Articles from TUHAT CRIS


Recent Submissions

  • Semenyuk, Pavel; Tiainen, Tony; Hietala, Sami; Tenhu, Heikki; Aseyev, Vladimir; Muronetz, Vladimir (2019)
    Stabilization of the enzymes under stress conditions is of special interest for modern biochemistry, bioengineering, as well as for formulation and target delivery of protein-based drugs. Aiming to achieve an efficient stabilization at elevated temperature with no influence on the enzyme under normal conditions, we studied chaperone-like activity of thermoresponsive polymers based on poly(dimethylaminoethyl methacrylate) (PDMAEMA) toward two different proteins, glyceraldehyde-3-phosphate dehydrogenase and chicken egg lysozyme. The polymers has been shown to do not interact with the folded protein at room temperature but form a complex upon heating to either protein unfolding or polymer phase transition temperature. A PDMAEMA-PEO block copolymer with a dodecyl end-group (d-PDMAEMA-PEO) as well as PDMAEMA-PEO without the dodecyl groups protected the denatured protein against aggregation in contrast to PDMAEMA homopolymer. No effect of the polymers on the enzymatic activity of the client protein was observed at room temperature. The polymers also partially protected the enzyme against inactivation at high temperature. The results provide a platform for creation of artificial chaperones with unfolded protein recognition which is a major feature of natural chaperones. (C) 2018 Elsevier B.V. All rights reserved.
  • Hyttinen, Tapani; Paolini, Gianluca (2018)
    Based on Crapo’s theory of one point extensions of combinatorial geometries, we find various classes of geometric lattices that behave very well from the point of view of stability theory. One of them, (K3, ), is ω-stable, it has a monster model and an independence calculus that satisfies all the usual properties of non-forking. On the other hand, these classes are rather unusual, e.g. in (K3, )the Smoothness Axiom fails, and so (K3, )is not an AEC.
  • Savvides, Rafael; Henelius, Andreas; Oikarinen, Emilia; Puolamäki, Kai (ACM, 2019)
    In this paper we consider the following important problem: when we explore data visually and observe patterns, how can we determine their statistical significance? Patterns observed in exploratory analysis are traditionally met with scepticism, since the hypotheses are formulated while viewing the data, rather than before doing so. In contrast to this belief, we show that it is, in fact, possible to evaluate the significance of patterns also during exploratory analysis, and that the knowledge of the analyst can be leveraged to improve statistical power by reducing the amount of simultaneous comparisons. We develop a principled framework for determining the statistical significance of visually observed patterns. Furthermore, we show how the significance of visual patterns observed during iterative data exploration can be determined. We perform an empirical investigation on real and synthetic tabular data and time series, using different test statistics and methods for generating surrogate data. We conclude that the proposed framework allows determining the significance of visual patterns during exploratory analysis.
  • Talvitie, Topi; Koivisto, Mikko (AAAI Press, 2019)
  • Paananen, Riku O.; Javanainen, Matti; Holopainen, Juha M.; Vattulainen, Ilpo (2019)
    Dry eye syndrome (DES), one of the most common ophthalmological diseases, is typically caused by excessive evaporation of tear fluid from the ocular surface. Excessive evaporation is linked to impaired function of the tear film lipid layer (TFLL) that covers the aqueous tear film. The principles of the evaporation resistance of the TFLL have remained unknown, however. We combined atomistic simulations with Brewster angle microscopy and surface potential experiments to explore the organization and evaporation resistance of films composed of wax esters, one of the main components of the TFLL. The results provide evidence that the evaporation resistance of the TFLL is based on crystalline-state layers of wax esters and that the evaporation rate is determined by defects in the TFLL and its coverage on the ocular surface. On the basis of the results, uncovering the nonequilibrium spreading and crystallization of TFLL films has potential to reveal new means of treating DES.
  • Filetti, Marco; Barral, Oswald; Jacucci, Giulio; Ravaja, Niklas (2019)
    Motivational intensity has been previously linked to information processing. In particular, it has been argued that affects which are high in motivational intensity tend to narrow cognitive scope. A similar effect has been attributed to negative affect, which has been linked to narrowing of cognitive scope. In this paper, we investigated how these phenomena manifest themselves during visual word search. We conducted three studies in which participants were instructed to perform word category identification. We manipulated motivational intensity by controlling reward expectations and affect via reward outcomes. Importantly, we altered visual search paradigms, assessing the effects of affective manipulations as modulated by information arrangement. We recorded multiple physiological signals (EEG, EDA, ECG and eye tracking) to assess whether motivational states can be predicted by physiology. Across the three studies, we found that high motivational intensity narrowed visual attentional scope by altering visual search strategies, especially when information was displayed sparsely. Instead, when information was vertically listed, approach-directed motivational intensity appeared to improve memory encoding. We also observed that physiology, in particular eye tracking, may be used to detect biases induced by motivational intensity, especially when information is sparsely organised.
  • Clayton-Smith, Jill; Bromley, Rebecca; Dean, John; Journel, Hubert; Odent, Sylvie; Wood, Amanda; Williams, Janet; Cuthbert, Verna; Hackett, Latha; Aslam, Neelo; Malm, Heli; James, Gregory; Westbom, Lena; Day, Ruth; Ladusans, Edmund; Jackson, Adam; Bruce, Iain; Walker, Robert; Sidhu, Sangeet; Dyer, Catrina; Ashworth, Jane; Hindley, Daniel; Diaz, Gemma Arca; Rawson, Myfanwy; Turnpenny, Peter (2019)
    Background: A pattern of major and minor congenital anomalies, facial dysmorphic features, and neurodevelopmental difficulties, including cognitive and social impairments has been reported in some children exposed to sodium valproate (VPA) during pregnancy. Recognition of the increased risks of in utero exposure to VPA for congenital malformations, and for the neurodevelopmental effects in particular, has taken many years but these are now acknowledged following the publication of the outcomes of several prospective studies and registries. As with other teratogens, exposure to VPA can have variable effects, ranging from a characteristic pattern of major malformations and significant intellectual disability to the other end of the continuum, characterised by facial dysmorphism which is often difficult to discern and a more moderate effect on neurodevelopment and general health. It has become clear that some individuals with FVSD have complex needs requiring multidisciplinary care but information regarding management is currently lacking in the medical literature. Methods: An expert group was convened by ERN-ITHACA, the European Reference Network for Congenital Malformations and Intellectual Disability comprised of professionals involved in the care of individuals with FVSD and with patient representation. Review of published and unpublished literature concerning management of FVSD was undertaken and the level of evidence from these sources graded. Management recommendations were made based on strength of evidence and consensus expert opinion, in the setting of an expert consensus meeting. These were then refined using an iterative process and wider consultation. Results: Whilst there was strong evidence regarding the increase in risk for major congenital malformations and neurodevelopmental difficulties there was a lack of high level evidence in other areas and in particular in terms of optimal clinical management.. The expert consensus approach facilitated the formulation of management recommendations, based on literature evidence and best practice. The outcome of the review and group discussions leads us to propose the term Fetal Valproate Spectrum Disorder (FVSD) as we feel this better encompasses the broad range of effects seen following VPA exposure in utero. Conclusion: The expert consensus approach can be used to define the best available clinical guidance for the diagnosis and management of rare disorders such as FVSD. FVSD can have medical, developmental and neuropsychological impacts with life-long consequences and affected individuals benefit from the input of a number of different health professionals.
  • Kalakoski, Virpi; Henelius, Andreas; Oikarinen, Emilia; Ukkonen, Antti; Puolamäki, Kai (2019)
    Today's ever-increasing amount of data places new demands on cognitive ergonomics and requires new design ideas to ensure successful human-data interaction. Our aim was to identify the cognitive factors that must be considered when designing systems to improve decision-making based on large amounts of data. We constructed a task that simulates the typical cognitive demands people encounter in data analysis situations. We demonstrate some essential cognitive limitations using a behavioural experiment with 20 participants. The studied task presented the participants with critical and noncritical attributes that contained information on two groups of people. They had to select the response option (group) with the higher level of critical attributes. The results showed that accuracy of judgement decreased as the amount of information increased, and that judgement was affected by irrelevant information. Our results thus demonstrate critical cognitive limitations when people utilise data and suggest a cognitive bias in data-based decision-making. Therefore, when designing for cognition, we should consider the human cognitive limitations that are manifested in a data analysis context. Furthermore, we need general cognitive ergonomic guidelines for design that support the utilisation of data and improve data-based decision-making.
  • Palanca, Ana; Castelblanco, Esmeralda; Betriu, Angels; Perpinan, Hector; Soldevila, Berta; Manuel Valdivielso, Jose; Bermudez-Lopez, Marcelino; Puig-Jove, Carlos; Puig-Domingo, Manel; Groop, Per-Henrik; Fernandez, Elvira; Alonso, Nuria; Mauricio, Didac (2019)
    Background: Individuals with diabetes have remarkably high rates of cardiovascular morbidity and mortality. However, the incremental cardiovascular risk in diabetes is heterogeneous and has often been related to renal involvement. The purpose of this study was to analyse the prognostic value of subclinical atherosclerosis in determining the incidence of first cardiovascular events (CVEs) in individuals with diabetes and chronic kidney disease (CKD) compared to CKD individuals without diabetes. Methods: We included data from individuals with CKD with and without diabetes, free from pre-existing cardiovascular disease, from the NEFRONA cohort. Participants underwent baseline carotid and femoral ultrasound and were followed up for 4 years. All CVEs during follow-up were registered. Bivariate analysis and Fine-Gray competing risk models were used to perform the statistical analysis. Results: During the mean follow-up time of 48 months, a total of 203 CVE was registered. 107 CVE occurred among participants without diabetes (19.58 per 1000 person-years) and 96 CVE occurred among participants with diabetes (44.44 per 1000 person-years). Following the competing risk analysis, the variables predicting CVEs in CKD individuals without diabetes were the number of territories with plaque at baseline (HR 1.862, 95% CI [1.432;2.240]), age (HR 1.026, 95% CI [1.003;1.049]) and serum concentrations of 25-OH vitamin D (HR 0.963, 95% CI [0.933;0.094]). The only variable predicting CVEs among CKD participants with diabetes was the number of territories with plaque at baseline (HR 1.782, 95% CI [1.393, 2.278]). For both models, concordance (C) index yielded was over 0.7. Conclusions: The burden of subclinical atherosclerosis is the strongest predictor of future CVEs in diabetic individuals with CKD. Early detection of subclinical atherosclerotic burden by multiterritorial vascular ultrasound could improve CVE prediction in this population.
  • Räihä, Juulia; Helanterä, Ilkka; Ekstrand, Agneta; Nordin, Arno; Sallinen, Ville; Lempinen, Marko (2019)
    Background: Pretransplant dialysis modality may affect outcome after simultaneous pancreas-kidney transplantation (SPKT), and it has been suspected that peritoneal dialysis (PD) is associated with more postoperative complications compared to hemodialysis (HD). The aim of this study was to evaluate whether pretransplant dialysis modality affects the risk for postoperative complications in SPKT recipients. Material/ Methods: This was a retrospective longitudinal cohort study of all patients undergoing SPKT from 2010 to 2017, during which 99 simultaneous pancreas-kidney transplantations were performed. Three pre-emptive transplantations were excluded. Patient groups receiving PD (n=59) or HD (n=37) were similar regarding baseline characteristics. All complications occurring during the first 3 months after transplantation, as well as patient and graft survival, were analyzed. Results: There were no significant differences in postoperative complications between groups, with similar rates of intraabdominal infections (8% in HD vs. 10% in PD), pancreatitis (16% in HD vs. 17% in PD), gastrointestinal bleedings (22% in HD vs. 10% in PD), and relaparotomies (27% in HD vs. 24% in PD). None of the patients had venous graft thrombosis. Past peritonitis was not associated with increased risk for postoperative complications in PD patients. Patient and graft survival were similar between PD and HD groups. Conclusions: Peritoneal dialysis is not a risk factor for postoperative complications after SPKT.
  • Gonzalez, Marta Lopez; Oosterhoff, Dinja; Lindenberg, Jelle J.; Milenova, Ioanna; Lougheed, Sinead M.; Martianez, Tania; Dekker, Henk; Quixabeira, Dafne Carolina Alves; Hangalapura, Basav; Joore, Jos; Piersma, Sander R.; Cervera-Carrascon, Victor; Santos, Joao Manuel; Scheper, Rik J.; Verheul, Henk M. W.; Jimenez, Connie R.; Van De Ven, Rieneke; Hemminki, Akseli; Van Beusechem, Victor W.; De Gruijl, Tanja D. (2019)
    In patients with cancer, the functionality of Dendritic Cells (DC) is hampered by high levels of tumor-derived suppressive cytokines, which interfere with DC development and maturation. Poor DC development can limit the efficacy of immune checkpoint blockade and in vivo vaccination approaches. Interference in intracellular signaling cascades downstream from the receptors of major tumor-associated suppressive cytokines like IL-10 and IL-6, might improve DC development and activation, and thus enhance immunotherapy efficacy. We performed exploratory functional screens on arrays consisting of >1000 human kinase peptide substrates to identify pathways involved in DC development and its inhibition by IL-10 or IL-6. The resulting alterations in phosphorylation of the kinome substrate profile pointed to glycogen-synthase kinase-3 beta (GSK3 beta) as a pivotal kinase in both DC development and suppression. GSK3 beta inhibition blocked human DC differentiation in vitro, which was accompanied by decreased levels of IL-12p70 secretion, and a reduced capacity for T cell priming. More importantly, adenoviral transduction of monocytes with a constitutively active form of GSK3 beta induced resistance to the suppressive effects of IL-10 and melanoma-derived supernatants alike, resulting in improved DC development, accompanied by up-regulation of co-stimulatory markers, an increase in CD83 expression levels in mature DC, and diminished release of IL-10. Moreover, adenovirus-mediated intratumoral manipulation of this pathway in an in vivo melanoma model resulted in DC activation and recruitment, and in improved immune surveillance and tumor control. We propose the induction of constitutive GSK3 beta activity as a novel therapeutic means to bolster DC functionality in the tumor microenvironment.
  • Döntgen, Malte; Pekkanen, Timo T.; Joshi, Satya P.; Timonen, Raimo S.; Eskola, Arkke J. (2019)
    The kinetics and thermochemistry of the pent-1-en-3-yl radical reaction with molecular oxygen (CH2CHCHCH2CH3 + O-2) has been studied by both experimental and computational methods. The bimolecular rate coefficient of the reaction was measured as a function of temperature (198-370 K) and pressure (0.2-4.5 Torr) using laser photolysis-photoionization mass-spectrometry. Quantum chemical calculations were used to explore the potential energy surface of the reaction, after which Rice-Ramsperger-Kassel-Marcus theory/master equation simulations were performed to investigate the reaction. The experimental data were used to adjust key parameters, such as well depths, in the master equation model within methodological uncertainties. The master equation simulations suggest that the formation rates of the two potential RO2 adducts are equal and that the reaction to QOOH is slower than for saturated hydrocarbons. The initial addition reaction, CH2CHCHCH2CH3 + O-2, is found to be barrierless when accounting for multireference effects. This is in agreement with the current experimental data, as well as with past experimental data for the allyl + O-2 reaction. Finally, we conducted numerical simulations of the pent-1-en-3-yl + O-2 reaction system and observed significant amounts of penta-1,3-diene being formed under engine-relevant conditions.
  • Doshi, Bhairavi; Hietala, Sami; Sirviö, Juho Antti; Repo, Eveliina; Sillanpää, Mika (2019)
    The traces of hazardous chemicals used in oil spill response have harmed marine creatures with long-term cytoxic impacts, so, a greener alternative is to use biodegradable components in the dispersant formulation. This study demonstrates the efficiency of carboxymethylated and acylated chitosan combined with powdered orange peel (OP-D) in the emulsification of marine diesel and 2 T-oil with different qualities of water. OP-D particles undergo Pickering emulsions, whereas the amphiphilic behaviour of the Blend and hydrophobically modified carboxymethyl chitosan-orange peels (CSOP-A) favours conventional emulsions through steric and electrostatic stabilization. The emulsion formation rate was maximum with OP-D in saline water and autonomous of the water quality with Blend. Additionally, different hydrophobic moieties on the surface of the Blend and CSOP-A affected the oil droplets' stabilization rate. Changing pH altered the surface properties of particles and hence the nature of the formed emulsion range from gel-like to creamy, suggesting particle-particle to particle-oil interactions. An increase in electrolyte concentration enhanced the coalescence rate of marine diesel with CSOP-A. The oil droplet size in the formed emulsion increases with a temperature decrease up to 2 °C, and the emulsion stabilization rate was
  • Ren, Hao; Qiu, Xing-Ping; Shi, Yan; Yang, Peng; Winnik, Francoise M. (2019)
    Azopyridines (AzPy) act as light-sensitive groups that undergo reversible cis-trans isomerization upon UV irradiation, as hydrogen-bond acceptors, and as ionizable moieties. The kinetics of the thermal cis- to trans-AzPy deactivation are slow except when the Py nitrogen is H-bonded or cationic. The properties of AzPy were used here to control the phase transition of aqueous solutions of alpha-azopyridine-omega-n-dodecyl-poly(N-isopropylacrylamides) (C12-PN-AzPy) with the molar mass (M-n) ranging from 5800 to 19 700 g mol(-1). The C12-PN-AzPy polymers form cationic star-micelles in solutions of pH 3 and flower-micelles in neutral and basic solutions. This diversity of micelle morphology underlies the temperature-, pH- and UV-irradiation-driven phase transition of aqueous C12-PN-AzPy solutions as demonstrated by turbidimetry, H-1 NMR spectroscopy, and microcalorimetry. Unlike azobenzene, the commonly used photoresponsive moiety to actuate amphiphilic polymers, AzPy can affect the thermoresponsive behavior of polymers in response to three orthogonal triggers: pH, through changes in ionization; light, via trans-cis photoisomerization; and time, from hours to a few ms, via the kinetics of the dark cis-trans relaxation. The study leads the way to responsive sensors or actuators in the form of aqueous fluids, hydrogels, or films by the application of light and changes of temperature and pH in permutable sequences.
  • Porcu, Eleonora; Rüeger, Sina; Lepik, Kaido; Agbessi, Mawusse; Ahsan, Habibul; Alves, Isabel; Andiappan, Anand; Arindrarto, Wibowo; Awadalla, Philip; Battle, Alexis; Beutner, Frank; Bonder, Marc Jan; Boomsma, Dorret; Christiansen, Mark; Claringbould, Annique; Deelen, Patrick; Esko, Tonu; Fave, Marie-Julie; Franke, Lude; Frayling, Timothy; Gharib, Sina A.; Gibson, Gregory; Heijmans, Bastiaan T.; Hemani, Gibran; Jansen, Rick; Kahonen, Mika; Kalnapenkis, Anette; Kasela, Silva; Kettunen, Johannes; Kim, Yungil; Kirsten, Holger; Kovacs, Peter; Krohn, Knut; Kronberg-Guzman, Jaanika; Kukushkina, Viktorija; Lee, Bernett; Lehtimaki, Terho; Loeffler, Markus; Marigorta, Urko M.; Mei, Hailang; Milani, Lili; Montgomery, Grant W.; Mueler-Nurasyid, Martina; Nauck, Matthias; Nivard, Michel; Penninx, Brenda; Perola, Markus; Pervjakova, Natalia; Pierce, Brandon L.; Ripatti, Samuli (2019)
    Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most of these variants overlap with expression QTLs, indicating their potential involvement in regulation of gene expression. Here, we propose a transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) that uses multiple SNPs as instruments and multiple gene expression traits as exposures, simultaneously. Applied to 43 human phenotypes, it uncovers 3,913 putatively causal gene-trait associations, 36% of which have no genome-wide significant SNP nearby in previous GWAS. Using independent association summary statistics, we find that the majority of these loci were missed by GWAS due to power issues. Noteworthy among these links is educational attainment-associated BSCL2, known to carry mutations leading to a Mendelian form of encephalopathy. We also find pleiotropic causal effects suggestive of mechanistic connections. TWMR better accounts for pleiotropy and has the potential to identify biological mechanisms underlying complex traits.
  • Tiainen, Leena; Korhonen, Emilia A.; Leppänen, Veli-Matti; Luukkaala, Tiina; Hämäläinen, Mari; Tanner, Minna; Lahdenperä, Outi; Vihinen, Pia; Jukkola, Arja; Karihtala, Peeter; Aho, Sonja; Moilanen, Eeva; Alitalo, Kari; Kellokumpu-Lehtinen, Pirkko-Liisa (2019)
    BackgroundAngiopoietin growth factors (Angs) regulate angiogenesis and lymphangiogenesis by binding to the endothelial Tie2 receptor. Ang2 expression is elevated in tissue hypoxia and inflammation, which also induce cleavage of the extracellular domain of the orphan Tie1 receptor. Here we have examined if the concentrations of Ang2 and the soluble extracellular domain of Tie1 in patient plasma are associated with the prognosis of patients with metastatic breast cancer.MethodsPlasma Tie1 and Ang2 levels were measured in metastatic breast cancer patients treated in a phase II trial with a taxane-bevacizumab combination chemotherapy in the first-line treatment setting. They were analyzed before treatment, after 6weeks and 6months of treatment, and at the final study visit. Using the median concentrations as cutoffs, Tie1 and Ang2 data were dichotomized into low and high concentration groups. Additionally, we analyzed Tie1 concentrations in plasma from 10 healthy women participating in a breast cancer primary prevention study.ResultsPlasma samples were available from 58 (89%) of the 65 patients treated in the trial. The baseline Tie1 levels of the healthy controls were significantly lower than those of the metastatic patients (p
  • Baars, Adája E.; Rubio-Valverde, Jose R.; Hu, Yannan; Bopp, Matthias; Brønnum-Hansen, Henrik; Kalediene, Ramune; Leinsalu, Mall; Martikainen, Pekka; Regidor, Enrique; White, Chris; Wojtyniak, Bogdan; Mackenbach, Johan P.; Nusselder, Wilma J. (2019)
    ObjectivesTo assess to what extent educational differences in total life expectancy (TLE) and disability-free life expectancy (DFLE) could be reduced by improving fruit and vegetable consumption in ten European countries.MethodsData from national census or registries with mortality follow-up, EU-SILC, and ESS were used in two scenarios to calculate the impact: the upward levelling scenario (exposure in low educated equals exposure in high educated) and the elimination scenario (no exposure in both groups). Results are estimated for men and women between ages 35 and 79years.ResultsVarying by country, upward levelling reduced inequalities in DFLE by 0.1-1.1years (1-10%) in males, and by 0.0-1.3years (0-18%) in females. Eliminating exposure reduced inequalities in DFLE between 0.6 and 1.7years for males (6-15%), and between 0.1years and 1.8years for females (3-20%).ConclusionsUpward levelling of fruit and vegetable consumption would have a small, positive effect on both TLE and DFLE, and could potentially reduce inequalities in TLE and DFLE.
  • Vaara, Martti (2019)
    The discovery of polymyxins, highly basic lipodecapeptides, was published independently by three laboratories in 1947. Their clinical use, however, was abandoned in the sixties because of nephrotoxicity and because better-tolerated drugs belonging to other antibiotic classes were discovered. Now polymyxins have resurged as the last-resort drugs against extremely multi-resistant strains, even though their nephrotoxicity forces clinicians to administer them at doses that are lower than those required for optimal efficacy. As their therapeutic windows are very narrow, the use of polymyxins has received lots of justified criticism. To address this criticism, consensus guidelines for the optimal use of polymyxins have just been published. Quite obviously, too, improved polymyxins with increased efficacy and lowered nephrotoxicity would be more than welcome. Over the last few years, more than USD 40 million of public money has been used in programs that aim at the design of novel polymyxin derivatives. This perspective article points out that polymyxins do have potential for further development and that the novel derivatives already now at hand might offer major advantages over the old polymyxins.
  • Chakroborty, Deepankar; Emani, Maheswara Reddy; Klen, Riku; Bockelman, Camilla; Hagström, Jaana; Haglund, Caj; Ristimäki, Ari; Lahesmaa, Riitta; Elo, Laura L. (2019)
    BackgroundPrognostic markers specific to a particular cancer type can assist in the evaluation of survival probability of patients and help clinicians to assess the available treatment modalities.MethodsGene expression data was analyzed from three independent colon cancer microarray gene expression data sets (N=1052). Survival analysis was performed for the three data sets, stratified by the expression level of the LINE-1 type transposase domain containing 1 (L1TD1). Correlation analysis was performed to investigate the role of the interactome of L1TD1 in colon cancer patients.ResultsWe found L1TD1 as a novel positive prognostic marker for colon cancer. Increased expression of L1TD1 associated with longer disease-free survival in all the three data sets. Our results were in contrast to a previous study on medulloblastoma, where high expression of L1TD1 was linked with poor prognosis. Notably, in medulloblastoma L1TD1 was co-expressed with its interaction partners, whereas our analysis revealed lack of co-expression of L1TD1 with its interaction partners in colon cancer.ConclusionsOur results identify increased expression of L1TD1 as a prognostic marker predicting longer disease-free survival in colon cancer patients.
  • Hietala, Ville; Horsma-Heikkinen, Jenni; Carron, Annelie; Skurnik, Mikael; Kiljunen, Saija (2019)
    The production of phages for therapeutic purposes demands fast, efficient and scalable purification procedures. Phage lysates have a wide range of impurities, of which endotoxins of gram-negative bacteria and protein toxins produced by many pathogenic bacterial species are harmful to humans. The highest allowed endotoxin concentration for parenterally applied medicines is 5 EU/kg/h. The aim of this study was to evaluate the feasibility of different purification methods in endotoxin and protein toxin removal in the production of phage preparations for clinical use. In the purification assays, we utilized three phages: Escherichia phage vB_EcoM_fHoEco02, Acinetobacter phage vB_ApiMiHyAci03, and Staphylococcus phage vB_SauMiRuSau02. The purification methods tested in the study were precipitation with polyethylene glycol, ultracentrifugation, ultrafiltration, anion exchange chromatography, octanol extraction, two different endotoxin removal columns, and different combinations thereof. The efficiency of the applied purification protocols was evaluated by measuring phage titer and either endotoxins or staphylococcal enterotoxins A and C (SEA and SEC, respectively) from samples taken from different purification steps. The most efficient procedure in endotoxin removal was the combination of ultrafiltration and EndoTrap HD affinity column, which was able to reduce the endotoxin-to-phage ratio of vB_EcoM_HoEco02 lysate from 3.5 x 10(4) Endotoxin Units (EU)/10(9) plaque forming units (PFU) to 0.09 EU/10 9 PFU. The combination of ultrafiltration and anion exchange chromatography resulted in ratio 96 EU/10(9) PFU, and the addition of octanol extraction step into this procedure still reduced this ratio threefold. The other methods tested either resulted to less efficient endotoxin removal or required the use of harmful chemicals that should be avoided when producing phage preparations for medical use. Ultrafiltration with 100,000 MWCO efficiently removed enterotoxins from vB_SauM_fRuSau02 lysate (from 1.3 to 0.06 ng SEA/10(9) PFU), and anion exchange chromatography reduced the enterotoxin concentration below 0.25 ng/ml, the detection limit of the assay.

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