analysis for quantifying the expression of IP3R type 3 and type 2 in tissues from breast cancer patients (n = 40). Principal Component Analysis (PCA) and Partial Least Square-Discriminant Analysis (PLS-DA) clearly distinguished patients with high/low IP3R expression from healthy subjects. The present study revealed high expression of IP3R type 2 and type 3 in human breast tumor tissue compared to adjacent non-tumorous tissue. Moreover, patients with ≥ 2-fold increase in IP3R (high IP3R group) had significantly higher concentration of metabolic intermediates compared to those with < 2-fold increase in IP3R (low IP3R group). We observed an increase in lipoprotein content and the levels of metabolites like lactate, lysine and alanine and a decrease in the levels of pyruvate and glucose in serum of high IP3R group patients when compared to those in healthy subjects. Receiver operating characteristic (ROC) curve analysis was performed to show the clinical utility of metabolites. In addition to the human studies, functional relevance of IP3Rs in causing metabolic disruption was observed in MCF-7 and MDA MB-231 cells. Results from our studies bring forth the importance of metabolic (or metabolomics) profiling of serum by 1H NMR in conjunction with tissue expression studies for characterizing breast cancer patients. The results from this study provide new insights into relationship of breast cancer metabolites with IP3R.
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Affiliation(s)
- Aru Singh
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | | | - Megha Chagtoo
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Gaurav Agarwal
- Department of Endocrine Surgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Nelson George
- Department of Endocrine Surgery, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
| | - Neeraj Sinha
- Centre of Biomedical Research, Raebareli Road, Lucknow, India
| | - Madan M. Godbole
- Department of Molecular Medicine and Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
- * E-mail:
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Gajbhiye A, Dabhi R, Taunk K, Vannuruswamy G, RoyChoudhury S, Adhav R, Seal S, Mane A, Bayatigeri S, Santra MK, Chaudhury K, Rapole S. Urinary proteome alterations in HER2 enriched breast cancer revealed by multipronged quantitative proteomics. Proteomics 2016; 16:2403-18. [DOI: 10.1002/pmic.201600015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/27/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Akshada Gajbhiye
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
- Savitribai Phule Pune University; Ganeshkhind Pune Maharashtra India
| | - Raju Dabhi
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Khushman Taunk
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Sourav RoyChoudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Ragini Adhav
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Anupama Mane
- Grant Medical Foundation; Ruby Hall Clinic; Pune Maharashtra India
| | | | - Manas K. Santra
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Koel Chaudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Srikanth Rapole
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
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Prica F, Radon T, Cheng Y, Crnogorac-Jurcevic T. The life and works of S100P - from conception to cancer. Am J Cancer Res 2016; 6:562-576. [PMID: 27186425 PMCID: PMC4859681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/10/2016] [Indexed: 06/05/2023] Open
Abstract
Since its discovery in 1992, the small, 10.4 kDa calcium-binding protein S100P has gained the attention of researchers from different scientific fields due to its potential roles in both healthy and neoplastic tissues. Although not ubiquitously expressed, in tissues where it is present, S100P is associated with distinct changes in cellular behaviour. In this review we have summarized the evolutionary history of S100P, its expression and involvement in implantation and human embryonic development, as well as important functions in normal tissue and cancer. Finally, we have demonstrated its pivotal role as a potential diagnostic and therapeutic target, which opens promising avenues for further fruitful research on S100P.
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Affiliation(s)
- Filip Prica
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of LondonLondon, UK
| | - Tomasz Radon
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of LondonLondon, UK
| | - Yuzhu Cheng
- Institute of Genetic Medicine, Newcastle UniversityNewcastle, UK
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Pendharkar N, Gajbhiye A, Taunk K, RoyChoudhury S, Dhali S, Seal S, Mane A, Abhang S, Santra MK, Chaudhury K, Rapole S. Quantitative tissue proteomic investigation of invasive ductal carcinoma of breast with luminal B HER2 positive and HER2 enriched subtypes towards potential diagnostic and therapeutic biomarkers. J Proteomics 2015; 132:112-30. [PMID: 26642762 DOI: 10.1016/j.jprot.2015.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/16/2015] [Accepted: 11/26/2015] [Indexed: 02/09/2023]
Abstract
Worldwide, breast cancer is one of the frequently diagnosed cancers in women with high mortality if not diagnosed at early stage. Although biomarker discoveries through various proteomic approaches have been studied in breast cancer, a limited number of studies have explored the invasive ductal carcinoma with Luminal B HER2 positive (LB) and HER2 enriched (HE) subtypes. The present study employed the complementary quantitative proteomic approaches to find a panel of markers that could discriminate LB and HE subtypes as well as early (ES) and late stages (LS) of these subtypes. A total of 67 and 68 differentially expressed proteins were identified by DIGE for the subtype and stage wise categories, respectively. Multivariate statistical analysis was employed to identify the set of most significant proteins, which could discriminate between these two subtypes and also early and late stages under study. Immunoblotting and MRM based validation in a separate cohort of samples confirmed that panel of biosignatures for LB are APOA1, GELS, HS90B, EF1A1, NHRF1 and PRDX3 and for HE are PRDX1, CATD, CALR, ATPB and CH60. For the diagnosis of early and late stages the potential markers are TPM4, CATD, PRDX3, ANXA3, HSPB1 and CALR, TRFE, GELS, CH60, CAPG, NHRF1, 1433G, GRP78 respectively.
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Affiliation(s)
- Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; B. J. Medical College, Sassoon Hospital, Pune 411001, MH, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Sourav RoyChoudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune 411001, MH, India
| | | | - Manas K Santra
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
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A novel truncated form of S100P predicts disease-free survival in patients with lymph node positive breast cancer. Cancer Lett 2015; 368:64-70. [PMID: 26276712 DOI: 10.1016/j.canlet.2015.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/19/2015] [Accepted: 07/22/2015] [Indexed: 11/23/2022]
Abstract
The calcium-binding protein S100P is overexpressed in various cancers and may contribute to the oncogenic phenotype. This study used mass spectrometry to characterize a novel 9.2-kDa C-terminally truncated form of S100P (t-S100P), and to investigate its potential prognostic value in breast cancer. Univariate analysis demonstrated the association between breast tissue t-S100P levels (n = 148) and conventional pathological markers. Across all tumor samples, high t-S100P was strongly prognostic for poor disease-free survival (P = 0.005), its efficacy confined to lymph node-positive tumors (n = 74, P = 0.007). Matrix-assisted laser desorption/ionization imaging mass spectrometry confirmed differential t-S100P abundance between breast cancer and unaffected adjacent tissue. t-S100P was exclusively located in the cell nucleus of breast cancer tissue, and full-length S100P was essentially undetectable by mass spectrometry. We conclude that t-S100P is the predominant form of S100P in breast cancer tissue and is strongly prognostic for disease-free survival in women with lymph node-positive disease.
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Fung SY, Lee ML, Tan NH. Molecular mechanism of cell death induced by king cobra (Ophiophagus hannah) venom l-amino acid oxidase. Toxicon 2015; 96:38-45. [PMID: 25615711 DOI: 10.1016/j.toxicon.2015.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/09/2015] [Accepted: 01/20/2015] [Indexed: 01/11/2023]
Abstract
Snake venom LAAOs have been reported to exhibit a wide range of pharmacological activities, including cytotoxic, edema-inducing, platelet aggregation-inducing/platelet aggregation-inhibiting, bactericidal and antiviral activities. A heat-stable form of l-amino acid oxidase isolated from king cobra (Ophiophagus hannah) venom (OH-LAAO) has been shown to exhibit very potent cytotoxicity against human tumorigenic cells but not in their non-tumorigenic counterparts, and the cytotoxicity was due to the apoptosis-inducing effect of the enzyme. In this work, the molecular mechanism of cell death induced by OH-LAAO was investigated. The enzyme exerts its apoptosis-inducing effect presumably via both intrinsic and extrinsic pathways as suggested by the increase in caspase-8 and -9 activities. Oligonucleotide microarray analysis showed that the expression of a total of 178 genes was significantly altered as a result of oxidative stress induced by the hydrogen peroxide generated by the enzyme. Of the 178 genes, at least 27 genes are involved in apoptosis and cell death. These alterations of gene expression was presumably caused by the direct cytotoxic effect of H2O2 generated during the enzymatic reaction, as well as the non-specific oxidative modifications of signaling molecules that eventually lead to apoptosis and cell death. The very substantial up-regulation of cytochrome P450 genes may also contribute to the potent cytotoxic action of OH-LAAO by producing excessive reactive oxygen species (ROS). In conclusion, the potent apoptosis inducing activity of OH-LAAO was likely due to the direct cytotoxic effect of H2O2 generated during the enzymatic reaction, as well as the non-specific oxidation of signalling molecules.
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Affiliation(s)
- Shin Yee Fung
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Mui Li Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nget Hong Tan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
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Kotłowska A. Application of Chemometric Techniques in Search of Clinically Applicable Biomarkers of Disease. Drug Dev Res 2014; 75:283-90. [DOI: 10.1002/ddr.21213] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alicja Kotłowska
- Department of Food Sciences; Faculty of Pharmacy; Medical University of Gdańsk; Gdańsk 80-416 Poland
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15
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Chung L, Moore K, Phillips L, Boyle FM, Marsh DJ, Baxter RC. Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer. Breast Cancer Res 2014; 16:R63. [PMID: 24935269 PMCID: PMC4095593 DOI: 10.1186/bcr3676] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/02/2014] [Indexed: 12/15/2022] Open
Abstract
Introduction Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel. Methods Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated. Results From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up. Conclusions Protein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.
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Houška J, Peña-Méndez EM, Hernandez-Fernaud JR, Salido E, Hampl A, Havel J, Vaňhara P. Tissue profiling by nanogold-mediated mass spectrometry and artificial neural networks in the mouse model of human primary hyperoxaluria 1. J Appl Biomed 2014. [DOI: 10.1016/j.jab.2013.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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17
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Araújo TG, Paiva CE, Rocha RM, Maia YCP, Sena AAS, Ueira-Vieira C, Carneiro AP, Almeida JF, de Faria PR, Santos DW, Calábria L, Alcântara TM, Soares FA, Goulart LR. A novel highly reactive Fab antibody for breast cancer tissue diagnostics and staging also discriminates a subset of good prognostic triple-negative breast cancers. Cancer Lett 2013; 343:275-85. [PMID: 24099914 DOI: 10.1016/j.canlet.2013.09.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 09/26/2013] [Accepted: 09/26/2013] [Indexed: 01/01/2023]
Abstract
The discovery of novel markers for breast cancer (BC) has been recently relied on antibody combinatorial libraries and selection through phage display. We constructed a recombinant Fab library, and after selections against BC tissues, the FabC4 clone was thoroughly investigated by immunohistochemistry in 232 patients with long-term follow-up. The FabC4 ligand was determined by mass spectrometry. The FabC4 expression was associated with younger age, lack of progesterone receptor, higher histological grades and non-luminal subtypes, and it also identified a subset of good prognostic triple-negative BCs, possibly targeting a conformational epitope of Cytokeratin-10 (CK10). This new CK10-epitope specific antibody may open new possibilities in diagnostic and therapeutic strategies.
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Affiliation(s)
- Thaise G Araújo
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Carlos E Paiva
- Division of Breast and Gynecological Tumors, Department of Clinical Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Yara C P Maia
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Angela A S Sena
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Carlos Ueira-Vieira
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Ana Paula Carneiro
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Juliana F Almeida
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil
| | - Paulo R de Faria
- Federal University of Uberlandia, Biomedical Sciences Institute, Uberlandia, MG, Brazil
| | - Donizeti W Santos
- Obstetric Division, Internal Medicine, University Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Luanda Calábria
- Obstetric Division, Internal Medicine, University Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | - Tânia M Alcântara
- Pathology Division, Internal Medicine, University Hospital, Federal University of Uberlandia, Uberlandia, MG, Brazil
| | | | - Luiz R Goulart
- Federal University of Uberlandia, Institute of Genetics and Biochemistry, Nanobiotechnology Laboratory, Campus Umuarama, Bloco 2E, Sala 248, 38400-902 Uberlandia, MG, Brazil; University of California Davis, Dept. of Medical Microbiology and Immunology, Davis, CA, USA.
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Ngounou Wetie AG, Sokolowska I, Wormwood K, Beglinger K, Michel TM, Thome J, Darie CC, Woods AG. Mass spectrometry for the detection of potential psychiatric biomarkers. J Mol Psychiatry 2013; 1:8. [PMID: 25408901 PMCID: PMC4223884 DOI: 10.1186/2049-9256-1-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 12/20/2022] Open
Abstract
The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identification of protein markers. While significant progress has been made in the understanding of biomarkers for neurodegenerative diseases such as Alzheimer's disease, multiple sclerosis and Parkinson's disease, psychiatric disorders have not been as extensively investigated. Recent and successful applications of mass spectrometry-based proteomics in fields such as cardiovascular disease, cancer, infectious diseases and neurodegenerative disorders suggest a similar path for psychiatric disorders. In this brief review, we describe mass spectrometry and its use in psychiatric biomarker research and highlight some of the possible challenges of undertaking this type of work. Further, specific examples of candidate biomarkers are highlighted. A short comparison of proteomic with genomic methods for biomarker discovery research is presented. In summary, mass spectrometry-based techniques may greatly facilitate ongoing efforts to understand molecular mechanisms of psychiatric disorders.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Kelly Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katherine Beglinger
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Tanja Maria Michel
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany
| | - Johannes Thome
- Department of Psychiatry, University of Rostock, Rostock, Gehlsheimer Straße 20, D-18147 Germany ; College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA ; Neuropsychology Clinic and Psychoeducation Services, SUNY Plattsburgh, 101 Broad St, Plattsburgh, 12901 NY USA
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Chung L, Baxter RC. Breast cancer biomarkers: proteomic discovery and translation to clinically relevant assays. Expert Rev Proteomics 2013; 9:599-614. [PMID: 23256671 DOI: 10.1586/epr.12.62] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Although the molecular classification and prognostic assessment of breast tumors based on gene expression profiling is well established, a number of proteomic studies that propose potential breast cancer biomarkers has not yet led to any new diagnostic, prognostic or predictive test in wide clinical use. This review examines the current status of breast cancer biomarkers, discusses sample types (including plasma, tumor tissue, nipple aspirate and ductal lavage, as well as cell culture models) and different electrophoretic and mass spectrometry methods that have been widely used for the discovery of proteomic biomarkers in breast cancer, and also considers several approaches to biomarker validation. The pathway leading from the initial proteomic discovery and validation process to translation into a clinically useful test is also discussed.
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Affiliation(s)
- Liping Chung
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
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