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Wierzbicka A, Semik-Gurgul E, Świątkiewicz M, Szmatoła T, Steg A, Oczkowicz M. Changes in DNA Methylation and mRNA Expression in Lung Tissue after Long-Term Supplementation with an Increased Dose of Cholecalciferol. Int J Mol Sci 2023; 25:464. [PMID: 38203636 PMCID: PMC10778667 DOI: 10.3390/ijms25010464] [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: 12/08/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Maintaining an appropriate concentration of vitamin D is essential for the proper functioning of the body, regardless of age. Nowadays, there are more and more indications that vitamin D supplementation at higher than standard doses may show protective and therapeutic effects. Our study identified differences in the body's response to long-term supplementation with cholecalciferol at an increased dose. Two groups of pigs were used in the experiment. The first group received a standard dose of cholecalciferol (grower, 2000 IU/kg feed, and finisher, 1500 IU/kg feed), and the second group received an increased dose (grower, 3000 IU/kg feed, and finisher, 2500 IU/kg feed). After slaughter, lung samples were collected and used for RRBS and mRNA sequencing. Analysis of the methylation results showed that 2349 CpG sites had significantly altered methylation patterns and 1116 (47.51%) identified DMSs (Differentially Methylated Sites) were related to genes and their regulatory sites. The mRNA sequencing results showed a significant change in the expression of 195 genes. The integrated analysis identified eleven genes with DNA methylation and mRNA expression differences between the analyzed groups. The results of this study suggested that an increased vitamin D intake may be helpful for the prevention of lung cancer and pulmonary fibrosis. These actions may stem from the influence of vitamin D on the expression of genes associated with collagen production, such as SHMT1, UGT1A6, and ITIH2.The anti-cancer properties of vitamin D are also supported by changes in KLHL3 and TTPA gene expression.
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Affiliation(s)
- Alicja Wierzbicka
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland; (A.W.); (E.S.-G.); (T.S.); (A.S.)
| | - Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland; (A.W.); (E.S.-G.); (T.S.); (A.S.)
| | - Małgorzata Świątkiewicz
- Department of Animal Nutrition and Feed Science, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland;
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland; (A.W.); (E.S.-G.); (T.S.); (A.S.)
- Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248 Kraków, Poland
| | - Anna Steg
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland; (A.W.); (E.S.-G.); (T.S.); (A.S.)
| | - Maria Oczkowicz
- Department of Animal Molecular Biology, National Research Institute of Animal Production, ul. Krakowska 1, 32-083 Balice, Poland; (A.W.); (E.S.-G.); (T.S.); (A.S.)
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Feng Q, Xia W, Wang S, Dai G, Jiao W, Guo N, Li H, Zhang G. Etodolac improves collagen induced rheumatoid arthritis in rats by inhibiting synovial inflammation, fibrosis and hyperplasia. MOLECULAR BIOMEDICINE 2021; 2:33. [PMID: 35006449 PMCID: PMC8607370 DOI: 10.1186/s43556-021-00052-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Synovial hyperplasia is the main cause of chronic rheumatoid arthritis (RA), but the mechanism of synovial hyperplasia is still unclear. Etodolac (ETD) is a selective COX-2 inhibitor for relieving pain and stiffness in RA, but the disease modifying effect is still lack of evidence. Proteomics method was used to study the differential proteome of synovial tissue in collagen induced arthritis (CIA) in rats. With the help of STRING analysis, the upregulated proteins enriched in the cluster of complement and coagulation cascades and platelet degranulation were highlighted, these proteins with fibrogenic factors Lum, CIV, CXI and Tgfbi participated in the synovial inflammation, fibrosis and hyperplasia in CIA. Based on KOG function class analysis, the proteins involved in the events of the central dogma was explored. They might be hyperplasia related proteins for most of them are related to the proliferation of cancer. ETD significantly attenuated synovial inflammation, fibrosis and hyperplasia in CIA rats by downregulating these proteins. Several proteins have not been observed in RA so far, such as Tmsb4x, Pura, Nfic, Ruvbl1, Snrpd3, U2af2, Srrm2, Srsf7, Elavl1, Hnrnph1, Wars, Yars, Bzw2, Mcts1, Eif4b, Ctsh, Lamp1, Dpp7, Ptges3, Cdc37 and Septin9, they might be potentials targets for RA. Blood biochemistry tests showed the safety of 7 months use of ETD on rats. In conclusion, present study displayed a comprehensive mechanism of synovial hyperplasia in CIA rats, on this basis, the clinical value of ETD in the treatment of RA was well confirmed.
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Affiliation(s)
- Qin Feng
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Wenkai Xia
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Shenglan Wang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guoxin Dai
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Weimei Jiao
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Na Guo
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Honghua Li
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guimin Zhang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China. .,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China. .,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.
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Nguon LS, Seo K, Lim JH, Song TJ, Cho SH, Park JS, Park S. Deep Learning-Based Differentiation between Mucinous Cystic Neoplasm and Serous Cystic Neoplasm in the Pancreas Using Endoscopic Ultrasonography. Diagnostics (Basel) 2021; 11:diagnostics11061052. [PMID: 34201066 PMCID: PMC8229855 DOI: 10.3390/diagnostics11061052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 12/12/2022] Open
Abstract
Mucinous cystic neoplasms (MCN) and serous cystic neoplasms (SCN) account for a large portion of solitary pancreatic cystic neoplasms (PCN). In this study we implemented a convolutional neural network (CNN) model using ResNet50 to differentiate between MCN and SCN. The training data were collected retrospectively from 59 MCN and 49 SCN patients from two different hospitals. Data augmentation was used to enhance the size and quality of training datasets. Fine-tuning training approaches were utilized by adopting the pre-trained model from transfer learning while training selected layers. Testing of the network was conducted by varying the endoscopic ultrasonography (EUS) image sizes and positions to evaluate the network performance for differentiation. The proposed network model achieved up to 82.75% accuracy and a 0.88 (95% CI: 0.817–0.930) area under curve (AUC) score. The performance of the implemented deep learning networks in decision-making using only EUS images is comparable to that of traditional manual decision-making using EUS images along with supporting clinical information. Gradient-weighted class activation mapping (Grad-CAM) confirmed that the network model learned the features from the cyst region accurately. This study proves the feasibility of diagnosing MCN and SCN using a deep learning network model. Further improvement using more datasets is needed.
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Affiliation(s)
- Leang Sim Nguon
- School of Electrical and Electronics Engineering, Chung-Ang University, Seoul 06974, Korea; (L.S.N.); (K.S.)
| | - Kangwon Seo
- School of Electrical and Electronics Engineering, Chung-Ang University, Seoul 06974, Korea; (L.S.N.); (K.S.)
| | - Jung-Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Inha University School of Medicine, Incheon 22332, Korea;
| | - Tae-Jun Song
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.-J.S.); (S.-H.C.)
| | - Sung-Hyun Cho
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.-J.S.); (S.-H.C.)
| | - Jin-Seok Park
- Division of Gastroenterology, Department of Internal Medicine, Inha University School of Medicine, Incheon 22332, Korea;
- Correspondence: (J.-S.P.); (S.P.)
| | - Suhyun Park
- Department of Electronic and Electrical Engineering, Ewha Womans University, Seoul 03760, Korea
- Correspondence: (J.-S.P.); (S.P.)
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Yang KS, Ciprani D, O'Shea A, Liss AS, Yang R, Fletcher-Mercaldo S, Mino-Kenudson M, Fernández-Del Castillo C, Weissleder R. Extracellular Vesicle Analysis Allows for Identification of Invasive IPMN. Gastroenterology 2021; 160:1345-1358.e11. [PMID: 33301777 PMCID: PMC7956058 DOI: 10.1053/j.gastro.2020.11.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/21/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Advances in cross-sectional imaging have resulted in increased detection of intraductal papillary mucinous neoplasms (IPMNs), and their management remains controversial. At present, there is no reliable noninvasive method to distinguish between indolent and high risk IPMNs. We performed extracellular vesicle (EV) analysis to identify markers of malignancy in an attempt to better stratify these lesions. METHODS Using a novel ultrasensitive digital extracellular vesicle screening technique (DEST), we measured putative biomarkers of malignancy (MUC1, MUC2, MUC4, MUC5AC, MUC6, Das-1, STMN1, TSP1, TSP2, EGFR, EpCAM, GPC1, WNT-2, EphA2, S100A4, PSCA, MUC13, ZEB1, PLEC1, HOOK1, PTPN6, and FBN1) in EV from patient-derived cell lines and then on circulating EV obtained from peripheral blood drawn from patients with IPMNs. We enrolled a total of 133 patients in two separate cohorts: a clinical discovery cohort (n = 86) and a validation cohort (n = 47). RESULTS From 16 validated EV proteins in plasma samples collected from the discovery cohort, only MUC5AC showed significantly higher levels in high-grade lesions. Of the 11 patients with invasive IPMN (inv/HG), 9 had high MUC5AC expression in plasma EV of the 11 patients with high-grade dysplasia alone, only 1 had high MUC5AC expression (sensitivity of 82%, specificity of 100%). These findings were corroborated in a separate validation cohort. The addition of MUC5AC as a biomarker to imaging and high-riskstigmata allowed detection of all cases requiring surgery, whereas imaging and high-risk stigmata alone would have missed 5 of 14 cases (36%). CONCLUSIONS MUC5AC in circulating EV can predict the presence of invasive carcinoma within IPMN. This approach has the potential to improve the management and follow-up of patients with IPMN including avoiding unnecessary surgery.
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Affiliation(s)
- Katherine S Yang
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Aileen O'Shea
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Robert Yang
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.
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