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Akgul Caglar T, Gunal MY, Turhan MU, Ozturk G, Cagavi E. Experimental data of labeling the heart and cardiac cultures with a retrograde tracer in vitro and in vivo. Data Brief 2021; 35:106834. [PMID: 33748355 PMCID: PMC7960933 DOI: 10.1016/j.dib.2021.106834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 11/01/2022] Open
Abstract
Retrograde dyes are often used in basic research to investigate neuronal innervations of an organ. This article describes the experimental data on the application of retrograde dyes on the mouse heart in vivo and on the cardiac or neuronal cultures in vitro. By providing this information, cardiac or inneinnervations can be evaluated in vivo. Therefore, unknown cellular and molecular mechanisms and systemic interactions in the body can be investigated. In particular, we provided practical tips to lower mortality risks following the cardiac surgery and evaluated the staining capacity and fluorescent characteristics of the Di-8-ANEPPQ dye in the cardiac tissue and cell cultures. First, primary cultures of mouse nodose ganglia (NG) neurons and mouse neonatal cardiomyocytes were stained with Di-8-ANEPPQ. The Di-8-ANEPPQ signal from live cultures were visualized using spinning disk confocal microscopy to verify the lipophilic and fluorescent labeling capacity of Di-8-ANEPPQ. Next, the excitation and emission data of Di-8-ANEPPQ were collected between 415 nm and 690 nm using power spectrum module of confocal microscopy. This spectrum analysis could be useful for the researchers who plan to use Di-8-ANEPPQ in combination with other fluorescent dyes to eliminate any florescent overlap. In order to label the heart tissue with tracer dyes Di-8-ANEPPQ or DiI in vivo, the heart was exposed without damaging lungs or other tissues following anesthetization, then the retrograde dye was applied as a paste for DiI or injected to the apex of the heart for Di-8-ANEPPQ and the operation area was sutured. The surgical procedure required intubation to control the respiratory reflex without the need to perform a tracheotomy and yielded high viability. Following labeling the heart in vivo, the heart was dissected, and images of injection area were captured using confocal microscopy. All fluorescent images of Di-8-ANEPPQ labeled cells were analyzed by using the Fiji software. Overall, these data provide applicable data to other investigators to trace the sensory neurons innervating not only the heart but also other organs using Di-8-ANEPPQ. These data support the original research article titled "Evaluation of bilateral cardiac afferent distribution at the spinal and vagal ganglia by retrograde labeling" that was accepted for publication in Brain Research Journal [1].
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Affiliation(s)
- Tuba Akgul Caglar
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Neuroscience Program, Institute of Health Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Mehmet Yalcin Gunal
- Department of Physiology, School of Medicine, Alanya Alaaddin Keykubat University, Antalya, Turkey
| | - Mehmet Ugurcan Turhan
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Gurkan Ozturk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Neuroscience Program, Institute of Health Sciences, Istanbul Medipol University, Istanbul, Turkey.,Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Esra Cagavi
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Medical Biology and Genetics Program, Institute of Health Sciences, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
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Syed N, Chavan S, Sahasrabuddhe NA, Renuse S, Sathe G, Nanjappa V, Radhakrishnan A, Raja R, Pinto SM, Srinivasan A, Prasad TSK, Srikumar K, Gowda H, Santosh V, Sidransky D, Califano JA, Pandey A, Chatterjee A. Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics 2015; 15:383-93. [PMID: 25327479 DOI: 10.1002/pmic.201400338] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/24/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022]
Abstract
Dysregulation of protein expression is associated with most diseases including cancer. MS-based proteomic analysis is widely employed as a tool to study protein dysregulation in cancers. Proteins that are differentially expressed in head and neck squamous cell carcinoma (HNSCC) cell lines compared to the normal oral cell line could serve as biomarkers for patient stratification. To understand the proteomic complexity in HNSCC, we carried out iTRAQ-based MS analysis on a panel of HNSCC cell lines in addition to a normal oral keratinocyte cell line. LC-MS/MS analysis of total proteome of the HNSCC cell lines led to the identification of 3263 proteins, of which 185 proteins were overexpressed and 190 proteins were downregulated more than twofold in at least two of the three HNSCC cell lines studied. Among the overexpressed proteins, 23 proteins were related to DNA replication and repair. These included high-mobility group box 2 (HMGB2) protein, which was overexpressed in all three HNSCC lines studied. Overexpression of HMGB2 has been reported in various cancers, yet its role in HNSCC remains unclear. Immunohistochemical labeling of HMGB2 in a panel of HNSCC tumors using tissue microarrays revealed overexpression in 77% (54 of 70) of tumors. The HMGB proteins are known to bind to DNA structure resulting from cisplatin-DNA adducts and affect the chemosensitivity of cells. We observed that siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-FU. We hypothesize that targeting HMGB2 could enhance the efficacy of existing chemotherapeutic regimens for treatment of HNSCC. All MS data have been deposited in the ProteomeXchange with identifier PXD000737 (http://proteomecentral.proteomexchange.org/dataset/PXD000737).
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Affiliation(s)
- Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, India; Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
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Subbannayya Y, Mir SA, Renuse S, Manda SS, Pinto SM, Puttamallesh VN, Solanki HS, Manju HC, Syed N, Sharma R, Christopher R, Vijayakumar M, Veerendra Kumar KV, Keshava Prasad TS, Ramaswamy G, Kumar RV, Chatterjee A, Pandey A, Gowda H. Identification of differentially expressed serum proteins in gastric adenocarcinoma. J Proteomics 2015; 127:80-8. [PMID: 25952687 DOI: 10.1016/j.jprot.2015.04.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/14/2015] [Accepted: 04/21/2015] [Indexed: 01/01/2023]
Abstract
UNLABELLED Gastric adenocarcinoma is an aggressive cancer with poor prognosis. Blood based biomarkers of gastric cancer have the potential to improve diagnosis and monitoring of these tumors. Proteins that show altered levels in the circulation of gastric cancer patients could prove useful as putative biomarkers. We used an iTRAQ-based quantitative proteomic approach to identify proteins that show altered levels in the sera of patients with gastric cancer. Our study resulted in identification of 643 proteins, of which 48 proteins showed increased levels and 11 proteins showed decreased levels in serum from gastric cancer patients compared to age and sex matched healthy controls. Proteins that showed increased expression in gastric cancer included inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), Mannose-binding protein C (MBL2), sex hormone-binding globulin (SHBG), insulin-like growth factor-binding protein 2 (IGFBP2), serum amyloid A protein (SAA1), Orosomucoid 1 (ORM1) and extracellular superoxide dismutase [Cu-Zn] (SOD3). We used multiple reaction monitoring assays and validated elevated levels of ITIH4 and SAA1 proteins in serum from gastric cancer patients. BIOLOGICAL SIGNIFICANCE Gastric cancer is a highly aggressive cancer associated with high mortality. Serum-based biomarkers are of considerable interest in diagnosis and monitoring of various diseases including cancers. Gastric cancer is often diagnosed at advanced stages resulting in poor prognosis and high mortality. Pathological diagnosis using biopsy specimens remains the gold standard for diagnosis of gastric cancer. Serum-based biomarkers are of considerable importance as they are minimally invasive. In this study, we carried out quantitative proteomic profiling of serum from gastric cancer patients to identify proteins that show altered levels in gastric cancer patients. We identified more than 50 proteins that showed altered levels in gastric cancer patient sera. Validation in a large cohort of well classified patient samples would prove useful in identifying novel blood based biomarkers for gastric cancers. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore 560041, Karnataka, India; Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka, India
| | - Sartaj Ahmad Mir
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Manipal 576 104, Karnataka, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Srikanth S Manda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Manipal 576 104, Karnataka, India
| | | | | | - H C Manju
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Rakesh Sharma
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore 560029, Karnataka, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bangalore 560029, Karnataka, India
| | - M Vijayakumar
- Department of Surgery, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka, India
| | - K V Veerendra Kumar
- Department of Surgery, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Girija Ramaswamy
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka, India
| | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
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