Browsing by Subject "Proteomics"

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  • Miettinen, Juho; Kumari, Romika; Traustadottir, Gunnhildur Asta; Huppunen, Maiju-Emilia Anniina; Sergeev, Philipp; Majumder, Muntasir M.; Schepsky, Alexander; Gudjonsson, Thorarinn; Lievonen, Juha; Bazou, Despina; Dowling, Paul; O'Gorman, Peter; Slipicevic, Ana; Anttila, Pekka; Silvennoinen, Raija; Nupponen, Nina N.; Lehmann, Fredrik; Heckman, Caroline (2021)
    Multiple myeloma (MM) is characterized by extensive immunoglobulin production leading to an excessive load on protein homeostasis in tumor cells. Aminopeptidases contribute to proteolysis by catalyzing the hydrolysis of amino acids from proteins or peptides and function downstream of the ubiquitin–proteasome pathway. Notably, aminopeptidases can be utilized in the delivery of antibody and peptide-conjugated drugs, such as melflufen, currently in clinical trials. We analyzed the expression of 39 aminopeptidase genes in MM samples from 122 patients treated at Finnish cancer centers and 892 patients from the CoMMpass database. Based on ranked abundance, LAP3, ERAP2, METAP2, TTP2, and DPP7 were highly expressed in MM. ERAP2, XPNPEP1, DPP3, RNPEP, and CTSV were differentially expressed between relapsed/refractory and newly diagnosed MM samples (p < 0.05). Sensitivity to melflufen was detected ex vivo in 11/15 MM patient samples, and high sensitivity was observed, especially in relapsed/refractory samples. Survival analysis revealed that high expression of XPNPEP1, RNPEP, DPP3, and BLMH (p < 0.05) was associated with shorter overall survival. Hydrolysis analysis demonstrated that melflufen is a substrate for aminopeptidases LAP3, LTA4H, RNPEP, and ANPEP. The sensitivity of MM cell lines to melflufen was reduced by aminopeptidase inhibitors. These results indicate critical roles of aminopeptidases in disease progression and the activity of melflufen in MM.
  • Finndiane Study Grp; SDRN Type 1 Bioresource Collabora; Colombo, Marco; Valo, Erkka; Sandholm, Niina; Groop, Per-Henrik; Forsblom, Carol; Colhoun, Helen M. (2019)
    Aims/hypothesis We aimed to identify a sparse panel of biomarkers for improving the prediction of renal disease progression in type 1 diabetes. Methods We considered 859 individuals recruited from the Scottish Diabetes Research Network Type 1 Bioresource (SDRNT1BIO) and 315 individuals from the Finnish Diabetic Nephropathy (FinnDiane) study. All had an entry eGFR between 30 and 75 ml min(-1)[1.73 m](-2), with those from FinnDiane being oversampled for albuminuria. A total of 297 circulating biomarkers (30 proteins, 121 metabolites, 146 tryptic peptides) were measured in non-fasting serum samples using the Luminex platform and LC electrospray tandem MS (LC-MS/MS). We investigated associations with final eGFR adjusted for baseline eGFR and with rapid progression (a loss of more than 3 ml min(-1)[1.73 m](-2) year(-1)) using linear and logistic regression models. Panels of biomarkers were identified using a penalised Bayesian approach, and their performance was evaluated through 10-fold cross-validation and compared with using clinical record data alone. Results For final eGFR, 16 proteins and 30 metabolites or tryptic peptides showed significant association in SDRNT1BIO, and nine proteins and five metabolites or tryptic peptides in FinnDiane, beyond age, sex, diabetes duration, study day eGFR and length of follow-up (all at p <10(-4)). The strongest associations were with CD27 antigen (CD27), kidney injury molecule 1 (KIM-1) and alpha 1-microglobulin. Including the Luminex biomarkers on top of baseline covariates increased the r(2) for prediction of final eGFR from 0.47 to 0.58 in SDRNT1BIO and from 0.33 to 0.48 in FinnDiane. At least 75% of the increment in r(2) was attributable to CD27 and KIM-1. However, using the weighted average of historical eGFR gave similar performance to biomarkers. The LC-MS/MS platform performed less well. Conclusions/interpretation Among a large set of associated biomarkers, a sparse panel of just CD27 and KIM-1 contains most of the predictive information for eGFR progression. The increment in prediction beyond clinical data was modest but potentially useful for oversampling individuals with rapid disease progression into clinical trials, especially where there is little information on prior eGFR trajectories.
  • Prokopec, Stephenie D.; Lu, Aileen; Lee, Sandy Che-Eun S.; Yao, Cindy Q.; Sun, Ren X.; Watson, John D.; Soliymani, Rabah; de Borja, Richard; Wong, Ada; Sam, Michelle; Zuzarte, Philip; McPherson, John D.; Okey, Allan B.; Pohjanvirta, Raimo; Boutros, Paul C. (2019)
    The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify the other factors involved, we evaluated three transgenic mouse lines, each expressing a different rat AHR isoform (rWT, DEL, and INS) providing widely different resistance to TCDD toxicity, as well as C57BL/6 and DBA/2 mice which exhibit a similar to tenfold divergence in TCDD sensitivity (exposures of 5-1000 mu g/kg TCDD). We supplement these with whole-genome sequencing, together with transcriptomic and proteomic analyses of the corresponding rat models, Long-Evans (L-E) and Han/Wistar (H/W) rats (having a similar to 1000-fold difference in their TCDD sensitivities; 100 mu g/kg TCDD), to identify genes associated with TCDD-response phenotypes. Overall, we identified up to 50% of genes with altered mRNA abundance following TCDD exposure are associated with a single AHR isoform (33.8%, 11.7%, 5.2% and 0.3% of 3076 genes altered unique to rWT, DEL, C57BL/6 and INS respectively following 1000 mu g/kg TCDD). Hepatic Pxdc1 was significantly repressed in all three TCDD-sensitive animal models (C57BL/6 and rWT mice, and L-E rat) after TCDD exposure. Three genes, including Cxxc5, Sugp1 and Hgfac, demonstrated different AHRE-1 (full) motif occurrences within their promoter regions between rat strains, as well as different patterns of mRNA abundance. Several hepatic proteins showed parallel up- or downward alterations with their RNAs, with three genes (SNRK, IGTP and IMPA2) showing consistent, strain-dependent changes. These data show the value of integrating genomic, transcriptomic and proteomic evidence across multi-species models in toxicologic studies.
  • Mäkelä, Miia R.; Bouzid, Ourdia; Robl, Diogo; Post, Harm; Peng, Mao; Heck, Albert; Altelaar, Maarten; de Vries, Ronald P. (2017)
    The coprophilic ascomycete fungus Podospora anserina was cultivated on three different plant biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested plant biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in plant biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures. (C) 2017 Elsevier B.V. All rights reserved.
  • Holm, Matilda; Joenväärä, Sakari; Saraswat, Mayank; Tohmola, Tiialotta; Ristimäki, Ari; Renkonen, Risto; Haglund, Caj (BioMed Central, 2019)
    Abstract Background Colorectal cancer (CRC) is the third most common cancer worldwide, and its incidence is expected to increase to over 2.2 million new cases in 2030. Stage II CRC is classified as localized disease, while stage III CRC has spread to regional lymph nodes. The 5-year survival rate is over 80% for patients with stage II CRC, but less than 60% for patients with stage III CRC. Proteins, especially plasma proteins that are detectable in easily obtained blood samples, that differ between stage II and III CRC could be useful for predicting and monitoring disease progression. CRC displays differences depending on primary tumor location (right colon, left colon, or rectum), and how plasma protein expression changes during CRC progression from stage II to III depending on primary tumor location is not well-characterized. Methods In this study, we have used Ultra Performance Liquid Chromatography-Ultra Definition Mass Spectrometry (UPLC-UDMSE)-based proteomics to analyze plasma samples from 83 patients with stage II or III CRC, followed by statistical and pathway analysis (data are available via ProteomeXchange). The patients were divided into groups according to tumor stage (II or III) and changes in plasma protein expression between stage II and III (localized and regional disease) samples were studied both regardless of primary tumor location and also within each primary tumor location (right colon, left colon, rectum). Results We discovered differences in plasma protein expression within all groups analyzed and identified proteins whose levels changed in one, two, or all three primary tumor locations between stage II and III CRC. Proteins were identified that could separate the groups compared and pathway analysis by IPA discovered altered pathways involved in lipid metabolism and inflammation, among others. Conclusions Plasma protein expression changes significantly as CRC progresses from stage II to III. While the levels of certain plasma proteins changed during cancer progression in only one or two primary tumor locations, the levels of 13 proteins changed in all primary tumor locations and are therefore common to CRC progression.
  • Lundell, Taina K.; Mäkelä, Miia R.; de Vries, Ronald P.; Hilden, Kristiina S. (Academic Press, 2014)
    Advances in Botanical Research
    Saprobic (saprotrophic and saprophytic) wood-decay fungi are in majority species belonging to the fungal phylum Basidiomycota, whereas saprobic plant litter-decomposing fungi are species of both the Basidiomycota and the second Dikarya phylum Ascomycota. Wood-colonizing white rot and brown rot fungi are principally polypore, gilled pleurotoid, or corticioid Basidiomycota species of the class Agaricomycetes, which also includes forest and grassland soil-inhabiting and litter-decomposing mushroom species. In this chapter, examples of lignocellulose degradation patterns are presented in the current view of genome sequencing and comparative genomics of fungal wood-decay enzymes. Specific attention is given to the model white rot fungus, lignin-degrading species Phanerochaete chrysosporium and its wood decay-related gene expression (transcriptomics) on lignocellulose substrates. Types of fungal decay patterns on wood and plant lignocellulose are discussed in the view of fungal lifestyle strategies. Potentiality of the plant biomass-decomposing Basidiomycota species, their secreted enzymes and respective lignocellulose-attacking genes is evaluated in regard to development of biotechnological and industrial applications.
  • Weisell, Jonna; Ohukainen, Pauli; Näpänkangas, Juha; Ohlmeier, Steffen; Bergmann, Ulrich; Peltonen, Tuomas; Taskinen, Panu; Ruskoaho, Heikki; Rysä, Jaana (BioMed Central, 2019)
    Abstract Background Calcific aortic valve disease (CAVD) is an atheroinflammatory process; finally it leads to progressive calcification of the valve. There is no effective pharmacological treatment for CAVD and many of the underlying molecular mechanisms remain unknown. We conducted a proteomic study to reveal novel factors associated with CAVD. Methods We compared aortic valves from patients undergoing valvular replacement surgery due to non-calcified aortic insufficiency (control group, n = 5) to a stenotic group (n = 7) using two-dimensional difference gel electrophoresis (2D-DIGE). Protein spots were identified with mass spectrometry. Western blot and immunohistochemistry were used to validate the results in a separate patient cohort and Ingenuity Pathway Analysis (IPA) was exploited to predict the regulatory network of CAVD. Results We detected an upregulation of complement 9 (C9), serum amyloid P-component (APCS) and transgelin as well as downregulation of heat shock protein (HSP90), protein disulfide isomerase A3 (PDIA3), annexin A2 (ANXA2) and galectin-1 in patients with aortic valve stenosis. The decreased protein expression of HSP90 was confirmed with Western blot. Conclusions We describe here a novel data set of proteomic changes associated with CAVD, including downregulation of the pro-inflammatory cytosolic protein, HSP90.
  • Parviainen, Ville I.; Joenväärä, Sakari; Tohmola, Niina; Renkonen, Risto (2013)
  • Korvala, Johanna; Jee, Kowan; Porkola, Emmi; Almangush, Alhadi; Mosakhani, Neda; Bitu, Carolina; Cervigne, Nilva K.; Zandonadi, Flavia S.; Meirelles, Gabriela V.; Paes Leme, Adriana Franco; Coletta, Ricardo D.; Leivo, Ilmo; Salo, Tuula (2017)
    Complex molecular pathways regulate cancer invasion. This study overviewed proteins and microRNAs (miRNAs) involved in oral tongue squamous cell carcinoma (OTSCC) invasion. The human highly aggressive OTSCC cell line HSC-3 was examined in a 3D organotypic human leiomyoma model. Non-invasive and invasive cells were laser-captured and protein expression was analyzed using mass spectrometry-based proteomics and miRNA expression by microarray. In functional studies the 3D invasion assay was replicated after silencing candidate miRNAs, miR-498 and miR-940, in invasive OTSCC cell lines (HSC-3 and SCC-15). Cell migration, proliferation and viability were also studied in the silenced cells. In HSC-3 cells, 67 proteins and 53 miRNAs showed significant fold-changes between non-invasive vs. invasive cells. Pathway enrichment analyses allocated "Focal adhesion" and "ECM-receptor interaction" as most important for invasion. Significantly, in HSC-3 cells, miR-498 silencing decreased the invasion area and miR-940 silencing reduced invasion area and depth. Viability, proliferation and migration weren't significantly affected. In SCC-15 cells, down-regulation of miR-498 significantly reduced invasion and migration. This study shows HSC-3 specific miRNA and protein expression in invasion, and suggests that miR-498 and miR-940 affect invasion in vitro, the process being more influenced by mir-940 silencing in aggressive HSC-3 cells than in the less invasive SCC-15.
  • Teppo, Jaakko; Vaikkinen, Anu; Stratoulias, Vassilis; Mätlik, Kert; Anttila, Jenni E.; Smolander, Olli-Pekka; Pöhö, Päivi; Harvey, Brandon K.; Kostiainen, Risto; Airavaara, Mikko (2020)
    The peri-infarct region after ischemic stroke is the anatomical location for many of the endogenous recovery processes, and the molecular events in the peri-infarct region remain poorly characterized. In this study, we examine the molecular profile of the peri-infarct region on post-stroke day four, time when reparative processes are ongoing. We used a multiomics approach, involving RNA sequencing, and mass spectrometry-based proteomics and metabolomics to characterize molecular changes in the peri-infarct region. We also took advantage of our previously developed method to express transgenes in the peri-infarct region where self-complementary adeno-associated virus (AAV) vectors were injected into the brain parenchyma on post-stroke day 2. We have previously used this method to show that mesencephalic astrocyte-derived neurotrophic factor (MANF) enhances functional recovery from stroke and recruits phagocytic cells to the peri-infarct region. Here, we first analyzed the effects of stroke to the peri-infarct region on post-stroke day 4 in comparison to sham-operated animals, finding that stroke induced changes in 3345 transcripts, 341 proteins, and 88 metabolites. We found that after stroke genes related to inflammation, proliferation, apoptosis, and regeneration were upregulated, whereas genes encoding neuroactive ligand receptors and calcium-binding proteins were downregulated. In proteomics, we detected upregulation of proteins related to protein synthesis and downregulation of neuronal proteins. Metabolomic studies indicated that in after stroke tissue there is increase in saccharides, sugar phosphates, ceramides and free fatty acids and decrease of adenine, hypoxantine, adenosine and guanosine. We then compared the effects of post-stroke delivery AAV1-MANF delivery to AAV1-eGFP (enhanced green fluorescent protein). MANF administration increased the expression of 77 genes, most of which were related to immune response. In proteomics, MANF administration reduced S100A8 and S100A9 protein levels. In metabolomics, no significant differences between MANF and eGFP treatment were detected, but relative to sham surgery group, most of the changes in lipids were significant in the AAV-eGFP group only. This work describes the molecular profile of the peri-infarct region during recovery from ischemic stroke, and establishes a resource for further stroke studies. These results provide further support for parenchymal MANF as a modulator of phagocytic function.
  • Ikonen, Jani (Helsingin yliopisto, 2020)
    At the literary review, basic concepts of proteomics and mass spectrometry were covered. Different data-collection methods (DDA and DIA) were compared with each other including exploration of the possibilities of the DIA method. Characteristics of Fourier transformation mass spectrometry were discussed in detail beginning from the production of the protein spectra in FTMS instruments including features of the Orbitrap (hybrid) mass spectrometer. Features included modes of measurements, working principle, performance characteristics, operation modes and top-down experiments including large intact protein analysis (m/z range > 6000 Da). The working principles and performance in proteomic analyses of other mass spectrometer instruments were also briefly covered. Orbitrap MS instrumentation is compared with high-performance mass spectrometers including triple quadrupole, time of flight, ion trap, and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers. Lastly, operation and coupling of the LC instrumentation to the Orbitrap mass spectrometer were also briefly discussed. The experimental part of the thesis covers development and feasibility testing of a quality control method for protein analysis studied with PierceTM Intact Protein Standard Mix by using microflow liquid chromatography-Orbitrap mass spectrometry combination. Development and testing of the method includes optimization of the method for dried sample, robustness testing with variable LC eluent concentrations, and the method performance with a heavily contaminated instrument compared with the performance of a clean MS instrument. Tested heavily contaminated instrument had more than 2000 injections of protein samples without cleaning. In the end, the developed protein analysis method was tested with nine different Q Exactive HF Orbitrap instruments to measure the instrument variation. In the studies, the average mass of analyzed proteins varied from 9111.47 to 68001.15 kDa The mass range used for identification was 500 – 2000 Da.
  • Soderlund, Stina; Christiansson, Lisa; Persson, Inger; Hjorth-Hansen, Henrik; Richter, Johan; Simonsson, Bengt; Mustjoki, Satu; Olsson-Stromberg, Ulla; Loskog, Angelica (2016)
    Background and aims: The simultaneous measurement of many proteins is now possible using multiplex assays. In this pilot study we investigated a total of 124 proteins in plasma from chronic myeloid leukemia (CML) patients with the purpose of identifying proteins that are differently expressed at diagnosis and after tyrosine kinase inhibitor (TKI) treatment initiation. Methods: Samples were taken from 14 CML patients at diagnosis and after three months of TKI treatment (imatinib or dasatinib). Samples were analyzed by Mesoscale Discovery, Myriad RBM MAP technology and Olink Proseek. Results: Multiple plasma proteins were differentially expressed before and after initiation of TKI therapy. Protein patterns demonstrated a possible shift towards Th1-immunity and reduced angiogenic stimuli. Further, some plasma proteins were identified that can be of potential interest to study further for biologic, prognostic or therapeutic significance such as E-selectin, uPAR, growth hormone and carbonic anhydrase IX. Conclusions: Plasma proteomics seems feasible and useful in CML patients, both for studying patterns of protein expression and for identifying single proteins differentially expressed before and after treatment. Plasma proteomics may be useful to map disease activity and biological processes. Hence, plasma proteomics can be used to understand drug mechanisms and treatment responses in CML. (C) 2016 Elsevier Ltd. All rights reserved.
  • Soderlund, Stina; Persson, Inger; Ilanderd, Mette; Guilhot, Joelle; Hjorth-Hansen, Henrik; Koskenvesa, Perttu; Richter, Johan; Saussele, Susanne; Mustjoki, Satu; Olsson-Strömberg, Ulla (2020)
    Several studies have now shown that chronic myeloid leukaemia (CML) patients in deep molecular remission may discontinue tyrosine kinase inhibitor (TKI) treatment with a treatment free remission (TFR) rate of approximately 40-60 %. Some factors influencing the possibility of TFR have been described but better tools are needed for individual prediction of long-term TFR. Herein, two multiplex panels were utilised to analyse a total of 162 different plasma proteins from 56 patients included in the TKI stopping trial EURO-SKI (Saussele a al., 2018). The purpose was to identify possible plasma protein markers for prediction of successful TKI discontinuation and to evaluate effects of TKI discontinuation on plasma protein profiles. No protein biomarkers sampled before TKI discontinuation could separate relapse cases from non-relapse cases but some plasma proteins differed between patients who relapsed and those who remained in TFR when followed over time after TKI cessation. In conclusion, the plasma protein markers in this study could not predict relapse after TKI discontinuation but may be of use to understand the mechanisms involved in maintenance of TFR.
  • Holm, Matilda; Joenväärä, Sakari; Saraswat, Mayank; Tohmola, Tiialotta; Ristimäki, Ari; Renkonen, Risto; Haglund, Caj (2020)
    Introduction:Colorectal cancer (CRC) is the third most common cancer worldwide, accounting for 10% of the global cancer burden. Rectal cancer accounts for around 30% of CRC cases, and patients with resectable rectal cancer are often given preoperative radiotherapy (PRT) to reduce the rate of local recurrence. The human plasma proteome is an exceptionally complex proteome and ideal to study due to its ability to reflect the presence of diseases such as cancer and the ease of obtaining blood samples. Previous proteomic studies involving rectal cancer patients have mostly focused on the identification of proteins involved in resistance to radiotherapy.Objective:The aim of this study was to investigate the overall effects of PRT on plasma protein expression in rectal cancer patients, as there is a lack of such studies.Methods:Here, we have used mass spectrometry and subsequent statistical analyses to analyze the plasma samples of 30 rectal cancer patients according to PRT status (positive or negative) and tumor stage (II or III).Results and Conclusions:We discovered 42 proteins whose levels differed significantly between stage II and III rectal cancer patients who did or did not receive PRT. This study shows that PRT, although localized to the pelvis, leads to measurable, tumor stage-specific changes in plasma protein expression. Future studies of plasma proteins should, when relevant, take this into account and be aware of the widespread effects that PRT has on the plasma proteome.
  • Nyman, Tuula A.; Matikainen, Sampsa (2018)
    Viral infections are a major burden to human and animal health. Immune response against viruses consists of innate and adaptive immunity which are both critical for the eradication of the viral infection. The innate immune system is the first line of defense against viral infections. Proper innate immune response is required for the activation of adaptive, humoral and cell-mediated immunity. Macrophages are innate immune cells which have a central role in detecting viral infections including influenza A and human immunodeficiency viruses. Macrophages and other host cells respond to viral infection by modulating their protein expression levels, proteins' posttranslational modifications, as well as proteins' intracellular localization and secretion. Therefore the detailed characterization how viruses dynamically manipulate host proteome is needed for understanding the molecular mechanisms of viral infection. It is critical to identify cellular host factors which are exploited by different viruses, and which are less prone for mutations and could serve as potential targets for novel antiviral compounds. Here, we review how proteomics studies have enhanced our understanding of macrophage response to viral infection with special focus on Influenza A and Human immunodeficiency viruses, and virus infections of swine. (C) 2017 Elsevier B.V. All rights reserved.
  • Ahlström, Fredrik; Mätlik, Kert; Blomqvist, Kim; Liu, Xiaonan; Lilius, Tuomas; Sidorova, Yulia; Kalso, Eija; Rauhala, Pekka; Viisanen, Hanna (Helsingin yliopisto, 2020)
    Neuropatisk smärta (NS) är vanligare hos kvinnor. Fastän nyligen utförd forskning tyder på att patofysiologin är olik hos könen, har primärt handjur studerats tidigare. För att bättre förstå könsskillnader vid NS undersökte vi hon- och hanråttors smärtbeteende efter en perifer nerv-skada samt analyserade vävnader med systembiologiska metoder. En perifer nervskada orsakades hos hon- och hanråttor, sham-operationer utfördes på kontroll-grupperna. Mekanisk och köldallodyni mättes med von Frey filament, respektive acetontest före operationerna, efter sju och 21 dagar. Ryggmärgsprovers och dorsalrotsganglioners genexpress-ion analyserades sju dagar efter operationerna. L4-L5 ryggmärgssegment (IBA1 och GFAP) och dorsalrotsganglionerna (CGRP och IB-4) samlades för immunohistokemi och cerebrospinal-vätska för proteomik efter 21 dagar. En kraftigare mekanisk allodyni uppstod hos honråttorna. Bägge könen utvecklade en tidig kraf-tig köldallodyni. De immunohistokemiska markörerna påvisade en liknande nervskada i dorsal-rotganglierna och liknande mikroglia- och astrocytaktivitet i ryggmärgen hos könen. Cerebrospi-nalvätskans proteiner påverkades inte. Många gener i dorsalrotsganglierna visade könsspecifik genexpression efter nervskadan, exempelvis cd28, cd274, ctla4, dpp4, hrh3, il1b och thbs4; i ryggmärgen uppvisade bland annat generna atf3, ccl2, och pdyn könsspecifika förändringar. Hondjuren uppvisade kraftigare smärtbeteende, och vi identifierade många gener som kunde förklara den observerade skillnaden. T-lymfocytresponsen och flera andra till NS kopplade mekanismer verkar vara olika i de två könen. Generna är kandidater för vidare forskning och våra resultat understryker betydelsen av att könen undersöks skilt i smärtstudier. (219 ord)
  • Pontes, Maria Victoria Aguilar; Patyshakuliyeva, Aleksandrina; Post, Harm; Jurak, Edita; Hilden, Kristiina; Altelaar, Maarten; Heck, Albert; Kabel, Mirjam A.; de Vries, Ronald P.; Mäkelä, Miia R. (2018)
    The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.
  • Kuuskeri, Jaana; Häkkinen, Mari; Laine, Pia; Smolander, Olli-Pekka; Tamene, Fitsum; Miettinen, Sini; Nousiainen, Paula; Kemell, Marianna; Auvinen, Petri; Lundell, Taina (2016)
    Background The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC–MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus’ natural growth substrate. Results According to proteomics analyses, several CAZy oxidoreductase class-II peroxidases with glyoxal and alcohol oxidases were the most abundant proteins produced on wood together with enzymes important for cellulose utilization, such as GH7 and GH6 cellobiohydrolases. Transcriptome additionally displayed expression of multiple AA9 lytic polysaccharide monooxygenases indicative of oxidative cleavage of wood carbohydrate polymers. Large differences were observed for individual protein quantities at specific time points, with a tendency of enhanced production of specific peroxidases on the first 2 weeks of growth on wood. Among the 10 class-II peroxidases, new MnP1-long, characterized MnP2-long and LiP3 were produced in high protein abundances, while LiP2 and LiP1 were upregulated at highest level as transcripts on wood together with the oxidases and one acetyl xylan esterase, implying their necessity as primary enzymes to function against coniferous wood lignin to gain carbohydrate accessibility and fungal growth. Majority of the CAZy encoding transcripts upregulated on spruce wood represented activities against plant cell wall and were identified in the proteome, comprising main activities of white-rot decay. Conclusions Our data indicate significant changes in carbohydrate-active enzyme expression during the six-week surveillance of P. radiata growing on wood. Response to wood substrate is seen already during the first weeks. The immediate oxidative enzyme action on lignin and wood cell walls is supported by detected lignin substructure sidechain cleavages, release of phenolic units, and visual changes in xylem cell wall ultrastructure. This study contributes to increasing knowledge on fungal genetics and lignocellulose bioconversion pathways, allowing us to head for systems biology, development of biofuel production, and industrial applications on plant biomass utilizing wood-decay fungi.