Bioinformatics Analysis of Genes and Pathways of CD11b(+)/Ly6C(intermediate) Macrophages after Renal Ischemia-Reperfusion Injury
CURRENT MEDICAL SCIENCE
Authors: Sun, Dong; Wan, Xin; Pan, Bin-bin; Sun, Qing; Ji, Xiao-bing; Zhang, Feng; Zhang, Hao; Cao, Chang-chun
Abstract
Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury (AKI), which could induce the poor prognosis. The purpose of this study was to characterize the molecular mechanism of the functional changes of CD11b(+)/Ly6C(intermediate) macrophages after renal IRI. The gene expression profiles of CD11b(+)/Ly6C(intermcdiate) macrophages of the sham surgery mice, and the mice 4 h, 24 h and 9 days after renal IRI were downloaded from the Gene Expression Omnibus database. Analysis of mRNA expression profiles was conducted to identify differentially expressed genes (DEGs), biological processes and pathways by the series test of cluster. Protein-protein interaction network was constructed and analysed to discover the key genes. A total of 6738 DEGs were identified and assigned to 20 model profiles. DEGs in profile 13 were one of the predominant expression profiles, which are involved in immune cell chemotaxis and proliferation. Signet analysis showed that Atp5al, Atp5o, Cox4i, Cdc42, Rac2 and Nhp2 were the key genes involved in oxidation-reduction, apoptosis, migration, M1-M2 differentiation, and proliferation of macrophages. RPS18 may be an appreciate reference gene as it was stable in macrophages. The identified DEGs and their enriched pathways investigate factors that may participate in the functional changes of CD11b(+)/Ly6C(intermediate) macrophages after renal IRI. Moreover, the vital gene Nhp2 may involve the polarization of macrophages, which may be a new target to affect the process of AKI.
Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Authors: Balogh, Eszter; Chandler, Jennifer C.; Varga, Mate; Tahoun, Mona; Menyhard, Dora K.; Schay, Gusztav; Goncalves, Tomas; Hamar, Renata; Legradi, Regina; Szekeres, Akos; Gribouval, Olivier; Kleta, Robert; Stanescu, Horia; Bockenhauer, Detlef; Kerti, Andrea; Williams, Hywel; Kinsler, Veronica; Di, Wei-Li; Curtis, David; Kolatsi-Joannou, Maria; Hammid, Hafsa; Szocs, Anna; Perczel, Kristof; Maka, Erika; Toldi, Gergely; Sava, Florentina; Arrondel, Christelle; Kardos, Magdolna; Fintha, Attila; Hossain, Ahmed; D'Arco, Felipe; Kaliakatsos, Mario; Koeglmeier, Jutta; Mifsud, William; Moosajee, Mariya; Faro, Ana; Javorszky, Eszter; Rudas, Gabor; Saied, Marwa H.; Marzouk, Salah; Kelen, Kata; Gotze, Judit; Reusz, George; Tulassay, Tivadar; Dragon, Francois; Mollet, Geraldine; Motameny, Susanne; Thiele, Holger; Dorval, Guillaume; Nurnberg, Peter; Perczel, Andras; Szabo, Attila J.; Long, David A.; Tomita, Kazunori; Antignac, Corinne; Waters, Aoife M.; Tory, Kalman
Abstract
RNA modifications play a fundamental role in cellular function. Pseudouridylation, the most abundant RNA modification, is catalyzed by the H/ACA small ribonucleoprotein (snoRNP) complex that shares four core proteins, dyskerin (DKC1), NOP10, NHP2, and GAR1. Mutations in DKC1, NOP10, or NHP2 cause dyskeratosis congenita (DC), a disorder characterized by telomere attrition. Here, we report a phenotype comprising nephrotic syndrome, cataracts, sensorineural deafness, enterocolitis, and early lethality in two pedigrees: males with DKC1 p.Glu206Lys and two children with homozygous NOP10 p.Thr16Met. Females with heterozygous DKC1 p.Glu206Lys developed cataracts and sensorineural deafness, but nephrotic syndrome in only one case of skewed X-inactivation. We found telomere attrition in both pedigrees, but no mucocutaneous abnormalities suggestive of DC. Both mutations fall at the dyskerin-NOP10 binding interface in a region distinct from those implicated in DC, impair the dyskerin-NOP10 interaction, and disrupt the catalytic pseudouridylation site. Accordingly, we found reduced pseudouridine levels in the ribosomal RNA (rRNA) of the patients. Zebrafish dkc1 mutants recapitulate the human phenotype and show reduced 18S pseudouridylation, ribosomal dysregulation, and a cell-cycle defect in the absence of telomere attrition. We therefore propose that this human disorder is the consequence of defective snoRNP pseudouridylation and ribosomal dysfunction.