Heterozygous de novo dominant negative mutation of REXO2 results in interferonopathy.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
06 Aug 2024
Historique:
received: 03 06 2023
accepted: 22 07 2024
medline: 7 8 2024
pubmed: 7 8 2024
entrez: 6 8 2024
Statut: epublish

Résumé

Mitochondrial RNA (mtRNA) in the cytosol can trigger the innate immune sensor MDA5, and autoinflammatory disease due to type I IFN. Here, we show that a dominant negative mutation in the gene encoding the mitochondrial exonuclease REXO2 may cause interferonopathy by triggering the MDA5 pathway. A patient characterized by this heterozygous de novo mutation (p.T132A) presented with persistent skin rash featuring hyperkeratosis, parakeratosis and acanthosis, with infiltration of lymphocytes and eosinophils around small blood vessels. In addition, circulating IgE levels and inflammatory cytokines, including IFNα, are found consistently elevated. Transcriptional analysis highlights a type I IFN gene signature in PBMC. Mechanistically, REXO2 (T132A) lacks the ability to cleave RNA and inhibits the activity of wild-type REXO2. This leads to an accumulation of mitochondrial dsRNA in the cytosol, which is recognized by MDA5, leading to the associated type I IFN gene signature. These results demonstrate that in the absence of appropriate regulation by REXO2, aberrant cellular nucleic acids may accumulate and continuously trigger innate sensors, resulting in an inborn error of immunity.

Identifiants

pubmed: 39107301
doi: 10.1038/s41467-024-50878-w
pii: 10.1038/s41467-024-50878-w
doi:

Substances chimiques

Interferon-Induced Helicase, IFIH1 EC 3.6.4.13
IFIH1 protein, human EC 3.6.1.-
Interferon Type I 0
Exonucleases EC 3.1.-
Exoribonucleases EC 3.1.-
RNA, Double-Stranded 0
Immunoglobulin E 37341-29-0

Types de publication

Journal Article Case Reports

Langues

eng

Sous-ensembles de citation

IM

Pagination

6685

Subventions

Organisme : National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
ID : 32250410295
Organisme : National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
ID : 82125015

Informations de copyright

© 2024. The Author(s).

Références

Ablasser, A. & Hur, S. Regulation of cGAS- and RLR-mediated immunity to nucleic acids. Nat. Immunol. 21, 17–29 (2020).
doi: 10.1038/s41590-019-0556-1
Goubau, D., Deddouche, S. & Reis e Sousa, C. Cytosolic sensing of viruses. Immunity 38, 855–869 (2013).
doi: 10.1016/j.immuni.2013.05.007
Rodero, M. P. & Crow, Y. J. Type I interferon-mediated monogenic autoinflammation: the type I interferonopathies, a conceptual overview. J. Exp. Med. 213, 2527–2538 (2016).
doi: 10.1084/jem.20161596
Rice, G. I. et al. Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nat. Genet. 46, 503–509 (2014).
doi: 10.1038/ng.2933
Oda, H. et al. Aicardi-Goutieres syndrome is caused by IFIH1 mutations. Am. J. Hum. Genet 95, 121–125 (2014).
doi: 10.1016/j.ajhg.2014.06.007
Kuipers, D. J. S. et al. EIF2AK2 missense variants associated with early onset generalized dystonia. Ann. Neurol. 89, 485–497 (2021).
doi: 10.1002/ana.25973
Uggenti, C., Lepelley, A. & Crow, Y. J. Self-awareness: nucleic acid-driven inflammation and the type I interferonopathies. Annu. Rev. Immunol. 37, 247–267 (2019).
doi: 10.1146/annurev-immunol-042718-041257
Davidson, S., Steiner, A., Harapas, C. R. & Masters, S. L. An update on autoinflammatory diseases: interferonopathies. Curr. Rheumatol. Rep. 20, 38 (2018).
doi: 10.1007/s11926-018-0748-y
Fu, Y., Tigano, M. & Sfeir, A. Safeguarding mitochondrial genomes in higher eukaryotes. Nat. Struct. Mol. Biol. 27, 687–695 (2020).
doi: 10.1038/s41594-020-0474-9
Mai, N., Chrzanowska-Lightowlers, Z. M. & Lightowlers, R. N. The process of mammalian mitochondrial protein synthesis. Cell Tissue Res. 367, 5–20 (2017).
doi: 10.1007/s00441-016-2456-0
Pearce, S. F. et al. Regulation of mammalian mitochondrial gene expression: recent advances. Trends Biochem. Sci. 42, 625–639 (2017).
doi: 10.1016/j.tibs.2017.02.003
Borowski, L. S., Dziembowski, A., Hejnowicz, M. S., Stepien, P. P. & Szczesny, R. J. Human mitochondrial RNA decay mediated by PNPase-hSuv3 complex takes place in distinct foci. Nucleic Acids Res. 41, 1223–1240 (2013).
doi: 10.1093/nar/gks1130
Minczuk, M., Lilpop, J., Boros, J. & Stepien, P. P. The 5’ region of the human hSUV3 gene encoding mitochondrial DNA and RNA helicase: promoter characterization and alternative pre-mRNA splicing. Biochim. Biophys. Acta 1729, 81–87 (2005).
doi: 10.1016/j.bbaexp.2005.04.005
Szczesny, R. J. et al. Down-regulation of human RNA/DNA helicase SUV3 induces apoptosis by a caspase- and AIF-dependent pathway. Biol. Cell 99, 323–332 (2007).
doi: 10.1042/BC20060108
Kazak, L. et al. Alternative translation initiation augments the human mitochondrial proteome. Nucleic Acids Res. 41, 2354–2369 (2013).
doi: 10.1093/nar/gks1347
Wang, D. D., Shu, Z., Lieser, S. A., Chen, P. L. & Lee, W. H. Human mitochondrial SUV3 and polynucleotide phosphorylase form a 330-kDa heteropentamer to cooperatively degrade double-stranded RNA with a 3’-to-5’ directionality. J. Biol. Chem. 284, 20812–20821 (2009).
doi: 10.1074/jbc.M109.009605
Cameron, T. A., Matz, L. M. & De Lay, N. R. Polynucleotide phosphorylase: not merely an RNase but a pivotal post-transcriptional regulator. PLoS Genet 14, e1007654 (2018).
doi: 10.1371/journal.pgen.1007654
Dhir, A. et al. Mitochondrial double-stranded RNA triggers antiviral signalling in humans. Nature 560, 238–242 (2018).
doi: 10.1038/s41586-018-0363-0
Silva, S., Camino, L. P. & Aguilera, A. Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability. Proc. Natl Acad. Sci. USA 115, 11024–11029 (2018).
doi: 10.1073/pnas.1807258115
Vedrenne, V. et al. Mutation in PNPT1, which encodes a polyribonucleotide nucleotidyltransferase, impairs RNA import into mitochondria and causes respiratory-chain deficiency. Am. J. Hum. Genet. 91, 912–918 (2012).
doi: 10.1016/j.ajhg.2012.09.001
Ghosh, S. & Deutscher, M. P. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc. Natl Acad. Sci. USA 96, 4372–4377 (1999).
doi: 10.1073/pnas.96.8.4372
Mechold, U., Ogryzko, V. & Ngo, S. A. Danchin, Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells. Nucleic Acids Res. 34, 2364–2373 (2006).
doi: 10.1093/nar/gkl247
Chu, L. Y., Agrawal, S., Chen, Y. P., Yang, W. Z. & Yuan, H. S. Structural insights into nanoRNA degradation by human Rexo2. RNA 25, 737–746 (2019).
doi: 10.1261/rna.070557.119
Nguyen, L. H., Erzberger, J. P., Root, J. & Wilson, D. M. 3rd, The human homolog of Escherichia coli Orn degrades small single-stranded RNA and DNA oligomers. J. Biol. Chem. 275, 25900–25906 (2000).
doi: 10.1074/jbc.M002672200
Bruni, F., Gramegna, P., Oliveira, J. M., Lightowlers, R. N. & Chrzanowska-Lightowlers, Z. M. REXO2 is an oligoribonuclease active in human mitochondria. PLoS ONE 8, e64670 (2013).
doi: 10.1371/journal.pone.0064670
Szewczyk, M. et al. Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA. Nucleic Acids Res. 48, 5572–5590 (2020).
doi: 10.1093/nar/gkaa302
Mercer, T. R. et al. The human mitochondrial transcriptome. Cell 146, 645–658 (2011).
doi: 10.1016/j.cell.2011.06.051
Wanrooij, S. et al. In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication. EMBO Rep. 13, 1130–1137 (2012).
doi: 10.1038/embor.2012.161
Nicholls, T. J. et al. Dinucleotide degradation by REXO2 maintains promoter specificity in mammalian mitochondria. Mol. Cell 76, 784–796 e786 (2019).
doi: 10.1016/j.molcel.2019.09.010
Goldman, S. R. et al. NanoRNAs prime transcription initiation in vivo. Mol. Cell 42, 817–825 (2011).
doi: 10.1016/j.molcel.2011.06.005
Laitman, Y., Tzur, S., Attai, R., Tirosh, A. & Friedman, E. Germline variant in REXO2 is a novel candidate gene in familial pheochromocytoma. Genet Res. 102, e3 (2020).
doi: 10.1017/S0016672320000038
Wang, H., Wang, X., Xu, L., Zhang, J. & Cao, H. RUNX1 and REXO2 are associated with the heterogeneity and prognosis of IDH wild type lower grade glioma. Sci. Rep. 11, 11836 (2021).
doi: 10.1038/s41598-021-91382-1
Hulur, I. et al. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 16, 138 (2015).
doi: 10.1186/s12864-015-1292-z
Palmieri, O. et al. Genome-wide pathway analysis using gene expression data of colonic mucosa in patients with inflammatory Bowel disease. Inflamm. Bowel Dis. 21, 1260–1268 (2015).
Samarajiwa, S. A., Forster, S., Auchettl, K. & Hertzog, P. J. INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res. 37, D852–D857 (2009).
doi: 10.1093/nar/gkn732
Metz, P., Reuter, A., Bender, S. & Bartenschlager, R. Interferon-stimulated genes and their role in controlling hepatitis C virus. J. Hepatol. 59, 1331–1341 (2013).
doi: 10.1016/j.jhep.2013.07.033
Schoggins, J. W. & Rice, C. M. Interferon-stimulated genes and their antiviral effector functions. Curr. Opin. Virol. 1, 519–525 (2011).
doi: 10.1016/j.coviro.2011.10.008
Nelson, I., Hanna, M. G., Wood, N. W. & Harding, A. E. Depletion of mitochondrial DNA by ddC in untransformed human cell lines. Somat Cell Mol. Genet 23, 287–290 (1997).
doi: 10.1007/BF02674419
Nicolli, A., Basso, E., Petronilli, V., Wenger, R. M. & Bernardi, P. Interactions of cyclophilin with the mitochondrial inner membrane and regulation of the permeability transition pore, and cyclosporin A-sensitive channel. J. Biol. Chem. 271, 2185–2192 (1996).
doi: 10.1074/jbc.271.4.2185
Xian, H. et al. Oxidized DNA fragments exit mitochondria via mPTP- and VDAC-dependent channels to activate NLRP3 inflammasome and interferon signaling. Immunity 55, 1370–1385 e1378 (2022).
doi: 10.1016/j.immuni.2022.06.007
Kim, J. et al. VDAC oligomers form mitochondrial pores to release mtDNA fragments and promote lupus-like disease. Science 366, 1531–1536 (2019).
doi: 10.1126/science.aav4011
Arimatsu, Y. et al. Purification and properties of double-stranded RNA-degrading nuclease, dsRNase, from the digestive juice of the silkworm, Bombyx mori. J. Insect Biotechnol. Sericol. 76, 1_57–51_62 (2007).
Liu, J., Swevers, L., Iatrou, K., Huvenne, H. & Smagghe, G. Bombyx mori DNA/RNA non-specific nuclease: expression of isoforms in insect culture cells, subcellular localization and functional assays. J. Insect Physiol. 58, 1166–1176 (2012).
doi: 10.1016/j.jinsphys.2012.05.016
Podolska, K., Sedlak, D., Bartunek, P. & Svoboda, P. Fluorescence-based high-throughput screening of dicer cleavage activity. J. Biomol. Screen 19, 417–426 (2014).
doi: 10.1177/1087057113497400
Starokadomskyy, P. et al. DNA polymerase-alpha regulates the activation of type I interferons through cytosolic RNA:DNA synthesis. Nat. Immunol. 17, 495–504 (2016).
doi: 10.1038/ni.3409
Bursztejn, A. C. et al. Unusual cutaneous features associated with a heterozygous gain-of-function mutation in IFIH1: overlap between Aicardi-Goutieres and Singleton-Merten syndromes. Br. J. Dermatol. 173, 1505–1513 (2015).
doi: 10.1111/bjd.14073
Zahn, S. et al. Enhanced skin expression of melanoma differentiation-associated gene 5 (MDA5) in dermatomyositis and related autoimmune diseases. J. Am. Acad. Dermatol. 64, 988–989 (2011).
doi: 10.1016/j.jaad.2010.08.004
Chen, G. et al. Genetic variants in IFIH1 play opposite roles in the pathogenesis of psoriasis and chronic periodontitis. Int. J. Immunogenet. 39, 137–143 (2012).
doi: 10.1111/j.1744-313X.2011.01068.x
Liu, X., Li, C., Mou, C., Dong, Y. & Tu, Y. dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Med. 12, 103 (2020).
doi: 10.1186/s13073-020-00803-9
Yu, C. H. et al. TDP-43 triggers mitochondrial DNA release via mPTP to activate cGAS/STING in ALS. Cell 183, 636–649 e618 (2020).
doi: 10.1016/j.cell.2020.09.020
Davidson, S. et al. Protein kinase R is an innate immune sensor of proteotoxic stress via accumulation of cytoplasmic IL-24. Sci. Immunol. 7, eabi6763 (2022).
doi: 10.1126/sciimmunol.abi6763
Baker, P. J. & Masters, S. L. Generation of genetic knockouts in myeloid cell lines using a lentiviral CRISPR/Cas9 system. Methods Mol. Biol. 1714, 41–55 (2018).
doi: 10.1007/978-1-4939-7519-8_3
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
doi: 10.14806/ej.17.1.200
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
doi: 10.1093/bioinformatics/bty560
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
doi: 10.1093/bioinformatics/bts635
Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E. & Zanini, F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics 38, 2943–2945 (2022).
doi: 10.1093/bioinformatics/btac166
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
doi: 10.1186/s13059-014-0550-8

Auteurs

Elina Idiiatullina (E)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.
Department of Therapy and Nursing, Bashkir State Medical University, Ufa, Russia.
Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, USA.

Mahmoud Al-Azab (M)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.
Department of Medical Microbiology, Faculty of Medicine, University of Science and Technology, Aden, Yemen.

Meng Lin (M)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Katja Hrovat-Schaale (K)

Department of Therapy and Nursing, Bashkir State Medical University, Ufa, Russia.
Department of Medical Microbiology, Faculty of Medicine, University of Science and Technology, Aden, Yemen.

Ziyang Liu (Z)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Xiaotian Li (X)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Caiqin Guo (C)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Xixi Chen (X)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Yaoying Li (Y)

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center, Sun Yat-sen University Cancer Center, Guangzhou, China.

Song Gao (S)

State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center, Sun Yat-sen University Cancer Center, Guangzhou, China.

Jun Cui (J)

School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

Wenhao Zhou (W)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China.

Li Liu (L)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China. liliuchina@qq.com.

Yuxia Zhang (Y)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China. yuxia.zhang@gwcmc.org.

Seth L Masters (SL)

Department of Genetics and Endocrinology, Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China. seth.masters@hudson.org.au.
Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. seth.masters@hudson.org.au.
Department of Medical Biology, The University of Melbourne, Parkville, Australia. seth.masters@hudson.org.au.
Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia. seth.masters@hudson.org.au.
Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia. seth.masters@hudson.org.au.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH