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Wang G, Li P, Su SW, Xu R, Huang ZY, Yang TX, Li JM. Identification of key pathways and mRNAs in interstitial cystitis/bladder pain syndrome treatment with quercetin through bioinformatics analysis of mRNA-sequence data. Aging (Albany NY) 2024; 16:5949-5966. [PMID: 38526326 PMCID: PMC11042929 DOI: 10.18632/aging.205682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic condition with painful bladder. At present, the pathogenesis of IC/BPS is still unknown. Quercetin (QCT) is a kind of natural flavonoid with wide sources and multiple biological activities. The purpose of this study was to explore the effects of QCT on mRNA expression and related regulatory signal pathways in IC model rats. METHODS LL-37 was used to induce the IC/BPS model rats. 20 mg/kg QCT was injected intraperitoneally into IC/BPS rats. ELISA, HE, Masson and TB staining were used to evaluate the level of inflammation and pathology. The concentration of QCT in rats was detected by HPLC. The mRNA sequencing was used to detect the differentially expressed (DE) mRNA in each group. The over-expression experiment of Lpl was carried out in IC/BPS model rats. RESULTS QCT treatment significantly decreased the level of MPO, IL-1β, IL-6 and TNF-α induced by LL-37 in rats, and alleviated bladder injury and mast cell degranulation. There were significant differences in mRNA sequencing data between groups, and the hub gene Lpl were screened by Cytohubba. The expression of Lpl was downregulated in IC/BPS rats. QCT intervention promoted Lpl expression. Overexpression of Lpl reduced the bladder injury induced by LL-37, increased GAG level and decreased the expression of MPO, IL-1β, IL-6 and TNF-α. CONCLUSION In this study, we provided the DE mRNA in IC/BPS rats treated with QCT, the signaling pathways for DE enrichment, screened out the hub genes, and revealed that Lpl overexpression alleviated IC/BPS model rats.
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Affiliation(s)
- Guang Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Pei Li
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Si-Wei Su
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Rui Xu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Zi-Ye Huang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Tong-Xin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Jiong-Ming Li
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
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Kim YA, Mousavi K, Yazdi A, Zwierzyna M, Cardinali M, Fox D, Peel T, Coller J, Aggarwal K, Maruggi G. Computational design of mRNA vaccines. Vaccine 2024; 42:1831-1840. [PMID: 37479613 DOI: 10.1016/j.vaccine.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
mRNA technology has emerged as a successful vaccine platform that offered a swift response to the COVID-19 pandemic. Accumulating evidence shows that vaccine efficacy, thermostability, and other important properties, are largely impacted by intrinsic properties of the mRNA molecule, such as RNA sequence and structure, both of which can be optimized. Designing mRNA sequence for vaccines presents a combinatorial problem due to an extremely large selection space. For instance, due to the degeneracy of the genetic code, there are over 10632 possible mRNA sequences that could encode the spike protein, the COVID-19 vaccines' target. Moreover, designing different elements of the mRNA sequence simultaneously against multiple objectives such as translational efficiency, reduced reactogenicity, and improved stability requires an efficient and sophisticated optimization strategy. Recently, there has been a growing interest in utilizing computational tools to redesign mRNA sequences to improve vaccine characteristics and expedite discovery timelines. In this review, we explore important biophysical features of mRNA to be considered for vaccine design and discuss how computational approaches can be applied to rapidly design mRNA sequences with desirable characteristics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeff Coller
- Johns Hopkins University, Baltimore, MD, USA
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Tang Y, Wang Y, Wang S, Wang R, Xu J, Peng Y, Ding L, Zhao J, Zhou G, Sun S, Zhang Z. Methylation and transcriptomic expression profiles of HUVEC in the oxygen and glucose deprivation model and its clinical implications in AMI patients. Front Genet 2023; 14:1293393. [PMID: 38145212 PMCID: PMC10740152 DOI: 10.3389/fgene.2023.1293393] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/13/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
The obstructed coronary artery undergoes a series of pathological changes due to ischemic-hypoxic shocks during acute myocardial infarction (AMI). However, the altered DNA methylation levels in endothelial cells under these conditions and their implication for the etiopathology of AMI have not been investigated in detail. This study aimed to explore the relationship between DNA methylation and pathologically altered gene expression profile in human umbilical vein endothelial cells (HUVECs) subjected to oxygen-glucose deprivation (OGD), and its clinical implications in AMI patients. The Illumina Infinium MethylationEPIC BeadChip assay was used to explore the genome-wide DNA methylation profile using the Novaseq6000 platform for mRNA sequencing in 3 pairs of HUVEC-OGD and control samples. GO and KEGG pathway enrichment analyses, as well as correlation, causal inference test (CIT), and protein-protein interaction (PPI) analyses identified 22 hub genes that were validated by MethylTarget sequencing as well as qRT-PCR. ELISA was used to detect four target molecules associated with the progression of AMI. A total of 2,524 differentially expressed genes (DEGs) and 22,148 differentially methylated positions (DMPs) corresponding to 6,642 differentially methylated genes (DMGs) were screened (|Δβ|>0.1 and detection p < 0.05). After GO, KEGG, correlation, CIT, and PPI analyses, 441 genes were filtered. qRT-PCR confirmed the overexpression of VEGFA, CCL2, TSP-1, SQSTM1, BCL2L11, and TIMP3 genes, and downregulation of MYC, CD44, BDNF, GNAQ, RUNX1, ETS1, NGFR, MME, SEMA6A, GNAI1, IFIT1, and MEIS1. DNA fragments BDNF_1_ (r = 0.931, p < 0.0001) and SQSTM1_2_NEW (r = 0.758, p = 0.0043) were positively correlated with the expressions of corresponding genes, and MYC_1_ (r = -0.8245, p = 0.001) was negatively correlated. Furthermore, ELISA confirmed TNFSF10 and BDNF were elevated in the peripheral blood of AMI patients (p = 0.0284 and p = 0.0142, respectively). Combined sequencing from in vitro cellular assays with clinical samples, aiming to establish the potential causal chain of the causal factor (DNA methylation) - mediator (mRNA)-cell outcome (endothelial cell ischemic-hypoxic injury)-clinical outcome (AMI), our study identified promising OGD-specific genes, which provided a solid basis for screening fundamental diagnostic and prognostic biomarkers of coronary endothelial cell injury of AMI. Moreover, it furnished the first evidence that during ischemia and hypoxia, the expression of BNDF was regulated by DNA methylation in endothelial cells and elevated in peripheral blood.
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Affiliation(s)
- Yuning Tang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yongxiang Wang
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Shengxiang Wang
- School of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Runqing Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Jin Xu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yu Peng
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Liqiong Ding
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jing Zhao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Gang Zhou
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Shougang Sun
- Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zheng Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China
- Cardiovascular Clinical Research Center of Gansu Province, Lanzhou, China
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China
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Li J, Chen Q, Shi D, Lian X. Combined time-restricted feeding and cisplatin enhance the anti-tumor effects in cisplatin-resistant and -sensitive lung cancer cells. Med Oncol 2022; 40:63. [PMID: 36576605 DOI: 10.1007/s12032-022-01923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
Combination therapy as an important treatment option for lung cancer has been attracting attention due to the primary and acquired resistance of chemotherapeutic drugs in the clinical application. In the present study, as a new therapy strategy, concomitant treatment with time-restricted feeding (TRF) plus cisplatin (DDP) on lung cancer growth was investigated in DDP-resistant and DDP-sensitive lung cancer cells. We first found that TRF significantly enhanced the drug susceptibility of DDP in DDP-resistant A549 (A549/DDP) cell line, illustrated by reversing the inhibitory concentration 50 (IC50) values of A549/DDP cells to normal level of parental A549 cells. We also found that TRF markedly enhanced DDP inhibition on cell proliferation, migration, as well as promoted apoptosis compared to the DDP alone group in A549, H460 and A549/DDP cells lines. We further revealed that the synergistic anti-tumor effect of combined DDP and TRF was greater than that of combined DDP and simulated fasting condition (STS), a known anti-tumor cellular medium. Moreover, mRNA sequence analysis from A549/DDP cell line demonstrated the synergistic anti-tumor effect involved in upregulated pathways in p53 signaling pathway and apoptosis. Notably, compared with the DDP alone group, combination of TRF and DDP robustly upregulated the P53 protein expression without mRNA level change by regulating its stability via promoting protein synthesis and inhibiting degradation, revealed by cycloheximide and MG132 experiments. Collectively, our results suggested that TRF in combination with cisplatin might be an additional novel therapeutic strategy for patients with lung cancer.
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Ahn JC, Mathiyalagan R, Nahar J, Ramadhania ZM, Kong BM, Lee DW, Choi SK, Lee CS, Boopathi V, Yang DU, Kim BY, Park H, Yang DC, Kang SC. Transcriptome expression profile of compound-K-enriched red ginseng extract (DDK-401) in Korean volunteers and its apoptotic properties. Front Pharmacol 2022; 13:999192. [PMID: 36532751 PMCID: PMC9751427 DOI: 10.3389/fphar.2022.999192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2023] Open
Abstract
Ginseng and ginsenosides have been reported to have various pharmacological effects, but their efficacies depend on intestinal absorption. Compound K (CK) is gaining prominence for its biological and pharmaceutical properties. In this study, CK-enriched fermented red ginseng extract (DDK-401) was prepared by enzymatic reactions. To examine its pharmacokinetics, a randomized, single-dose, two-sequence, crossover study was performed with eleven healthy Korean male and female volunteers. The volunteers were assigned to take a single oral dose of one of two extracts, DDK-401 or common red ginseng extract (DDK-204), during the initial period. After a 7-day washout, they received the other extract. The pharmacokinetics of DDK-401 showed that its maximum plasma concentration (Cmax) occurred at 184.8 ± 39.64 ng/mL, Tmax was at 2.4 h, and AUC0-12h was 920.3 ± 194.70 ng h/mL, which were all better than those of DDK-204. The maximum CK absorption in the female volunteers was higher than that in the male volunteers. The differentially expressed genes from the male and female groups were subjected to a KEGG pathway analysis, which showed results in the cell death pathway, such as apoptosis and necroptosis. In cytotoxicity tests, DDK-401 and DDK-204 were not particularly toxic to normal (HaCaT) cells, but at a concentration of 250 μg/mL, DDK-401 had a much higher toxicity to human lung cancer (A549) cells than DDK-204. DDK-401 also showed a stronger antioxidant capacity than DDK-204 in both the DPPH and potassium ferricyanide reducing power assays. DDK-401 reduced the reactive oxygen species production in HaCaT cells with induced oxidative stress and led to apoptosis in the A549 cells. In the mRNA sequence analysis, a signaling pathway with selected marker genes was assessed by RT-PCR. In the HaCaT cells, DDK-401 and DDK-204 did not regulate FOXO3, TLR4, MMP-9, or p38 expression; however, in the A549 cells, DDK-401 downregulated the expressions of MMP9 and TLR4 as well as upregulated the expressions of the p38 and caspase-8 genes compared to DDK-204. These results suggest that DDK-401 could act as a molecular switch for these two cellular processes in response to cell damage signaling and that it could be a potential candidate for further evaluations in health promotion studies.
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Affiliation(s)
- Jong Chan Ahn
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Jinnatun Nahar
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Zelika Mega Ramadhania
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Byoung Man Kong
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, South Korea
| | | | - Sung Keun Choi
- Daedong Korea Ginseng Co., Ltd., Geumsan-gun, South Korea
| | - Chang Soon Lee
- Daedong Korea Ginseng Co., Ltd., Geumsan-gun, South Korea
| | - Vinothini Boopathi
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | | | - Bo Yeon Kim
- Exercise Nutrition & Biochemistry Lab, Kyung Hee University, Yongin-si, South Korea
| | - Hyon Park
- Exercise Nutrition & Biochemistry Lab, Kyung Hee University, Yongin-si, South Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, South Korea
| | - Se Chan Kang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
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Figueroa AC, Díaz MS, Alasino RV, Yang P, Soria NW, Beltramo DM. Expression and localization of tubulin isotypes and its mRNAs during Thecaphora frezii developments. FEMS Microbiol Ecol 2022; 98:6753202. [PMID: 36208160 DOI: 10.1093/femsec/fiac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/16/2022] [Revised: 07/13/2022] [Accepted: 10/05/2022] [Indexed: 01/21/2023] Open
Abstract
Thecaphora frezii is a phytopathogenic fungus that infects Arachys hypogaea L. and produces peanut smut. It has three ontological stages teliospores, basidiospores, and hyphae. Microtubules are cellular structures that participate in various important cellular processes. In this work, we analyzed the presence and location of α-tubulin isotypes and enzymes that participate in tyrosination-detyrosination in the three stages of T. frezii. Although both tyrosinated and detyrosinated tubulin seem to be associated with a membrane fraction component that gives it a similar behavior to integral proteins, in the soluble cytosolic fraction, only detyrosinated tubulin was detected, not tyrosinated tubulin. The presence of α-tubulin was not detected using the monoclonal antibody DM1A as neither acetylated tubulin. The RNA-Seq analysis showed the presence of α, β, and γ-tubulins and the genes that codes for tyrosine-tubulin ligase and cytosolic carboxypeptidase 1, enzymes that are involved in post-translational modification processes. These sequences showed a high percentage of identity and homology with Ustilago maydis, Thecaphora thlaspeos, and Anthracocystis flocculosa. This is the first report for tubulins subpopulations and the cellular distribution in T. frezii, which together with the data obtained by RNA-Seq contribute to the knowledge of the pathogen, which will allow the development of control strategies.
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Affiliation(s)
- Ana Cristina Figueroa
- Centro de Excelencia en Productos y Procesos de Córdoba - CEPROCOR- Complejo Hospitalario Santa María de Punilla X6154, Córdoba, Argentina
| | - María Soledad Díaz
- Centro de Excelencia en Productos y Procesos de Córdoba - CEPROCOR- Complejo Hospitalario Santa María de Punilla X6154, Córdoba, Argentina
| | - Roxana Valeria Alasino
- Centro de Excelencia en Productos y Procesos de Córdoba - CEPROCOR- Complejo Hospitalario Santa María de Punilla X6154, Córdoba, Argentina.,Consejo Nacional de Ciencia y Tecnología de Argentina, - CONICET, Argentina
| | - Pablo Yang
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Avenida Armada Argentina 3555, X5016DHK, Córdoba, Argentina
| | - Néstor Walter Soria
- Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Avenida Armada Argentina 3555, X5016DHK, Córdoba, Argentina
| | - Dante Miguel Beltramo
- Centro de Excelencia en Productos y Procesos de Córdoba - CEPROCOR- Complejo Hospitalario Santa María de Punilla X6154, Córdoba, Argentina.,Consejo Nacional de Ciencia y Tecnología de Argentina, - CONICET, Argentina.,Cátedra de Biotecnología, Facultad de Ciencias Químicas, Unidad Asociada al CONICET: Área de Cs. Agrarias, Ingeniería, Cs. Biológicas, Universidad Católica de Córdoba, Avenida Armada Argentina 3555, X5016DHK, Córdoba, Argentina
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Wu H, Liu Q, Meng C, Xia Q, Pan Y, Zhang H, Zhang F, Song W, Liu H. Web Crawling and mRNA Sequencing Analyze Mechanisms of Photobiomodulation. Photobiomodul Photomed Laser Surg 2022; 40:252-260. [PMID: 35452301 DOI: 10.1089/photob.2021.0142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Photobiomodulation (PBM) is praised as a promising physical therapy, which has many advantages, such as being noninvasive and painless. However, the mechanisms are not fully elucidated. Methods: Using web crawling, mRNA sequence, and bioinformatics analysis, we selected genes, functional annotation, and mechanisms. The expressions of inflammatory cytokines were measured using quantitative real-time PCR (RT-qPCR). Results: A total of 146 human genes and 57 pathways were identified about PBM. The 630 nm light-emitting diode (LED)-stimulated-MH7A cells were sequenced to further analyze the mechanism of PBM. Two thousand nine hundred fifty differentially expressed genes were identified, and the gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to better understand functions and pathways. The 12 pathways were matched with the KEGG results of PBM and MH7A cells. A protein-protein interaction network was performed among genes in 12 pathways, and 10 outstanding proteins were identified. Importantly, the 9 genes were predicted with potential research value. And we also demonstrated that expression of inflammatory factors [interleukin (IL)-6, IL-1β, IL-8, and matrix metalloproteinase-3 (MMP-3)] was reduced; meanwhile, the expression of anti-inflammatory factor IL-10 was promoted after 630 nm LED. Conclusions: Using web crawling, bioinformatics analysis, and mRNA sequence, we obtained 9 key genes and 12 important pathways about PBM. Importantly, we demonstrated the anti-inflammatory effect of 630 nm LED red light by RT-qPCR.
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Affiliation(s)
- Hao Wu
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Qiannan Liu
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Caiyun Meng
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Qing Xia
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Yue Pan
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Hanxu Zhang
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Fengmin Zhang
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Wuqi Song
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
| | - Hailiang Liu
- The Heilongjiang Key Laboratory of Immunity and Infection Harbin Medical University, Department of Microbiology, Wu Lien-Teh Institute, Harbin, P.R. China
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Li R, Li H, Feng X, Zhao R, Cheng Y. Study on the Influence of mRNA, the Genetic Language, on Protein Folding Rates. Front Genet 2021; 12:635250. [PMID: 33889178 PMCID: PMC8056030 DOI: 10.3389/fgene.2021.635250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/30/2020] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Many works have reported that protein folding rates are influenced by the characteristics of amino acid sequences and protein structures. However, few reports on the problem of whether the corresponding mRNA sequences are related to the protein folding rates can be found. An mRNA sequence is regarded as a kind of genetic language, and its vocabulary and phraseology must provide influential information regarding the protein folding rate. In the present work, linear regressions on the parameters of the vocabulary and phraseology of mRNA sequences and the corresponding protein folding rates were analyzed. The results indicated that D2 (the adjacent base-related information redundancy) values and the GC content values of the corresponding mRNA sequences exhibit significant negative relations with the protein folding rates, but D1 (the single base information redundancy) values exhibit significant positive relations with the protein folding rates. In addition, the results show that the relationships between the parameters of the genetic language and the corresponding protein folding rates are obviously different for different protein groups. Some useful parameters that are related to protein folding rates were found. The results indicate that when predicting protein folding rates, the information from protein structures and their amino acid sequences is insufficient, and some information for regulating the protein folding rates must be derived from the mRNA sequences.
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Affiliation(s)
- Ruifang Li
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot, China
| | - Hong Li
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| | - Xue Feng
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot, China
| | - Ruifeng Zhao
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot, China
| | - Yongxia Cheng
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot, China
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Li R, Li H, Yang S, Feng X. The Influences of Palindromes in mRNA on Protein Folding Rates. Protein Pept Lett 2020; 27:303-312. [PMID: 31612810 DOI: 10.2174/0929866526666191014144015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/13/2019] [Revised: 06/14/2019] [Accepted: 06/29/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND It is currently believed that protein folding rates are influenced by protein structure, environment and temperature, amino acid sequence and so on. We have been working for long to determine whether and in what ways mRNA affects the protein folding rate. A large number of palindromes aroused our attention in our previous research. Whether these palindromes do have important influences on protein folding rates and what's the mechanism? Very few related studies are focused on these problems. OBJECTIVE In this article, our motivation is to find out if palindromes have important influences on protein folding rates and what's the mechanism. METHODS In this article, the parameters of the palindromes were defined and calculated, the linear regression analysis between the values of each parameter and the experimental protein folding rates were done. Furthermore, to compare the results of different kinds of proteins, proteins were classified into the two-state proteins and the multi-state proteins. For the two kinds of proteins, the above linear regression analysis were performed respectively. RESULTS Protein folding rates were negatively correlated to the palindrome frequencies for all proteins. An extremely significant negative linear correlation appeared in the relationship between palindrome densities and protein folding rates. And the repeatedly used bases by different palindromes simultaneously have an important effect on the relationship between palindrome density and protein folding rate. CONCLUSION The palindromes have important influences on protein folding rates, and the repeatedly used bases in different palindromes simultaneously play a key role in influencing the protein folding rates.
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Affiliation(s)
- Ruifang Li
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot 010022, China
| | - Hong Li
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Sarula Yang
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xue Feng
- College of Physics and Electronic Information, Inner Mongolia Normal University, Hohhot 010022, China
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Hua C, Chen X, Yuan W, Li Y, Yu J, Li H, Ming L. Gene expression profiling by mRNA sequencing reveals dysregulation of core genes in Rictor deficient T-ALL mouse model. Leuk Res 2019; 87:106229. [PMID: 31698306 DOI: 10.1016/j.leukres.2019.106229] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/22/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a neoplastic disorder with peak incidence in children and young adults. The mTOR complex is an important component of the PI3K/Akt/mTOR signaling cascade and holds great promise for the treatment of hematopoietic malignancies. Previous studies have shown that the depression of Rictor, one of the components of the mTOR complex, prevents myeloproliferative disorders and leukemia However, knowledge of the progression of mTOR has not greatly improved the prognosis of T-ALL. To identify potential prognostic biomarkers for T-ALL, a whole-genome expression profile of Rictior deficient T-ALL mice was performed. As a result, 1475 differentially expressed genes (DEGs) were identified. Network analysis revealed 46 genes with a high network degree and fold-change value. Kaplan-Meier analysis identified ten crucial genes which significantly associated with survival in Rictor deficient T-ALL mice. These findings provide potential therapeutic targets in leukemia and bear immediate relevance to patients with leukemia.
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Affiliation(s)
- Chunlan Hua
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xiangyu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yang Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jing Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Haijun Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
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Han P, Xin H, Peng J, Hou J, Zhang L, Song Y, Li G, Cao B, An X. Identification and expression of X-linked inhibitor of apoptosis protein during follicular development in goat ovary. Theriogenology 2017; 98:30-35. [PMID: 28601152 DOI: 10.1016/j.theriogenology.2017.04.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/10/2016] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 11/28/2022]
Abstract
X-linked inhibitor of apoptosis protein (XIAP), an endogenous of inhibitor of caspases, plays crucial roles in regulating ovarian granulosa cell apoptosis during follicular atresia. The aim of the present study was to determine the presence and localization of XIAP in the goat ovary and its expression level during follicular development. The full length cDNA of XIAP from goat ovary cells was cloned using reverse transcription PCR. A total of 497 amino acid residues were encoded by open reading frame and had high identity with homologous sequences from other mammals. XIAP was widely expressed in adult goat tissues as determined by real-time PCR and it demonstrated higher expression in propagative organs. High level of XIAP was detected in large healthy follicles and corpus luteum in comparison with that in small antral follicles, which was in accordance with the immunohistochemistry results and atretic follicles had very low expression. XIAP was localized in both granulosa and theca cells in antral follicles but not in primordial follicles. Furthermore, luteinizing hormone stimulated the proliferation of mRNA encoding XIAP in granulosa cells in vitro. The present study demonstrated that XIAP was expressed in a follicular-stage-dependent manner in goat ovaries.
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Affiliation(s)
- Peng Han
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haiyun Xin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiayin Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinxing Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Soh KT, Tario JD, Colligan S, Maguire O, Pan D, Minderman H, Wallace PK. Simultaneous, Single-Cell Measurement of Messenger RNA, Cell Surface Proteins, and Intracellular Proteins. Curr Protoc Cytom 2016; 75:7.45.1-7.45.33. [PMID: 26742656 PMCID: PMC5556691 DOI: 10.1002/0471142956.cy0745s75] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleic acid content can be quantified by flow cytometry through the use of intercalating compounds; however, measuring the presence of specific sequences has hitherto been difficult to achieve by this methodology. The primary obstacle to detecting discrete nucleic acid sequences by flow cytometry is their low quantity and the presence of high background signals, rendering the detection of hybridized fluorescent probes challenging. Amplification of nucleic acid sequences by molecular techniques such as in situ PCR have been applied to single-cell suspensions, but these approaches have not been easily adapted to conventional flow cytometry. An alternative strategy implements a Branched DNA technique, comprising target-specific probes and sequentially hybridized amplification reagents, resulting in a theoretical 8,000- to 16,000-fold increase in fluorescence signal amplification. The Branched DNA technique allows for the quantification of native and unmanipulated mRNA content with increased signal detection and reduced background. This procedure utilizes gentle fixation steps with low hybridization temperatures, leaving the assayed cells intact to permit their concomitant immunophenotyping. This technology has the potential to advance scientific discovery by correlating potentially small quantities of mRNA with many biological measurements at the single-cell level.
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Affiliation(s)
- Kah Teong Soh
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Joseph D. Tario
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Sean Colligan
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Orla Maguire
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Dalin Pan
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Hans Minderman
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
| | - Paul K. Wallace
- Roswell Park Cancer Institute, Department of Flow and Image Cytometry, Elm & Carlton Street, Buffalo, New York 14263
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