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Rutkowska-Zapała M, Grabowska-Gurgul A, Lenart M, Szaflarska A, Kluczewska A, Mach-Tomalska M, Baj-Krzyworzeka M, Siedlar M. Gene Signature of Regulatory T Cells Isolated from Children with Selective IgA Deficiency and Common Variable Immunodeficiency. Cells 2024; 13:417. [PMID: 38474381 DOI: 10.3390/cells13050417] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Selective IgA deficiency (SIgAD) is the most common form and common variable immunodeficiency (CVID) is the most symptomatic form of predominant antibody deficiency. Despite differences in the clinical picture, a similar genetic background is suggested. A common feature of both disorders is the occurrence of autoimmune conditions. Regulatory T cells (Tregs) are the major immune cell type that maintains autoimmune tolerance. As the different types of abnormalities of Treg cells have been associated with autoimmune disorders in primary immunodeficiency (PID) patients, in our study we aimed to analyze the gene expression profiles of Treg cells in CVID and SIgAD patients compared to age-matched healthy controls. The transcriptome-wide gene profiling was performed by microarray technology. As a result, we analyzed and visualized gene expression patterns of isolated population of Treg cells. We showed the differences at the gene level between patients with and without autoimmunizations. Our findings suggest that the gene signatures of Treg cells isolated from SIgAD and CVID patients differ from age-matched healthy controls and from each other, presenting transcriptional profiles enriched in innate immune or Th response, respectively. The occurrence of autoimmunity in both types of PID is associated with down-regulation of class I IFNs signaling pathways. In summary, our findings improve our understanding of Treg dysfunctions in patients with common PIDs and associated autoimmunity.
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Affiliation(s)
- Magdalena Rutkowska-Zapała
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Agnieszka Grabowska-Gurgul
- Department of Medical Genetics, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Marzena Lenart
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Anna Szaflarska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Anna Kluczewska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Monika Mach-Tomalska
- Department of Clinical Immunology, University Children's Hospital, Wielicka 265, 30-663 Krakow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
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Zou X, Yang M, Ye Z, Li T, Jiang Z, Xia Y, Tan S, Long Y, Wang X. Uncovering lupus nephritis-specific genes and the potential of TNFRSF17-targeted immunotherapy: a high-throughput sequencing study. Front Immunol 2024; 15:1303611. [PMID: 38440734 PMCID: PMC10909935 DOI: 10.3389/fimmu.2024.1303611] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE). This study aimed to identify LN specific-genes and potential therapeutic targets. Methods We performed high-throughput transcriptome sequencing on peripheral blood mononuclear cells (PBMCs) from LN patients. Healthy individuals and SLE patients without LN were used as controls. To validate the sequencing results, qRT-PCR was performed for 5 upregulated and 5 downregulated genes. Furthermore, the effect of the TNFRSF17-targeting drug IBI379 on patient plasma cells and B cells was evaluated by flow cytometry. Results Our analysis identified 1493 and 205 differential genes in the LN group compared to the control and SLE without LN groups respectively, with 70 genes common to both sets, marking them as LN-specific. These LN-specific genes were significantly enriched in the 'regulation of biological quality' GO term and the cell cycle pathway. Notably, several genes including TNFRSF17 were significantly overexpressed in the kidneys of both LN patients and NZB/W mice. TNFRSF17 levels correlated positively with urinary protein levels, and negatively with complement C3 and C4 levels in LN patients. The TNFRSF17-targeting drug IBI379 effectively induced apoptosis in patient plasma cells without significantly affecting B cells. Discussion Our findings suggest that TNFRSF17 could serve as a potential therapeutic target for LN. Moreover, IBI379 is presented as a promising treatment option for LN.
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Affiliation(s)
- Xiaojuan Zou
- Department of Rheumatology and Immunology, The First Hospital of Jilin University, Changchun, China
| | - Mingyue Yang
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Zhuang Ye
- Department of Rheumatology and Immunology, The First Hospital of Jilin University, Changchun, China
| | - Tie Li
- Department of Rheumatology and Immunology, The First Hospital of Jilin University, Changchun, China
| | - Zhenyu Jiang
- Department of Rheumatology and Immunology, The First Hospital of Jilin University, Changchun, China
| | - Ying Xia
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
| | - Shenghai Tan
- Department of Surgical Intensive Care Unit (SICU), The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yu Long
- Department of Rheumatology and Immunology, The First Hospital of Jilin University, Changchun, China
| | - Xiaosong Wang
- Laboratory for Tumor Immunology, The First Hospital of Jilin University, Changchun, China
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Diaz-Villegas V, Pichardo-Macías LA, Juárez-Méndez S, Ignacio-Mejía I, Cárdenas-Rodríguez N, Vargas-Hernández MA, Mendoza-Torreblanca JG, Zamudio SR. Changes in the Dentate Gyrus Gene Expression Profile Induced by Levetiracetam Treatment in Rats with Mesial Temporal Lobe Epilepsy. Int J Mol Sci 2024; 25:1690. [PMID: 38338984 PMCID: PMC10855401 DOI: 10.3390/ijms25031690] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Temporal lobe epilepsy (TLE) is one of the most common forms of focal epilepsy. Levetiracetam (LEV) is an antiepileptic drug whose mechanism of action at the genetic level has not been fully described. Therefore, the aim of the present work was to evaluate the relevant gene expression changes in the dentate gyrus (DG) of LEV-treated rats with pilocarpine-induced TLE. Whole-transcriptome microarrays were used to obtain the differential genetic profiles of control (CTRL), epileptic (EPI), and EPI rats treated for one week with LEV (EPI + LEV). Quantitative RT-qPCR was used to evaluate the RNA levels of the genes of interest. According to the results of the EPI vs. CTRL analysis, 685 genes were differentially expressed, 355 of which were underexpressed and 330 of which were overexpressed. According to the analysis of the EPI + LEV vs. EPI groups, 675 genes were differentially expressed, 477 of which were downregulated and 198 of which were upregulated. A total of 94 genes whose expression was altered by epilepsy and modified by LEV were identified. The RT-qPCR confirmed that LEV treatment reversed the increased expression of Hgf mRNA and decreased the expression of the Efcab1, Adam8, Slc24a1, and Serpinb1a genes in the DG. These results indicate that LEV could be involved in nonclassical mechanisms involved in Ca2+ homeostasis and the regulation of the mTOR pathway through Efcab1, Hgf, SLC24a1, Adam8, and Serpinb1a, contributing to reduced hyperexcitability in TLE patients.
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Affiliation(s)
- Veronica Diaz-Villegas
- Departamento de Fisiología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 07738, Mexico; (V.D.-V.); (L.A.P.-M.)
- Laboratorio de Neurociencias, Subdirección de Medicina Experimental, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
| | - Luz Adriana Pichardo-Macías
- Departamento de Fisiología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 07738, Mexico; (V.D.-V.); (L.A.P.-M.)
| | - Sergio Juárez-Méndez
- Laboratorio de Oncología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea, Mexico City 11200, Mexico;
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Subdirección de Medicina Experimental, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
| | - Marco Antonio Vargas-Hernández
- Subdirección de Investigación, Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea, Mexico City 11200, Mexico;
| | | | - Sergio R. Zamudio
- Departamento de Fisiología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 07738, Mexico; (V.D.-V.); (L.A.P.-M.)
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Öztan G, Bozbuğa N, İşsever H, Oğuz F, Canıaz İ, Yazıksız N, Ertan M, Alpagut İU. Comparative Analysis of Transcriptome Profiles in Patients with Thromboangiitis Obliterans. Genes (Basel) 2023; 15:19. [PMID: 38275601 PMCID: PMC10815726 DOI: 10.3390/genes15010019] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Thromboangiitis obliterans (TAO) causes vascular insufficiency due to chronic inflammation and abrupt thrombosis of the medium and small arteries of the extremities. In our study, we aimed to determine biomarkers for the diagnosis of TAO by evaluating 15 male TAO patients with Shinoya diagnostic criteria and 5 healthy controls who did not have TAO-related symptoms in their family histories. METHODS The Clariom D Affymetrix platform was used to conduct microarray analysis on total RNA extracted from whole blood. A total of 477 genes (FC ≤ 5 or >5) common to the fifteen patient and five control samples were selected using comparative microarray analysis; among them, 79 genes were upregulated and 398 genes were downregulated. RESULTS According to FC ≤ 10 or >10, in the same TAO patient and control group, 13 genes out of 28 were upregulated, whereas 15 genes were downregulated. The 11 key genes identified according to their mean log2FC values were PLP2, RPL27A, CCL4, FMNL1, EGR1, EIF4A1, RPL9, LAMP2, RNF149, EIF4G2, and DGKZ. The genes were ranked according to their relative expression as follows: FMNL1 > RNF149 > RPL27A > EIF4G2 > EIF4A1 > LAMP2 > EGR1 > PLP2 > DGKZ > RPL9 > CCL4. Using protein-protein interaction network analysis, RPL9, RPL27A, and RPL32 were found to be closely related to EIF4G2 and EIF4A1. The Reactome pathway found pathways linked to 28 genes. These pathways included the immune system, cellular responses to stress, cytokine signaling in the immune system, and signaling by ROBO receptors. CONCLUSIONS By figuring out the protein expression levels of the genes that have been found to explain how TAO disease works at the molecular level, it will be possible to figure out how well these chosen transcripts can diagnose and predict the disease.
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Affiliation(s)
- Gözde Öztan
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - Nilgün Bozbuğa
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Halim İşsever
- Department of Public Health, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - Fatma Oğuz
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - İrem Canıaz
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Nilgün Yazıksız
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Melike Ertan
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - İbrahim Ufuk Alpagut
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
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Abarca-Barriga HH, Punil Luciano R, Vásquez Sotomayor F. Cornelia de Lange Syndrome Caused by an Intragenic Heterozygous Deletion in RAD21 Detected through Very-High-Resolution Chromosomal Microarray Analysis. Genes (Basel) 2023; 14:2212. [PMID: 38137034 PMCID: PMC10742884 DOI: 10.3390/genes14122212] [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: 10/03/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Cornelia de Lange syndrome is a genetic and clinically heterogeneous entity, caused by at least five genes. It is characterized by short stature, gestalt facies, microcephaly, neurodevelopmental disorders, and other anomalies. In this report, we present a 13-year-old female patient with microcephaly, cleft palate, polydactyly, short stature, triangular facies, frontal bossing, a bulbous nose, an overfolded helix, limited pronosupination, and an anomalous uterus. No neurodevelopmental disorders were reported. A chromosomal microarray analysis of 6.5 million markers was performed in the proband and her parents. The results showed a de novo heterozygous microdeletion of exons 9-14 within RAD21, which confirmed the diagnosis of Cornelia de Lange syndrome type 4. Our patient did not show any neurologic phenotype (until the time of diagnosis), although neurodevelopmental disorders are frequently present in patients with Cornelia de Lange syndrome type 4, and despite carrying a deletion that was larger than previously reported. Therefore, unknown genetic modifiers or intrinsic mechanisms of RAD21 variants may exist and should be studied.
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Affiliation(s)
- Hugo H. Abarca-Barriga
- Instituto de Investigaciones de Ciencias Biomédicas, Universidad Ricardo Palma, Lima 15039, Peru;
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
| | - Renzo Punil Luciano
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
| | - Flor Vásquez Sotomayor
- Instituto de Investigaciones de Ciencias Biomédicas, Universidad Ricardo Palma, Lima 15039, Peru;
- Servicio de Genética & Errores Innatos del Metabolismo, Instituto Nacional de Salud del Niño Breña, Lima 15083, Peru;
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Ryabov V, Gombozhapova A, Litviakov N, Ibragimova M, Tsyganov M, Rogovskaya Y, Kzhyshkowska J. Microarray Analysis for Transcriptomic Profiling of Myocardium in Patients with Fatal Myocardial Infarction. Biomedicines 2023; 11:3294. [PMID: 38137515 PMCID: PMC10740899 DOI: 10.3390/biomedicines11123294] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Transcriptomic evidence from human myocardium in myocardial infarction (MI) is still not sufficient. Thus, there is a need for studies on human cardiac samples in relation to the clinical data of patients. The purpose of our pilot study was to investigate the transcriptomic profile of myocardium in the infarct zone, in comparison to the remote myocardium, in patients with fatal MI, via microarray analysis. This study included four patients with fatal MI type 1. We selected histologically verified samples from within the infarct area (n = 4) and remote myocardium (n = 4). The whole transcriptome was evaluated using microarray analysis. Differentially expressed genes (DEGs) clustered in the infarct area and in the remote myocardium allowed their differentiation. We identified a total of 1785 DEGs (8.32%) in the infarct area, including 1692 up-regulated (94.79%) and 93 down-regulated (5.21%) genes. The top 10 up-regulated genes were TRAIL, SUCLA2, NAE1, PDCL3, OSBPL5, FCGR2C, SELE, CEP63, ST3GAL3 and C4orf3. In the infarct area, we found up-regulation of seventeen apoptosis-related genes, eleven necroptosis-related, and six necrosis-related genes. Transcriptome profiling of the myocardium in patients with MI remains a relevant area of research for the formation of new scientific hypotheses and a potential way to increase the translational significance of studies into myocardial infarction.
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Affiliation(s)
- Vyacheslav Ryabov
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Aleksandra Gombozhapova
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Nikolai Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Marina Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Matvey Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | | | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, 69117 Heidelberg, Germany;
- Laboratory of Translational and Cellular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia
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Rutkowska-Zapała M, Grabowska A, Lenart M, Kluczewska A, Szaflarska A, Kobylarz K, Pituch-Noworolska A, Siedlar M. Transcriptome profiling of regulatory T cells from children with transient hypogammaglobulinemia of infancy. Clin Exp Immunol 2023; 214:275-288. [PMID: 37936298 PMCID: PMC10719223 DOI: 10.1093/cei/uxad116] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
Transient hypogammaglobulinemia of infancy (THI) is one of the most common forms of hypogammaglobulinemia in the early childhood. THI is usually associated with chronic, recurrent bacterial and viral infections, life-threatening in some cases, yet its pathogenesis is still largely unknown. As our previous findings indicated the possible role of Treg cells in the pathomechanism of THI, the aim of the current study was to investigate gene expression profile of Treg cells isolated from THI patients. The transcriptome-wide gene profiling was performed using microarray technology on THI patients in two time-points: during (THI-1), and in resolution phase (THI-2) of hypogammaglobulinemia. As a result, a total of 1086 genes were differentially expressed in THI-1 patients, when compared to THI-2 as well as control group. Among them, 931 were up- and 155 downregulated, and part of them encodes genes important for Treg lymphocyte biology and function, i.e. transcription factors/cofactors that regulate FOXP3 expression. Thus, we postulate that Treg cells isolated from THI patients during hypogammaglobulinemia display enhanced suppressor transcriptome signature. Treg expression profile of THI children after normalization of Ig levels largely resembles the results obtained in healthy control group, suggesting THI Treg transcriptome seems to return to that observed in healthy children. Taken together, we suggest that THI pathomechanism is associated not only with transiently elevated Treg cell numbers, but also with their enhanced regulatory/inhibitory functions. These findings expand our knowledge of human Treg cells and may be useful for the future diagnosis or management of THI.
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Affiliation(s)
- Magdalena Rutkowska-Zapała
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Agnieszka Grabowska
- Department of Medical Genetics, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Marzena Lenart
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Anna Kluczewska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Anna Szaflarska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Krzysztof Kobylarz
- Department of Anesthesiology and Intensive Care, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Anna Pituch-Noworolska
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Wielicka, Krakow, Poland
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Dai F, He Y, Lei T, Jiang Y, Zhang Q, Qing Y. Identification and functional prediction of long non-coding RNA and mRNA related to connective tissue disease-associated interstitial lung diseases. Rheumatol Immunol Res 2023; 4:204-215. [PMID: 38125642 PMCID: PMC10729597 DOI: 10.2478/rir-2023-0030] [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] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/23/2023] [Indexed: 12/23/2023]
Abstract
Objective Recently, the role of long non-coding RNA (lncRNA) in rheumatic immune diseases has attracted widespread attention. However, knowledge of lncRNA in connective tissue disease-associated interstitial lung disease (CTD-ILD) is limited. This study explored the expression profile and possible mechanisms of lncRNA and mRNA in peripheral blood mononuclear cells (PBMCs) of CTD-ILD patients, especially systemic sclerosis (SSc)-ILD and rheumatoid arthritis (RA)-ILD. Methods LncRNA microarray analysis identified 240 diferentially expressed lncRNAs and 218 diferentially expressed mRNA in the CTD-ILD group and the connective tissue disease without associated interstitial lung disease (CTD-NILD) group. The bioinformatics analysis of diferential genes has identified several important biological processes and signal pathways, including nuclear factor kappa B (NF-kappa B) signaling pathway, interleukin 17 (IL-17) signaling pathway, B cell receptor signaling pathway. Relative expression levels of five diferentially expressed lncRNAs and one mRNA in 120 SSc and RA patients with or without ILD were detected by quantitative reverse-transcription (PCR). Results The ENST00000604692 expression level was significantly higher in the ILD than the without interstitial lung disease (NILD) group; T311354 and arginase-1 were significantly higher in SSc than RA group. Conclusion These data suggest that the specific profile of lncRNA in PBMCs of CTD-ILD patients and the potential signal pathways related to the pathogenesis of CTD-ILD, which may provide newfound insights for the diagnosis and treatment of CTD-ILD patients.
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Affiliation(s)
- Fei Dai
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Rheumatology and Immunology, the Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yixi He
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Rheumatology and Immunology, the Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Tianyi Lei
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Rheumatology and Immunology, the Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yi Jiang
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Rheumatology and Immunology, the Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Quanbo Zhang
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Geriatrics, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yufeng Qing
- Research Center of Hyperuricemia and Gout, the Afiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Rheumatology and Immunology, the Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
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Ibrahim S, van Rooij J, Verkerk AJ, de Vries J, Zuurbier L, Defesche J, Peter J, Schonck WA, Sedaghati-Khayat B, Kees Hovingh G, Uitterlinden AG, Stroes ES, Reeskamp LF. Low-Cost High-Throughput Genotyping for Diagnosing Familial Hypercholesterolemia. Circ Genom Precis Med 2023; 16:462-469. [PMID: 37675602 PMCID: PMC10581440 DOI: 10.1161/circgen.123.004103] [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] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is a common but underdiagnosed genetic disorder characterized by high low-density lipoprotein cholesterol levels and premature cardiovascular disease. Current sequencing methods to diagnose FH are expensive and time-consuming. In this study, we evaluated the accuracy of a low-cost, high-throughput genotyping array for diagnosing FH. METHODS An Illumina Global Screening Array was customized to include probes for 636 variants, previously classified as FH-causing variants. First, its theoretical coverage was assessed in all FH variant carriers diagnosed through next-generation sequencing between 2016 and 2022 in the Netherlands (n=1772). Next, the performance of the array was validated in another sample of FH variant carriers previously identified in the Dutch FH cascade screening program (n=1268). RESULTS The theoretical coverage of the array for FH-causing variants was 91.3%. Validation of the array was assessed in a sample of 1268 carriers of whom 1015 carried a variant in LDLR, 250 in APOB, and 3 in PCSK9. The overall sensitivity was 94.7% and increased to 98.2% after excluding participants with variants not included in the array design. Copy number variation analysis yielded a 89.4% sensitivity. In 18 carriers, the array identified a total of 19 additional FH-causing variants. Subsequent DNA analysis confirmed 5 of the additionally identified variants, yielding a false-positive result in 16 subjects (1.3%). CONCLUSIONS The FH genotyping array is a promising tool for genetically diagnosing FH at low costs and has the potential to greatly increase accessibility to genetic testing for FH. Continuous customization of the array will further improve its performance.
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Affiliation(s)
- Shirin Ibrahim
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Annemieke J.M.H. Verkerk
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Jard de Vries
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Linda Zuurbier
- Department of Human Genetics (L.Z., J.D.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Joep Defesche
- Department of Human Genetics (L.Z., J.D.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Jorge Peter
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine (J.P., G.K.H.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Willemijn A.M. Schonck
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Bahar Sedaghati-Khayat
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - G. Kees Hovingh
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine (J.P., G.K.H.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands (J.v.R., A.J.M.H.V., J.d.V., B.S.-K., A.G.U.)
| | - Erik S.G. Stroes
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Laurens F. Reeskamp
- Department of Vascular Medicine (S.I., J.P., W.A.M.S., G.K.H., E.S.G.S., L.F.R.), Amsterdam UMC, University of Amsterdam, the Netherlands
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O’Connor LM, O’Connor BA, Zeng J, Lo CH. Data Mining of Microarray Datasets in Translational Neuroscience. Brain Sci 2023; 13:1318. [PMID: 37759919 PMCID: PMC10527016 DOI: 10.3390/brainsci13091318] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Data mining involves the computational analysis of a plethora of publicly available datasets to generate new hypotheses that can be further validated by experiments for the improved understanding of the pathogenesis of neurodegenerative diseases. Although the number of sequencing datasets is on the rise, microarray analysis conducted on diverse biological samples represent a large collection of datasets with multiple web-based programs that enable efficient and convenient data analysis. In this review, we first discuss the selection of biological samples associated with neurological disorders, and the possibility of a combination of datasets, from various types of samples, to conduct an integrated analysis in order to achieve a holistic understanding of the alterations in the examined biological system. We then summarize key approaches and studies that have made use of the data mining of microarray datasets to obtain insights into translational neuroscience applications, including biomarker discovery, therapeutic development, and the elucidation of the pathogenic mechanisms of neurodegenerative diseases. We further discuss the gap to be bridged between microarray and sequencing studies to improve the utilization and combination of different types of datasets, together with experimental validation, for more comprehensive analyses. We conclude by providing future perspectives on integrating multi-omics, to advance precision phenotyping and personalized medicine for neurodegenerative diseases.
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Affiliation(s)
- Lance M. O’Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Blake A. O’Connor
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA;
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
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11
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Schneider BS, Petereit J, Zhang L, Voss JG. Crush Injury and Simulated Flight Effects on Muscle Gene Expression in Female Mice. Nurs Res 2023; 72:363-370. [PMID: 37625178 PMCID: PMC10542909 DOI: 10.1097/nnr.0000000000000667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND Aeromedical evacuation provides critical care during long-distance transport of injured victims between medical facilities. Often, these victims sustain muscle trauma related to mechanical insults, such as crush. Understanding the effects of flight on injured muscle is important because the aircraft cabin represents an external environment with mild hypoxia-the cabin's altitude is 2,438 m instead of sea level. Because mild hypobaric hypoxia can alter gene expression in normal muscle and affect recovery patterns, it is beneficial to examine whether this type of hypoxia may also alter injury-related genes. OBJECTIVE The objective of this study was to verify the hypothesis that differential gene expression occurs in response to mild hypobaric hypoxia exposure in crush-injured muscle during two early recovery (preregeneration stage) time points. METHODS Twenty-four female mice were anesthetized, and the right gastrocnemius muscle underwent crush injury. Approximately 24 hours later, mice were exposed to normobaric normoxia or hypobaric hypoxia for 8-9 hours. After 32 or 48 hours of recovery, the mice were euthanized, and the right and left lateral gastrocnemius muscles were collected for microarray and bioinformatics analyses. RESULTS The study hypothesis was verified. There were 353 highly upregulated, differentially expressed genes identified in the injured muscle compared to the uninjured muscle. Mid1 was upregulated in both pressure conditions regardless of injury status. There were 52 and 15 differentially expressed genes at 32 and 48 hours postinjury, respectively, in the hypobaric hypoxia-exposed, injured muscle compared to the normobaric normoxia-exposed, injured muscle. The macrophage gene Cd68 correlated with other leukocyte-related genes. DISCUSSION These findings expand our understanding of the genetic changes that occur in muscle in response to a crush injury, including those related to the macrophage protein CD68. Nursing interventions addressing adequate functioning after crush muscle injury may need to consider the effects on Cd68 and its closely related genes. In addition, our results suggest a responsiveness of the gene Mid1 to flight-relevant hypobaric hypoxia. Changes in the expression of Mid1 may be appropriate in assessing the long-term health of flight crew members.
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Hashemi KS, Aliabadi MK, Mehrara A, Talebi E, Hemmati AA, Rezaeiye RD, Ghanbary MJ, Motealleh M, Dayeri B, Alashti SK. A meta-analysis of microarray datasets to identify biological regulatory networks in Alzheimer's disease. Front Genet 2023; 14:1225196. [PMID: 37705610 PMCID: PMC10497115 DOI: 10.3389/fgene.2023.1225196] [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: 05/19/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Background: Alzheimer's Disease (AD) is an age-related progressive neurodegenerative disorder characterized by mental deterioration, memory deficit, and multiple cognitive abnormalities, with an overall prevalence of ∼2% among industrialized countries. Although a proper diagnosis is not yet available, identification of miRNAs and mRNAs could offer valuable insights into the molecular pathways underlying AD's prognosis. Method: This study aims to utilize microarray bioinformatic analysis to identify potential biomarkers of AD, by analyzing six microarray datasets (GSE4757, GSE5281, GSE16759, GSE28146, GSE12685, and GSE1297) of AD patients, and control groups. Furthermore, this study conducted gene ontology, pathways analysis, and protein-protein interaction network to reveal major pathways linked to probable biological events. The datasets were meta-analyzed using bioinformatics tools, to identify significant differentially expressed genes (DEGs) and hub genes and their targeted miRNAs'. Results: According to the findings, CXCR4, TGFB1, ITGB1, MYH11, and SELE genes were identified as hub genes in this study. The analysis of DEGs using GO (gene ontology) revealed that these genes were significantly enriched in actin cytoskeleton regulation, ECM-receptor interaction, and hypertrophic cardiomyopathy. Eventually, hsa-mir-122-5p, hsa-mir-106a-5p, hsa-mir-27a-3p, hsa-mir16-5p, hsa-mir-145-5p, hsa-mir-12-5p, hsa-mir-128-3p, hsa-mir 3200-3p, hsa-mir-103a-3p, and hsa-mir-9-3p exhibited significant interactions with most of the hub genes. Conclusion: Overall, these genes can be considered as pivotal biomarkers for diagnosing the pathogenesis and molecular functions of AD.
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Affiliation(s)
- Kimia Sadat Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohadese Koohi Aliabadi
- Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, Iran
| | - Arian Mehrara
- School of Pharmacy, Ramsar International Campus, Mazandaran University of Medical Sciences, Ramsar, Iran
| | - Elham Talebi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Akbar Hemmati
- Department of Biology and Biotechnology, Molecular Biology, and Genetics, Pavia University, Lombardi, Italy
| | | | | | - Maryam Motealleh
- Department of System Biology Lab, University of Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Behnaz Dayeri
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Biotechnology, University of Milan, Milan, Italy
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Correa-Arzate L, Portilla-Robertson J, Ramírez-Jarquín JO, Jacinto-Alemán LF, Mejía-Velázquez CP, Villanueva-Sánchez FG, Rodríguez-Vázquez M. LRP5, SLC6A3, and SOX10 Expression in Conventional Ameloblastoma. Genes (Basel) 2023; 14:1524. [PMID: 37628576 PMCID: PMC10453908 DOI: 10.3390/genes14081524] [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: 06/21/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Cell proliferation and invasion are characteristic of many tumors, including ameloblastoma, and are important features to target in possible future therapeutic applications. OBJECTIVE The objective of this study was the identification of key genes and inhibitory drugs related to the cell proliferation and invasion of ameloblastoma using bioinformatic analysis. METHODS The H10KA_07_38 gene profile database was analyzed by Rstudio and ShinyGO Gene Ontology enrichment. String, Cytoscape-MCODE, and Kaplan-Meier plots were generated, which were subsequently validated by RT-qPCR relative expression and immunoexpression analyses. To propose specific inhibitory drugs, a bioinformatic search using Drug Gene Budger and DrugBank was performed. RESULTS A total of 204 significantly upregulated genes were identified. Gene ontology enrichment analysis identified four pathways related to cell proliferation and cell invasion. A total of 37 genes were involved in these pathways, and 11 genes showed an MCODE score of ≥0.4; however, only SLC6A3, SOX10, and LRP5 were negatively associated with overall survival (HR = 1.49 (p = 0.0072), HR = 1.55 (p = 0.0018), and HR = 1.38 (p = 0.025), respectively). The RT-qPCR results confirmed the significant differences in expression, with overexpression of >2 for SLC6A3 and SOX10. The immunoexpression analysis indicated positive LRP5 and SLC6A3 expression. The inhibitory drugs bioinformatically obtained for the above three genes were parthenolide and vorinostat. CONCLUSIONS We identify LRP5, SLC6A3, and SOX10 as potentially important genes related to cell proliferation and invasion in the pathogenesis of ameloblastomas, along with both parthenolide and vorinostat as inhibitory drugs that could be further investigated for the development of novel therapeutic approaches against ameloblastoma.
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Affiliation(s)
- Lorena Correa-Arzate
- Department of Oral Medicine and Pathology, Postgraduate Division, Dental School, National Autonomous University of Mexico, Mexico City 04510, Mexico (J.P.-R.); (C.P.M.-V.)
| | - Javier Portilla-Robertson
- Department of Oral Medicine and Pathology, Postgraduate Division, Dental School, National Autonomous University of Mexico, Mexico City 04510, Mexico (J.P.-R.); (C.P.M.-V.)
| | - Josué Orlando Ramírez-Jarquín
- Neurosciences Division, Cellular Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Luis Fernando Jacinto-Alemán
- Department of Oral Medicine and Pathology, Postgraduate Division, Dental School, National Autonomous University of Mexico, Mexico City 04510, Mexico (J.P.-R.); (C.P.M.-V.)
| | - Claudia Patricia Mejía-Velázquez
- Department of Oral Medicine and Pathology, Postgraduate Division, Dental School, National Autonomous University of Mexico, Mexico City 04510, Mexico (J.P.-R.); (C.P.M.-V.)
| | | | - Mariana Rodríguez-Vázquez
- Infectomic and Molecular Pathogenesis Department, CINVESTAV, National Polytechnic Institute, Mexico City 07738, Mexico;
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Fan C, Gao Y, Sun Y. Integrated multiple- microarray analysis and mendelian randomization to identify novel targets involved in diabetic nephropathy. Front Endocrinol (Lausanne) 2023; 14:1191768. [PMID: 37492198 PMCID: PMC10363738 DOI: 10.3389/fendo.2023.1191768] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
Background Diabetic nephropathy (DN), which is the main cause of renal failure in end-stage renal disease, is becoming a common chronic renal disease worldwide. Mendelian randomization (MR) is a genetic tool that is widely used to minimize confounding and reverse causation when identifying the causal effects of complex traits. In this study, we conducted an integrated multiple microarray analysis and large-scale plasma proteome MR analysis to identify candidate biomarkers and evaluate the causal effects of prospective therapeutic targets in DN. Methods Five DN gene expression datasets were selected from the Gene Expression Omnibus. The robust rank aggregation (RRA) method was used to integrate differentially expressed genes (DEGs) of glomerular samples between patients with DN and controls, followed by functional enrichment analysis. Protein quantitative trait loci were incorporated from seven different proteomic genome-wide association studies, and genetic association data on DN were obtained from FinnGen (3676 cases and 283,456 controls) for two-sample MR analysis. External validation and clinical correlation were also conducted. Results A total of 82 DEGs (53 upregulated and 29 downregulated) were identified through RRA integrated analysis. The enriched Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways of the DEGs were significantly enriched in neutrophil degranulation, neutrophil activation, proteoglycan binding, collagen binding, secretory granule lumen, gluconeogenesis, tricarboxylic acid cycle, and pentose phosphate pathways. MR analysis revealed that the genetically predicted levels of MHC class I polypeptide-related sequence B (MICB), granzyme A (GZMA), cathepsin S (CTSS), chloride intracellular channel protein 5, and ficolin-1 (FCN1) were causally associated with DN risk. Expression validation and clinical correlation analysis showed that MICB, GZMA, FCN1, and insulin-like growth factor 1 may participate in the development of DN, and carbonic anhydrase 2 and lipoprotein lipase may play protective roles in patients with DN. Conclusion Our integrated analysis identified novel biomarkers, including MICB and GZMA, which may help further understand the complicated mechanisms of DN and identify new target pathways for intervention.
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Affiliation(s)
- Chenyu Fan
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
| | - Yuye Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ying Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
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Landzaat LJ, Emons JAM, Sonneveld LJH, Schreurs MWJ, Arends NJT. Early inhalant allergen sensitization at component level: an analysis in atopic Dutch children. Front Allergy 2023; 4:1173540. [PMID: 37470032 PMCID: PMC10352100 DOI: 10.3389/falgy.2023.1173540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/24/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023] Open
Abstract
Background Allergic rhinitis is a common respiratory disease in children and sensitization to inhalant allergens plays a significant role in its development. However, limited knowledge exists regarding sensitization profiles of inhalant allergen components in atopic children, particularly in the very young individuals. Understanding these profiles could provide insights into the early development of allergic rhinitis. The objective of this cross-sectional retrospective study was to evaluate the IgE-sensitization profiles to multiple inhalant allergen components and their clinical relevance in Dutch atopic children, with specific focus on children under the age of 4 years. Methods A total of 243 atopic children were included in the study and sensitization profiles were analyzed using multiplex microarray analysis (ISAC). Clinical information was obtained from records of a pediatric allergy outpatient clinic between 2011 and 2020. Specific IgE responses to inhalation allergen components from five allergen sources (grass pollen, tree pollen, house dust mite, cat and dog), were examined. The study encompassed children of different age groups and compared those with and without symptoms. Results The results demonstrated that sensitization to inhalant allergen components was present in 92% of the cohort. Sensitization was already evident at a young age (87%), including infancy, with a rapid increase in prevalence after 1 year of age. House dust mite emerged as the most predominant sensitizing allergen in early childhood, followed by tree pollen in later years. Sensitization patterns were similar between symptomatic and asymptomatic children, although symptomatic children exhibited higher frequencies and values. The sensitization profiles in very young children were comparable to those of children across all age groups. Conclusion These findings highlight the presence of sensitization to inhalant allergen components and the early onset of allergic rhinitis before the age of 4, including infancy, in Dutch atopic children. Notable allergen molecules in Dutch atopic children under the age of 4 years include Bet v 1, Fel d 1, Der f 1, Der p 1, Der p 10 and Phl p 4, with house dust mite sensitization being the most common among Dutch infants. Moreover, the prevalence of sensitization to inhalant allergens in this Dutch cohort surpassed that of general European populations, emphasizing the importance of early assessment and management of allergic rhinitis in young atopic children.
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Affiliation(s)
- Lonneke J. Landzaat
- Division of Pediatric Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Joyce A. M. Emons
- Division of Pediatric Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Laura J. H. Sonneveld
- Division of Pediatric Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marco W. J. Schreurs
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Nicolette J. T. Arends
- Division of Pediatric Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Azadeh M, Salehzadeh A, Ghaedi K, Talesh Sasani S. Integrated High-Throughput Bioinformatics (Microarray, RNA-Seq, and RNA Interaction) and qRT-PCR Investigation of BMPR1B Axis as a Potential Diagnostic Biomarker of Isfahan Breast Cancer. Adv Biomed Res 2023; 12:120. [PMID: 37434942 PMCID: PMC10331528 DOI: 10.4103/abr.abr_200_22] [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: 06/14/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 07/13/2023] Open
Abstract
Background According to the bioinformatics analyses and previous studies, bone morphogenetic protein receptor type 1B (BMPR1B) dysregulation could remarkably affect breast cancer (BC) status as a potential biomarker and tumor suppressor. Therefore, the analysis of the expression level of BMPR1B and other relevant biological factors such as microRNAs, long non-coding RNAs, downstream proteins in the relevant signaling pathways, and finding the accurate biological mechanism of BMPR1B could be helpful for a better understanding of BC pathogenicity and discovering the new treatment methods and drugs. Materials and Methods R Studio software (4.0.2) was used for microarray data analyses. GSE31448 dataset was downloaded by GEOquery package and analyzed by limma package. STRING and miRWalk online databases and Cytoscape software were used for interaction analyses. Quantitative measurement of BMPR1B expression level was performed by qRT-PCR experiment. Result Microarray and real-time PCR analysis revealed that BMPR1B has a significant downregulation in the transforming growth factor (TGF)-beta and bone morphogenic protein (BMP) signaling pathways in BC samples. BMPR1B is a potential diagnostic biomarker, regulated by hsa-miR-181a-5p. Also, BMPR1B regulates the function of BMP2, BMP6, SMAD4, SMAD5, and SMAD6 proteins. Discussion BMPR1B have a significant role in the development of BC by regulating the potential proteins' function, playing the diagnostic biomarker role, and regulation of TGF-beta and BMP signaling pathways. The high amount of BMPR1B protein helps in increasing the survival rate of the patients.
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Affiliation(s)
- Mansoureh Azadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Kamran Ghaedi
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
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Zhao F, Zhu S, Fang J, Dong H, Zhu C. Correlation of DNA methylation and lymph node metastasis in papillary thyroid carcinoma. Head Neck 2023. [PMID: 37097909 DOI: 10.1002/hed.27377] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/11/2023] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer with a primarily good prognosis, and its 10-year survival rate is over 90%. However, PTC is prone to early lymph node metastasis. METHODS Thyroid cancer tissues from PTC patients with lymphatic metastasis and normal tissues were collected for DNA methylation analysis. Different methylation sites, different methylation regions, gene-enriched pathways, and protein-protein interactions (PPIs) were analyzed. RESULTS There were 1004 differentially methylated sites in the PTC group versus the control group; these involved 479 hypermethylated sites in 415 related genes, 525 hypomethylated sites in 482 related genes, 64 differentially methylated regions located in the CpG island region, 34 differentially methylated genes closely related to thyroid cancer, and 17 genes with differentially methylated genes in the DNA promoter region. CONCLUSION NDRG4 hypermethylation and FOXO3, ZEB2, and CDK6 hypomethylation were associated with PTC lymph node metastasis.
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Affiliation(s)
- Feng Zhao
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyi Zhu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Fang
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huilei Dong
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Chenfang Zhu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Tian Y, Cui X, Guan X, Meng X, Zheng M, Wang X, Cheng G, Xia Y, Ye M. Differential expression profile of microRNAs in the lung tissues of coal workers with pneumoconiosis and patients with silicosis. Toxicol Ind Health 2023; 39:204-217. [PMID: 36840710 DOI: 10.1177/07482337231156281] [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] [Indexed: 02/26/2023]
Abstract
The purpose of this study was to characterize the microRNA (miRNA) profile of the lung tissues from coal workers' pneumoconiosis (CWP) and silicosis and to analyze the changes in downstream genes, biological processes, and signaling pathways based on the differently expressed miRNAs. Lung tissues from three CWP patients, eight silicosis patients, and four healthy controls were collected and analyzed for their miRNA profiles using Affymetrix® GeneChip® miRNA Arrays. Differentially expressed miRNAs (DEMs) were identified between the different groups. The miRanda and TargetScan databases were used to predict the putative target genes, and volcano and heat maps were drawn. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were then performed to screen the DEMs-associated biological process and signaling pathways, respectively. Further identification with a comprehensive literature research involving particle exposure, fibrosis, inflammation and lung cancer were used to further screen DEMs of CWP and silicosis. Microarray data showed that 375 and 88 miRNAs were differentially expressed in CWP and silicosis lung tissues compared with healthy lung tissues, while 34 miRNAs were differentially expressed in CWP compared with silicosis lung tissues. The GO and KEGG pathway analyses showed that, the target genes were mainly enriched in the TGF-β, MAPK, p53 and other signal pathways. These results provided insight into the miRNA-related underlying mechanisms of CWP and silicosis, and they provided new clues for miRNAs as biomarkers for the diagnosis and differential diagnosis of these two diseases.
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Affiliation(s)
- Yilin Tian
- National Institute for Occupational Health and Poison Control, 12415Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqing Cui
- Hubei Provincial Key Laboratory for Applied Toxicology, 498598Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - Xin Guan
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Xiang Meng
- National Institute for Occupational Health and Poison Control, 12415Chinese Center for Disease Control and Prevention, Beijing, China
| | - Min Zheng
- National Institute for Occupational Health and Poison Control, 12415Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Wang
- National Institute for Occupational Health and Poison Control, 12415Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoping Cheng
- Ward II of Respiratory and Critical Care Medicine, Huangshi Second Hospital, Huangshi, China
| | - Ying Xia
- Hubei Provincial Key Laboratory for Applied Toxicology, 498598Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - Meng Ye
- National Institute for Occupational Health and Poison Control, 12415Chinese Center for Disease Control and Prevention, Beijing, China
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Wang Q, Li X, Chen Y, Gong J, Hu B. Classification and survival prediction in early-stage cirrhosis by gene expression profiling. J Viral Hepat 2023; 30:116-128. [PMID: 36355440 DOI: 10.1111/jvh.13769] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/29/2022] [Indexed: 11/12/2022]
Abstract
Liver cirrhosis has been increasingly diagnosed at an early stage owing to the non-invasive diagnostic techniques. However, it is difficult to identify patients at high risk of disease progression. Screening cirrhotic patients with poor prognosis who are most in need of surveillance is still challenging. Gene expression data GSE15654 and GSE14520 were downloaded for performing unsupervised clustering analysis. The prognostic differences between the different clusters were explored by Cox regression. Integrative analysis of gene expression signature, immune cell enrichments and clinical characterization was performed for different clusters. Two distinctive subclasses were identified in HCV-related GSE15654, and Kaplan-Meier analysis indicated that subtype 2 had lower survival rates than subtype 1 (p = 0.0399). Further analysis revealed subtype 2 had a higher density of follicular T helper cells, resting natural killer cells and M0, M2 macrophages while subtype 1 with a higher fraction of naive B cells, memory B cells, resting memory CD 4 T cells, activated natural killer cells and monocytes. 226 differentially expressed genes were identified between the two subtypes, and Reactome analysis showed the mainly enriched pathways were biological oxidations and fatty acid metabolism. Five hub genes (AKT1, RPS16, CDC42, CCND1 and PCBP2) and three significant modules were extracted from the PPI network. The results were validated in HBV-related GSE14520 cohort. We identified two subtypes of patients with different prognosis for hepatitis C-related early-stage liver cirrhosis. Bioinformatics analysis of the gene expression and immune cell profile may provide fresh insight into understanding the prognosis difference.
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Affiliation(s)
- Qingliang Wang
- Department of General Surgery, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaojie Li
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yaqiong Chen
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiao Gong
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bo Hu
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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20
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Ambrocio-Ortiz E, Pérez-Rubio G, Ramírez-Venegas A, Hernández-Zenteno RJ, Fernández-López JC, Ramírez-Díaz ME, Cruz-Vicente F, Martínez-Gómez ML, Sansores R, Pérez-Ramos J, Falfán-Valencia R. SNPs Sets in Codifying Genes for Xenobiotics-Processing Enzymes Are Associated with COPD Secondary to Biomass-Burning Smoke. Curr Issues Mol Biol 2023; 45:799-819. [PMID: 36825998 DOI: 10.3390/cimb45020053] [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: 12/09/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide; the main risk factors associated with the suffering are tobacco smoking (TS) and chronic exposure to biomass-burning smoke (BBS). Different biological pathways have been associated with COPD, especially xenobiotic or drug metabolism enzymes. This research aims to identify single nucleotide polymorphisms (SNPs) profiles associated with COPD from two expositional sources: tobacco smoking and BBS. One thousand-five hundred Mexican mestizo subjects were included in the study and divided into those exposed to biomass-burning smoke and smokers. Genome-wide exome genotyping was carried out using Infinium Exome-24 kit arrays v. 1.2. Data quality control was conducted using PLINK 1.07. For clinical and demographic data analysis, Rstudio was used. Eight SNPs were found associated with COPD secondary to TS and seven SNPs were conserved when data were analyzed by genotype. When haplotype analyses were carried out, five blocks were predicted. In COPD secondary to BBS, 24 SNPs in MGST3 and CYP family genes were associated. Seven blocks of haplotypes were associated with COPD-BBS. SNPs in the ARNT2 and CYP46A1 genes are associated with COPD secondary to TS, while in the BBS comparison, SNPs in CYP2C8, CYP2C9, MGST3, and MGST1 genes were associated with increased COPD risk.
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Gotoh H, Maruyama K, Yoshii K, Yamauchi N, Nomura T, Ohtsuka S, Shirasaki R, Takebayashi H, Ono K. Disruption of the anterior commissure in Olig2 deficient mice. Eur J Neurosci 2023; 57:5-16. [PMID: 36370145 DOI: 10.1111/ejn.15861] [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: 08/10/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/15/2022]
Abstract
In the present study, we examined neural circuit formation in the forebrain of the Olig2 knockout (Olig2-KO) mouse model and found disruption of the anterior commissure at the late foetal stage. Axon bundles of the anterior commissure encountered the wall of the third ventricle and ceased axonal extension. L1-CAM immunohistochemistry showed that Olig2-KO mice lose decussation formation in the basal forebrain. DiI tracing revealed that the thin bundles of the anterior commissure axons crossed the midline but ceased further extension into the deep part of the contralateral side. Furthermore, some fractions of DiI-labelled axons were oriented dorsolaterally, which was not observed in the control mouse forebrain. The rostral part of the third ventricle was much wider in the Olig2-KO mice than in wild-type mice, which likely resulted in the delay of midline fusion and subsequent delay and malformation of the anterior commissure. We analysed gene expression alterations in the Olig2-KO mice using a public database and found multiple genes, which are related to axon guidance and epithelial-mesenchymal transition, showing subtle expression changes. These results suggest that Olig2 is essential for anterior commissure formation, likely by regulating multiple biological processes.
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Affiliation(s)
- Hitoshi Gotoh
- Developmental Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kohei Maruyama
- Developmental Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kengo Yoshii
- Mathematics and Statistics in Medical Sciences, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nao Yamauchi
- Developmental Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Okayama University Medical School, Okayama, Japan
| | - Tadashi Nomura
- Developmental Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Ohtsuka
- Laboratory for Experimental Animals, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuichi Shirasaki
- Developmental Neurobiology Group, Graduate School of Frontier Biosciences Osaka University, Osaka, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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22
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Tsyganov MM, Ibragimova MK, Garbukov EY, Bragina OD, Karchevskaya AA, Usynin EA, Litvyakov NV. Determination of BRCAness Phenotype in Breast Tumors for the Appointment of Neoadjuvant Chemotherapy Based on Platinum and Taxanes. Int J Mol Sci 2022; 24. [PMID: 36613648 DOI: 10.3390/ijms24010207] [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: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
The concept of BRCAness was developed because of similarities between sporadic and hereditary breast cancer. BRCAness defines the pathogenesis and treatment sensitivity of many types of cancer, as well as the presence of a defect in the homologous recombination repair of tumor cells simulating the loss of BRCA1 or BRCA2, as in the presence of germline mutations. The question of treatment effectiveness for BRCA-like tumors is controversial and open. Thus, the aim of this work was to study the effectiveness of neoadjuvant chemotherapy (NAC) in BRCA-deficient breast cancer patients without germline mutations. The study involved 130 patients with breast cancer in stages IIA-IIIB. The treatment regimen included neoadjuvant chemotherapy, surgery, and adjuvant chemotherapy. The materials used were tumor samples from before and after chemotherapy. DNA and RNA were isolated from the tumor material. RNA was used to assess the expression level of BRCA1, while DNA was used for methyl-sensitive PCR. A microarray analysis was performed on high-density DNA chips from an Affymetrix CytoScanTM HD Array to assess DNA copy number aberration (CNA status) and loss of heterozygosity. A statistical analysis was performed using the Statistica 8.0 application package. It was noted that the existence of copy number aberrations in genes was statistically significantly associated with tumor treatment response and disease prognosis. Patients with partial regression had a statistically significantly higher amount of deletion than patients without an objective response (5/25 patients; 16%), as shown in the general sample of patients (52.9% versus 27.1%, respectively) at p = 0.0001 and in patients treated with anthracycline-containing regimen (p = 0.0001). In addition, it was shown that patients with BRCA1 deletion had higher rates of metastatic-free survival (log rank test, p = 0.009). BRCAness patients had a higher rate of 5-year metastatic survival, but not of treatment efficacy. The prospective study showed the positive effect of assessing the BRCAness phenotype of a tumor before treatment and of prescribing personalized NAC regimens. The objective response rate was statistically significantly more often observed in the group of patients with personalized chemotherapy (85.0% (34/40 patients) versus 62.3% (56/90 patients); p = 0.007). Despite the controversial effectiveness of BRCA-like tumor treatment, our data showed high predictive and prognostic significance of the BRCAness phenotype for the personalization of platinum and taxane regimens.
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Mankovich N, Kehoe E, Peterson A, Kirby M. Pathway expression analysis. Sci Rep 2022; 12:21839. [PMID: 36528702 PMCID: PMC9759056 DOI: 10.1038/s41598-022-26381-x] [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: 08/20/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
This paper introduces a pathway expression framework as an approach for constructing derived biomarkers. The pathway expression framework incorporates the biological connections of genes leading to a biologically relevant model. Using this framework, we distinguish between shedding subjects post-infection and all subjects pre-infection in human blood transcriptomic samples challenged with various respiratory viruses: H1N1, H3N2, HRV (Human Rhinoviruses), and RSV (Respiratory Syncytial Virus). Additionally, pathway expression data is used for selecting discriminatory pathways from these experiments. The classification results and selected pathways are benchmarked against standard gene expression based classification and pathway ranking methodologies. We find that using the pathway expression data along with selected pathways, which have minimal overlap with high ranking pathways found by traditional methods, improves classification rates across experiments.
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Affiliation(s)
- Nathan Mankovich
- grid.47894.360000 0004 1936 8083Colorado State University, Mathematics, Fort Collins, 80523 USA
| | - Eric Kehoe
- grid.47894.360000 0004 1936 8083Colorado State University, Mathematics, Fort Collins, 80523 USA
| | - Amy Peterson
- grid.47894.360000 0004 1936 8083Colorado State University, Mathematics, Fort Collins, 80523 USA
| | - Michael Kirby
- grid.47894.360000 0004 1936 8083Colorado State University, Mathematics, Fort Collins, 80523 USA
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24
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Jurado-Castañeda E, Ramírez-Martínez CM, Alonso-Moctezuma A, Páramo-Sánchez JT, Rivera-Reza DI, Chanes-Cuevas OA, Ortiz-Solís CL, Téliz-Meneses MA, Hernández-Ortega OR, Vizzuete-Bolaños MX, Olmedo-Bastidas P, Jacinto-Alemán LF. Conventional Ameloblastoma. A Case Report with Microarray and Bioinformatic Analysis. Diagnostics (Basel) 2022; 12. [PMID: 36553196 DOI: 10.3390/diagnostics12123190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Ameloblastoma is a rare benign epithelial odontogenic neoplasm, but with great clinical implications, as despite its benignity and slow growth, most cases are locally aggressive with a significant recurrence rate. Histological, cellular, or molecular analyses of its pathogenesis have confirmed the complexity of this neoplasm. We present the case of a 20-year-old patient with a suggestive clinical and radiographic diagnosis of ameloblastoma. An incisional biopsy was obtained confirming the diagnosis of conventional ameloblastoma. Left hemimandibulectomy and plate reconstruction were performed. Histopathological analysis of the surgical specimen confirmed the conventional ameloblastoma with a plexiform pattern and significant areas of cystic degeneration and amyloid-like-like deposits. Additionally, a microarray was carried out with bioinformatic analysis for the enrichment, protein interaction, and determination of eight hub genes (CRP, BCHE, APP, AKT1, AGT, ACTC1, ADAM10, and APOA2) related to their pathogenesis.
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Lun Y, Hu J, Zuming Y. Circular RNAs expression profiles and bioinformatics analysis in bronchopulmonary dysplasia. J Clin Lab Anal 2022; 37:e24805. [PMID: 36514862 PMCID: PMC9833990 DOI: 10.1002/jcla.24805] [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: 06/07/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) has long been considered the most challenging chronic lung disease for neonatologists and researchers due to its complex pathological mechanisms and difficulty in prediction. Growing evidence indicates that BPD is associated with the dysregulation of circular RNAs (circRNAs). Therefore, we aimed to explore the expression profiles of circRNAs and investigate the underlying molecular network associated with BPD. METHODS Peripheral blood was collected from very-low-birth-weight (VLBW) infants at 5-8 days of life to extract PBMCs. Microarray analysis and qRT-PCR tests were performed to determine the differentially expressed circRNAs (DEcircRNAs) between BPD and non-BPD VLBW infants. Simultaneous analysis of GSE32472 was conducted to obtain differentially expressed mRNAs (DEmRNA) from BPD infants. The miRNAs were predicted by DEcircRNAs and DEmRNAs of upregulated, respectively, and then screened for overlapping ones. GO and KEGG analysis was performed following construction of the competing endogenous RNA regulatory network (ceRNA) for further investigation. RESULTS A total of 65 circRNAs (52 upregulated and 13 downregulated) were identified as DEcircRNAs between the two groups (FC >2.0 and p.adj <0.05). As a result, the ceRNA network was constructed based on three upregulated DEcircRNAs validated by qRT-PCR (hsa_circ_0007054, hsa_circ_0057950, and hsa_circ_0120151). Bioinformatics analysis indicated these DEcircRNAs participated in response to stimulus, IL-1 receptor activation, neutrophil activation, and metabolic pathways. CONCLUSIONS In VLBW infants with a high risk for developing BPD, the circRNA expression profiles in PBMCs were significantly altered in the early post-birth period, suggesting immune dysregulation caused by infection and inflammatory response already existed.
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Affiliation(s)
- Yu Lun
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
| | - Junlong Hu
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
| | - Yang Zuming
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
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26
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Wu P, Jiao F, Huang H, Liu D, Tang W, Liang J, Chen W. Morinda officinalis polysaccharide enable suppression of osteoclastic differentiation by exosomes derived from rat mesenchymal stem cells. Pharm Biol 2022; 60:1303-1316. [PMID: 35801991 PMCID: PMC9272931 DOI: 10.1080/13880209.2022.2093385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
CONTEXT Morinda officinalis F.C. How. (MO) (Rubiaceae) can strengthen bone function. OBJECTIVE To examine the functional mechanism and effect of MO polysaccharides (MOPs) in rats with glucocorticoid-induced osteoporosis (GIOP). MATERIALS AND METHODS Rats with GIOP were treated with 5, 15 or 45 mL/kg of MOP [n = 15 for each dose, intraperitoneal (i.p.) injection every other day for 8 weeks]. The body weight of rats and histomorphology of bone tissues were examined. Bone marrow mesenchymal stem cells (BMSCs)-derived exosomes (Exo) were collected and identified. Bone marrow-derived macrophages (BMMs) were induced to differentiate into osteoclasts and treated with BMSC-Exo for in vitro studies. RESULTS MOP reduced the body weight (5, 15, or 45 mg/kg MOP vs. phosphate-buffered saline: 8%, 15% and 25%, p < 0.01), elevated the bone volume to tissue volume (BV/TV), mean trabecular thickness (Tb.Th), mean trabecular number (Tb.N) and mean connectivity density (Conn.D) (40-86%, p < 0.01), decreased the mean trabecular separation/spacing (Tb.Sp) (22-37%, p < 0.01), increased the cortical bone continuity (35-90%, p < 0.01) and elevated RUNX family transcription factor 2 and RANK levels (5-12%, p < 0.01), but suppressed matrix metallopeptidase 9 and cathepsin K levels (9-20%, p < 0.01) in femur tissues. BMSC-Exo from MOP-treated rats (MOP-Exo) suppressed osteoclastic differentiation and proliferation of BMMs. The downregulation of microRNA-101-3p (miR-101-3p) or the upregulation of prostaglandin-endoperoxide synthase 2 (PTGS2) blocked the functions of MOP-Exo. DISCUSSION AND CONCLUSIONS MOP inhibits osteoclastic differentiation and could potentially be used for osteoporosis management. This suppression may be enhanced by the upregulation of miR-101-3p or the inhibition of PTGS2.
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Affiliation(s)
- Peiyu Wu
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
- CONTACT Peiyu Wu Wen Chen Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, No. 87, Yingbin Road, Huadu District, Guangzhou510800, Guangdong, PR China
| | - Feng Jiao
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
| | - He Huang
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
| | - Donghua Liu
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
| | - Wang Tang
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
| | - Jie Liang
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
| | - Wen Chen
- Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, PR China
- CONTACT Peiyu Wu Wen Chen Department of Orthopedic Surgery, Guangzhou Hospital of Integrated Traditional and Western Medicine, No. 87, Yingbin Road, Huadu District, Guangzhou510800, Guangdong, PR China
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Yuan L, Tang Y, Yin L, Lin X, Luo Z, Wang S, Li J, Liang P, Jiang B. Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy. Genes (Basel) 2022; 13:genes13122258. [PMID: 36553526 PMCID: PMC9778384 DOI: 10.3390/genes13122258] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Background: tRNA-derived small RNAs (tsRNAs) as a novel non-coding RNA have been studied in many cardiovascular diseases, but the relationship between tsRNAs and septic cardiomyopathy has not been investigated. We sought to analyze changes of the expression profile of tsRNAs in septic cardiomyopathy and reveal an important role for tsRNAs. Methods: We constructed a sepsis model by cecal ligation and puncture (CLP) in mice, and microarray analysis was used to find differentially expressed tsRNAs. Quantitative real-time PCR was used to verify the expression of tsRNAs and the interference effect of angiogenin (ANG), a key nuclease producing tsRNAs. Bioinformatics analysis was used to predict target genes and functions. CCK-8 and LDH release assays were used to detect cell viability and cell death. Results: A total of 158 tsRNAs were screened, of which 101 were up-regulated and 57 were down-regulated. A total of 8 tsRNAs were verified by qPCR, which was consistent with microarray results. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses suggest that these tsRNAs may be associated with the Wnt signaling pathway and participate in cellular process. The expression of tsRNAs decreased after the interference of the key nuclease ANG, while CCK-8 suggested a corresponding decrease in cell viability and an increase in the release of LDH (cell death), indicating that tsRNAs can protect cardiomyocytes during the development of septic cardiomyopathy, reduced cardiomyocyte death. Conclusions: A total of 158 tsRNAs changed significantly in septic cardiomyopathy, and these tsRNAs may play a protective role in the development of septic cardiomyopathy.
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Affiliation(s)
- Ludong Yuan
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Yuting Tang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Leijing Yin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Xiaofang Lin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Zhengyang Luo
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Shuxin Wang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Jing Li
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bimei Jiang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, National Medicine Functional Experimental Teaching Center, Xiangya School of Medicine, Central South University, Changsha 410008, China
- Correspondence: ; Tel./Fax: +86-0731-82355019
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Chen Y, Zhao G, Li N, Luo Z, Wang X, Gu J. [Corrigendum] Role of 4‑aminobutyrate aminotransferase (ABAT) and the lncRNA co‑expression network in the development of myelodysplastic syndrome. Oncol Rep 2022; 49:10. [PMID: 36416343 PMCID: PMC9685366 DOI: 10.3892/or.2022.8447] [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: 10/11/2018] [Accepted: 05/20/2019] [Indexed: 11/18/2022] Open
Abstract
Subsequently to the publication of the above article, and a Corrigendum that has already been published with the intention of showing corrected versions of Figs. 1 and 8 (DOI: 10.3892/or.2022.8348; published online on June 14, 2022), the authors have belatedly realized that the revisions made to Fig. 8 necessitated changes that should have been introduced into Fig. 9, although these were not attended to in the first corrigendum. Essentially, Fig. 8 was revised as the cell apoptosis and cell proliferation assays therein were poorly presented, which made the interpretation of the data difficult; Fig. 9 showed the fractions of apoptotic cells in the SKM‑1 and THP‑1 cell lines with lncENST00000444102 overexpression as this pertained to Fig. 8. A revised version of Fig. 9, presenting the analysis of the data shown in the revised version of Fig. 8, is shown opposite. In addition to the revision of Fig. 9, the sentence starting on p. 517, left‑hand column, line 12 ["The flow cytometric apoptosis assay revealed that lncENST00000444102 overexpression promoted tumor cells to undergo apoptosis compared to control cells (P<0.001, Fig. 9)"] should be replaced with the following text, to reflect the change in the level of statistical significance: 'The flow cytometric apoptosis assay revealed that lncENST00000444102 overexpression promoted tumor cells to undergo apoptosis compared to control cells (P<0.01, Fig. 9)". Note that the revisions made to Figs. 8 and 9 in this paper have not had a major impact on the reported results, and do not affect the overall conclusions reported in the study. All the authors agree to the publication of this corrigendum. The authors are grateful to the Editor of Oncology Reports for allowing them the opportunity to publish this additional Corrigendum; furthermore, they apologize for any inconvenience caused to the readership of the Journal. [Oncology Reports 42: 509‑520, 2019; DOI: 10.3892/or.2019.7175].
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Luan C, Jin S, Hu Y, Zhou X, Liu L, Li R, Ju M, Huang D, Chen K. Whole-genome identification and construction of the lncRNA-mRNA co-expression network in patients with actinic keratosis. Transl Cancer Res 2022; 11:4070-4078. [PMID: 36523309 PMCID: PMC9745357 DOI: 10.21037/tcr-22-842] [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: 03/28/2022] [Accepted: 08/17/2022] [Indexed: 08/30/2023]
Abstract
BACKGROUND Actinic keratosis (AK) is a common premalignant lesion induced by chronic exposure to ultraviolet radiation and may develop into invasive cutaneous squamous carcinoma (cSCC). The identification of specific biomarkers in AK are still unclear. Long non-coding RNAs (lncRNAs), as transcripts of more than 200 nucleotides, significantly involving in multiple biologic processes, especially in the development of tumors. METHODS In our study, we obtained data from RNA-sequencing analysis using two AK lesion tissues and three normal cutaneous tissues to comparatively analyze the differentially expressed (DE) lncRNAs and messenger RNAs (mRNAs). Firstly, we used microarray analyses to identify DE lncRNAs and DE mRNAs. Secondly, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to analyze the primary function and find out significant pathways of these DE mRNA and lncRNAs. Finally, we used the top ten DE lncRNAs to construct a lncRNA-mRNA co-expression network. RESULTS Our results showed that there were a total of 2,097 DE lncRNAs and 2,043 DE mRNAs identified. GO and KEGG analysis and the lncRNA-mRNA co-expression network (using the top 10 DE lncRNAs comprises 130 specific co-expressed mRNAs to construct) indicated that lncRNA uc011fnr.2 may negatively regulate SCIMP and Toll-like receptor 4 (TLR4) and play an important role in Janus kinase-signal transducer and activator of transcription 3 (JAK-STAT3) signaling pathway of AK. CONCLUSIONS lncRNA uc011fnr.2 may play an important role in JAK-STAT3 signaling pathway of AK by modulating SCIMP, TLR4 and IL-6. Further research is required to validate the value of lncRNA uc011fnr.2 in the progression of AK.
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Affiliation(s)
- Chao Luan
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Shuang Jin
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Yu Hu
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Xuyue Zhou
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Lingxi Liu
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Rong Li
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Mei Ju
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Dan Huang
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
| | - Kun Chen
- Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China
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Zu Y, Guo S, Li G, Gao Q, Wang X, Zhang C, Liu D. Serum microRNAs as non-invasive diagnostic biomarkers for intrahepatic cholestasis of pregnancy. Am J Transl Res 2022; 14:6763-6773. [PMID: 36247288 PMCID: PMC9556493] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVES Intrahepatic cholestasis of pregnancy (IHCP) causes itching, preterm birth, and stillbirth. However, there is no accurate diagnostic method for IHCP. Currently, circulating microRNAs (miRNAs) have become candidate biomarkers for the diagnosis of multiple diseases. Here, we investigated the diagnostic value of miRNAs in IHCP and aimed to predict the molecular mechanism of IHCP pathogenesis. METHODS We analyzed differentially expressed miRNAs in both women with IHCP and normal pregnant women. The selected candidate miRNAs were validated in 46 IHCP cases and 46 normal pregnant subjects, and we constructed receiver operator characteristic curves of miRNAs. Pearson correlations between levels of total bile acid (TBA) and differentially expressed miRNAs were also calculated. In addition, we clustered functionally significant biological pathways using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. RESULTS The expression levels of 13 miRNAs were remarkably upregulated while the other 35 miRNAs were significantly downregulated, in women with IHCP (P≤0.05) when compared with healthy pregnant women. The areas under the curves of miRNA-7706, miRNA-877-3p, and miRNA-128-3p were higher than 0.90, indicating more reliable diagnosis of IHCP. The Pearson analysis showed that the levels of these miRNAs were positively correlated to TBA level. Additionally, the results of bioinformatics analysis revealed that the differentially expressed miRNAs mainly influenced fatty acid biosynthesis, the endoplasmic reticulum ubiquitin ligase complex, and the p53, and mammalian target of rapamycin (mTOR) and AMP-activated protein kinase (AMPK) signaling pathways. CONCLUSION The panel of three-miRNAs (miRNA-7706, miRNA-877-3p, and miRNA-128-3p) may be a useful noninvasive diagnostic biomarker of IHCP.
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Affiliation(s)
- Yue Zu
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Sheng Guo
- The First Affiliated Hospital of Xinxiang Medical UniversityWeihui, Henan, China
| | - Guodong Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Qianyan Gao
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Ximin Wang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Chengliang Zhang
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
| | - Dong Liu
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei, China
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31
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Rahimpour A, Heidarzadehpilehrood R, Abdollahi S, Ranjbari H, Shams Z, Ghasemi SA, Najmaei S, Pirhoushiaran M. A comprehensive bioinformatic analysis revealed novel MicroRNA biomarkers of Parkinson's disease. Cell Biol Int 2022; 46:1841-1851. [PMID: 36098337 DOI: 10.1002/cbin.11869] [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: 03/02/2022] [Revised: 06/18/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022]
Abstract
Parkinson's disease (PD) is categorized as a neurodegenerative disorder. Different studies have focused on the role of microRNAs (miRNAs) on PD progression. Due to its complexity in initiation and progression, a considerable requirement has arisen to identify novel miRNA biomarkers in a noninvasive manner. In silico analysis has been used to select differentially expressed miRNAs (DE-miRNAs) and key pathways in this disease. In this manner, several data sets of different neurodegenerative diseases have been analyzed to purify the findings of the present study. Totally, 15 DE miRNAs showed significant changes compared to healthy controls and other neurodegenerative diseases. Then, the targets of the miRNAs were predicted through miRTarBase and TargetScan databases. Besides, enrichment analysis was implemented for predicted target genes. Most of the target genes were enriched in the TRAIL signaling pathway, Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, protein serine/threonine kinase activity, and Cytoplasm. Moreover, a protein-protein interaction network was constructed to find the most key DE miRNAs and targets in this disease. The results of the present study may help researchers shed light on the discovery of novel biomarkers for PD.
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Affiliation(s)
- Alireza Rahimpour
- Islamic Azad University of science and research branch Tehran, Tehran, Iran
| | - Roozbeh Heidarzadehpilehrood
- Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Sepideh Abdollahi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Haidar Ranjbari
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Zinat Shams
- Department of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Seyed Abbas Ghasemi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Shima Najmaei
- University of Rostock, Institute of Biological Sciences, Division of Microbiology, A.-Einstein-Str. 3, Rostock, Germany
| | - Maryam Pirhoushiaran
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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32
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DiSalvo M, Cortés-Llanos B, LaBelle CA, Murdoch DM, Allbritton NL. Scalable Additive Construction of Arrayed Microstructures with Encoded Properties for Bioimaging. Micromachines (Basel) 2022; 13:1392. [PMID: 36144015 PMCID: PMC9500771 DOI: 10.3390/mi13091392] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Microarrays are essential components of analytical instruments. The elements of microarrays may be imbued with additional functionalities and encodings using composite materials and structures, but traditional microfabrication methods present substantial barriers to fabrication, design, and scalability. In this work, a tool-free technique was reported to additively batch-construct micromolded, composite, and arrayed microstructures. The method required only a compatible carrier fluid to deposit a material onto a substrate with some topography. Permutations of this basic fabrication approach were leveraged to gain control over the volumes and positions of deposited materials within the microstructures. As a proof of concept, cell micro-carrier arrays were constructed to demonstrate a range of designs, compositions, functionalities, and applications for composite microstructures. This approach is envisioned to enable the fabrication of complex composite biological and synthetic microelements for biosensing, cellular analysis, and biochemical screening.
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Affiliation(s)
- Matthew DiSalvo
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Belén Cortés-Llanos
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Cody A. LaBelle
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - David M. Murdoch
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
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Chen Y, Zhao G, Li N, Luo Z, Wang X, Gu J. [Corrigendum] Role of 4‑aminobutyrate aminotransferase (ABAT) and the lncRNA co‑expression network in the development of myelodysplastic syndrome. Oncol Rep 2022; 48:137. [PMID: 35703350 PMCID: PMC9245076 DOI: 10.3892/or.2022.8348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/20/2019] [Indexed: 11/27/2022] Open
Affiliation(s)
- Yanzhen Chen
- WorldWide Medical Center, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Guangjie Zhao
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Nianyi Li
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Zhongguang Luo
- Department of Digestive Diseases, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Xiaoqin Wang
- Department of Hematology, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
| | - Jingwen Gu
- WorldWide Medical Center, Huashan Hospital of Fudan University, Shanghai 200040, P.R. China
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Elia I, Realini G, Di Mauro V, Borghi S, Bottoni L, Tornambè S, Vitiello L, Weiss SJ, Chiariello M, Tamburrini A, Oliviero S, Neri F, Orlandini M, Galvagni F. SNAI1 is upregulated during muscle regeneration and represses FGF21 and ATF3 expression by directly binding their promoters. FASEB J 2022; 36:e22401. [PMID: 35726676 DOI: 10.1096/fj.202200215r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/09/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022]
Abstract
During skeletal myogenesis, the zinc-finger transcription factors SNAI1 and SNAI2, are expressed in proliferating myoblasts and regulate the transition to terminally differentiated myotubes while repressing pro-differentiation genes. Here, we demonstrate that SNAI1 is upregulated in vivo during the early phase of muscle regeneration induced by bupivacaine injury. Using shRNA-mediated gene silencing in C2C12 myoblasts and whole-transcriptome microarray analysis, we identified a collection of genes belonging to the endoplasmic reticulum (ER) stress pathway whose expression, induced by myogenic differentiation, was upregulated in absence of SNAI1. Among these, key ER stress genes, such as Atf3, Ddit3/Chop, Hspa5/Bip, and Fgf21, a myokine involved in muscle differentiation, were strongly upregulated. Furthermore, by promoter mutant analysis and Chromatin immune precipitation assay, we demonstrated that SNAI1 represses Fgf21 and Atf3 in proliferating myoblasts by directly binding to multiple E boxes in their respective promoter regions. Together, these data describe a new regulatory mechanism of myogenic differentiation involving the direct repressive action of SNAI1 on ER stress and Fgf21 expression, ultimately contributing to maintaining the proliferative and undifferentiated state of myoblasts.
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Affiliation(s)
- Ines Elia
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Giulia Realini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Vittoria Di Mauro
- IRCCS-Humanitas Research Hospital, Rozzano, Italy.,Institute of Genetic and Biomedical Research (IRGB), Milan Unit, National Research Council, Via Fantoli 16/15, Milan, 20138, Italy
| | - Sara Borghi
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA.,Immune Monitoring Laboratory, NYU Langone Health, 550 First Avenue, New York, NY, 10016, USA
| | - Laura Bottoni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Salvatore Tornambè
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Stephen J Weiss
- Division of Genetic Medicine, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Mario Chiariello
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR) and Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Siena, Italy
| | - Annalaura Tamburrini
- Department of Life Science and Systems Biology, Università degli Studi di Torino, Turin, Italy.,IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
| | - Salvatore Oliviero
- Department of Life Science and Systems Biology, Università degli Studi di Torino, Turin, Italy.,IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
| | - Francesco Neri
- Department of Life Science and Systems Biology, Università degli Studi di Torino, Turin, Italy
| | - Maurizio Orlandini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
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Seki S, Iwasaki M, Makino H, Yahara Y, Kondo M, Kamei K, Futakawa H, Nogami M, Watanabe K, Tran Canh Tung N, Hirokawa T, Tsuji M, Kawaguchi Y. Association of Ligamentum Flavum Hypertrophy with Adolescent Idiopathic Scoliosis Progression-Comparative Microarray Gene Expression Analysis. Int J Mol Sci 2022; 23. [PMID: 35563428 DOI: 10.3390/ijms23095038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
The role of the ligamentum flavum (LF) in the pathogenesis of adolescent idiopathic scoliosis (AIS) is not well understood. Using magnetic resonance imaging (MRI), we investigated the degrees of LF hypertrophy in 18 patients without scoliosis and on the convex and concave sides of the apex of the curvature in 22 patients with AIS. Next, gene expression was compared among neutral vertebral LF and LF on the convex and concave sides of the apex of the curvature in patients with AIS. Histological and microarray analyses of the LF were compared among neutral vertebrae (control) and the LF on the apex of the curvatures. The mean area of LF in the without scoliosis, apical concave, and convex with scoliosis groups was 10.5, 13.5, and 20.3 mm2, respectively. There were significant differences among the three groups (p < 0.05). Histological analysis showed that the ratio of fibers (Collagen/Elastic) was significantly increased on the convex side compared to the concave side (p < 0.05). Microarray analysis showed that ERC2 and MAFB showed significantly increased gene expression on the convex side compared with those of the concave side and the neutral vertebral LF cells. These genes were significantly associated with increased expression of collagen by LF cells (p < 0.05). LF hypertrophy was identified in scoliosis patients, and the convex side was significantly more hypertrophic than that of the concave side. ERC2 and MAFB genes were associated with LF hypertrophy in patients with AIS. These phenomena are likely to be associated with the progression of scoliosis.
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36
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Scott CH, Amarillo IE. Identification of Small Regions of Overlap from Copy Number Variable Regions in Patients with Hypospadias. Int J Mol Sci 2022; 23:4246. [PMID: 35457073 PMCID: PMC9027593 DOI: 10.3390/ijms23084246] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Hypospadias is a common form of congenital atypical sex development that is often associated with other congenital comorbidities. Many genes have been associated with the condition, most commonly single sequence variations. Further investigations of recurrent and overlapping copy number variations (CNVs) have resulted in the identification of genes and chromosome regions associated with various conditions, including differences of sex development (DSD). In this retrospective study, we investigated the DECIPHER database, as well as an internal institutional database, to identify small recurrent CNVs among individuals with isolated and syndromic hypospadias. We further investigated these overlapping recurrent CNVs to identify 75 smallest regions of overlap (SROs) on 18 chromosomes. Some of the genes within these SROs may be considered potential candidate genes for the etiology of hypospadias and, occasionally, additional comorbid phenotypes. This study also investigates for the first time additional common phenotypes among individuals with hypospadias and overlapping CNVs. This study provides data that may aid genetic counseling and management of individuals with hypospadias, as well as improve understanding of its underlying genetic etiology and human genital development overall.
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Affiliation(s)
- Carter H. Scott
- Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Ina E. Amarillo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Zheng L, Yue X, Li M, Hu J, Zhang B, Zhang R, Zheng G, Chen R, Dong H. Contribution of FBLN5 to Unstable Plaques in Carotid Atherosclerosis via mir128 and mir532-3p Based on Bioinformatics Prediction and Validation. Front Genet 2022; 13:821650. [PMID: 35356421 PMCID: PMC8959633 DOI: 10.3389/fgene.2022.821650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
FBLN5, a member of the short fibulins in the fibulin family of extracellular matrix/matricellular proteins, is involved in interactions with components of the basement membrane and extracellular matrix proteins. It plays key roles in endothelial tissues in many vascular diseases. In this study, the relationship between FBLN5 and carotid atherosclerotic plaque stability as well as the regulatory roles of miRNAs were evaluated. Differential gene expression analyses and weighted gene co-expression network analysis (WGCNA) based on the GSE163154 dataset (including 16 samples without intraplaque hemorrhage and 27 samples with intraplaque hemorrhage) in GEO revealed that FBLN5 is related to plaque stability and is the most significantly differentially expressed gene. LASSO regression was used to evaluate genes obtained from the intersection of differentially expressed genes and clinically significant modules identified by WGCNA. A prediction model based on eight genes, including FBLN5, was constructed and showed an accuracy of 0.951 based on an ROC analysis. Low FBLN5 expression in plaque tissues was confirmed by immunohistochemistry and western blotting. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that FBLN5 acted mainly by the maintenance of the cellular matrix and reactive oxygen species production. miRNAs upstream of these eight predictive genes, including FBLN5, were identified and used to construct a network diagram. These results revealed that hsa-mir-128 and hsa-mir-532–3p were upstream regulatory factors of FBLN5, as verified by PCR assays of human plaque tissues demonstrating that both miRNAs were significantly up-regulated. Therefore, FBLN5 may play an important role in carotid atherosclerosis via hsa-mir-128 and hsa-mir-532–3p as well as become an essential target for treatment.
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Affiliation(s)
- Lin Zheng
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinyang Yue
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Minhui Li
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jie Hu
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Bojin Zhang
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Ruijing Zhang
- Department of Nephrology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Guoping Zheng
- The Second Hospital of Shanxi Medical University, Taiyuan, China
| | | | - Honglin Dong
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
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Cheng T, Li X, Chen J, Yang L, Liu J, Song G, Ma H. Investigation of hub genes involved in Turner syndrome using biological informatics methods. Medicine (Baltimore) 2022; 101:e29069. [PMID: 35356930 PMCID: PMC10684194 DOI: 10.1097/md.0000000000029069] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database. METHODS GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using R and subsequently annotated by Gene Ontology. Functional enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database for annotation, visualization, and integrated discovery. A protein-protein interaction network of different genes was constructed based on the STRING database, in which hub genes were explored through Cytoscape software. The expression of the hub genes was verified by analyzing the gene expression in the GSE46687 data set. RESULTS A total of 733 differential genes were identified. These differentially expressed genes were significantly enriched in nucleoplasm and nucleus. Their molecular function was concentrated on DNA binding and transcription, coronary artery, and adipose tissue development. According to the annotation of Kyoto Encyclopedia of Genes and Genomes, the identified DEGs were mainly enriched in inflammatory mediator regulation of TRP channels, osteoclast differentiation. A total of 10 hub genes (HIST1H2BA, TRIM71, HIST1H2BB, HIST1H4D, TNF, TP53BP1, CDCA8, EGF, HMG20B, and BCL9) were identified from the constructed protein-protein interaction network. These genes were discovered to be highly expressed in osteoclasts, ovaries, digestive tract, blood, and lymphatic tissues through the online application of human protein atlas. CONCLUSION In this study, 733 DEGs and 10 hub genes were identified. They would be new candidate targets in Turner syndrome.
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Affiliation(s)
| | | | | | | | | | | | - Huijuan Ma
- Correspondence: Huijuan Ma, Hebei General Hospital, Shijiazhuang, Hebei, China (e-mail: ).
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Ma Q, Wang L, Wang Z, Su Y, Hou Q, Xu Q, Cai R, Wang T, Gong X, Yi Q. Long non-coding RNA screening and identification of potential biomarkers for type 2 diabetes. J Clin Lab Anal 2022; 36:e24280. [PMID: 35257412 PMCID: PMC8993646 DOI: 10.1002/jcla.24280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/20/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND To investigate new lncRNAs as molecular markers of T2D. METHODS We used microarrays to identify differentially expressed lncRNAs and mRNAs from five patients with T2D and paired controls. Through bioinformatics analysis, qRT-PCR validation, ELISA, and receiver operating characteristic (ROC) curve analysis of 100 patients with T2D and 100 controls to evaluate the correlation between lncRNAs and T2D, and whether lncRNAs could be used in the diagnosis of T2D patients. RESULTS We identified 68 and 74 differentially expressed lncRNAs and mRNAs, respectively. The top five upregulated lncRNAs are ENST00000381108.3, ENST00000515544.1, ENST00000539543.1, ENST00000508174.1, and ENST00000564527.1, and the top five downregulated lncRNAs are TCONS_00017539, ENST00000430816.1, ENST00000533203.1, ENST00000609522.1, and ENST00000417079.1. The top five upregulated mRNAs are Q59H50, CYP27A1, DNASE1L3, GRIP2, and lnc-TMEM18-12, and the top five downregulated mRNAs are GSTM4, PODN, GLYATL2, ZNF772, and CLTC. Examination of lncRNA-mRNA interaction pairs indicated that the target gene of lncRNA XR_108954.2 is E2F2. Multiple linear regression analysis showed that XR_108954.2 (r = 0.387, p < 0.01) and E2F2 (r = 0.368, p < 0.01) expression levels were positively correlated with glucose metabolism indicators. Moreover, E2F2 was positively correlated with lipid metabolism indicators (r = 0.333, p < 0.05). The area under the ROC curve was 0.704 (95% CI: 0.578-0.830, p = 0.05) for lncRNA XR_108954.2 and 0.653 (95% CI: 0.516-0.790, p = 0.035) for E2F2. CONCLUSIONS This transcriptome analysis explored the aberrantly expressed lncRNAs and identified E2F2 and lncRNA XR_108954.2 as potential biomarkers for patients with T2D.
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Affiliation(s)
- Qi Ma
- Xinjiang Key Laboratory of Metabolic Disease, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Li Wang
- Xinjiang Key Laboratory of Metabolic Disease, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Wang
- Kuntuo Medical Research and Development Company, Shanghai, China
| | - Yinxia Su
- Hospital of Public Health, Xinjiang Medical University, Urumqi, China
| | - Qinqin Hou
- Department of pathology, Fudan university Shanghai cancer center, Shanghai, China
| | - Qiushuang Xu
- Psychological Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Ren Cai
- Specimen Bank of Xinjiang Key Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Tingting Wang
- School of Nursing & Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xueli Gong
- Department of Pathophysiology, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Qizhong Yi
- Psychological Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Singh HN, Swarup V, Dubey NK, Jha NK, Singh AK, Lo WC, Kumar S. Differential Transcriptome Profiling Unveils Novel Deregulated Gene Signatures Involved in Pathogenesis of Alzheimer's Disease. Biomedicines 2022; 10. [PMID: 35327413 DOI: 10.3390/biomedicines10030611] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder that is characterized by a progressive loss of cognitive functions at a higher level than normal aging. Although the apolipoprotein (APOE) gene is a major risk factor in developing AD, other genes have also been reported to be linked with complex phenotypes. Therefore, this genome-wide expression study explored differentially expressed genes as possible novel biomarkers involved in AD. The mRNA expression dataset, GSE28146, containing 15 sample data composed of 7 AD cases from the hippocampus region with age-matched control (n = 8, >80 years), was analyzed. Using “affy” R-package, mRNA expression was calculated, while pathway enrichment analysis was performed to determine related biological processes. Of 58 differentially expressed genes, 44 downregulated and 14 upregulated genes were found to be significantly (p < 0.001) altered. The pathway enrichment analysis revealed two altered genes, i.e., dynein light chain 1 (DYNLL1) and kalirin (KLRN), associated with AD in the elderly population. The majority of genes were associated with retrograde endocannabinoid as well as vascular endothelial growth factors affecting the complex phenotypes. The DYNLL1 and KLRN genes may be involved with AD and Huntington’s disease (HD) phenotypes and represent a common genetic basis of these diseases. However, the hallmark of AD is dementia, while the classic motor sign of HD includes chorea. Our data warrant further investigation to identify the role of these genes in disease pathogenesis.
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Rahimmanesh I, Fatehi R, Khanahmad H. Identification of Significant Genes and Pathways Associated with Tenascin-C in Cancer Progression by Bioinformatics Analysis. Adv Biomed Res 2022; 11:17. [PMID: 35386538 PMCID: PMC8977614 DOI: 10.4103/abr.abr_201_20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022] Open
Abstract
Background Tenascin-C (TNC) is a large glycoprotein of the extracellular matrix which associated with poor clinical outcomes in several malignancies. TNC over-expression is repeatedly observed in several cancer tissues and promotes several processes in tumor progression. Until quite recently, more needs to be known about the potential mechanisms of TNC as a key player in cancer progression and metastasis. Materials and Methods In the present study, we performed a bioinformatics analysis of breast and colorectal cancer expression microarray data to survey TNC role and function with holistic view. Gene expression profiles were analyzed to identify differentially expressed genes (DEGs) between normal samples and cancer biopsy samples. The protein-protein interaction (PPI) networks of the DEGs with CluePedia plugin of Cytoscape software were constructed. Furthermore, after PPI network construction, gene-regulatory networks analysis was performed to predict long noncoding RNAs and microRNAs associated with TNC and cluster analysis was performed. Using the Clue gene ontology (GO) plugin of Cytoscape software, the GO and pathway enrichment analysis were performed. Results PPI and DEGs-miRNA-lncRNA regulatory networks showed TNC is a significant node in a huge network, and one of the main gene with high centrality parameters. Furthermore, from the regulatory level perspective, TNC could be significantly impressed by miR-335-5p. GO analysis results showed that TNC was significantly enriched in cancer-related biological processes. Conclusions It is important to identify the TNC underlying molecular mechanisms in cancer progression, which may be clinically useful for tumor-targeting strategies. Bioinformatics analysis provides an insight into the significant roles that TNC plays in cancer progression scenarios.
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Affiliation(s)
- Ilnaz Rahimmanesh
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran,Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Razieh Fatehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non- Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran,Address for correspondence: Dr. Hossein Khanahmad, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. E-mail:
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Li D, Zhen F, Le J, Chen G, Zhu J. Identification of hub genes and pathways in bladder cancer using bioinformatics analysis. Am J Clin Exp Urol 2022; 10:13-24. [PMID: 35291419 PMCID: PMC8918393] [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] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/30/2020] [Indexed: 06/14/2023]
Abstract
Bladder cancer (BC) is the most common malignant tumor of urinary tract system. The aim of this study was to investigate the genetic signatures of bladder cancer (BC) and identify its potential molecular mechanisms. The gene expression profiles of GSE3167 (50 samples, including 41BC and 9 non-cancerous urothelial cells) was downloaded from the GEO database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) were performed to identify enriched pathways, and a protein-protein interaction (PPI) network was used to identify hub genes and for module analysis. Moreover, we conducted expression and survival analyses to screen and validate hub genes. In total, 1528 DEGs were identified in bladder cancer (BC), including 1212 up-regulated genes and 316 down-regulated genes. Up-regulated differentially expressed genes (DEGs) were significantly enriched in negative regulation of macromolecule metabolic process, macromolecule catabolic process, proteolysis and regulation of cell death, while the down-regulated differentially expressed genes (DEGs) were mainly involved in cell surface receptor linked signal transduction, ion transport, cell-cell signaling and defense response. The top 10 hub genes with the highest degrees were selected from the PPI network. These genes included HSP90AA1, MYH11, MYL9, CNN1, ACTC1, RAN, ENO1, HNRNPC, ACTG2 and YWHAZ. From sub-networks, we found these genes were involved in the proteasome, pathways in cancer and cell cycle. Hence, the identified DEGs and hub genes may be beneficial to elucidate the mechanisms underlying BC.
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Affiliation(s)
- Danhui Li
- Department of ICU, Ningbo First Hospital Ningbo, Zhejiang Province, P. R. China
| | - Fan Zhen
- Department of ICU, Ningbo First Hospital Ningbo, Zhejiang Province, P. R. China
| | - Jianwei Le
- Department of ICU, Ningbo First Hospital Ningbo, Zhejiang Province, P. R. China
| | - Guodong Chen
- Department of ICU, Ningbo First Hospital Ningbo, Zhejiang Province, P. R. China
| | - Jianhua Zhu
- Department of ICU, Ningbo First Hospital Ningbo, Zhejiang Province, P. R. China
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Jazdarehee A, Huget-Penner S, Pawlowska M. Pseudo-pheochromocytoma due to obstructive sleep apnea: a case report. Endocrinol Diabetes Metab Case Rep 2022; 2022:21-0100. [PMID: 35212265 PMCID: PMC8897593 DOI: 10.1530/edm-21-0100] [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: 12/17/2021] [Accepted: 02/02/2022] [Indexed: 11/11/2022] Open
Abstract
SUMMARY Obstructive sleep apnea (OSA) is a condition of intermittent nocturnal upper airway obstruction. OSA increases sympathetic drive which may result in clinical and biochemical features suggestive of pheochromocytoma. We present the case of a 65-year-old male with a 2.9-cm left adrenal incidentaloma on CT, hypertension, symptoms of headache, anxiety and diaphoresis, and persistently elevated 24-h urine norepinephrine (initially 818 nmol/day (89-470)) and normetanephrine (initially 11.2 µmol/day (0.6-2.7)). He was started on prazosin and underwent left adrenalectomy. Pathology revealed an adrenal corticoadenoma with no evidence of pheochromocytoma. Over the next 2 years, urine norepinephrine and normetanephrine remained significantly elevated with no MIBG avid disease. Years later, he was diagnosed with severe OSA and treated with continuous positive airway pressure. Urine testing done once OSA was well controlled revealed complete normalization of urine norepinephrine and normetanephrine with substantial symptom improvement. It was concluded that the patient never had a pheochromocytoma but rather an adrenal adenoma with biochemistry and symptoms suggestive of pheochromocytoma due to untreated severe OSA. Pseudo-pheochromocytoma is a rare presentation of OSA and should be considered on the differential of elevated urine catecholamines and metanephrines in the right clinical setting. LEARNING POINTS Obstructive sleep apnea (OSA) is a common condition among adults. OSA may rarely present as pseudo-pheochromocytoma with symptoms of pallor, palpitations, perspiration, headache, or anxiety. OSA should be considered on the differential of elevated urine catecholamines and metanephrines, especially in patients with negative metaiodobenzylguanidine (MIBG) scan results.
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Key Words
- adolescent/young adult
- adult
- geriatric
- neonatal
- paediatric
- pregnant adult
- female
- male
- american indian or alaska native
- asian - bangladeshi
- asian - chinese
- asian - filipino
- asian - indian
- asian - japanese
- asian - korean
- asian - pakistani
- asian - vietnamese
- asian - other
- black - african
- black - caribbean
- black - other
- hispanic or latino - central american or south american
- hispanic or latino - cuban
- hispanic or latino - dominican
- hispanic or latino - mexican, mexican american, chicano
- hispanic or latino - puerto rican
- hispanic or latino - other
- native hawaiian/other pacific islander
- white
- other
- afghanistan
- aland islands
- albania
- algeria
- american samoa
- andorra
- angola
- anguilla
- antarctica
- antigua and barbuda
- argentina
- armenia
- aruba
- australia
- austria
- azerbaijan
- bahamas
- bahrain
- bangladesh
- barbados
- belarus
- belgium
- belize
- benin
- bermuda
- bhutan
- bolivia
- bosnia and herzegovina
- botswana
- bouvet island
- brazil
- british indian ocean territory
- brunei darussalam
- bulgaria
- burkina faso
- burundi
- cambodia
- cameroon
- canada
- cape verde
- cayman islands
- central african republic
- chad
- chile
- china
- christmas island
- cocos (keeling) islands
- colombia
- comoros
- congo
- congo, the democratic republic of the
- cook islands
- costa rica
- côte d'ivoire
- croatia
- cuba
- cyprus
- czech republic
- denmark
- djibouti
- dominica
- dominican republic
- ecuador
- egypt
- el salvador
- equatorial guinea
- eritrea
- estonia
- ethiopia
- falkland islands (malvinas)
- faroe islands
- fiji
- finland
- france
- french guiana
- french polynesia
- french southern territories
- gabon
- gambia
- georgia
- germany
- ghana
- gibraltar
- greece
- greenland
- grenada
- guadeloupe
- guam
- guatemala
- guernsey
- guinea
- guinea-bissau
- guyana
- haiti
- heard island and mcdonald islands
- holy see (vatican city state)
- honduras
- hong kong
- hungary
- iceland
- india
- indonesia
- iran, islamic republic of
- iraq
- ireland
- isle of man
- israel
- italy
- jamaica
- japan
- jersey
- jordan
- kazakhstan
- kenya
- kiribati
- korea, democratic people's republic of
- korea, republic of
- kuwait
- kyrgyzstan
- lao people's democratic republic
- latvia
- lebanon
- lesotho
- liberia
- libyan arab jamahiriya
- liechtenstein
- lithuania
- luxembourg
- macao
- macedonia, the former yugoslav republic of
- madagascar
- malawi
- malaysia
- maldives
- mali
- malta
- marshall islands
- martinique
- mauritania
- mauritius
- mayotte
- mexico
- micronesia, federated states of
- moldova, republic of
- monaco
- mongolia
- montenegro
- montserrat
- morocco
- mozambique
- myanmar
- namibia
- nauru
- nepal
- netherlands
- netherlands antilles
- new caledonia
- new zealand
- nicaragua
- niger
- nigeria
- niue
- norfolk island
- northern mariana islands
- norway
- oman
- pakistan
- palau
- palestinian territory, occupied
- panama
- papua new guinea
- paraguay
- peru
- philippines
- pitcairn
- poland
- portugal
- puerto rico
- qatar
- réunion
- romania
- russian federation
- rwanda
- saint barthélemy
- saint helena
- saint kitts and nevis
- saint lucia
- saint martin
- saint pierre and miquelon
- saint vincent and the grenadines
- samoa
- san marino
- sao tome and principe
- saudi arabia
- senegal
- serbia
- seychelles
- sierra leone
- singapore
- slovakia
- slovenia
- solomon islands
- somalia
- south africa
- south georgia and the south sandwich islands
- spain
- sri lanka
- sudan
- suriname
- svalbard and jan mayen
- swaziland
- sweden
- switzerland
- syrian arab republic
- taiwan, province of china
- tajikistan
- tanzania, united republic of
- thailand
- timor-leste
- togo
- tokelau
- tonga
- trinidad and tobago
- tunisia
- turkey
- turkmenistan
- turks and caicos islands
- tuvalu
- uganda
- ukraine
- united arab emirates
- united kingdom
- united states
- united states minor outlying islands
- uruguay
- uzbekistan
- vanuatu
- vatican city state
- venezuela
- viet nam
- virgin islands, british
- virgin islands, u.s.
- wallis and futuna
- western sahara
- yemen
- zambia
- zimbabwe
- maylaysia
- adipose tissue
- adrenal
- bone
- duodenum
- heart
- hypothalamus
- kidney
- liver
- ovaries
- pancreas
- parathyroid
- pineal
- pituitary
- placenta
- skin
- stomach
- testes
- thymus
- thyroid
- andrology
- autoimmunity
- cardiovascular endocrinology
- developmental endocrinology
- diabetes
- emergency
- endocrine disruptors
- endocrine-related cancer
- epigenetics
- genetics and mutation
- growth factors
- gynaecological endocrinology
- immunology
- infectious diseases
- late effects of cancer therapy
- mineral
- neuroendocrinology
- obesity
- ophthalmology
- paediatric endocrinology
- puberty
- tumours and neoplasia
- vitamin d
- 17ohp
- acth
- adiponectin
- adrenaline
- aldosterone
- amh
- androgens
- androstenedione
- androsterone
- angiotensin
- antidiuretic hormone
- atrial natriuretic hormone
- avp
- beta-endorphin
- big igf2
- brain natriuretic peptide
- calcitonin
- calcitriol
- cck
- corticosterone
- corticotrophin
- cortisol
- cortisone
- crh
- dehydroepiandrostenedione
- deoxycorticosterone
- deoxycortisol
- dhea
- dihydrotestosterone
- dopamine
- endothelin
- enkephalin
- epitestosterone
- epo
- fgf23
- fsh
- gastrin
- gh
- ghrelin
- ghrh
- gip
- glp1
- glp2
- glucagon
- glucocorticoids
- gnrh
- gonadotropins
- hcg
- hepcidin
- histamine
- human placental lactogen
- hydroxypregnenolone
- igf1
- igf2
- inhibin
- insulin
- kisspeptin
- leptin
- lh
- melanocyte-stimulating hormone
- melatonin
- metanephrines
- mineralocorticoids
- motilin
- nandrolone
- neuropeptide y
- noradrenaline
- normetanephrine
- oestetrol (e4)
- oestradiol (e2)
- oestriol (e3)
- oestrogens
- oestrone (e1)
- osteocalcin
- oxyntomodulin
- oxytocin
- pancreatic polypeptide
- peptide yy
- pregnenolone
- procalcitonin
- progesterone
- prolactin
- prostaglandins
- pth
- relaxin
- renin
- resistin
- secretin
- somatostatin
- testosterone
- thpo
- thymosin
- thymulin
- thyroxine (t4)
- trh
- triiodothyronine (t3)
- tsh
- vip
- 17-alpha hydroxylase/17,20 lyase deficiency
- 17-beta-hydroxysteroid dehydrogenase type 3 deficiency
- 3-m syndrome
- 22q11 deletion syndrome
- 49xxxxy syndrome
- abscess
- acanthosis nigricans
- acromegaly
- acute adrenocortical insufficiency
- addisonian crisis
- addison's disease
- adenocarcinoma
- aip gene mutation
- adrenal insufficiency
- adrenal salt-wasting crisis
- adrenarche
- adrenocortical adenoma
- adrenocortical carcinoma
- adrenoleukodystrophy
- aip gene variant
- amenorrhoea (primary)
- amenorrhoea (secondary)
- amyloid goitre
- amyloidosis
- anaplastic thyroid cancer
- anaemia
- aneuploidy
- androgen insensitivity syndrome
- anti-phospholipid antibody syndrome
- asthma
- autoimmune disorders
- autoimmune polyendocrine syndrome 1
- autoimmune polyendocrine syndrome 2
- autoimmune polyglandular syndrome
- autoimmune hypophysitis
- autosomal dominant hypophosphataemic rickets
- autosomal dominant osteopetrosis
- bardet-biedl syndrome
- bartter syndrome
- bilateral adrenal hyperplasia
- biliary calculi
- breast cancer
- brenner tumour
- brown tumour
- burkitt's lymphoma
- casr gene mutation
- catecholamine secreting carotid body paraganglionoma
- cancer-prone syndrome
- carcinoid syndrome
- carcinoid tumour
- carney complex
- carotid body paraganglioma
- c-cell hyperplasia
- cerebrospinal fluid leakage
- chronic fatigue syndrome
- circadian rhythm sleep disorders
- congenital adrenal hyperplasia
- congenital hypothyroidism
- congenital hyperinsulinism
- conn's syndrome
- corticotrophic adenoma
- craniopharyngioma
- cretinism
- crohn's disease
- cryptorchidism
- cushing's disease
- cushing's syndrome
- cystolithiasis
- de quervain's thyroiditis
- denys-drash syndrome
- desynchronosis
- developmental abnormalities
- diabetes - lipoatrophic
- diabetes - mitochondrial
- diabetes - steroid-induced
- diabetes insipidus - dipsogenic
- diabetes insipidus - gestational
- diabetes insipidus - nephrogenic
- diabetes insipidus - neurogenic/central
- diabetes mellitus type 1
- diabetes mellitus type 2
- diabetic foot syndrome
- diabetic hypoglycaemia
- diabetic ketoacidosis
- diabetic muscle infarction
- diabetic nephropathy
- diverticular disease
- donohue syndrome
- down syndrome
- eating disorders
- ectopic acth syndrome
- ectopic cushing's syndrome
- ectopic parathyroid adenoma
- empty sella syndrome
- endometrial cancer
- endometriosis
- eosinophilic myositis
- euthyroid sick syndrome
- familial hypocalciuric hypercalcaemia
- familial dysalbuminaemic hyperthyroxinaemia
- familial euthyroid hyperthyroxinaemia
- fat necrosis
- female athlete triad syndrome
- fetal demise
- fetal macrosomia
- follicular thyroid cancer
- fractures
- frasier syndrome
- friedreich's ataxia
- functional parathyroid cyst
- galactorrhoea
- gastrinoma
- gastritis
- gastrointestinal perforation
- gastrointestinal stromal tumour
- gck mutation
- gender identity disorder
- gestational diabetes mellitus
- giant ovarian cysts
- gigantism
- gitelman syndrome
- glucagonoma
- glucocorticoid remediable aldosteronism
- glycogen storage disease
- goitre
- goitre (multinodular)
- gonadal dysgenesis
- gonadoblastoma
- gonadotrophic adenoma
- gorham's disease
- granuloma
- granulosa cell tumour
- graves' disease
- graves' ophthalmopathy
- growth hormone deficiency (adult)
- growth hormone deficiency (childhood onset)
- gynaecomastia
- hamman's syndrome
- haemorrhage
- hajdu-cheney syndrome
- hashimoto's disease
- hemihypertrophy
- hepatitis c
- hereditary multiple osteochondroma
- hirsutism
- histiocytosis
- huntington's disease
- hürthle cell adenoma
- hyperaldosteronism
- hyperandrogenism
- hypercalcaemia
- hypercalcaemic crisis
- hyperglucogonaemia
- hyperglycaemia
- hypergonadotropic hypogonadism
- hypergonadotropism
- hyperinsulinaemia
- hyperinsulinaemic hypoglycaemia
- hyperkalaemia
- hyperlipidaemia
- hypernatraemia
- hyperosmolar hyperglycaemic state
- hyperparathyroidism (primary)
- hyperparathyroidism (secondary)
- hyperparathyroidism (tertiary)
- hyperpituitarism
- hyperprolactinaemia
- hypersexuality
- hypertension
- hyperthyroidism
- hypoaldosteronism
- hypocalcaemia
- hypoestrogenism
- hypoglycaemia
- hypoglycaemic coma
- hypogonadism
- hypogonadotrophic hypogonadism
- hypoinsulinaemia
- hypokalaemia
- hyponatraemia
- hypoparathyroidism
- hypophosphataemia
- hypophosphatasia
- hypophysitis
- hypopituitarism
- hypothyroidism
- iatrogenic disorder
- idiopathic bilateral adrenal hyperplasia
- idiopathic pituitary hyperplasia
- igg4-related systemic disease
- inappropriate tsh secretion
- incidentaloma
- infertility
- insulin autoimmune syndrome
- insulin resistance
- insulinoma
- intracranial vasospasm
- intrauterine growth retardation
- iodine allergy
- ischaemic heart disease
- kallmann syndrome
- ketoacidosis
- klinefelter syndrome
- kwashiorkor
- kwashiorkor (marasmic)
- leg ulcer
- laron syndrome
- latent autoimmune diabetes of adults (lada)
- laurence-moon syndrome
- left ventricular hypertrophy
- leukocytoclastic vasculitis
- leydig cell tumour
- lipodystrophy
- lipomatosis
- liver failure
- lung metastases
- luteoma
- lymphadenopathy
- macronodular adrenal hyperplasia
- macronodular hyperplasia
- macroprolactinoma
- marasmus
- maturity onset diabetes of young (mody)
- mccune-albright syndrome
- mckittrick-wheelock syndrome
- medullary thyroid cancer
- meigs syndrome
- membranous nephropathy
- men1
- men2a
- men2b
- men4
- menarche
- meningitis
- menopause
- metabolic acidosis
- metabolic syndrome
- metastatic carcinoma
- metastatic chromaffin cell tumour
- metastatic gastrinoma
- metastatic melanoma
- metastatic tumour
- microadenoma
- microprolactinoma
- motor neurone disease
- myasthenia gravis
- myelolipoma
- myocardial infarction
- myositis
- myotonic dystrophy type 1
- myotonic dystrophy type 2
- myxoedema
- myxoedema coma
- nelson's syndrome
- neonatal diabetes
- nephrolithiasis
- neuroblastoma
- neuroendocrine tumour
- neurofibromatosis
- nodular hyperplasia
- non-functioning pituitary adenoma
- non-hodgkin lymphoma
- non-islet-cell tumour hypoglycaemia
- noonan syndrome
- oculocerebrorenal syndrome
- osteogenesis imperfecta
- osteomalacia
- osteomyelitis
- osteoporosis
- osteoporosis (pregnancy/lactation-associated)
- osteosclerosis
- ovarian cancer
- ovarian dysgenesis
- ovarian hyperstimulation syndrome
- ovarian tumour
- paget's disease
- paget's disease (juvenille)
- pancreatic neuroendocrine tumour
- pancreatitis
- panhypopituitarism
- papillary thyroid cancer
- paraganglioma
- paranasal sinus lesion
- paraneoplastic syndromes
- parasitic thyroid nodules
- parathyroid adenoma
- parathyroid adenoma (ectopic)
- parathyroid carcinoma
- parathyroid cyst
- parathroid hyperplasia
- pcos
- periodontal disease
- phaeochromocytoma
- phaeochromocytoma crisis
- pickardt syndrome
- pituitary abscess
- pituitary adenoma
- pituitary apoplexy
- pituitary carcinoma
- pituitary cyst
- pituitary haemorrhage
- pituitary hyperplasia
- pituitary hypoplasia
- pituitary tumour (malignant)
- plurihormonal pituitary adenoma
- poems syndrome
- polycythaemia
- porphyria
- pneumonia
- posterior reversible encephalopathy syndrome
- post-prandial hypoglycaemia
- prader-willi syndrome
- prediabetes
- pre-eclampsia
- pregnancy
- premature ovarian failure
- premenstrual dysphoric disorder
- premenstrual syndrome
- primary hypertrophic osteoarthropathy
- prolactinoma
- prostate cancer
- pseudohypoaldosteronism type 1
- pseudohypoaldosteronism type 2
- pseudohypoparathyroidism
- psychosocial short stature
- puberty (delayed or absent)
- puberty (precocious)
- pulmonary oedema
- quadrantanopia
- rabson-mendenhall syndrome
- rhabdomyolysis
- rheumatoid arthritis
- rickets
- schwannoma
- sellar reossification
- sertoli cell tumour
- sertoli-leydig cell tumour
- sexual development disorders
- sheehan's syndrome
- short stature
- siadh
- small-cell carcinoma
- small intestine neuroendocrine tumour
- solitary fibrous tumour
- solitary sellar plasmacytoma
- somatostatinoma
- somatotrophic adenoma
- squamous cell thyroid carcinoma
- stiff person syndrome
- struma ovarii
- subcutaneous insulin resistance
- systemic lupus erythematosus
- takotsubo cardiomyopathy
- tarts
- testicular cancer
- thecoma
- thyroid adenoma
- thyroid carcinoma
- thyroid cyst
- thyroid dysgenesis
- thyroid fibromatosis
- thyroid hormone resistance syndrome
- thyroid lymphoma
- thyroid nodule
- thyroid storm
- thyroiditis
- thyrotoxicosis
- thyrotrophic adenoma
- traumatic brain injury
- tuberculosis
- tuberous sclerosis complex
- tumour-induced osteomalacia
- turner syndrome
- unilateral adrenal hyperplasia
- ureterolithiasis
- urolithiasis
- von hippel-lindau disease
- wagr syndrome
- waterhouse-friderichsen syndrome
- williams syndrome
- wolcott-rallison syndrome
- wolfram syndrome
- xanthogranulomatous hypophysitis
- xlaad/ipex
- zollinger-ellison syndrome
- abdominal adiposity
- abdominal distension
- abdominal cramp
- abdominal discomfort
- abdominal guarding
- abdominal lump
- abdominal pain
- abdominal tenderness
- abnormal posture
- abdominal wall defects
- abrasion
- acalculia
- accelerated growth
- acne
- acrochorda
- acroosteolysis
- acute stress reaction
- adverse breast development
- aggression
- agitation
- agnosia
- akathisia
- akinesia
- albuminuria
- alcohol intolerance
- alexia
- alopecia
- altered level of consciousness
- amaurosis
- amaurosis fugax
- ambiguous genitalia
- amblyopia
- amenorrhoea
- ameurosis
- amnesia
- amusia
- anasarca
- angiomyxoma
- anhedonia
- anisocoria
- ankle swelling
- anorchia
- anorectal malformations
- anorexia
- anosmia
- anosognosia
- anovulation
- antepartum haemorrhage
- anuria
- anxiety
- apathy
- aphasia
- aphonia
- apnoea
- appendicitis
- appetite increase
- appetite reduction/loss
- apraxia
- aqueductal stenosis
- arteriosclerosis
- arthralgia
- articulation impairment
- ascites
- asperger syndrome
- asphyxia
- asthenia
- astigmatism
- asymptomatic
- ataxia
- atrial fibrillation
- atrial myxoma
- atrophy
- adhd
- autism
- autonomic neuropathy
- avulsion
- babinski's sign
- back pain
- bacteraemia
- behavioural problems
- belching
- bifid scrotum
- biliary colic
- bitemporal hemianopsia
- blindness
- blistering
- bloating
- bloody show
- boil(s)
- bone cyst
- bone fracture(s)
- bone lesions
- bone pain
- bony metastases
- borborygmus
- bowel movements - bleeding
- bowel movements - increased frequency
- bowel movements - pain
- bowel obstruction
- bowel perforation
- brachycephaly
- brachydactyly
- bradycardia
- bradykinesia
- bradyphrenia
- bradypnea
- breast contour change
- breast enlargement
- breast lump
- breast reduction
- breast tenderness
- breastfeeding difficulties
- breathing difficulties
- bronchospasms
- brushfield spots
- bruxism
- buffalo hump
- cachexia
- calcification
- cardiac fibrosis
- cardiac malformations
- cardiac tamponade
- cardiogenic shock
- cardiomegaly
- cardiomyopathy
- cardiopulmonary arrest
- carpal tunnel syndrome
- caruncle - inflammation
- cataplexy
- cataract(s)
- catathrenia
- central obesity
- cerebrospinal fluid rhinorrhoea
- cervical pain
- cheeks - full
- cheiloschisis
- chemosis
- chest pain
- chest pain (pleuritic)
- chest pain (precordial)
- cheyne-stokes respiration
- chills
- cholecystitis
- cholestasis
- chondrocalcinosis
- chordee
- chorea
- choroidal atrophy
- chronic pain
- circulatory collapse
- cirrhosis
- citraturia
- claudication
- clitoromegaly
- cloacal exstrophy
- clonus
- club foot
- clumsiness
- coagulopathy
- coarctation
- coeliac disease
- cognitive problems
- cold intolerance
- collapse
- colour blindness
- coma
- concentration difficulties
- confusion
- congenital heart defect
- conjunctivitis
- constipation
- convulsions
- coordination difficulties
- coughing
- crackles
- cramps
- craniofacial abnormalities
- craniotabes
- cutaneous ischaemia
- cutaneous myxoma
- cutaneous pigmentation
- cyanosis
- dalrymple's sign
- deafness
- deep vein thrombosis
- dehydration
- delayed puberty
- delirium
- dementia
- dental abscess(es)
- dental problems
- depression
- diabetes insipidus
- diabetic neuropathy
- diabetic foot infection
- diabetic foot neuropathy
- diabetic foot ulceration
- diarrhoea
- diplopia
- dizziness
- duodenal atresia
- duplex kidney(s)
- dysarthria
- dysdiadochokinesia
- dysgraphia
- dyslexia
- dyslipidaemia
- dysmenorrhoea
- dyspareunia
- dyspepsia
- dysphagia
- dysphonia
- dysphoria
- dyspnoea
- dystonia
- dysuria
- ear, nose and/or throat infection
- early menarche
- ears - low set
- ears - pinna abnormalities
- ears - small
- ecchymoses
- ectopic ureter
- emotional immaturity
- encopresis
- endometrial hyperplasia
- enlarged bladder
- enlarged prostate
- eosinophilia
- epicanthic fold
- epilepsy
- epistaxis
- erectile dysfunction
- erythema
- euphoria
- eyebrows - bushy
- eyelid retraction
- eyelid swelling
- eyelids - redness
- eyes - almond-shaped
- eyes - dry
- eyes - feeling of grittiness
- eyes - inflammation
- eyes - irritation
- eyes - itching
- eyes - pain (gazing down)
- eyes - pain (gazing up)
- eyes - redness
- eyes - watering
- face - change in appearance
- face - coarse features
- face - numbness
- facial fullness
- facial palsy
- facial plethora
- facial weakness
- facies - abnormal
- facies - hippocratic
- facies - moon
- faecal incontinence
- failure to thrive
- fallopian tube hyperplasia
- fasciculation
- fatigue
- fatigue (post-exertional)
- feet - cold
- feet - increased size
- feet - large
- feet - pain
- feet - small
- fingers - thick
- flaccid paralysis
- flatulence
- flushing
- fontanelles - enlarged
- frontal bossing
- fungating lesion
- fungating mass
- funny turns
- gait abnormality
- gait unsteadiness
- gallbladder calculi
- gallstones
- gangrene
- gastro-oesophageal reflux
- genital oedema
- genu valgum
- genu varum
- gestational diabetes
- glaucoma
- glucose intolerance
- glucosuria
- growth hormone deficiency
- growth retardation
- haematemesis
- haematochezia
- haematoma
- haematuria
- haemoglobinuria
- haemoptysis
- hair - coarse
- hair - dry
- hair - temporal balding
- hairline - low
- hallucination
- hands - enlargement
- hands - large
- hands - single palmar crease
- hands - small
- head - large
- headache
- hearing loss
- heart failure
- heart murmur
- heat intolerance
- height loss
- hemiballismus
- hemianopia
- hemiparesis
- hemispatial neglect
- hepatic cysts
- hepatic metastases
- hepatomegaly
- hidradenitis suppurativa
- high-arched palate
- hip dislocation
- hippocampal dysgenesis
- hirschsprung's disease
- hot flushes
- hydronephrosis
- hypolipidaemia
- hyperactivity
- hyperacusis
- hyperandrogenaemia
- hypercalciuria
- hypercapnea
- hypercholesterolaemia
- hypercortisolaemia
- hyperflexibility
- hyperglucagonaemia
- hyperhidrosis
- hyperhomocysteinaemia
- hypernasal speech
- hyperopia
- hyperoxaluria
- hyperpigmentation
- hyperplasia
- hyperpnoea
- hypersalivation
- hyperseborrhea
- hypersomnia
- hyperthermia
- hypertrichosis
- hypertrophy
- hyperuricaemia
- hyperventilation
- hypoadrenalism
- hypoalbuminaemia
- hypocalciuria
- hypocitraturia
- hypomagnesaemia
- hypopigmentation
- hypoplastic scrotum
- hypopotassaemia
- hypoprolactinaemia
- hyporeflexia
- hyposmia
- hypospadias
- hypotension
- hypothermia
- hypotonia
- hypoventilation
- hypovitaminosis d
- hypovolaemia
- hypovolaemic shock
- hypoxia
- immunodeficiency
- impulsivity
- inattention
- infections
- inflexibility
- insomnia
- instability
- intussusception
- irritability
- ischaemia
- ischuria
- itching
- jaundice
- keratoconus
- ketonuria
- ketotic odour
- kidney dysplasia
- kidney stones
- kyphoscoliosis
- kyphosis
- labioscrotal fold abnormalities
- laceration
- late dentition
- learning difficulties
- leg pain
- legs - increased length
- leukaemia
- leukocytosis
- libido increase
- libido reduction/loss
- lichen sclerosus
- lips - dry
- lips - thin
- little finger - in-curved
- little finger - short
- liver masses
- lordosis
- lordosis (loss of)
- lymphadenectomy
- lymphadenitis
- lymphocytosis
- lymphoedema
- macroglossia
- malaise
- malaise (post-exertional)
- malodorous perspiration
- mania
- marcus gunn pupil
- mastalgia
- meckel's diverticulum
- melena
- menorrhagia
- menstrual disorder
- mesenteric ischaemia
- metabolic alkalosis
- microalbuminuria
- microcephaly
- micrognathia
- micropenis
- milk-alkali syndrome
- miscarriage
- mood changes/swings
- mouth - down-turned
- mouth - small
- movement - limited range of
- mucosal pigmentation
- muscle atrophy
- muscle freezing
- muscle hypertrophy
- muscle rigidity
- myalgia
- myasthaenia
- mydriasis
- myelodysplasia
- myeloma
- myoclonus
- myodesopsia
- myokymia
- myopathy
- myopia
- myosis
- nail clubbing
- nail dystrophy
- nasal obstruction
- nausea
- neck - loose skin (nape)
- neck - short
- neck mass
- neck pain/discomfort
- necrolytic migratory erythema
- necrosis
- nephrocalcinosis
- nephropathy
- neurofibromas
- night terrors
- nipple change
- nipple discharge
- nipple inversion
- nipple retraction
- nipples widely spaced
- nocturia
- normochromic normocytic anaemia
- nose - depressed bridge
- nose - flat bridge
- nose - thickening
- nystagmus
- obsessive-compulsive disorder
- obstetrical haemorrhage
- obstructive sleep apnoea
- odynophagia
- oedema
- oesophageal atresia
- oesophagitis
- oligomenorrhoea
- oliguria
- onychauxis
- oophoritis
- ophthalmoplegia
- optic atrophy
- orbital fat prolapse
- orbital hypertelorism
- orthostatic hypotension
- osteoarthritis
- osteopenia
- otitis media
- ovarian cysts
- ovarian hyperplasia
- palatoschisis
- pallor
- palmar erythema
- palpebral fissure (downslanted)
- palpebral fissure (extended)
- palpebral fissure (reduced)
- palpebral fissure (upslanted)
- palpitations
- pancreatic fibrosis
- pancytopaenia
- panic attacks
- papilloedema
- paraesthesia
- paralysis
- paranoia
- patellar dislocation
- patellar subluxation
- pedal ulceration
- pellagra
- pelvic mass
- pelvic pain
- penile agenesis
- peptic ulcer
- pericardial effusion
- periodontitis
- periosteal bone reactions
- peripheral oedema
- personality change
- pes cavus
- petechiae
- peyronie's disease
- pharyngitis
- philtrum - long
- philtrum - short
- phosphaturia
- photophobia
- photosensitivity
- pleurisy
- poikiloderma
- polydactyly
- polydipsia
- polyphagia
- polyuria
- poor wound healing
- postmenopausal bleeding
- post-nasal drip
- postprandial fullness
- postural instability
- prehypertension
- premature birth
- premature labour
- prenatal growth retardation
- presbyopia
- pretibial myxoedema
- proctalgia fugax
- prognathism
- proptosis
- prosopagnosia
- proteinuria
- pruritus
- pruritus scroti
- pruritus vulvae
- pseudarthrosis
- psoriatic arthritis
- psychiatric problems
- psychomotor retardation
- psychosis
- pterygium colli
- ptosis
- puberty (delayed/absent)
- puberty (early/precocious)
- puffiness
- pulmonary embolism
- purpura
- pyelonephritis
- pyloric stenosis
- pyrexia
- pyrosis
- pyuria
- rash
- rectal pain
- rectorrhagia
- refractory anemia
- reluctance to weight-bear
- renal agenesis
- renal clubbing
- renal colic
- renal cyst
- renal failure
- renal insufficiency
- renal phosphate wasting (isolated)
- renal tubular acidosis
- respiratory failure
- reticulocytosis
- retinitis pigmentosa
- retinopathy
- retrobulbar pain
- retrograde ejaculation
- retroperitoneal fibrosis
- salivary gland swelling
- salpingitis
- salt craving
- salt wasting
- sarcoidosis
- schizophrenia
- scoliosis
- scotoma
- seborrhoeic dermatitis
- seizures
- sensory loss
- sepsis
- septic arthritis
- septic shock
- shivering
- singultus
- sinusitis
- sixth nerve palsy
- skeletal deformity
- skeletal dysplasia
- skin - texture change
- skin infections
- skin necrosis
- skin pigmentation - spotty
- skin thickening
- skin thinning
- sleep apnoea
- sleep difficulties
- sleep disturbance
- sleep hyperhidrosis
- slow growth
- slurred speech
- social difficulties
- soft tissue swelling
- somnambulism
- somniloquy
- somnolence
- sore throat
- spasms
- spastic paraplegia
- spasticity
- speech delay
- spider naevi
- splenomegaly
- sputum production
- steatorrhoea
- stomatitis
- strabismus
- strangury
- striae
- stridor
- stroke
- subfertility
- suicidal ideation
- supraclavicular fat pads
- supranuclear gaze palsy
- sweating
- syncope
- syndactyly
- tachycardia
- tachypnoea
- teeth gapping
- telangiectasias
- telecanthus
- tetraparesis
- t-reflex (absent)
- t-reflex (depressed)
- tetany
- thermodysregulation
- thrombocytopenia
- thrombocytosis
- thrombophilia
- thrush
- tics
- tinnitus
- toe clubbing
- toe deformities
- toes - thick
- toes - widely spaced
- tongue - protruding
- tracheo-oesophageal compression
- tracheo-oesophageal fistula
- tremulousness
- tricuspid insufficiency
- umbilical hernia
- uraemia
- ureter duplex
- uricaemia
- urinary frequency
- urinary incontinence
- urogenital sinus
- urticaria
- uterine hyperplasia
- uterus duplex
- vagina duplex
- vaginal bleeding
- vaginal discharge
- vaginal dryness
- vaginal pain/tenderness
- vaginism
- ventricular fibrillation
- ventricular hypertrophy
- vertigo
- viraemia
- virilisation (abnormal)
- vision - acuity reduction
- vision - blurred
- visual disturbance
- visual field defect
- visual impairment
- visual loss
- vitiligo
- vocal cord paresis
- vomiting
- von graefe's sign
- weight gain
- weight loss
- wheezing
- widened joint space(s)
- xeroderma
- xerostomia
- 3-methoxy 4-hydroxy mandelic acid
- 17-hydroxypregnenolone (urine)
- 17-ketosteroids
- 25-hydroxyvitamin-d3
- 5hiaa
- aberrant adrenal receptors
- acid-base balance
- acth stimulation
- activated partial thromboplastin time
- acyl-ghrelin
- adrenal antibodies
- adrenal function
- adrenal scintigraphy
- adrenal venous sampling
- afp tumour marker
- alanine aminotransferase
- albumin
- albumin to creatinine ratio
- aldosterone (24-hour urine)
- aldosterone (blood)
- aldosterone (plasma)
- aldosterone (serum)
- aldosterone to renin ratio
- alkaline phosphatase
- alkaline phosphatase (bone-specific)
- alpha-fetoprotein
- ammonia
- amniocentesis
- amylase
- angiography
- anion gap
- anti-acetylcholine antibodies
- anticardiolipin antibody
- anti-insulin antibodies
- anti-islet cell antibody
- anti-gh antibodies
- antinuclear antibody
- anti-tyrosine phosphatase antibodies
- asvs
- barium studies
- basal insulin
- base excess
- apolipoprotein h
- beta-hydroxybutyrate
- bicarbonate
- bilirubin
- biopsy
- blood film
- blood pressure
- bmi
- body fat mass
- bone age
- bone biopsy
- bone mineral content
- bone mineral density
- bone mineral density test
- bone scintigraphy
- bone sialoprotein
- bound insulin
- brca1/brca2
- c1np
- c3 complement
- c4 complement
- ca125
- calcifediol
- calcium (serum)
- calcium (urine)
- calcium to creatinine clearance ratio
- carcinoembryonic antigen
- cardiac index
- catecholamines (24-hour urine)
- catecholamines (plasma)
- cd-56
- chemokines
- chest auscultation
- chloride
- chorionic villus sampling
- chromatography
- chromogranin a
- chromosomal analysis
- clomid challenge
- clonidine suppression
- collagen
- colonoscopy
- colposcopy
- continuous glucose monitoring
- core needle biopsy
- corticotropin-releasing hormone stimulation test
- cortisol (9am)
- cortisol (plasma)
- cortisol (midnight)
- cortisol (salivary)
- cortisol (serum)
- cortisol day curve
- cortisol, free (24-hour urine)
- c-peptide (24-hour urine)
- c-peptide (blood)
- c-reactive protein
- creatinine
- creatine kinase
- creatinine (24-hour urine)
- creatinine (serum)
- creatinine clearance
- crh stimulation
- ctpa scan
- ct scan
- c-telopeptide
- cytokines
- deoxypyridinoline
- dexa scan
- dexamethasone suppression
- dexamethasone suppression (high dose)
- dexamethasone suppression (low dose)
- dhea sulphate
- discectomy
- dldl cholesterol
- dmsa scan
- dna sequencing
- domperidone
- down syndrome screening
- ductal lavage
- echocardiogram
- eeg
- electrocardiogram
- electrolytes
- electromyography
- endoscopic ultrasound
- endoscopy
- endosonography
- enzyme immunoassay
- epinephrine (plasma)
- epinephrine (urine)
- erythrocyte sedimentation rate
- estimated glomerular filtration rate
- ethanol ablation
- ewing and clarke autonomic function
- exercise tolerance
- fbc
- ferritin
- fine needle aspiration biopsy
- flow cytometry
- fludrocortisone suppression
- fluticasone-propionate-17-beta carboxylic acid
- fmri
- folate
- ft3
- ft4
- gada
- gallium nitrate
- gallium scan
- gastric biopsy
- genetic analysis
- genitography
- gh day curve
- gh stimulation
- gh suppression
- glp-1
- glp-2
- glucose suppression test
- glucose (blood)
- glucose (blood, fasting)
- glucose (blood, postprandial)
- glucose (urine)
- glucose tolerance
- glucose tolerance (intravenous)
- glucose tolerance (oral)
- glucose tolerance (prolonged)
- gluten sensitivity
- gnrh stimulation
- gonadotrophins
- growth hormone-releasing peptide-2 test
- gut hormones (fasting)
- haematoxylin and eosin staining
- haemoglobin
- haemoglobin a1c
- hcg (serum)
- hcg (urine)
- hcg stimulation
- hdl cholesterol
- hearing test
- heart rate
- hepatic venous sampling with arterial stimulation
- high-sensitivity c-reactive protein
- histopathology
- hla genotyping
- holter monitoring
- homa
- homocysteine
- hyaluronic acid
- hydrocortisone day curve
- hydroxyproline
- hydroxyprogesterone
- hysteroscopy
- igfbp2
- igfbp3
- igg4/igg ratio
- immunocytochemistry
- immunohistochemistry
- immunoglobulins
- immunoglobulin g2
- immunoglobulin g4
- immunoglobulin a
- immunoglobulin m
- immunostaining
- inferior petrosal sinus sampling
- inhibin b
- insulin (fasting)
- insulin suppression
- insulin tissue resistance tests
- insulin tolerance
- intracranial pressure
- irm imaging
- ketones (plasma)
- ketones (urine)
- kidney function
- lactate
- lactate dehydrogenase
- laparoscopy
- laparoscopy and dye
- laparotomy
- ldl cholesterol
- leuprolide acetate stimulation
- leukocyte esterase (urine)
- levothyroxine absorption
- lipase (serum)
- lipid profile
- liquid-based cytology
- liquid chromatography-mass spectrometry
- liver biopsy
- liver function
- lumbar puncture
- lung function testing
- luteinising hormone releasing hormone test
- macroprolactin
- magnesium
- mag3 scan
- mammogram
- mantoux test
- metanephrines (plasma)
- metanephrines (urinary)
- methoxytyramine
- metoclopramide
- metyrapone cortisol day curve
- metyrapone suppression
- metyrapone test dose
- mibg scan
- microarray analysis
- molecular genetic analysis
- mri
- myocardial biopsy
- nerve conduction study
- neuroendocrine markers
- neuron-specific enolase
- norepinephrine
- ntx
- oct
- octreotide scan
- octreotide suppression test
- osmolality
- ovarian venous sampling
- p1np
- palpation
- pap test
- parathyroid scintigraphy
- pentagastrin
- perchlorate discharge
- percutaneous umbilical blood sampling
- peripheral blood film
- pet scan
- ph (blood)
- phosphate (serum)
- phosphate (urine)
- pituitary function
- plasma osmolality
- plasma viscosity
- platelet count
- pneumococcal antigen
- pneumococcal pcr
- polymerase chain reaction
- polysomnography
- porter-silber chromogens
- potassium
- pregnancy test
- proinsulin
- prostate-specific antigen
- protein electrophoresis
- protein fingerprinting
- protein folding analysis
- psychiatric assessment
- psychometric assessment
- pulse oximetry
- pyelography
- pyridinium crosslinks
- quicki
- plasma renin activity
- radioimmunoassay
- radionuclide imaging
- raiu test
- red blood cell count
- renal biopsy
- renin (24-hour urine)
- respiratory status
- renin (blood)
- renin plasma activity
- rheumatoid factor
- salt loading
- sdldl cholesterol
- secretin stimulation
- selective parathyroid venous sampling
- selective transhepatic portal venous sampling
- semen analysis
- serotonin
- serum osmolality
- serum free insulin
- sestamibi scan
- sex hormone binding globulin
- shbg
- skeletal muscle mass
- skin biopsy
- sleep diary
- sodium
- spect scan
- supervised 72-hour fast
- surgical biopsy
- sweat test
- synaptophysin
- systemic vascular resistance index
- tanner scale
- thoracocentesis
- thyroid transcription factor-1
- thyroglobulin
- thyroid antibodies
- thyroid function
- thyroid scintigraphy
- thyroid ultrasonography
- total cholesterol
- total ghrelin
- total t3
- total t4
- trabecular thickness
- transaminase
- transvaginal ultrasound
- trap 5b
- trh stimulation
- triglycerides
- triiodothyronine (t3) suppression
- troponin
- tsh receptor antibodies
- type 3 precollagen
- type 4 collagen
- ultrasound-guided biopsy
- ultrasound scan
- urea and electrolytes
- uric acid (blood)
- uric acid (urine)
- urinalysis
- urinary free cortisol
- urine 24-hour volume
- urine osmolality
- vaginal examination
- vanillylmandelic acid (24-hour urine)
- visual field assessment
- vitamin b12
- vitamin e
- waist circumference
- water deprivation
- water load
- weight
- western blotting
- white blood cell count
- white blood cell differential count
- x-ray
- zinc
- abscess drainage
- acetic acid injection
- adhesiolysis
- adrenalectomy
- amputation
- analgesics
- angioplasty
- arthrodesis
- assisted reproduction techniques
- bariatric surgery
- bilateral salpingo-oophorectomy
- blood transfusion
- bone grafting
- caesarean section
- cardiac transplantation
- cardiac pacemaker
- cataract extraction
- chemoembolisation
- chemotherapy
- chemoradiotherapy
- clitoroplasty
- continuous renal replacement therapy
- contraception
- cordotomy
- counselling
- craniotomy
- cryopreservation
- cryosurgical ablation
- debridement
- dialysis
- diazoxide
- diet
- duodenotomy
- endonasal endoscopic surgery
- exercise
- external fixation
- extracorporeal shock wave lithotripsy
- extraocular muscle surgery
- eye surgery
- eyelid surgery
- fasciotomy
- fluid repletion
- fluid restriction
- gamma knife radiosurgery
- gastrectomy
- gastrostomy
- gender reassignment surgery
- gonadectomy
- heart transplantation
- hormone replacement
- hormone suppression
- hypophysectomy
- hysterectomy
- inguinal orchiectomy
- internal fixation
- intra-cardiac defibrillator
- islet transplantation
- ivf
- kidney transplantation
- laparoscopic adrenalectomy
- laryngoplasty
- laryngoscopy
- laser lithotripsy
- light treatment
- liver transplantation
- lumpectomy
- lymph node dissection
- mastectomy
- molecularly targeted therapy
- neuroendoscopic surgery
- oophorectomy
- orbital decompression
- orbital radiation
- orchidectomy
- orthopaedic surgery
- osteotomy
- ovarian cystectomy
- ovarian diathermy
- oxygen therapy
- pancreas transplantation
- pancreatectomy
- pancreaticoduodenectomy
- parathyroidectomy
- percutaneous adrenal ablation
- percutaneous nephrolithotomy
- pericardiocentesis
- pericardiotomy
- physiotherapy
- pituitary adenomectomy
- plasma exchange
- plasmapheresis
- psychotherapy
- radiofrequency ablation
- radionuclide therapy
- radiotherapy
- reconstruction of genitalia
- resection of tumour
- right-sided hemicolectomy
- salpingo-oophorectomy
- small bowel resection
- speech and language therapy
- spinal surgery
- splenectomy
- stereotactic radiosurgery
- termination of pregnancy
- thymic transplantation
- thyroidectomy
- tracheostomy
- transcranial surgery
- transsphenoidal surgery
- transtentorial surgery
- vaginoplasty
- vagotomy
- 5-alpha-reductase inhibitors
- 17?-estradiol
- abiraterone
- acarbose
- acetazolamide
- acetohexamide
- adalimumab
- albiglutide
- alendronate
- alogliptin
- alpha-blockers
- alphacalcidol
- alpha-glucosidase inhibitors
- amiloride
- amlodipine
- amoxicillin
- anastrozole
- angiotensin-converting enzyme inhibitors
- angiotensin receptor antagonists
- anthracyclines
- antiandrogens
- antibiotics
- antiemetics
- antiepileptics
- antipsychotics
- antithyroid drugs
- antiseptic
- antivirals
- aripiprazole
- aromatase inhibitors
- aspirin
- astragalus membranaceus
- ativan
- atenolol
- atorvastatin
- avp receptor antagonists
- axitinib
- azathioprine
- bendroflumethiazide
- benzodiazepines
- beta-blockers
- betamethasone
- bexlosteride
- bicalutamide
- bisphosphonates
- bleomycin
- botulinum toxin
- bromocriptine
- cabergoline
- cabozantinib
- calcimimetics
- calcitonin (salmon)
- calcium
- calcium carbonate
- calcium chloride
- calcium dobesilate
- calcium edta
- calcium gluconate
- calcium-l-aspartate
- calcium polystyrene sulphonate
- canagliflozin
- capecitabine
- captopril
- carbimazole
- carboplatin
- carbutamide
- carvedilol
- ceftriaxone
- chlorothiazide
- chlorpropamide
- cholecalciferol
- cholinesterase inhibitors
- ciclosporin
- cinacalcet
- cisplatin
- clodronate
- clomifene
- clomiphene citrate
- clopidogrel
- co-cyprindiol
- codeine
- colonic polyps
- combined oral contraceptive pill
- conivaptan
- cortisone acetate
- continuous subcutaneous hydrocortisone infusion
- continuous subcutaneous insulin infusion
- coumadin
- corticosteroids
- cortisol
- cyproterone acetate
- dacarbazine
- danazol
- dapagliflozin
- daunorubicin
- deferiprone
- demeclocycline
- denosumab
- desmopressin
- dexamethasone
- diazepam
- diethylstilbestrol
- digoxin
- diltiazem
- diphenhydramine
- diuretics
- docetaxel
- dopamine agonists
- dopamine antagonists
- dopamine receptor agonists
- doxazosin
- doxepin
- doxorubicin
- dpp4 inhibitors
- dutasteride
- dutogliptin
- eflornithine
- enoxaparin
- empagliflozin
- epinephrine
- epirubicin
- eplerenone
- epristeride
- equilenin
- equilin
- erlotinib
- ethinylestradiol
- etidronate
- etomidate
- etoposide
- everolimus
- exenatide
- fenofibrate
- finasteride
- fluconazole
- fluticasone
- fludrocortisone
- fluorouracil
- fluoxetine
- flutamide
- furosemide
- gaba receptor antagonists
- gefitinib
- gemcitabine
- gemigliptin
- ginkgo biloba
- glibenclamide
- glibornuride
- gliclazide
- glimepiride
- glipizide
- gliquidone
- glisoxepide
- glp1 agonists
- glucose
- glyclopyramide
- gnrh analogue
- gnrh antagonists
- heparin
- hrt (menopause)
- hydrochlorothiazide
- hydrocortisone
- ibandronate
- ibuprofen
- idarubicin
- idebenone
- imatinib
- immunoglobulin therapy
- implanon
- indapamide
- infliximab
- iron supplements
- isoniazid
- insulin aspart
- insulin glargine
- insulin glulisine
- insulin lispro
- interferon
- intrauterine system
- iopanoic acid
- ipilimumab
- ipragliflozin
- irbesartan
- izonsteride
- ketoconazole
- labetalol
- lactulose
- lanreotide
- leuprolide acetate
- levatinib
- levodopa
- levonorgestrel
- levothyroxine
- linagliptin
- liothyronine
- liraglutide
- lithium
- lisinopril
- lixivaptan
- loperamide
- loprazolam
- lormetazepam
- losartan
- low calcium formula
- magnesium glycerophosphate
- magnesium sulphate
- mecasermin
- medronate
- medroxyprogesterone acetate
- meglitinides
- menotropin
- metformin
- methadone
- methimazole
- methylprednisolone
- metoprolol
- metyrapone
- miglitol
- mitotane
- mitoxantrone
- mozavaptan
- mtor inhibitors
- multivitamins
- naproxen
- natalizumab
- nateglinide
- nelivaptan
- neridronate
- nifedipine
- nilutamide
- nitrazepam
- nivolumab
- nsaid
- octreotide
- oestradiol valerate
- olanzapine
- olpadronate
- omeprazole
- opioids
- oral contraceptives
- orlistat
- ornipressin
- otelixizumab
- oxandrolone
- oxidronate
- oxybutynin
- paclitaxel
- pamidronate
- pancreatic enzymes
- pantoprazole
- paracetamol
- paroxetine
- pasireotide
- pegvisomant
- perindopril
- phenobarbital
- phenoxybenzamine
- phosphate binders
- phosphate supplements
- phytohaemagglutinin induced interferon gamma
- pioglitazone
- plicamycin
- potassium chloride
- potassium iodide
- pramlintide
- prazosin
- prednisolone
- prednisone
- premarin
- promethazine
- propranolol
- propylthiouracil
- protease inhibitors
- proton pump inhibitors
- pyridostigmine
- quetiapine
- quinagolide
- quinestrol
- radioactive mibg
- radioactive octreotide
- radioiodine
- raloxifene
- ramipril
- relcovaptan
- remogliflozin etabonate
- repaglinide
- risperidone
- risedronate
- rituximab
- romidepsin
- rosiglitazone
- salbutamol
- saline
- salmeterol
- salt supplements
- satavaptan
- saxagliptin
- selective progesterone receptor modulators
- selenium
- sglt2 inhibitors
- sildenafil
- simvastatin
- sirolimus
- sitagliptin
- sodium bicarbonate
- sodium chloride
- sodium polystyrene sulfonate (kayexalate)
- somatostatin analogues
- sorafenib
- spironolactone
- ssris
- statins
- streptozotocin
- steroids
- strontium ranelate
- sucralfate
- sulphonylureas
- sunitinib
- tamoxifen
- taspoglutide
- temazepam
- temozolomide
- teplizumab
- terazosin
- teriparatide
- testolactone
- testosterone enanthate esters
- tetrabenazine
- thalidomide
- thiazolidinediones
- thyrotropin alpha
- tibolone
- tiludronate
- tiratricol (triac)
- tofogliflozin
- tolazamide
- tolbutamide
- tolvaptan
- tramadol
- trastuzumab
- trazodone
- triamcinolone
- triamterene
- trimipramine
- troglitazone
- tryptophan
- turosteride
- tyrosine-kinase inhibitors
- valproic acid
- valrubicin
- vandetanib
- vaptans
- vildagliptin
- vinorelbine
- voglibose
- vorinostat
- warfarin
- zaleplon
- z-drugs
- zoledronic acid
- zolpidem
- zopiclone
- cardiology
- dermatology
- gastroenterology
- general practice
- genetics
- geriatrics
- gynaecology
- nephrology
- neurology
- nursing
- obstetrics
- oncology
- otolaryngology
- paediatrics
- pathology
- podiatry
- psychology/psychiatry
- radiology/rheumatology
- rehabilitation
- surgery
- urology
- insight into disease pathogenesis or mechanism of therapy
- novel diagnostic procedure
- novel treatment
- unique/unexpected symptoms or presentations of a disease
- new disease or syndrome: presentations/diagnosis/management
- unusual effects of medical treatment
- error in diagnosis/pitfalls and caveats
- february
- 2022
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Affiliation(s)
- Aria Jazdarehee
- Department of Medicine and Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Sawyer Huget-Penner
- Division of Endocrinology and Metabolism, Fraser Health Authority, British Columbia, Canada
| | - Monika Pawlowska
- Division of Endocrinology and Metabolism, University of British Columbia, British Columbia, Canada
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Ma G, Zhang L, Seoka M, Nakata A, Yahata M, Shimada T, Fujii H, Endo T, Yoshioka T, Kan T, Kato M. Characterization of a Caffeic Acid 8- O-Methyltransferase from Citrus and Its Function in Nobiletin Biosynthesis. J Agric Food Chem 2022; 70:543-553. [PMID: 34964635 DOI: 10.1021/acs.jafc.1c06513] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nobiletin (3',4',5,6,7,8-hexamethoxyflavone) is a polymethoxylated flavonoid specifically accumulated in citrus fruit with numerous beneficial effects to human health. In this study, a novel O-methyltransferase (CitOMT2) was isolated from three citrus varieties, Ponkan mandarin (Citrus reticulata Blanco), Nou 6 ("King mandarin" × "Mukaku-kishu"), and Satsuma mandarin (Citrus unshiu Marc.), and its functions were characterized in vitro. The gene expression results showed that CitOMT2 was highly expressed in the two nobiletin abundant varieties of Ponkan mandarin and Nou 6. However, the expression level of CitOMT2 was low in the flavedo of Satsuma mandarin, in which only a small amount of nobiletin was accumulated. Functional analysis suggested that CitOMT2 was a caffeic acid 8-O-methyltransferase, and it catalyzed the O-methylation of 7,8-dihydroxyflavone at 8-OH. As the methylation of flavone at 8-OH was required for nobiletin biosynthesis, the results presented in this study suggested that CitOMT2 was a key gene regulating nobiletin accumulation in citrus fruit.
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Affiliation(s)
- Gang Ma
- Department of Bioresource Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Lancui Zhang
- Department of Bioresource Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Mao Seoka
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Akari Nakata
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Masaki Yahata
- Department of Bioresource Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Takehiko Shimada
- NARO Institute of Fruit Tree and Tea Science, Shizuoka 424-0292, Japan
| | - Hiroshi Fujii
- NARO Institute of Fruit Tree and Tea Science, Shizuoka 424-0292, Japan
| | - Tomoko Endo
- NARO Institute of Fruit Tree and Tea Science, Shizuoka 424-0292, Japan
| | - Terutaka Yoshioka
- NARO Institute of Fruit Tree and Tea Science, Shizuoka 424-0292, Japan
| | - Toshiyuki Kan
- School of Pharmaceutical Sciences University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Masaya Kato
- Department of Bioresource Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
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45
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Du Y, Zhu Y, Liu Y, Liu J, Hu C, Sun Y, Zhang D, Lv S, Cheng Y, Han H, Zhang J, Zhao Y, Zhou Y. Expression profiles of long noncoding and messenger RNAs in epicardial adipose tissue derived from patients with coronary atherosclerosis. Curr Vasc Pharmacol 2022; 20:189-200. [PMID: 35049433 DOI: 10.2174/1570161120666220114095320] [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: 06/22/2021] [Revised: 08/21/2021] [Accepted: 12/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Given its close anatomical location to the heart and its endocrine properties, attention on epicardial adipose tissue (EAT) has increased. OBJECTIVE This study investigated the expression profiles of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in EAT derived from patients with coronary artery disease (CAD). METHODS EAT samples from 8 CAD and 8 non-CAD patients were obtained during open-heart surgery. The expression of lncRNAs and mRNAs in each EAT sample was investigated using microarray analysis and further verified using reverse transcription-quantitative polymerase chain reaction. RESULTS Overall, 1,093 differentially expressed mRNAs and 2,282 differentially expressed lncRNAs were identified in EAT from CAD vs non-CAD patients. Analysis using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes showed that these differentially expressed genes were mainly enriched in various inflammatory, immune, and metabolic processes. They were also involved in osteoclast differentiation, B cell receptor and adipocytokine signaling, and insulin resistance pathways. Additionally, lncRNA-mRNA and lncRNA-target pathway networks were built to identify potential core genes (e.g. Lnc-CCDC68-2:1, AC010148.1, NONHSAT104810) involved in atherosclerosis pathogenesis. CONCLUSION In summary, lncRNA and mRNA profiles in EAT were markedly different between CAD and non-CAD patients. Our study identifies several potential key genes and pathways that may participate in atherosclerosis development.
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Affiliation(s)
- Yu Du
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yong Zhu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yan Liu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Jinxing Liu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Chengping Hu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yan Sun
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Dai Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Sai Lv
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yujing Cheng
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Hongya Han
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Jianwei Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yingxin Zhao
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
| | - Yujie Zhou
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic Disease, Clinical Center for Coronary Heart Disease, Capital Medical University, Beijing100029, China
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Xu S, Dong H, Zhao Y, Feng W. Differential Expression of Long Non-Coding RNAs and Their Role in Rodent Neuropathic Pain Models. J Pain Res 2022; 14:3935-3950. [PMID: 35002313 PMCID: PMC8722684 DOI: 10.2147/jpr.s344339] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Neuropathic pain, which is accompanied by an unpleasant sensation, affects the patient’s quality of life severely. Considering the complexity of the neuropathic pain, there are huge unmet medical needs for it while current effective therapeutics remain far from satisfactory. Accordingly, exploration of mechanisms of neuropathic pain could provide new therapeutic insights. While numerous researches have pointed out the contribution of sensory neuron-immune cell interactions, other mechanisms of action, such as long non-coding RNAs (lncRNAs), also could contribute to the neuropathic pain observed in vivo. LncRNAs have more than 200 nucleotides and were originally considered as transcriptional byproducts. However, recent studies have suggested that lncRNAs played a significant role in gene regulation and disease pathogenesis. A substantial number of long non-coding RNAs were expressed differentially in neuropathic pain models. Besides, therapies targeting specific lncRNAs can significantly ameliorate the development of neuropathic pain, which reveals the contribution of lncRNAs in the generation and maintenance of neuropathic pain and provides a new therapeutic strategy. The primary purpose of this review is to introduce recent studies of lncRNAs on different neuropathic pain models.
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Affiliation(s)
- Songchao Xu
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People's Republic of China
| | - He Dong
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People's Republic of China
| | - Yang Zhao
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People's Republic of China
| | - Wei Feng
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People's Republic of China
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Gan J, Chen Z, Feng X, Wei Z, Zhang S, Du Y, Xu C, Zhao H. Expression profiling of lncRNAs and mRNAs in placental site trophoblastic tumor (PSTT) by microarray. Int J Med Sci 2022; 19:1-12. [PMID: 34975294 PMCID: PMC8692111 DOI: 10.7150/ijms.65002] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
As a rare type of gestational trophoblastic disease, placental site trophoblastic tumor (PSTT) is originated from intermediate trophoblast cells. Long noncoding RNAs (lncRNAs) regulate numerous biological process. However, the role of lncRNAs in PSTT remains poorly understood. In the present study, expression levels of lncRNAs and mRNAs in four human PSTT tissues and four normal placental villi were investigated. The results of microarray were validated by the reverse transcription and quantitative real-time polymerase reaction (RT-qPCR) and immunohistochemistry analyses. Furthermore, GO and KEGG pathway analyses were performed to identify the underlying biological processes and signaling pathways of aberrantly expressed lncRNAs and mRNAs. We also conducted the coding-non-coding gene co-expression (CNC) network to explore the interaction of altered lncRNAs and mRNAs. In total, we identified 1247 up-regulated lncRNAs and 1013 down-regulated lncRNAs as well as 828 up-regulated mRNAs and 1393 down-regulated mRNAs in PSTT tissues compared to normal villi (fold change ≥ 2.0, p < 0.05). GO analysis showed that mitochondrion was the most significantly down-regulated GO term, and immune response was the most significantly up-regulated term. A CNC network profile based on six confirmed lncRNAs (NONHSAT114519, NR_103711, NONHSAT003875, NONHSAT136587, NONHSAT134431, NONHSAT102500) as well as 354 mRNAs was composed of 497 edges. GO and KEGG analyses indicated that interacted mRNAs were enriched in the signal-recognition particle (SRP)-dependent cotranslational protein targeting to membrane and Ribosome pathway. It contributes to expand the understanding of the aberrant lncRNAs and mRNAs profiles of PSTT, which may be helpful for the exploration of new diagnosis and treatment of PSTT.
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Affiliation(s)
- Jianfeng Gan
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Zhixian Chen
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Xuan Feng
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Zhi Wei
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Sai Zhang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Yan Du
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Congjian Xu
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Hongbo Zhao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
- Department of Obstetrics and Gynecology of Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
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Shen Z, Zhu W, Du L. Analysis of Gene Expression Profiles in the Liver of Rats With Intrauterine Growth Retardation. Front Pediatr 2022; 10:801544. [PMID: 35321016 PMCID: PMC8934861 DOI: 10.3389/fped.2022.801544] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) is highly associated with fetal as well as neonatal morbidity, mortality, and an increased risk metabolic disease development later in life. The mechanism involved in the increased risk has not been established. We compared differentially expressed genes between the liver of appropriate for gestational age (AGA) and IUGR rat models and identified their effects on molecular pathways involved in the metabolic syndrome. METHODS We extracted RNA from the liver of IUGR and AGA rats and profiled gene expression by microarray analysis. GO function and KEGG pathway enrichment analyses were conducted using the Search Tool for the Retrieval of Interacting Genes database. Then, the Cytoscape software was used to visualize regulatory interaction networks of IUGR-related genes. The results were further verified via quantitative reverse transcriptase PCR analysis. RESULTS In this study, 815 genes were found to be markedly differentially expressed (fold-change >1.5, p < 0.05) between IUGR and AGA, with 347 genes elevated and 468 suppressed in IUGR, relative to AGA. Enrichment and protein-protein interaction network analyses of target genes revealed that core genes including Ppargc1a, Prkaa2, Slc2a1, Rxrg, and Gcgr, and pathways, including the PPAR signaling pathway and FoxO signaling pathway, had a potential association with metabolic syndrome development in IUGR. We also confirmed that at the mRNA level, five genes involved in glycometabolism were differentially expressed between IUGR and AGA. CONCLUSION Our findings elucidate on differential gene expression profiles in IUGR and AGA. Moreover, they elucidate on the pathogenesis of IUGR-associated metabolic syndromes. The suggested candidates are potential biomarkers and eventually intended to treat them appropriately.
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Affiliation(s)
- Zheng Shen
- Department of Clinical Laboratory, Zhejiang University School of Medicine Children's Hospital, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Weifen Zhu
- Department of Endocrinology, Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou, China
| | - Lizhong Du
- National Clinical Research Center for Child Health, Hangzhou, China.,Department of Neonatology, Zhejiang University School of Medicine Children's Hospital, Hangzhou, China
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Yuan Y, Yang X, Xie D. Role of hsa_circ_0066966 in proliferation and migration of hepatitis B virus-related liver cancer cells. Exp Ther Med 2022; 23:87. [PMID: 34976133 PMCID: PMC8674973 DOI: 10.3892/etm.2021.11010] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
A large proportion of liver cancer cases is caused by hepatitis B virus (HBV) infection. In recent years, an increasing number of reports have indicated that circular RNAs (circRNAs) exert regulatory effects in cancer development, whereas the role of circRNAs in HBV-positive liver cancer requires further investigation. In the present study, abnormally expressed circRNAs were identified in HBV-positive liver cancer cells through microarray analysis. A total of 1,493 differentially expressed circRNAs [absolute fold-change (FC) ≥2] in HBV-positive liver cancer cells were detected, of which 171 were upregulated and 1,322 were downregulated. Subsequently, Gene Ontology enrichment analysis indicated that the genes of dysregulated circRNAs were mainly involved in regulating Sertoli cell differentiation and development, as well as telomeric DNA binding. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that most of these genes were enriched in cancer-related signaling pathways, including the MAPK and Hippo signaling pathways. Next, the expression levels of the top-10 dysregulated circRNAs were verified in HBV-positive liver cancer cells through reverse transcription-quantitative PCR. Among them, hsa_circ_0066966 had the highest absolute Log2FC value and was abnormally increased in HBV-positive liver cancer cells. Functional experiments further verified that knockdown of hsa_circ_0066966 had a significant inhibitory effect on the proliferation and migration of HBV-positive liver cancer cells. By contrast, overexpression of hsa_circ_0066966 in HBV-negative liver cancer cells resulted in the opposite effect. In conclusion, in the present study, comprehensive circRNA profiling in HBV-positive liver cancer cells indicated that hsa_circ_0066966 may regulate the progression of HBV-positive liver cancer.
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Affiliation(s)
- Yinghua Yuan
- Department of Infectious Diseases, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, P.R. China
| | - Xiaojin Yang
- Department of Infectious Diseases, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, P.R. China
| | - Desheng Xie
- Department of Infectious Diseases, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, P.R. China
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Raza SHA, Liang C, Guohua W, Pant SD, Mohammedsaleh ZM, Shater AF, Alotaibi MA, Khan R, Schreurs N, Cheng G, Mei C, Zan L. Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis. Front Vet Sci 2021; 8:794628. [PMID: 34966817 PMCID: PMC8710720 DOI: 10.3389/fvets.2021.794628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 01/17/2023] Open
Abstract
Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.
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Affiliation(s)
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wang Guohua
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sameer D Pant
- School of Animal & Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Zuhair M Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdullah F Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Nicola Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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