Increased interferon I signaling, DNA damage response and evidence of T-cell exhaustion in a patient with combined interferonopathy (Aicardi-Goutières Syndrome, AGS) and cohesinopathy (Cornelia de Lange Syndrome, CdLS)

Crow YJ, Chase DS, Lowenstein Schmidt J, Szynkiewicz M, Forte GM, Gornall HL, Oojageer A, Anderson B, Pizzino A, Helman G, et al. Characterization of human disease phenotypes associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1. Am J Med Genet A. 2015;167A(2):296–312.

Article  PubMed  Google Scholar 

Uggenti C, Lepelley A, Depp M, Badrock AP, Rodero MP, El-Daher MT, Rice GI, Dhir S, Wheeler AP, Dhir A, et al. cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing. Nat Genet. 2020;52(12):1364–72.

Article  CAS  PubMed  Google Scholar 

Dell’Isola GB, Dini G, Culpepper KL, Portwood KE, Ferrara P, Di Cara G, Verrotti A, Lodolo M. Clinical spectrum and currently available treatment of type I interferonopathy Aicardi-Goutieres Syndrome. World J Pediatr. 2023;19(7):635–43.

Article  PubMed  PubMed Central  Google Scholar 

Kline AD, Moss JF, Selicorni A, Bisgaard AM, Deardorff MA, Gillett PM, Ishman SL, Kerr LM, Levin AV, Mulder PA, et al. Diagnosis and management of Cornelia de Lange Syndrome: first international consensus statement. Nat Rev Genet. 2018;19(10):649–66.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu Z, Wang X. Roles of cohesin in chromosome architecture and gene expression. Semin Cell Dev Biol. 2019;90:187–93.

Article  CAS  PubMed  Google Scholar 

Neven B, Al Adba B, Hully M, Desguerre I, Pressiat C, Boddaert N, Duffy D, Rice GI, Seabra L, Fremond ML, et al. JAK inhibition in the Aicardi-Goutieres Syndrome. N Engl J Med. 2020;383(22):2190–1.

Article  PubMed  Google Scholar 

Vanderver A, Adang L, Gavazzi F, McDonald K, Helman G, Frank DB, Jaffe N, Yum SW, Collins A, Keller SR, et al. Janus kinase inhibition in the Aicardi-Goutieres Syndrome. N Engl J Med. 2020;383(10):986–9.

Article  PubMed  PubMed Central  Google Scholar 

Cattalini M, Galli J, Zunica F, Ferraro RM, Carpanelli M, Orcesi S, Palumbo G, Pinelli L, Giliani S, Fazzi E, Badolato R. Case report: the JAK-Inhibitor Ruxolitinib use in Aicardi-Goutieres Syndrome due to ADAR1 mutation. Front Pediatr. 2021;9:725868.

Article  PubMed  PubMed Central  Google Scholar 

Rice GI, Meyzer C, Bouazza N, Hully M, Boddaert N, Semeraro M, Zeef LAH, Rozenberg F, Bondet V, Duffy D, et al. Reverse-transcriptase inhibitors in the Aicardi-Goutieres Syndrome. N Engl J Med. 2018;379(23):2275–7.

Article  PubMed  Google Scholar 

Xu B, Sowa N, Cardenas ME, Gerton JL. L-leucine partially rescues translational and developmental defects associated with zebrafish models of Cornelia de Lange Syndrome. Hum Mol Genet. 2015;24(6):1540–55.

Article  CAS  PubMed  Google Scholar 

Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–60.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome Project Data Processing S: The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.

Article  PubMed  PubMed Central  Google Scholar 

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.

Article  PubMed  PubMed Central  Google Scholar 

Nezos A, Gravani F, Tassidou A, Kapsogeorgou EK, Voulgarelis M, Koutsilieris M, Crow MK, Mavragani CP. Type I and II interferon signatures in Sjogren’s Syndrome pathogenesis: contributions in distinct clinical phenotypes and Sjogren’s related lymphomagenesis. J Autoimmun. 2015;63:47–58.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andrews S: FastQC: a quality control tool for high throughput sequence data. In.: Cambridge, United Kingdom; 2010.

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1):10–2.

Article  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.

Article  CAS  PubMed  Google Scholar 

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I. GENCODE 2021. Nucleic Acids Res. 2021;49(D1):D916–23.

Article  CAS  PubMed  Google Scholar 

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008.

Article  PubMed  PubMed Central  Google Scholar 

Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.

Article  CAS  PubMed  Google Scholar 

Sentis G, Loukogiannaki C, Malissovas N, Nikolopoulos D, Manolakou T, Flouda S, Grigoriou M, Banos A, Boumpas DT, Filia A. A network-based approach reveals long non-coding RNAs associated with disease activity in lupus nephritis: key pathways for flare and potential biomarkers to be used as liquid biopsies. Front Immunol. 2023;14:1203848.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.

Article  CAS  PubMed  Google Scholar 

Team RC: R: A language and environment for statistical computing. URL. R Foundation for Statistical Computing: Vienna, Austria 2021.

Wickham H. Mastering the grammar. ggplot2: elegant graphics for data analysis 2009:27–40. https://link.springer.com/book/10.1007/978-0-387-98141-3.

Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32(18):2847–9.

Article  CAS  PubMed  Google Scholar 

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database hallmark gene set collection. Cell Syst. 2015;1(6):417–25.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545–50.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:1–15.

Article  Google Scholar 

Chiche L, Jourde-Chiche N, Whalen E, Presnell S, Gersuk V, Dang K, Anguiano E, Quinn C, Burtey S, Berland Y. Modular transcriptional repertoire analyses of adults with systemic lupus erythematosus reveal distinct type I and type II interferon signatures. Arthritis Rheumatol. 2014;66(6):1583–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vakrakou AG, Paschalidis N, Pavlos E, Giannouli C, Karathanasis D, Tsipota X, Velonakis G, Stadelmann-Nessler C, Evangelopoulos M-E, Stefanis L. Specific myeloid signatures in peripheral blood differentiate active and rare clinical phenotypes of multiple sclerosis. Front Immunol. 2023;14: 1071623.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP, Robinson MD: CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Res 2017, 6:748.

Bagwell CB, Hunsberger B, Hill B, Herbert D, Bray C, Selvanantham T, Li S, Villasboas JC, Pavelko K, Strausbauch M, et al. Multi-site reproducibility of a human immunophenotyping assay in whole blood and peripheral

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