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Kalyoncu S, Yilmaz S, Kuyucu AZ, Sayili D, Mert O, Soyturk H, Gullu S, Akinturk H, Citak E, Arslan M, Taskinarda MG, Tarman IO, Altun GY, Ozer C, Orkut R, Demirtas A, Tilmensagir I, Keles U, Ulker C, Aralan G, Mercan Y, Ozkan M, Caglar HO, Arik G, Ucar MC, Yildirim M, Yildirim TC, Karadag D, Bal E, Erdogan A, Senturk S, Uzar S, Enul H, Adiay C, Sarac F, Ekiz AT, Abaci I, Aksoy O, Polat HU, Tekin S, Dimitrov S, Ozkul A, Wingender G, Gursel I, Ozturk M, Inan M. Process development for an effective COVID-19 vaccine candidate harboring recombinant SARS-CoV-2 delta plus receptor binding domain produced by Pichia pastoris. Sci Rep 2023; 13:5224. [PMID: 36997624 PMCID: PMC10062263 DOI: 10.1038/s41598-023-32021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Recombinant protein-based SARS-CoV-2 vaccines are needed to fill the vaccine equity gap. Because protein-subunit based vaccines are easier and cheaper to produce and do not require special storage/transportation conditions, they are suitable for low-/middle-income countries. Here, we report our vaccine development studies with the receptor binding domain of the SARS-CoV-2 Delta Plus strain (RBD-DP) which caused increased hospitalizations compared to other variants. First, we expressed RBD-DP in the Pichia pastoris yeast system and upscaled it to a 5-L fermenter for production. After three-step purification, we obtained RBD-DP with > 95% purity from a protein yield of > 1 g/L of supernatant. Several biophysical and biochemical characterizations were performed to confirm its identity, stability, and functionality. Then, it was formulated in different contents with Alum and CpG for mice immunization. After three doses of immunization, IgG titers from sera reached to > 106 and most importantly it showed high T-cell responses which are required for an effective vaccine to prevent severe COVID-19 disease. A live neutralization test was performed with both the Wuhan strain (B.1.1.7) and Delta strain (B.1.617.2) and it showed high neutralization antibody content for both strains. A challenge study with SARS-CoV-2 infected K18-hACE2 transgenic mice showed good immunoprotective activity with no viruses in the lungs and no lung inflammation for all immunized mice.
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Affiliation(s)
| | - Semiramis Yilmaz
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | | | - Dogu Sayili
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Olcay Mert
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | - Seyda Gullu
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | - Erhan Citak
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | | | - Ceren Ozer
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ridvan Orkut
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | | | - Umur Keles
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Lund University, Lund, Sweden
| | - Ceren Ulker
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Gizem Aralan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Yavuz Mercan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Muge Ozkan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Hasan Onur Caglar
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Erzurum Technical University, Erzurum, Turkey
| | - Gizem Arik
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Ankara Medipol University, Ankara, Turkey
| | - Mehmet Can Ucar
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Imperial College London, London, UK
| | | | | | | | - Erhan Bal
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir Tinaztepe University, Izmir, Turkey
| | - Aybike Erdogan
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Serdar Uzar
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Hakan Enul
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Cumhur Adiay
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | - Fahriye Sarac
- Pendik Veterinary Research and Control Institute, Istanbul, Turkey
| | | | - Irem Abaci
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
| | - Ozge Aksoy
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
| | | | - Saban Tekin
- Marmara Research Center, TUBITAK, Kocaeli, Turkey
- University of Health Sciences, Istanbul, Turkey
| | | | | | | | - Ihsan Gursel
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir Tinaztepe University, Izmir, Turkey
| | - Mehmet Inan
- Izmir Biomedicine and Genome Center, Izmir, Turkey.
- Akdeniz University, Antalya, Turkey.
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Keles U, Ow JR, Kuentzel KB, Zhao LN, Kaldis P. Liver-derived metabolites as signaling molecules in fatty liver disease. Cell Mol Life Sci 2022; 80:4. [PMID: 36477411 PMCID: PMC9729146 DOI: 10.1007/s00018-022-04658-8] [Citation(s) in RCA: 6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Abstract
Excessive fat accumulation in the liver has become a major health threat worldwide. Unresolved fat deposition in the liver can go undetected until it develops into fatty liver disease, followed by steatohepatitis, fibrosis, cirrhosis, and eventually hepatocellular carcinoma. Lipid deposition in the liver is governed by complex communication, primarily between metabolic organs. This can be mediated by hormones, organokines, and also, as has been more recently discovered, metabolites. Although how metabolites from peripheral organs affect the liver is well documented, the effect of metabolic players released from the liver during the development of fatty liver disease or associated comorbidities needs further attention. Here we focus on interorgan crosstalk based on metabolites released from the liver and how these molecules act as signaling molecules in peripheral tissues. Due to the liver's specific role, we are covering lipid and bile mechanism-derived metabolites. We also discuss the high sucrose intake associated with uric acid release from the liver. Excessive fat deposition in the liver during fatty liver disease development reflects disrupted metabolic processes. As a response, the liver secretes a variety of signaling molecules as well as metabolites which act as a footprint of the metabolic disruption. In the coming years, the reciprocal exchange of metabolites between the liver and other metabolic organs will gain further importance and will help to better understand the development of fatty liver disease and associated diseases.
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Affiliation(s)
- Umur Keles
- Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden
| | - Jin Rong Ow
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Katharina Barbara Kuentzel
- Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden
| | - Li Na Zhao
- Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden
| | - Philipp Kaldis
- Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden. .,Lund University Diabetes Centre (LUDC), Clinical Research Centre (CRC), Lund University, Box 50332, 202 13, Malmö, Sweden.
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3
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Iscan E, Ekin U, Yildiz G, Oz O, Keles U, Suner A, Cakan-Akdogan G, Ozhan G, Nekulova M, Vojtesek B, Uzuner H, Karakülah G, Alotaibi H, Ozturk M. TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation. Cancers (Basel) 2021; 13:cancers13040783. [PMID: 33668566 PMCID: PMC7918882 DOI: 10.3390/cancers13040783] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/12/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is a highly complex and heterogeneous type of cancer. Hepatocyte dedifferentiation is one of the important steps in the development of HCC. However, its molecular mechanisms are not well known. In this study, we report that transcriptionally active TAp73 isoforms are overexpressed in HCC. We also show that TAp73β suppresses the expression of the hepatocyte markers including CYP3A4, AFP, ALB, HNF4α, while increasing the expression of several cholangiocyte markers in HCC cell lines. In conclusion, this report reveals a pro-oncogenic role for TAp73β in liver cancer. Abstract Hepatocyte dedifferentiation is a major source of hepatocellular carcinoma (HCC), but its mechanisms are unknown. We explored the p73 expression in HCC tumors and studied the effects of transcriptionally active p73β (TAp73β) in HCC cells. Expression profiles of p73 and patient clinical data were collected from the Genomic Data Commons (GDC) data portal and the TSVdb database, respectively. Global gene expression profiles were determined by pan-genomic 54K microarrays. The Gene Set Enrichment Analysis method was used to identify TAp73β-regulated gene sets. The effects of TAp73 isoforms were analyzed in monolayer cell culture, 3D-cell culture and xenograft models in zebrafish using western blot, flow cytometry, fluorescence imaging, real-time polymerase chain reaction (RT-PCR), immunohistochemistry and morphological examination. TAp73 isoforms were significantly upregulated in HCC, and high p73 expression correlated with poor patient survival. The induced expression of TAp73β caused landscape expression changes in genes involved in growth signaling, cell cycle, stress response, immunity, metabolism and development. Hep3B cells overexpressing TAp73β had lost hepatocyte lineage biomarkers including ALB, CYP3A4, AFP, HNF4α. In contrast, TAp73β upregulated genes promoting cholangiocyte lineage such as YAP, JAG1 and ZO-1, accompanied with an increase in metastatic ability. Our findings suggest that TAp73β may promote malignant dedifferentiation of HCC cells.
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Affiliation(s)
- Evin Iscan
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Umut Ekin
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Gokhan Yildiz
- Department of Medical Biology, Faculty of Medicine, Karadeniz Technical University, Trabzon 61000, Turkey;
| | - Ozden Oz
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
- Izmir Bozyaka Education and Research Hospital, University of Health Sciences, Izmir 35000, Turkey
| | - Umur Keles
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Aslı Suner
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir 35000, Turkey;
| | - Gulcin Cakan-Akdogan
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Izmir 35000, Turkey
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Marta Nekulova
- RECAMO, Masaryk Memorial Cancer Institute, 60200 Brno, Czech Republic; (M.N.); (B.V.)
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, 60200 Brno, Czech Republic; (M.N.); (B.V.)
| | - Hamdiye Uzuner
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35000, Turkey
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Izmir 35000, Turkey; (E.I.); (U.E.); (O.O.); (U.K.); (G.C.-A.); (G.O.); (H.U.); (G.K.); (H.A.)
- Correspondence:
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4
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Keles U, Iscan E, Yilmaz HE, Karakülah G, Suner A, Bal E, Tasdemir N, Cavga AD, Ekin U, Mutlu Z, Kahyaoglu S, Serdar MA, Atabey N, Ozturk M. Differential expression of full-length and NH 2 terminally truncated FAM134B isoforms in normal physiology and cancer. Am J Physiol Gastrointest Liver Physiol 2020; 319:G733-G747. [PMID: 33052704 PMCID: PMC7864244 DOI: 10.1152/ajpgi.00094.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Selective autophagy of the endoplasmic reticulum (ER), namely ER-phagy, is mediated by ER-localized receptors, which are recognized and sequestered by GABARAP/LC3B-decorated phagophores and transferred to lysosomes for degradation. Being one such receptor, FAM134B plays critical roles in cellular processes such as protein quality control and neuronal survival. FAM134B has also been associated with different cancers, although its exact role remains elusive. We report here that the FAM134B gene encodes not one but at least two different protein isoforms: the full-length and the NH2 terminally truncated forms. Their relative expression shows extreme variation, both within normal tissues and among cancer types. Expression of full-length FAM134B is restricted to the brain, testis, spleen, and prostate. In contrast, NH2 terminally truncated FAM134B is dominant in the heart, skeletal muscle, kidney, pancreas, and liver. We compared wild-type and knockout mice to study the role of the Fam134b gene in starvation. NH2 terminally truncated FAM134B-2 was induced in the liver, skeletal muscle, and heart but not in the pancreas and stomach following starvation. Upon starvation, Fam134b-/- mice differed from wild-type mice by less weight loss and less hyperaminoacidemic and hypocalcemic response but increased levels of serum albumin, total serum proteins, and α-amylase. Interestingly, either NH2 terminally truncated FAM134B or both isoforms were downregulated in liver, lung, and colon cancers. In contrast, upregulation was observed in stomach and chromophobe kidney cancers.NEW & NOTEWORTHY We reported tissues expressing FAM134B-2 such as the kidney, muscle, heart, and pancreas, some of which exhibit stimulated expression upon nutrient starvation. We also demonstrated the effect of Fam134b deletion during ad libitum and starvation conditions. Resistance to weight loss and hypocalcemia, accompanied by an increase in serum albumin and α-amylase levels, indicate critical roles of Fam134b in physiology. Furthermore, the differential expression of FAM134B isoforms was shown to be significantly dysregulated in human cancers.
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Affiliation(s)
- Umur Keles
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey,2Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Evin Iscan
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey,2Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Huriye Erbak Yilmaz
- 2Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Gökhan Karakülah
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey,2Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Aslı Suner
- 3Department of Biostatistics and Medical Informatics, Ege University, Izmir, Turkey
| | - Erhan Bal
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Nilgun Tasdemir
- 4Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ayse Derya Cavga
- 4Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Umut Ekin
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey,2Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Zeynep Mutlu
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey
| | | | | | - Nese Atabey
- 1Izmir Biomedicine and Genome Center, Izmir, Turkey
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