(t)RNA epitranscriptome and disease group

Unravelling the wonders of (t)RNA molecules and their modifications in the context of disease

Publications

Most relevant publications

  • Pereira M, Ribeiro DR, Berg M, Tsai AP, Dong C, Nho K, Kaiser S, Moutinho M, Soares AR. Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis in Alzheimer’s disease models. BBA Molecular Basis of Disease, 2023. doi: 10.1016/j.bbadis.2023.16685
  • Marques M, Ramos B, Albuquerque H, Pereira M, Ribeiro DR, Nunes A, Sarabando J, Bras D, Ferreira AR, Vitorino R, Amorim MJ, Silva A, Soares AR, Ribeiro D. Influenza A virus propagation requires the activation of the unfolded protein response and the accumulation of insoluble protein aggregates. iScience. Jan 2024. doi.org/10.1016/j.isci.2024.109100 
  • Ribeiro DR, Nunes A, Ribeiro D, Soares AR. The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections. Frontiers in genetics. 2023. doi: 10.3389/fgene.2023.1245683 
  • Soares AR, Kikkert M, Kellner-Kaiser S, Ribeiro D. Editorial: Viruses and Epitranscriptomes: Regulation of Infection and Antiviral Response. Front Cell Dev Biol. 2022 May 9;10:917894. doi: 10.3389/fcell.2022.917894. 
  • Santos M, Fidalgo A, Varanda AS, Soares AR, Almeida GM, Martins D, Mendes N, Oliveira C, Santos MAS. Upregulation of tRNA-Ser-AGA-2-1 Promotes Malignant Behavior in Normal Bronchial Cells. Front Mol Biosci. 2022 May 2;9:809985. doi: 10.3389/fmolb.2022.809985
  • Francisco S, Martinho V, Ferreira M, Reis A, Moura G, Soares AR, Santos MAS. The Role of MicroRNAs in Proteostasis Decline and Protein Aggregation during Brain and Skeletal Muscle Aging. Int J Mol Sci. 2022 Mar 17;23(6):3232. doi: 10.3390/ijms23063232
  • Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR. m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci. 2021 Mar 14;22(6):2941. doi: 10.3390/ijms22062941
  • Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. RNA Biol. 2021 Apr;18(4):563-575. doi: 10.1080/15476286.2020.1819671
  • Francisco S, Ferreira M, Moura G, Soares AR, Santos MAS. Does proteostasis get lost in translation? Implications for protein aggregation across the lifespan. Ageing Res Rev. 2020 Sep;62:101119. doi: 10.1016/j.arr.2020.101119
  • Nunes A, Ribeiro DR, Marques M, Santos MAS, Ribeiro D, Soares AR. Emerging Roles of tRNAs in RNA Virus Infections. Trends Biochem Sci. 2020 Sep;45(9):794-805. doi: 10.1016/j.tibs.2020.05.007
  • Pereira M, Francisco S, Varanda AS, Santos M, Santos MAS, Soares AR. Impact of tRNA Modifications and tRNA-Modifying Enzymes on Proteostasis and Human Disease. Int J Mol Sci. 2018 Nov 24;19(12):3738. doi: 10.3390/ijms19123738
  • Pereira, P, Tomé D, Domingues AS, Varanda AS, Paulo C, Santos MS, Soares AR. A fluorescence-based sensor assay that monitors general protein aggregation in human cells. Biotechnology Journal – 2018 Jan 18. doi: 10.1002/biot.201700676 
  • Soares AR, Santos MA. Discovery and function of tRNA derived fragments and their role in disease. Wires RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1423 
  • Reverendo M, Soares AR, Pereira PM, Carreto L, Ferreira V, Gatti E, Pierre P, Moura GR, Santos MA. TRNA mutations that affect decoding fidelity deregulate development and the proteostasis network in zebrafish. RNA Biology. 2014;11(9):1199-213. doi: 10.4161/rna.32199. 
  • Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics. 2009 Apr 27;10:195. doi: 10.1186/1471-2164-10-195

Other publications

  • Malafaia D et al. Design, Synthesis and Biological Evaluation of Chromeno[3,4- b]xanthones as Multifunctional Agents for Alzheimer’s Disease. ACS Chem Neurosci, 2025. doi: 10.1021/acschemneuro.5c00425
  • Gonçalves B, Pires D, Fernandes L, Pacheco M, Ferreira T, Osório H, Soares AR, Henriques M, Silva S. Biofilm matrix regulation by Candida glabrata Zap1 under acidic conditions: transcriptomic and proteomic analyses. Microbiology Spectrum. Nov 2024. doi.org/10.1128/spectrum.01201-24 
  • Silva ARR, Silva PV, Soares AR, González-Alcaraz MN, van Gestel CAM, Roelofs D, Moura G, Soares AMVM, Loureiro S. Daphnia magna Multigeneration Exposure to Carbendazim: Gene Transcription Responses. Nov 10;11(11):918. Toxics. 2023. doi: 10.3390/toxics11110918
  • Gonçalves B, Barbosa A, Soares AR, Henriques M, Silva S. Sfl1 is required for Candida albicans biofilm formation under acidic conditions. Biochimie. 2023 Jan 18;209:37-43. doi: 10.1016/j.biochi.2023.01.011 
  • Salazar SB, Pinheiro MJF, Sotti-Novais D, Soares AR, Lopes MM, Ferreira T, Rodrigues V, Fernandes F, Mira NP. Disclosing azole resistance mechanisms in resistant Candida glabrata strains encoding wild-type or gain-of-function CgPDR1 alleles through comparative genomics and transcriptomics. G3 (Bethesda). 2022 Jul 6;12(7):jkac110. doi: 10.1093/g3journal/jkac110
  • Albuquerque HMT, Nunes da Silva R, Pereira M, Maia A, Guieu S, Soares AR, Santos CMM, Vieira SI, Silva AMS. Steroid-Quinoline Hybrids for Disruption and Reversion of Protein Aggregation Processes. ACS Med Chem Lett. 2022 Feb 14;13(3):443-448. doi: 10.1021/acsmedchemlett.1c00604. eCollection 2022 Mar 10. 
  • Magalhães S, Almeida I, Martins F, Camões F, Soares AR, Goodfellow BJ, Rebelo S, Nunes A. FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice. Molecules. 2021 Oct 23;26(21):6410. doi: 10.3390/molecules26216410. 
  • Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. Aging (Albany NY). 2021 Jul 29;13(14):18150-18190. doi: 10.18632/aging.203379. 
  • Varanda AS, Santos M, Soares AR, Vitorino R, Oliveira P, Oliveira C, Santos MAS. Human cells adapt to translational errors by modulating protein synthesis rate and protein turnover. RNA Biol. 2020 Jan;17(1):135-149. doi: 10.1080/15476286.2019.1670039. 
  • Marques M, Ramos B, Soares AR, Ribeiro D. Cellular Proteostasis During Influenza A Virus Infection-Friend or Foe? Cells. 2019 Mar 9;8(3):228. doi: 10.3390/cells8030228. 
  • Ferreira C, Soares AR, Lamosa P, Santos MA, da Costa MS. Comparison of the compatible solute pool of two slightly halophilic planctomycetes species, Gimesia maris and Rubinisphaera brasiliensis. Extremophiles. 2016 Nov;20(6):811-820. doi: 10.1007/s00792-016-0868-0 
  • Matos JC, Soares AR, Domingues I, Monteiro GA, Gonçalves MC. ORMOPLEXEs for gene therapy: in vitro and in vivo assays. Materials Science and Engineering: C Materials for Biological Applications. 2016 Jun;63:546-53. doi:10.1016/j.msec.2016.03.006 
  • Soares AR, Fernandes N, Reverendo M, Araujo, H, Oliveira JL, Moura G, Santos MA. Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Molecular Biology. 2015 Dec 22;16(1):22. doi: 10.1186/s12867-015-0050-8
  • Terawaki S, Camosseto V, Prete F, Wenger T, Papadopoulos A, Rondeau C, Combes A, Rodriguez Rodrigues C, Vu Manh TP, Fallet M, English L, Santamaria R, Soares AR, Weil T, Hammad H, Desjardins M, Gorvel JP, Santos MA, Gatti E, Pierre P. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. Journal of Cell Biology. 2015 Sep 28;210(7):1133-52. doi: 10.1083/jcb.201501059
  • Soares AR, Reverendo M, Pereira PM, Nivelles O, Pendeville H, Bezerra AR, Moura GR, Struman I, Santos MA. Dre-miR-2188 targets Nrp2a and mediates proper intersegmental vessel development in zebrafish embryos. PLoS One. 2012;7(6):e39417. doi: 10.1371/journal.pone.0039417 
  • Soares AR, Pereira PM, Ferreira V, Reverendo M, Simões J, Bezerra AR, Moura GR, Santos MA. Ethanol exposure induces upregulation of specific microRNAs in zebrafish embryos. Toxicological Sciences. 2012 May;127(1):18-28. doi: 10.1093/toxsci/kfs068 
  • Moura GR, Pinheiro M, Freitas A, Oliveira JL, Frommlet JC, Carreto L, Soares AR, Bezerra AR, Santos MA. Species-specific codon context rules unveil non-neutrality effects of synonymous mutations. 
    PLoS One. 2011;6(10):e26817. doi: 10.1371/journal.pone.0026817 
  • Pereira PM, Marques JP, Soares AR, Carreto L, Santos MA. MicroRNA expression variability in human cervical tissues. PLoS One. 2010 Jul 26;5(7):e11780. doi: 10.1371/journal.pone.0011780 

Preprints

  • Marques M, Ramos B, Albuquerque H, Pereira M, Ribeiro DR, Nunes A, Sarabando J, Bras D, Ferreira AR, Vitorino R, Amorim MJ, Silva A, Soares AR, Ribeiro D. Influenza A virus activates the unfolded protein response and induces the accumulation of insoluble protein aggregates that are essential for efficient viral propagation. BioRXiv. Sept 2023.doi: https://doi.org/10.1101/2023.09.11.557148
  • Pereira M, Ribeiro DR, Berg M, Tsai AP, Nho K, Kaiser S, Moutinho M, Soares AR. Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis in Alzheimer’s disease models. BioRXiv. May 2023. bioRxiv 2023.05.02.538928; doi: https://doi.org/10.1101/2023.05.02.538928 
  • Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. BioRXiv. Feb 2021. doi: https://doi.org/10.1101/2021.02.18.431793 
  • Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. BioRXiv. Jul 2020 doi: https://doi.org/10.1101/2020.07.13.200121