Browsing by Subject "TRANSLATION"

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  • Genome Aggregation Database Prod T; Genome Aggregation Database Consor; Whiffin, Nicola; Karczewski, Konrad J.; Zhang, Xiaolei; Ware, James S.; Färkkilä, Martti; Groop, Leif; Holi, Matti M.; Hiltunen, Mikko; Kallela, Kaarlo Mikko; Kaprio, Jaakko; Koskinen, Seppo; Laakso, Markku; Lehtimäki, Tero; Mattila, Kari; Palotie, Aarno; Remes, Anne M.; Ripatti, Samuli; Salomaa, Veikko; Soininen, Hilkka; Suvisaari, Jaana; Wessman, Maija; Tuomi, Tiinamaija; Vartiainen, Erkki (2020)
    Upstream open reading frames (uORFs) are tissue-specific cis-regulators of protein translation. Isolated reports have shown that variants that create or disrupt uORFs can cause disease. Here, in a systematic genome-wide study using 15,708 whole genome sequences, we show that variants that create new upstream start codons, and variants disrupting stop sites of existing uORFs, are under strong negative selection. This selection signal is significantly stronger for variants arising upstream of genes intolerant to loss-of-function variants. Furthermore, variants creating uORFs that overlap the coding sequence show signals of selection equivalent to coding missense variants. Finally, we identify specific genes where modification of uORFs likely represents an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in neurofibromatosis. Our results highlight uORF-perturbing variants as an under-recognised functional class that contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data in studying non-coding variant classes. Upstream open reading frames (uORFs), located in 5' untranslated regions, are regulators of downstream protein translation. Here, Whiffin et al. use the genomes of 15,708 individuals in the Genome Aggregation Database (gnomAD) to systematically assess the deleteriousness of variants creating or disrupting uORFs.
  • Lohmus, Andres; Hafren, Anders; Mäkinen, Kristiina (2017)
    We demonstrate here that both coat protein (CP) phosphorylation by protein kinase CK2 and a chaperone system formed by two heat shock proteins, CP-interacting protein (CPIP) and heat shock protein 70 (HSP70), are essential for potato virus A (PVA; genus Potyvirus) replication and that all these host proteins have the capacity to contribute to the level of PVA CP accumulation. An E3 ubiquitin ligase called carboxyl terminus Hsc70-interacting protein (CHIP), which may participate in the CPIP-HSP70-mediated CP degradation, is also needed for robust PVA gene expression. Residue Thr243 within the CK2 consensus sequence of PVA CP was found to be essential for viral replication and to regulate CP protein stability. Substitution of Thr243 either with a phosphorylation-mimicking Asp (CPADA) or with a phosphorylation-deficient Ala (CPAAA) residue in CP expressed from viral RNA limited PVA gene expression to the level of nonreplicating PVA. We found that both the CPAAA mutant and CK2 silencing inhibited, whereas CPADA mutant and overexpression of CK2 increased, PVA translation. From our previous studies, we know that phosphorylation reduces the RNA binding capacity of PVA CP and an excess of CP fully blocks viral RNA translation. Together, these findings suggest that binding by nonphosphorylated PVA CP represses viral RNA translation, involving further CP phosphorylation and CPIP-HSP70 chaperone activities as prerequisites for PVA replication. We propose that this mechanism contributes to shifting potyvirus RNA from translation to replication. IMPORTANCE Host protein kinase CK2, two host chaperones, CPIP and HSP70, and viral coat protein (CP) phosphorylation at Thr243 are needed for potato virus A (PVA) replication. Our results show that nonphosphorylated CP blocks viral translation, likely via binding to viral RNA. We propose that this translational block is needed to allow time and space for the formation of potyviral replication complex around the 3' end of viral RNA. Progression into replication involves CP regulation by both CK2 phosphorylation and chaperones CPIP and HSP70.
  • Hulkkonen, S.; Repo, J. P.; Häkkinen, A.; Karppinen, J.; Ryhänen, J. (2020)
    Background and Aims: Michigan Hand Outcomes Questionnaire is a widely used patient-reported outcome measure in hand surgery. The aim of this study was to translate and validate the Michigan Hand Outcomes Questionnaire into Finnish for Finnish patients with hand problems following international standards and guidelines. Material and Methods: The original English Michigan Hand Outcomes Questionnaire was translated into Finnish. Altogether, 115 patients completed the Finnish Michigan Hand Outcomes Questionnaire, and reference outcomes: Disabilities of the Arm and Shoulder, EQ-5D 3L and pain intensity on a visual analog scale. Grip and key pinch forces were measured. After 1-2 weeks, 63 patients completed the Finnish Michigan Hand Outcomes Questionnaire the second time. The Michigan Hand Outcomes Questionnaire was analyzed for internal consistency, repeatability, correlations with the reference outcomes, and factor analysis. Results: Cronbach's alpha ranged from 0.90 to 0.97 in all the Michigan Hand Outcomes Questionnaire subscales, showing high internal consistency. The intraclass correlation coefficient showed good to excellent test-retest reliability ranging from 0.66 to 0.91 in all the Michigan Hand Outcomes Questionnaire subscales. In factor analysis, the structure with six subscales was not confirmed. All the subscales correlated with Disabilities of the Arm and Shoulder score, and five subscales correlated with EQ-5D index. Conclusion: The Finnish version of the Michigan Hand Outcomes Questionnaire showed similar properties compared to the original English version and thus can be used as patient-reported outcome measure for Finnish patients with hand problems.
  • Ramilowski, Jordan A.; Yip, Chi Wai; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan V.; Mendez, Mickael; Ooi, Jasmine Li Ching; Ouyang, John F.; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Brombacher, Frank; Cameron, Chris J. F.; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josee; Ducoli, Luca; Favorov, Alexander; Fort, Alexandre; Garrido, Diego; Gil, Noa; Gimenez, Juliette; Guler, Reto; Handoko, Lusy; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Kosuke; Hayatsu, Norihito; Heutink, Peter; Hirose, Tetsuro; Imada, Eddie L.; Itoh, Masayoshi; Kaczkowski, Bogumil; Kanhere, Aditi; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S. Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; Lopez-Redondo, Fernando; Luginbuhl, Joachim; Maeda, Shiori; Makeev, Vsevolod J.; Marchionni, Luigi; Medvedeva, Yulia A.; Minoda, Aki; Mueller, Ferenc; Munoz-Aguirre, Manuel; Murata, Mitsuyoshi; Nishiyori, Hiromi; Nitta, Kazuhiro R.; Noguchi, Shuhei; Noro, Yukihiko; Nurtdinov, Ramil; Okazaki, Yasushi; Orlando, Valerio; Paquette, Denis; Parr, Callum J. C.; Rackham, Owen J. L.; Rizzu, Patrizia; Martinez, Diego Fernando Sanchez; Sandelin, Albin; Sanjana, Pillay; Semple, Colin A. M.; Shibayama, Youtaro; Sivaraman, Divya M.; Suzuki, Takahiro; Szumowski, Suzannah C.; Tagami, Michihira; Taylor, Martin S.; Terao, Chikashi; Thodberg, Malte; Thongjuea, Supat; Tripathi, Vidisha; Ulitsky, Igor; Verardo, Roberto; Vorontsov, Ilya E.; Yamamoto, Chinatsu; Young, Robert S.; Baillie, J. Kenneth; Forrest, Alistair R. R.; Guigo, Roderic; Hoffman, Michael M.; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; Hoon, Michiel J. L. de; Shin, Jay W.; Carninci, Piero (2020)
    Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-todate lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
  • Lorey, Martina B.; Rossi, Katriina; Eklund, Kari; Nyman, Tuula A.; Matikainen, Sampsa (2017)
    Gram-negative bacteria are associated with a wide spectrum of infectious diseases in humans. Inflammasomes are cytosolic protein complexes that are assembled when the cell encounters pathogens or other harmful agents. The non-canonical caspase-4/5 inflammasome is activated by Gram-negative bacteria-derived lipopolysaccharide (LPS) and by endogenous oxidized phospholipids. Protein secretion is a critical component of the innate immune response. Here, we have used label-free quantitative proteomics to characterize global protein secretion in response to non-canonical inflammasome activation upon intracellular LPS recognition in human primary macrophages. Before proteomics, the total secretome was separated into two fractions, enriched extracellular vesicle (EV) fraction and rest-secretome (RS) fraction using size-exclusion centrifugation. We identified 1048 proteins from the EV fraction and 1223 proteins from the RS fraction. From these, 640 were identified from both fractions suggesting that the non-canonical inflammasome activates multiple, partly overlapping protein secretion pathways. We identified several secreted proteins that have a critical role in host response against severe Gram-negative bacterial infection. The soluble secretome (RS fraction) was highly enriched with inflammation-associated proteins upon intracellular LPS recognition. Several ribosomal proteins were highly abundant in the EV fraction upon infection, and our data strongly suggest that secretion of translational machinery and concomitant inhibition of translation are important parts of host response against Gram-negative bacteria sensing caspase-4/5 inflammasome. Intracellular recognition of LPS resulted in the secretion of two metalloproteinases, a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) and MMP14, in the enriched EV fraction. ADAM10 release was associated with the secretion of TNF, a key inflammatory cytokine, and M-CSF, an important growth factor for myeloid cells probably through ADAM10-dependent membrane shedding of these cytokines. Caspase-4/5 inflammasome activation also resulted in secretion of danger-associated molecules S100A8 and prothymosin- in the enriched EV fraction. Both S100A8 and prothymosin- are ligands for toll-like receptor 4 recognizing extracellular LPS, and they may contribute to endotoxic shock during non-canonical inflammasome activation.
  • Selberg, Simona; Zusinaite, Eva; Herodes, Koit; Seli, Neinar; Kankuri, Esko; Merits, Andres; Karelson, Mati (2021)
    The N6-methyladenosine (m(6)A) modifications in both viral and host cell RNAs play an important role in HIV-1 virus genome transcription and virus replication. We demonstrate here that activators of the METTL3/METTL14/WTAP RNA methyltransferase complex enhance the production of virus particles in cells harboring HIV-1 provirus. In parallel, the amount of m(6)A residues in the host cell mRNA was increased in the presence of these activator compounds. Importantly, the m(6)A methylation of the HIV-1 RNA was also enhanced significantly (about 18%). The increase of virus replication by the small-molecule activators of the METTL3/METTL14/WTAP complex excludes them as potential anti-HIV-1 drug candidates. However, the compounds may be of large interest as activators for the latent HIV-1 provirus copies deposited in host cells' genome and the subsequent virus eradication by an antiviral compound.
  • Miikkulainen, Petra; Högel, Heidi; Seyednasrollah, Fatemeh; Rantanen, Krista; Elo, Laura L.; Jaakkola, Panu M. (2019)
    Most clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL), resulting in the accumulation of hypoxia-inducible factor -subunits (HIF-) and their downstream targets. HIF-2 expression is particularly high in ccRCC and is associated with increased ccRCC growth and aggressiveness. In the canonical HIF signaling pathway, HIF-prolyl hydroxylase 3 (PHD3) suppresses HIF-2 protein by post-translational hydroxylation under sufficient oxygen availability. Here, using immunoblotting and immunofluorescence staining, qRT-PCR, and siRNA-mediated gene silencing, we show that unlike in the canonical pathway, PHD3 silencing in ccRCC cells leads to down-regulation of HIF-2 protein and mRNA. Depletion of other PHD family members had no effect on HIF-2 expression, and PHD3 knockdown in non-RCC cells resulted in the expected increase in HIF-2 protein expression. Accordingly, PHD3 knockdown decreased HIF-2 target gene expression in ccRCC cells and expression was restored upon forced HIF-2 expression. The effect of PHD3 depletion was pinpointed to HIF2A mRNA stability. In line with these in vitro results, a strong positive correlation of PHD3 and HIF2A mRNA expression in ccRCC tumors was detected. Our results suggest that in contrast to the known negative regulation of HIF-2 in most cell types, high PHD3 expression in ccRCC cells maintains elevated HIF-2 expression and that of its target genes, which may enhance kidney cancer aggressiveness.
  • Xu, Guanglang (2020)
    Fast, accurate, and stable computation of the Clebsch-Gordan (C-G) coefficients is always desirable, for example, in light scattering simulations, the translation of the multipole fields, quantum physics and chemistry. Current recursive methods for computing the C-G coefficients are often unstable for large quantum numbers due to numerical overflow or underflow. In this paper, we present an improved method, called the sign-exponent recurrence, for the recursive computation of C-G coefficients. The result shows that the proposed method can significantly improve the stability of the computation without losing its efficiency, producing accurate values for the C-G coefficients even with very large quantum numbers. (C) 2020 The Author. Published by Elsevier Ltd.
  • Bakula, Daniela; Ablasser, Andrea; Aguzzi, Adriano; Antebi, Adam; Barzilai, Nir; Bittner, Martin-Immanuel; Jensen, Martin Borch; Calkhoven, Cornelis F.; Chen, Danica; de Grey, Aubrey D. N. J.; Feige, Jerome N.; Georgievskaya, Anastasia; Gladyshev, Vadim N.; Golato, Tyler; Gudkov, Andrei V.; Hoppe, Thorsten; Kaeberlein, Matt; Katajisto, Pekka; Kennedy, Brian K.; Lal, Unmesh; Martin-Villalba, Ana; Moskalev, Alexey A.; Ozerov, Ivan; Petr, Michael A.; Reason, Matthew; Rubinsztein, David C.; Tyshkovskiy, Alexander; Vanhaelen, Quentin; Zhavoronkov, Alex; Scheibye-Knudsen, Morten (2019)
    An increasing aging population poses a significant challenge to societies worldwide. A better understanding of the molecular, cellular, organ, tissue, physiological, psychological, and even sociological changes that occur with aging is needed in order to treat age-associated diseases. The field of aging research is rapidly expanding with multiple advances transpiring in many previously disconnected areas. Several major pharmaceutical, biotechnology, and consumer companies made aging research a priority and are building internal expertise, integrating aging research into traditional business models and exploring new go-to-market strategies. Many of these efforts are spearheaded by the latest advances in artificial intelligence, namely deep learning, including generative and reinforcement learning. To facilitate these trends, the Center for Healthy Aging at the University of Copenhagen and Insilico Medicine are building a community of Key Opinion Leaders (KOLs) in these areas and launched the annual conference series titled "Aging Research and Drug Discovery (ARDD)" held in the capital of the pharmaceutical industry, Basel, Switzerland (www.agingpharma.org). This ARDD collection contains summaries from the 6th annual meeting that explored aging mechanisms and new interventions in age-associated diseases. The 7th annual ARDD exhibition will transpire 2nd-4th of September, 2020, in Basel.
  • Bayoumi, Ali; Elsayed, Asmaa; Han, Shuanglin; Petta, Salvatore; Adams, Leon A.; Aller, Rocio; Khan, Anis; Garcia-Monzon, Carmelo; Arias-Loste, Maria Teresa; Miele, Luca; Latchoumanin, Olivier; Alenizi, Shafi; Gallego-Duran, Rocio; Fischer, Janett; Berg, Thomas; Craxi, Antonio; Metwally, Mayada; Qiao, Liang; Liddle, Christopher; Yki-Järvinen, Hannele; Bugianesi, Elisabetta; Romero-Gomez, Manuel; George, Jacob; Eslam, Mohammed (2021)
    Fibroblast growth factor 21 (FGF21) is a liver-derived hormone with pleiotropic beneficial effects on metabolism. Paradoxically, FGF21 levels are elevated in metabolic diseases. Interventions that restore metabolic homeostasis reduce FGF21. Whether abnormalities in FGF21 secretion or resistance in peripheral tissues is the initiating factor in altering FGF21 levels and function in humans is unknown. A genetic approach is used to help resolve this paradox. The authors demonstrate that the primary event in dysmetabolic phenotypes is the elevation of FGF21 secretion. The latter is regulated by translational reprogramming in a genotype- and context-dependent manner. To relate the findings to tissues outcomes, the minor (A) allele of rs838133 is shown to be associated with increased hepatic inflammation in patients with metabolic associated fatty liver disease. The results here highlight a dominant role for translation of the FGF21 protein to explain variations in blood levels that is at least partially inherited. These results provide a framework for translational reprogramming of FGF21 to treat metabolic diseases.
  • Kemppainen, Esko; George, Jack; Garipler, Görkem; Tuomela, Tea; Kiviranta, Essi; Soga, Tomoyoshi; Dunn, Cory D.; Jacobs, Howard T. (2016)
    The Drosophila mutant tko(25t) exhibits a deficiency ofmitochondrial protein synthesis, leading to a global insufficiency of respiration and oxidative phosphorylation. This entrains an organismal phenotype of developmental delay and sensitivity to seizures induced bymechanical stress. We found that the mutant phenotype is exacerbated in a dose-dependent fashion by high dietary sugar levels. tko(25t) larvae were found to exhibit severe metabolic abnormalities that were further accentuated by high-sugar diet. These include elevated pyruvate and lactate, decreased ATP and NADPH. Dietary pyruvate or lactate supplementation phenocopied the effects of high sugar. Based on tissue-specific rescue, the crucial tissue in which this metabolic crisis initiates is the gut. It is accompanied by down-regulation of the apparatus of cytosolic protein synthesis and secretion at both the RNA and post-translational levels, including a novel regulation of S6 kinase at the protein level.
  • Tapaninen, Anna-Maria; Halme-Tuomisaari, Miia; Kankaanpaa, Viljami (2019)
  • Melvin, Richard G.; Lamichane, Nicole; Havula, Essi; Kokki, Krista; Soeder, Charles; Jones, Corbin D.; Hietakangas, Ville (2018)
    How dietary selection affects genome evolution to define the optimal range of nutrient intake is a poorly understood question with medical relevance. We have addressed this question by analyzing Drosophila simulans and sechellia, recently diverged species with differential diet choice. D. sechellia larvae, specialized to a nutrient scarce diet, did not survive on sugar-rich conditions, while the generalist species D. simulans was sugar tolerant. Sugar tolerance in D. simulans was a tradeoff for performance on low-energy diet and was associated with global reprogramming of metabolic gene expression. Hybridization and phenotype-based introgression revealed the genomic regions of D. simulans that were sufficient for sugar tolerance. These regions included genes that are involved in mitochondrial ribosome biogenesis and intracellular signaling, such as PPP1R15/Gadd34 and SERCA, which contributed to sugar tolerance. In conclusion, genomic variation affecting genes involved in global metabolic control defines the optimal range for dietary macronutrient composition.
  • Cosentino, Cristina; Toivonen, Sanna; Villamil, Esteban Diaz; Atta, Mohamed; Ravanat, Jean-Luc; Demine, Stephane; Schiavo, Andrea Alex; Pachera, Nathalie; Deglasse, Jean-Philippe; Jonas, Jean-Christophe; Balboa, Diego; Otonkoski, Timo; Pearson, Ewan R.; Marchetti, Piero; Eizirik, Decio L.; Cnop, Miriam; Igoillo-Esteve, Mariana (2018)
    Transfer RNAs (tRNAs) are non-coding RNA molecules essential for protein synthesis. Post-transcriptionally they are heavily modified to improve their function, folding and stability. Intronic polymorphisms in CDKAL1, a tRNA methylthiotransferase, are associated with increased type 2 diabetes risk. Loss-of-function mutations in TRMT10A, a tRNA methyltransferase, are a monogenic cause of early onset diabetes and microcephaly. Here we confirm the role of TRMT10A as a guanosine 9 tRNA methyltransferase, and identify tRNA(Gln) and tRNA(iMeth) as two of its targets. Using RNA interference and induced pluripotent stem cell-derived pancreatic beta-like cells from healthy controls and TRMT10A-deficient patients we demonstrate that TRMT10A deficiency induces oxidative stress and triggers the intrinsic pathway of apoptosis in beta-cells. We show that tRNA guanosine 9 hypomethylation leads to tRNA(Gln) fragmentation and that 5'-tRNA(Gln) fragments mediate TRMT10A deficiency-induced beta-cell death. This study unmasks tRNA hypomethylation and fragmentation as a hitherto unknown mechanism of pancre-atic beta-cell demise relevant to monogenic and polygenic forms of diabetes.
  • Multanen, J.; Ylinen, J.; Karjalainen, T.; Kautiainen, H.; Repo, J. P.; Häkkinen, A. (2020)
    Background and Aims: The Boston Carpal Tunnel Questionnaire is the most commonly used outcome measure in the assessment of carpal tunnel syndrome. The purpose of this study was to translate the original Boston Carpal Tunnel Questionnaire into Finnish and validate its psychometric properties. Materials and Methods: We translated and culturally adapted the Boston Carpal Tunnel Questionnaire into Finnish. Subsequently, 193 patients completed the Finnish version of the Boston Carpal Tunnel Questionnaire, 6-Item CTS Symptoms Scale, and EuroQol 5 Dimensions 12 months after carpal tunnel release. The Boston Carpal Tunnel Questionnaire was re-administered after a 2-week interval. We calculated construct validity, internal consistency, test-retest reliability, and coefficient of repeatability. We also examined floor and ceiling effects. Results: The cross-cultural adaptation required only minor modifications to the questions. Both subscales of the Boston Carpal Tunnel Questionnaire (Symptom Severity Scale and Functional Status Scale) correlated significantly with the CTS-6 and EuroQol 5 Dimensions, indicating good construct validity. The Cronbach's alpha was 0.93 for both the Symptom Severity Scale and Functional Status Scale, indicating high internal consistency. Test-retest reliability was excellent, with an intraclass correlation coefficient greater than 0.8 for both scales. The coefficient of repeatability was 0.80 for the Symptom Severity Scale and 0.68 for the Functional Status Scale. We observed a floor effect in the Functional Status Scale in 28% of participants. Conclusion: Our study shows that the present Finnish version of the Boston Carpal Tunnel Questionnaire is reliable and valid for the evaluation of symptom severity and functional status among surgically treated carpal tunnel syndrome patients. However, owing to the floor effect, the Functional Status Score may have limited ability to detect differences in patients with good post-operative outcomes.
  • Mutso, Margit; Nikonov, Andrei; Pihlak, Arno; Zusinaite, Eva; Viru, Liane; Selyutina, Anastasia; Reintamm, Tonu; Kelve, Merike; Saarma, Mart; Karelson, Mati; Merits, Andres (2015)
    The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV) RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA) residues at its termini (LNA/DNA gapmer) by inserting 8-oxo-2'-deoxyguanosine (8-oxo-dG) residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3 degrees C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC50) : 0.13 nM), whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC50 : 5.5 and 7.1 nM, respectively). However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide: RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.
  • Richter, Uwe; Evans, Molly E.; Clark, Wesley C.; Marttinen, Paula; Shoubridge, Eric A.; Suomalainen, Anu; Wredenberg, Anna; Wedell, Anna; Pan, Tao; Battersby, Brendan J. (2018)
    Post-transcriptional RNA modifications play a critical role in the pathogenesis of human mitochondrial disorders, but the mechanisms by which specific modifications affect mitochondrial protein synthesis remain poorly understood. Here we used a quantitative RNA sequencing approach to investigate, at nucleotide resolution, the stoichiometry and methyl modifications of the entire mitochondrial tRNA pool, and establish the relevance to human disease. We discovered that a N-1 -methyladenosine (m(1)A) modification is missing at position 58 in the mitochondrial tRNA(LYs) of patients with the mitochondrial DNA mutation m.8344 A > G associated with MERRF (myoclonus epilepsy, ragged-red fibers). By restoring the modification on the mitochondrial tRNA(LYs), we demonstrated the importance of the m(1)A58 to translation elongation and the stability of selected nascent chains. Our data indicates regulation of post-transcriptional modifications on mitochondrial tRNAs is finely tuned for the control of mitochondrial gene expression. Collectively, our findings provide novel insight into the regulation of mitochondrial tRNAs and reveal greater complexity to the molecular pathogenesis of MERRF.
  • Koh, Cha San; Sarin, Leif Peter (2018)
    Transfer RNA (tRNA) molecules are sumptuously decorated with evolutionary conserved post-transcriptional nucleoside modifications that are essential for structural stability and ensure efficient protein translation. The tRNA modification levels change significantly in response to physiological stresses, altering translation in a number of ways. For instance, tRNA hypomodification leads to translational slowdown, disrupting protein homeostasis and reducing cellular fitness. This highlights the importance of proper tRNA modification as a determinant for maintaining cellular function and viability during stress. Furthermore, the expression of several microbial virulence factors is induced by changes in environmental conditions; a process where tRNA 2-thiolation is unequivocal for pathogenicity. In this review, we discuss the multifaceted implications of tRNA modification for infection by examining the roles of nucleoside modification in tRNA biology. Future development of novel methods and combinatory utilization of existing technologies will bring tRNA modification-mediated regulation of cellular immunity and pathogenicity to the limelight.
  • Repo, J. P.; Homsy, P.; Uimonen, M. M.; Roine, R. P.; Jahkola, T.; Popov, P. (2019)
    Background: Massive weight loss can notably affect patients' health-related quality of life (HRQoL) and body image. Yet, no body contouring specific instruments to assess HRQoL and body image after massive weight loss have been validated in Finnish. The BODY-Q includes 26 independently functioning scales and a single checklist that measure appearance, HRQoL, and experience of care. The aim of the present study was to translate and validate a Finnish version of the BODY-Q among patients who underwent abdominoplasty. Methods: The BODY-Q was translated into Finnish using recommended guidelines. Eighty-two patients who underwent abdominoplasty due to massive weight loss were identified from hospital records using procedure codes. A postal survey including the BODY-Q, the 15D, and general health and pain instruments was used. Criterion validity, Cronbach's alpha, and floor and ceiling effects were analyzed. Results: The BODY-Q translated well into Finnish. Fifty-three patients returned the questionnaires (response rate 65%) and were included. All but the Scars subscale correlated significantly with the 15D mean score, thus indicating strong criterion validity against a generic HRQoL tool. The Excess Skin and the Physical Function scales reached the ceiling effect (>15% of maximum points) in our postoperative sample. No floor effects were observed. Internal consistency of the BODY-Q scales was high (Cronbach's alpha range, 0.81-0.95). Conclusions: The Finnish version of the BODY-Q instrument is equivalent in terms of content, accuracy, and comprehensiveness to the original English version. The findings of the present study indicate that the BODY-Q has psychometric properties suitable for assessing outcomes and treatment effectiveness of abdominoplasty. (C) 2019 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.