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Garg P, Krishna M, Subbalakshmi AR, Ramisetty S, Mohanty A, Kulkarni P, Horne D, Salgia R, Singhal SS. Emerging biomarkers and molecular targets for precision medicine in cervical cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189106. [PMID: 38701936 DOI: 10.1016/j.bbcan.2024.189106] [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: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cervical cancer remains a significant global health burden, necessitating innovative approaches for improved diagnostics and personalized treatment strategies. Precision medicine has emerged as a promising paradigm, leveraging biomarkers and molecular targets to tailor therapy to individual patients. This review explores the landscape of emerging biomarkers and molecular targets in cervical cancer, highlighting their potential implications for precision medicine. By integrating these biomarkers into comprehensive diagnostic algorithms, clinicians can identify high-risk patients at an earlier stage, enabling timely intervention and improved patient outcomes. Furthermore, the identification of specific molecular targets has paved the way for the development of targeted therapies aimed at disrupting key pathways implicated in cervical carcinogenesis. In conclusion, the evolving landscape of biomarkers and molecular targets presents exciting opportunities for advancing precision medicine in cervical cancer. By harnessing these insights, clinicians can optimize treatment selection, enhance patient outcomes, and ultimately transform the management of this devastating disease.
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Affiliation(s)
- Pankaj Garg
- Department of Chemistry, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Madhu Krishna
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ayalur Raghu Subbalakshmi
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sravani Ramisetty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Departments of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
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Kabir MWU, Alawad DM, Pokhrel P, Hoque MT. DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues. Comput Biol Med 2024; 170:108081. [PMID: 38295475 PMCID: PMC10922697 DOI: 10.1016/j.compbiomed.2024.108081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/12/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
Abstract
DNA-binding and RNA-binding proteins are essential to an organism's normal life cycle. These proteins have diverse functions in various biological processes. DNA-binding proteins are crucial for DNA replication, transcription, repair, packaging, and gene expression. Likewise, RNA-binding proteins are essential for the post-transcriptional control of RNAs and RNA metabolism. Identifying DNA- and RNA-binding residue is essential for biological research and understanding the pathogenesis of many diseases. However, most DNA-binding and RNA-binding proteins still need to be discovered. This research explored various properties of the protein sequences, such as amino acid composition type, Position-Specific Scoring Matrix (PSSM) values of amino acids, Hidden Markov model (HMM) profiles, physiochemical properties, structural properties, torsion angles, and disorder regions. We utilized a sliding window technique to extract more information from a target residue's neighbors. We proposed an optimized Light Gradient Boosting Machine (LightGBM) method, named DRBpred, to predict DNA-binding and RNA-binding residues from the protein sequence. DRBpred shows an improvement of 112.00 %, 33.33 %, and 6.49 % for the DNA-binding test set compared to the state-of-the-art method. It shows an improvement of 112.50 %, 16.67 %, and 7.46 % for the RNA-binding test set regarding Sensitivity, Mathews Correlation Coefficient (MCC), and AUC metric.
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Affiliation(s)
- Md Wasi Ul Kabir
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
| | - Duaa Mohammad Alawad
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
| | - Pujan Pokhrel
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
| | - Md Tamjidul Hoque
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
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Danishuddin, Khan S, Kim JJ. From cancer big data to treatment: Artificial intelligence in cancer research. J Gene Med 2024; 26:e3629. [PMID: 37940369 DOI: 10.1002/jgm.3629] [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: 08/25/2023] [Revised: 09/12/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
In recent years, developing the idea of "cancer big data" has emerged as a result of the significant expansion of various fields such as clinical research, genomics, proteomics and public health records. Advances in omics technologies are making a significant contribution to cancer big data in biomedicine and disease diagnosis. The increasingly availability of extensive cancer big data has set the stage for the development of multimodal artificial intelligence (AI) frameworks. These frameworks aim to analyze high-dimensional multi-omics data, extracting meaningful information that is challenging to obtain manually. Although interpretability and data quality remain critical challenges, these methods hold great promise for advancing our understanding of cancer biology and improving patient care and clinical outcomes. Here, we provide an overview of cancer big data and explore the applications of both traditional machine learning and deep learning approaches in cancer genomic and proteomic studies. We briefly discuss the challenges and potential of AI techniques in the integrated analysis of omics data, as well as the future direction of personalized treatment options in cancer.
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Affiliation(s)
- Danishuddin
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, South Korea
| | - Shawez Khan
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Jong Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, South Korea
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Kumarasamy G, Mohd Salim NH, Mohd Afandi NS, Hazlami Habib MA, Mat Amin ND, Ismail MN, Musa M. Glycoproteomics-based liquid biopsy: translational outlook for colorectal cancer clinical management in Southeast Asia. Future Oncol 2023; 19:2313-2332. [PMID: 37937446 DOI: 10.2217/fon-2023-0704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Colorectal cancer (CRC) signifies a significant healthcare challenge in Southeast Asia. Despite advancements in screening approaches and treatment modalities, significant medical gaps remain, ranging from prevention and early diagnosis to determining targeted therapy and establishing personalized approaches to managing CRC. There is a need to expand more validated biomarkers in clinical practice. An advanced technique incorporating high-throughput mass spectrometry as a liquid biopsy to unravel a repertoire of glycoproteins and glycans would potentially drive the development of clinical tools for CRC screening, diagnosis and monitoring, and it can be further adapted to the existing standard-of-care procedure. Therefore this review offers a perspective on glycoproteomics-driven liquid biopsy and its potential integration into the clinical care of CRC in the southeast Asia region.
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Affiliation(s)
- Gaayathri Kumarasamy
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
| | - Nurul Hakimah Mohd Salim
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
| | - Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Nor Datiakma Mat Amin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
- Nature Products Division, Forest Research Institute Malaysia, Kepong, Selangor, 52109, Malaysia
| | - Mohd Nazri Ismail
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Pulau Pinang, 11800, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, 11900, Malaysia
| | - Marahaini Musa
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, 16150, Malaysia
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Chaithanya P, Meshram RJ. Chemo Markers as Biomarkers in Septic Shock: A Comprehensive Review of Their Utility and Clinical Applications. Cureus 2023; 15:e42558. [PMID: 37637638 PMCID: PMC10460194 DOI: 10.7759/cureus.42558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Sepsis is a life-threatening condition characterized by a dysregulated host response to infection, often leading to septic shock. Early diagnosis and prompt intervention are crucial for improving patient outcomes. Chemo markers, which are measurable biological substances associated with the pathophysiology of septic shock, have emerged as potential biomarkers for the identification, risk stratification, and management of this condition. This comprehensive review aims to thoroughly evaluate the utility and clinical applications of chemo markers in septic shock. The review begins by discussing the criteria for ideal chemo markers, including specificity, sensitivity, dynamic range, stability, non-invasiveness, and prognostic value. These characteristics ensure accurate diagnosis, early detection, effective monitoring, and prediction of clinical outcomes. Furthermore, the review explores the role of chemo markers in monitoring treatment response and disease progression, highlighting their ability to serve as objective indicators for assessing the effectiveness of interventions and making timely adjustments in management strategies. Moreover, the prognostic value of chemo markers in predicting outcomes is discussed, emphasizing their association with mortality, hospital stays, and the development of complications. Integration of chemo markers into prognostic models or scoring systems enhances risk stratification and informs therapeutic decisions. The review also delves into recent advances in chemo marker research and technology, emphasizing the potential for discovering novel chemo markers with enhanced diagnostic and prognostic capabilities. It highlights the use of high-throughput proteomics, genomics, and transcriptomics in identifying specific molecular signatures associated with septic shock. This contributes to a deeper understanding of the complex immune and inflammatory responses involved. In conclusion, chemo markers have emerged as valuable biomarkers in septic shock, offering potential utility in diagnosis, risk stratification, treatment monitoring, and prediction of outcomes. Continued research, validation, and integration into clinical practice are necessary to fully realize their potential in improving patient care and outcomes in septic shock.
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Affiliation(s)
- Pulivarthi Chaithanya
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Revat J Meshram
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Wardha, IND
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Ahmad A, Imran M, Ahsan H. Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases. Pharmaceutics 2023; 15:1630. [PMID: 37376078 DOI: 10.3390/pharmaceutics15061630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
A biomarker is any measurable biological moiety that can be assessed and measured as a potential index of either normal or abnormal pathophysiology or pharmacological responses to some treatment regimen. Every tissue in the body has a distinct biomolecular make-up, which is known as its biomarkers, which possess particular features, viz., the levels or activities (the ability of a gene or protein to carry out a particular body function) of a gene, protein, or other biomolecules. A biomarker refers to some feature that can be objectively quantified by various biochemical samples and evaluates the exposure of an organism to normal or pathological procedures or their response to some drug interventions. An in-depth and comprehensive realization of the significance of these biomarkers becomes quite important for the efficient diagnosis of diseases and for providing the appropriate directions in case of multiple drug choices being presently available, which can benefit any patient. Presently, advancements in omics technologies have opened up new possibilities to obtain novel biomarkers of different types, employing genomic strategies, epigenetics, metabolomics, transcriptomics, lipid-based analysis, protein studies, etc. Particular biomarkers for specific diseases, their prognostic capabilities, and responses to therapeutic paradigms have been applied for screening of various normal healthy, as well as diseased, tissue or serum samples, and act as appreciable tools in pharmacology and therapeutics, etc. In this review, we have summarized various biomarker types, their classification, and monitoring and detection methods and strategies. Various analytical techniques and approaches of biomarkers have also been described along with various clinically applicable biomarker sensing techniques which have been developed in the recent past. A section has also been dedicated to the latest trends in the formulation and designing of nanotechnology-based biomarker sensing and detection developments in this field.
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Affiliation(s)
- Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC), Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Hotchkiss Brain Institute, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad Imran
- Therapeutics Research Group, Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane 4102, Australia
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Mir MA, Qayoom H, Sofi S, Jan N. Proteomics: A groundbreaking development in cancer biology. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00004-3] [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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Arip M, Tan LF, Jayaraj R, Abdullah M, Rajagopal M, Selvaraja M. Exploration of biomarkers for the diagnosis, treatment and prognosis of cervical cancer: a review. Discov Oncol 2022; 13:91. [PMID: 36152065 PMCID: PMC9509511 DOI: 10.1007/s12672-022-00551-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 12/19/2022] Open
Abstract
As the fourth most diagnosed cancer, cervical cancer (CC) is one of the major causes of cancer-related mortality affecting females globally, particularly when diagnosed at advanced stage. Discoveries of CC biomarkers pave the road to precision medicine for better patient outcomes. High throughput omics technologies, characterized by big data production further accelerate the process. To date, various CC biomarkers have been discovered through the advancement in technologies. Despite, very few have successfully translated into clinical practice due to the paucity of validation through large scale clinical studies. While vast amounts of data are generated by the omics technologies, challenges arise in identifying the clinically relevant data for translational research as analyses of single-level omics approaches rarely provide causal relations. Integrative multi-omics approaches across different levels of cellular function enable better comprehension of the fundamental biology of CC by highlighting the interrelationships of the involved biomolecules and their function, aiding in identification of novel integrated biomarker profile for precision medicine. Establishment of a worldwide Early Detection Research Network (EDRN) system helps accelerating the pace of biomarker translation. To fill the research gap, we review the recent research progress on CC biomarker development from the application of high throughput omics technologies with sections covering genomics, transcriptomics, proteomics, and metabolomics.
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Affiliation(s)
- Masita Arip
- Allergy & Immunology Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, 40170 Shah Alam, Selangor, Malaysia
| | - Lee Fang Tan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Rama Jayaraj
- Charles Darwin University, Darwin, NT, 0909, Australia
| | - Maha Abdullah
- Immunology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Jalan Serdang, 43400, Serdang, Selangor, Malaysia
| | - Mogana Rajagopal
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Malarvili Selvaraja
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, 56000 Cheras, Kuala Lumpur, Malaysia.
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Endoplasmic Reticulum Stress and Impairment of Ribosome Biogenesis Mediate the Apoptosis Induced by Ocimum x africanum Essential Oil in a Human Gastric Cancer Cell Line. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58060799. [PMID: 35744062 PMCID: PMC9227199 DOI: 10.3390/medicina58060799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Background and Objectives: Gastric cancer remains a major unmet clinical problem worldwide. Although conventional medical treatments are available, their curative effects are generally unsatisfactory. Consequently, it remains necessary to search natural products for potential alternatives in treating gastric cancer patients. Ocimum x africanum Lour. is a culinary herb that has been used in folk medicine for various diseases, but little is known regarding its anti-cancer activity against gastric cancer cells. In the current study, we focus on the anti-cancer mechanisms of O. x africanum essential oil (OAEO) in the AGS human gastric cancer cell line. Materials and Methods: After OAEO treatment, AGS cell viability was evaluated by MTT assay. Cell migration and apoptotic nuclear morphology were determined by wound-healing assay and DAPI staining, respectively. Gene expression levels of apoptosis-related genes were quantified by qRT–PCR. Differential protein expression was determined with an LC–MS/MS-based proteomics approach to identify the key proteins that may be important in the anti-cancer mechanisms of OAEO on AGS cells. The chemical constituents of OAEO were identified by GC–MS analysis. Results: We found OAEO to exhibit a potent growth-inhibiting effect on AGS cells, with an IC50 value of 42.73 µg/mL. After OAEO treatment for 24 h, AGS cell migration was significantly decreased relative to the untreated control. OAEO-treated AGS cells exhibited common features of apoptotic cell death, including cell shrinkage, membrane blebbing, chromatin condensation, and nuclear fragmentation. Apoptotic cell death was confirmed by qRT–PCR for apoptosis-related genes, revealing that OAEO decreased the expression of anti-apoptotic genes (BCL2 and BCL-xL) and activated pro-apoptotic genes and apoptotic caspase genes (TP53, BAX, CASP9, CASP12, and CASP3). Moreover, expression of CASP8 was not changed after treatment. Proteomic analysis revealed that OAEO may produce a signature effect on protein clusters relating to unfolded protein accumulation, thereby inducing severe ER stress and also impairing ribosome synthesis. STRING analysis revealed seven up-regulated and 11 down-regulated proteins, which were significantly associated with protein folding and ribosome biogenesis, respectively. Using GC–MS analysis, 6-methyl-5-hepten-2-one, citral, neral, and linalool were found to be the major chemical constituents in OAEO. Conclusions: Taken together, these results indicate that OAEO has a potential anti-proliferative effect on AGS cells. Our molecular findings show evidence supporting an important role of ER stress and ribosome biogenesis impairment in mediating the induction of cell death by OAEO through the mitochondrial-apoptotic pathway. This study, therefore, provides fundamental knowledge for future applications using OAEO as an alternative therapy in gastric cancer management.
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Stiving AQ, Harvey SR, Jones BJ, Bellina B, Brown JM, Barran PE, Wysocki VH. Coupling 193 nm Ultraviolet Photodissociation and Ion Mobility for Sequence Characterization of Conformationally-Selected Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2313-2320. [PMID: 32959654 PMCID: PMC8127984 DOI: 10.1021/jasms.0c00259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a useful technique for characterizing peptide, protein, and protein complex primary and secondary structure. 193 nm UVPD, specifically, enables extensive covalent fragmentation of the peptide backbone without the requirement of a specific side chain chromophore and with no precursor charge state dependence. We have modified a commercial quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer to include 193 nm UVPD following ion mobility. Ion mobility (IM) is a gas-phase separation technique that enables separation of ions by their size, shape, and charge, providing an orthogonal dimension of separation to mass analysis. Following instrument modifications, we characterized the performance of, and information that could be generated from, this new setup using the model peptides substance P, melittin, and insulin chain B. These experiments show extensive fragmentation across the peptide backbone and a variety of ion types as expected from 193 nm UVPD. Additionally, y-2 ions (along with complementary a+2 and b+2 ions) N-terminal to proline were observed. Combining the IM separation and mobility gating capabilities with UVPD, we demonstrate the ability to accomplish both mass- and mobility-selection of bradykinin des-Arg9 and des-Arg1 peptides followed by complete sequence characterization by UVPD. The new capabilities of this modified instrument demonstrate the utility of combining IM with UVPD because isobaric species cannot be independently selected with a traditional quadrupole alone.
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Affiliation(s)
- Alyssa Q Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | | | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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Cantor DI, Cheruku HR, Westacott J, Shin JS, Mohamedali A, Ahn SB. Proteomic investigations into resistance in colorectal cancer. Expert Rev Proteomics 2020; 17:49-65. [PMID: 31914823 DOI: 10.1080/14789450.2020.1713103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Despite advances in screening and treatment options, colorectal cancer (CRC) remains one of the most prevalent and lethal cancer subtypes. Resistance to cytotoxic or targeted therapy has remained a constant challenge to the treatment and long-term management of patients, attracting intense worldwide investigation since the 1950s. Through extensive investigations into the proteomic mechanisms and functions that convey resistance to therapy/s, researchers have become able to implicate alterations in several signaling pathways that provide and sustain resistance to treatment.Areas covered: In this review, we summarize how protein alterations are associated with resistance to therapy, with particular emphasis on CRC. An overview of the mechanisms of therapeutic resistance is described, highlighting recent studies which endeavor to elucidate the proteomic changes that are associated with the acquisition and promulgation of therapeutic resistance.Expert opinion: While cancers such as CRC have been intensively studied for decades, unresponsiveness and the resistance to therapy remain critical obstacles in the treatment of patients. Due to the inherent biological and clinical heterogeneity of individual CRCs, proteomic methods stand to become powerful tools to provide biological insights that may guide therapeutic strategies with the ultimate goal of refining emergent immunotherapeutic treatments.
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Affiliation(s)
- David I Cantor
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | | | - Jack Westacott
- Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Joo-Shik Shin
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Abidali Mohamedali
- Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Seong Boem Ahn
- Faculty of Health and Medical Sciences, Macquarie University, Sydney, Australia
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Jun J, Gim J, Kim Y, Kim H, Yu SJ, Yeo I, Park J, Yoo JJ, Cho YY, Lee DH, Cho EJ, Lee JH, Kim YJ, Lee S, Yoon JH, Kim Y, Park T. Analysis of significant protein abundance from multiple reaction-monitoring data. BMC SYSTEMS BIOLOGY 2018; 12:123. [PMID: 30598095 PMCID: PMC6311902 DOI: 10.1186/s12918-018-0656-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background Discovering reliable protein biomarkers is one of the most important issues in biomedical research. The ELISA is a traditional technique for accurate quantitation of well-known proteins. Recently, the multiple reaction-monitoring (MRM) mass spectrometry has been proposed for quantifying newly discovered protein and has become a popular alternative to ELISA. For the MRM data analysis, linear mixed modeling (LMM) has been used to analyze MRM data. MSstats is one of the most widely used tools for MRM data analysis that is based on the LMMs. However, LMMs often provide various significance results, depending on model specification. Sometimes it would be difficult to specify a correct LMM method for the analysis of MRM data. Here, we propose a new logistic regression-based method for Significance Analysis of Multiple Reaction Monitoring (LR-SAM). Results Through simulation studies, we demonstrate that LMM methods may not preserve type I error, thus yielding high false- positive errors, depending on how random effects are specified. Our simulation study also shows that the LR-SAM approach performs similarly well as LMM approaches, in most cases. However, LR-SAM performs better than the LMMs, particularly when the effects sizes of peptides from the same protein are heterogeneous. Our proposed method was applied to MRM data for identification of proteins associated with clinical responses of treatment of 115 hepatocellular carcinoma (HCC) patients with the tyrosine kinase inhibitor sorafenib. Of 124 candidate proteins, LMM approaches provided 6 results varying in significance, while LR-SAM, by contrast, yielded 18 significant results that were quite reproducibly consistent. Conclusion As exemplified by an application to HCC data set, LR-SAM more effectively identified proteins associated with clinical responses of treatment than LMM did.
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Affiliation(s)
- Jongsu Jun
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Jungsoo Gim
- Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Hyunsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Injun Yeo
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea
| | - Jiyoung Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong-Ju Yoo
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Young Youn Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Dong Hyeon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Eun Ju Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Seoul, South Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, South Korea. .,Interdisciplinary program in Bioinformatics, Seoul National University, Seoul, South Korea.
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14
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Differential expression of NPM, GSTA3, and GNMT in mouse liver following long-term in vivo irradiation by means of uranium tailings. Biosci Rep 2018; 38:BSR20180536. [PMID: 30061177 PMCID: PMC6200700 DOI: 10.1042/bsr20180536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/21/2018] [Accepted: 07/26/2018] [Indexed: 12/19/2022] Open
Abstract
Uranium tailings (UT) are formed as a byproduct of uranium mining and are of potential risk to living organisms. In the present study, we sought to identify potential biomarkers associated with chronic exposure to low dose rate γ radiation originating from UT. We exposed C57BL/6J mice to 30, 100, or 250 μGy/h of gamma radiation originating from UT samples. Nine animals were included in each treatment group. We observed that the liver central vein was significantly enlarged in mice exposed to dose rates of 100 and 250 μGy/h, when compared with nonirradiated controls. Using proteomic techniques, we identified 18 proteins that were differentially expressed (by a factor of at least 2.5-fold) in exposed animals, when compared with controls. We chose glycine N-methyltransferase (GNMT), glutathione S-transferase A3 (GSTA3), and nucleophosmin (NPM) for further investigations. Our data showed that GNMT (at 100 and 250 μGy/h) and NPM (at 250 μGy/h) were up-regulated, and GSTA3 was down-regulated in all of the irradiated groups, indicating that their expression is modulated by chronic gamma radiation exposure. GNMT, GSTA3, and NPM may therefore prove useful as biomarkers of gamma radiation exposure associated with UT. The mechanisms underlying those changes need to be further studied.
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15
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Průcha M, Zazula R, Russwurm S. Sepsis Diagnostics in the Era of "Omics" Technologies. Prague Med Rep 2018; 119:9-29. [PMID: 29665344 DOI: 10.14712/23362936.2018.2] [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] [Indexed: 10/17/2022] Open
Abstract
Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy. Current progress in the use of systems biology technologies brings us hope that by using big data from clinical trials such biomarkers will be found.
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Affiliation(s)
- Miroslav Průcha
- Department of Clinical Biochemistry, Haematology and Immunology, Na Homolce Hospital, Prague, Czech Republic.
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Stefan Russwurm
- Department of Anesthesiology and Intensive Care, University Hospital Jena, Jena, Germany
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16
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Lee J, Geiss GK, Demirkan G, Vellano CP, Filanoski B, Lu Y, Ju Z, Yu S, Guo H, Bogatzki LY, Carter W, Meredith RK, Krishnamurthy S, Ding Z, Beechem JM, Mills GB. Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies. Mol Cell Proteomics 2018. [PMID: 29531020 DOI: 10.1074/mcp.ra117.000291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting.
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Affiliation(s)
- Jinho Lee
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030;
| | - Gary K Geiss
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109;
| | - Gokhan Demirkan
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Christopher P Vellano
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Brian Filanoski
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Yiling Lu
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Zhenlin Ju
- ¶The University of Texas M.D. Anderson Cancer Center, Department of Pathology, 1515 Holcombe Blvd, Houston, Texas 77030
| | - Shuangxing Yu
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Huifang Guo
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Lisa Y Bogatzki
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Warren Carter
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Rhonda K Meredith
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Savitri Krishnamurthy
- ¶The University of Texas M.D. Anderson Cancer Center, Department of Pathology, 1515 Holcombe Blvd, Houston, Texas 77030
| | - Zhiyong Ding
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030
| | - Joseph M Beechem
- §NanoString Technologies, Inc., 530 Fairview Ave N., Seattle, Washington 98109
| | - Gordon B Mills
- From the ‡The University of Texas M.D. Anderson Cancer Center, Department of Systems Biology, 1300 Moursund St., Houston, Texas 77030;
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17
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Duran-Ortiz S, Brittain AL, Kopchick JJ. The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies. Clin Proteomics 2017; 14:24. [PMID: 28670222 PMCID: PMC5492507 DOI: 10.1186/s12014-017-9160-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.
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Affiliation(s)
- Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA
| | - Alison L Brittain
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
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18
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Kumar M, Singh R, Meena A, Patidar BS, Prasad R, Chhabra SK, Bansal SK. An Improved 2-Dimensional Gel Electrophoresis Method for Resolving Human Erythrocyte Membrane Proteins. PROTEOMICS INSIGHTS 2017; 8:1178641817700880. [PMID: 28469466 PMCID: PMC5398320 DOI: 10.1177/1178641817700880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
The 2-dimensional gel electrophoresis (2-DE) technique is widely used for the analysis of complex protein mixtures extracted from biological samples. It is one of the most commonly used analytical techniques in proteomics to study qualitative and quantitative protein changes between different states of a cell or an organism (eg, healthy and diseased), conditionally expressed proteins, posttranslational modifications, and so on. The 2-DE technique is used for its unparalleled ability to separate thousands of proteins simultaneously. The resolution of the proteins by 2-DE largely depends on the quality of sample prepared during protein extraction which increases results in terms of reproducibility and minimizes protein modifications that may result in artifactual spots on 2-DE gels. The buffer used for the extraction and solubilization of proteins influences the quality and reproducibility of the resolution of proteins on 2-DE gel. The purification by cleanup kit is another powerful process to prevent horizontal streaking which occurs during isoelectric focusing due to the presence of contaminants such as salts, lipids, nucleic acids, and detergents. Erythrocyte membrane proteins serve as prototypes for multifunctional proteins in various erythroid and nonerythroid cells. In this study, we therefore optimized the selected major conditions of 2-DE for resolving various proteins of human erythrocyte membrane. The modification included the optimization of conditions for sample preparation, cleanup of protein sample, isoelectric focusing, equilibration, and storage of immobilized pH gradient strips, which were further carefully examined to achieve optimum conditions for improving the quality of protein spots on 2-DE gels. The present improved 2-DE analysis method enabled better detection of protein spots with higher quality and reproducibility. Therefore, the conditions established in this study may be used for the 2-DE analysis of erythrocyte membrane proteins for different diseases, which may help to identify the proteins that may serve as markers for diagnostics as well as targets for development of new therapeutic potential.
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Affiliation(s)
- Manoj Kumar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Singh
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Anil Meena
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Bhagwan S Patidar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,A28, Sector 3, Aliganj, Lucknow, UP, India
| | - Sunil K Chhabra
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,Department of Pulmonary, Sleep and Critical Care Medicine, Primus Super Speciality Hospital, Chanakyapuri, New Delhi, India
| | - Surendra K Bansal
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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19
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Lin F, Li Z, Hua Y, Lim YP. Proteomic profiling predicts drug response to novel targeted anticancer therapeutics. Expert Rev Proteomics 2016; 13:411-20. [PMID: 26954459 DOI: 10.1586/14789450.2016.1164043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most recently approved anti-cancer drugs by the US FDA are targeted therapeutic agents and this represents an important trend for future anticancer therapy. Unlike conventional chemotherapy that rarely considers individual differences, it is crucial for targeted therapies to identify the beneficial subgroup of patients for the treatment. Currently, genomics and transcriptomics are the major 'omic' analytics used in studies of drug response prediction. However, proteomic profiling excels both in its advantages of directly detecting an instantaneous dynamic of the whole proteome, which contains most current diagnostic markers and therapeutic targets. Moreover, proteomic profiling improves understanding of the mechanism for drug resistance and helps finding optimal combination therapy. This article reviews the recent success of applications of proteomic analytics in predicting the response to targeted anticancer therapeutics, and discusses the potential avenues and pitfalls of proteomic platforms and techniques used most in the field.
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Affiliation(s)
- Fan Lin
- a Department of Cell Biology , Nanjing Medical University , Nanjing , China.,b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Zilin Li
- b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Yunfen Hua
- c College of Pharmaceutical Science, Zhejiang University of Technology , Hangzhou , China
| | - Yoon Pin Lim
- b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore.,d Bioinformatics Institute, Agency for Science and Technology , Singapore.,e NUS Graduate School of Integrative Sciences and Technology , Singapore
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20
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Abstract
Precision medicine is an emerging approach for prevention and treatment of diseases considering individuals’ uniqueness. Omics provide one step forward toward advanced precision medicine and include technologies such as genomics, proteomics and metabolomics generating valuable data through characterization of entire biological systems. With the aid of omics, a major shift has been started to occur in understanding of diseases followed by potential fundamental changes in medical care strategies. This short review aims at providing some examples of current omics that are applied in the field of pain in terms of new biomarkers for diagnosis of different pain types, stratification of patients and new therapeutic targets. Implementation of omics would most likely offer breakthrough in the future of pain management.
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Affiliation(s)
- Parisa Gazerani
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
| | - Hye Sook Han Vinterhøj
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
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21
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Precision or Personalized Medicine for Cancer Chemotherapy: Is there a Role for Herbal Medicine. Molecules 2016; 21:molecules21070889. [PMID: 27399658 PMCID: PMC6273869 DOI: 10.3390/molecules21070889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/26/2016] [Accepted: 07/01/2016] [Indexed: 12/15/2022] Open
Abstract
Although over 100 chemotherapeutic agents are currently available for the treatment of cancer patients, the overall long term clinical benefit is disappointing due to the lack of effectiveness or severe side effects from these agents. In order to improve the therapeutic outcome, a new approach called precision medicine or personalized medicine has been proposed and initiated by the U.S. National Institutes of Health. However, the limited availability of effective medications and the high cost are still the major barriers for many cancer patients. Thus alternative approaches such as herbal medicines could be a feasible and less costly option. Unfortunately, scientific evidence for the efficacy of a majority of herbal medicines is still lacking and their development to meet FDA approval or other regulatory agencies is a big challenge. However, herbal medicines may be able to play an important role in precision medicine or personalized medicine. This review will focus on the existing and future technologies that could speed the development of herbal products for treatment of resistant cancer in individual patients. Specifically, it will concentrate on reviewing the phenotypic (activity based) rather than genotypic (mechanism based) approach to develop herbal medicine useful for personalized cancer chemotherapy.
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22
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Xia M, Broek JAC, Jouroukhin Y, Schoenfelder J, Abazyan S, Jaaro-Peled H, Sawa A, Bahn S, Pletnikov M. Cell Type-Specific Effects of Mutant DISC1: A Proteomics Study. MOLECULAR NEUROPSYCHIATRY 2016; 2:28-36. [PMID: 27606318 DOI: 10.1159/000444587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/08/2016] [Indexed: 12/19/2022]
Abstract
Despite the recent progress in psychiatric genetics, very few studies have focused on genetic risk factors in glial cells that, compared to neurons, can manifest different molecular pathologies underlying psychiatric disorders. In order to address this issue, we studied the effects of mutant disrupted in schizophrenia 1 (DISC1), a genetic risk factor for schizophrenia, in cultured primary neurons and astrocytes using an unbiased mass spectrometry-based proteomic approach. We found that selective expression of mutant DISC1 in neurons affects a wide variety of proteins predominantly involved in neuronal development (e.g., SOX1) and vesicular transport (Rab proteins), whereas selective expression of mutant DISC1 in astrocytes produces changes in the levels of mitochondrial (GDPM), nuclear (TMM43) and cell adhesion (ECM2) proteins. The present study demonstrates that DISC1 variants can perturb distinct molecular pathways in a cell type-specific fashion to contribute to psychiatric disorders through heterogenic effects in diverse brain cells.
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Affiliation(s)
- Meng Xia
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Preclinical College, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Jantine A C Broek
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Yan Jouroukhin
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Jeannine Schoenfelder
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sofya Abazyan
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Hanna Jaaro-Peled
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Akira Sawa
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Mikhail Pletnikov
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Departments of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md., USA
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