eRapport

The Proteomics Core Facility at Oslo University Hospital (Rikshospitalet)

Prosjekt
Prosjektnummer
2015098
Ansvarlig person
Tuula Nyman
Institusjon
Oslo universitetssykehus HF
Prosjektkategori
Regional teknologisk kjernefasilitet
Helsekategori
Generic Health Relevance
Forskningsaktivitet
1. Underpinning
Rapporter
2023
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet and University of Oslo provides advanced mass spectrometry-based proteomic services to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis.Proteomics is of fundamental importance to modern life science research. Proteome level information is needed to elucidate disease mechanisms, find new drug targets, and develop personalized medicine, and is integral to numerous other research fields with potential societal benefits. PCF provides a range of proteomics services to our users, with specialist knowledge in protein identification and quantification, as well as the analysis of proteins’ post-translational modifications and protein interactions. The unit has strong expertise with proteomics applied to immunology and cell signalling research, as well as in clinical proteomics applications. PCF personnel in 2023 included leader of the unit, Dr Tuula Nyman, head engineers Dr Maria Stensland and Dr Sachin Kumar Singh, and senior researcher Jorunn Stamnæs (50% position). All personnel are highly experienced with different proteomics methods and mass spectrometry (MS)-instruments, and have direct contact with our users to provide advice on experimental set-up, sample preparation and discuss the results of experiments. PCF leader Tuula Nyman is the Project Manager for the National Network for Advanced Proteomics Infrastructure (NAPI, https://www.napi.uio.no/) funded by the Research Council of Norway (RCN) in the end of 2019. To keep up with latest developments within proteomics a continuation application, NAPI2 with focus on clinical proteomics applications was submitted to INFRASTRUKTUR 2023 call from RCN. Proteomics is a constantly evolving field, with new methods, techniques, and instruments developed on a regular basis. PCF is equipped with three advanced mass spectrometry instruments; these allow for novel proteomics and spatial mass spectrometry techniques such as data independent acquisition (DIA) and mass spectrometry imaging. Mass spectrometry imaging (MSI) is an innovative MS methodology that generates unique in situ information on abundance and spatial distribution of molecules such as peptides, lipids and metabolites. MSI is thus a label-free method for spatial tissue analysis which complements e.g. antibody based imaging and spatial transcriptomics. MSI holds great potential for basic and translational research and future clinical applications. In 2023 we have set up basic protocols with the aim to launch MSI as a new research service in 2024. To complement MS-based techniques we purchased a Proximity Extension Assay- based proteomics technology, namely Olink Signature in December 2022. This technology is especially suitable for clinical samples like blood and serum, which still pose challenges for MS analysis. During 2023 PCF personnel were trained to carry out Olink experiments and several Olink projects were initiated in collaboration with groups from OUS, NTNU, Folkehelseinstituttet and one biotech company in Oslo. PCF services have an important role for top-level research in HSØ region; this is reflected in the number of users (e.g. 44 from UiO/OUS and 9 from abroad in 2023), as well as strong publication record. We also play an important role in the research activities of many local research centres like ‘CanCell’ Centre of Excellence (where Dr Nyman is an associate member) and K.G. Jebsen Coeliac Disease Research Centre. Also the newly funded Centre of Excellence Precision Immunotherapy Alliance (PRIMA) has an integral component, immunopeptidomics, relying on advanced proteomics and MS analyses provided by PCF.
2022
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet and University of Oslo provides advanced mass spectrometry-based proteomic services to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis.Proteomics is of fundamental importance to modern life science research. Proteome level information is needed to elucidate disease mechanisms, find new drug targets, and develop personalized medicine, and is integral to numerous other research fields with potential societal benefits. PCF provides a range of proteomics services to our users, including protein identification and quantification, as well as the analysis of proteins’ post-translational modifications and protein interactions. The unit has strong expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. PCF personnel in 2022 included leader of the unit, Dr Tuula Nyman, and head engineers Dr Maria Stensland and Dr Sachin Kumar Singh. All personnel are highly experienced with different proteomics methods and mass spectrometry (MS)-instruments, and all have direct contact with our users to provide advice on experimental set-up, sample preparation and discuss the results of experiments. PCF leader Tuula Nyman is the Project Manager for the National Network for Advanced Proteomics Infrastructure (NAPI, https://www.napi.uio.no/) funded by the Research Council of Norway in the end of 2019. NAPI’s main office is located at PCF, where both Dr Nyman and the NAPI Administrative Manager, Dr Joseph Robertson, are based. This positions PCF as a central hub in Norwegian proteomics research. Proteomics is a constantly evolving field, with new methods, techniques, and instruments developed on a regular basis. PCF is equipped with two advanced mass spectrometry instruments; one purchased in 2014 (with a major upgrade in 2020), the other installed in 2021. The second instrument, a timsTOF fleX from Bruker, represents the latest state-of-the-art proteomic technology available, which gives our users access to cutting-edge analytical techniques not previously available in Norway. This includes a technique called mass spectrometry imaging (MSI) which we have started to set up to PCF in 2022 together with several collaborators. MSI is a next-generation analytical technique enabling researchers to determine specific molecular masses in tissues in 2D-space with moderate to high resolution. This information can be overlaid with tissue morphology and used in clinical/diagnostic settings, for example in the detection of disease biomarkers as well as in basic and translational research. To complement MS-based techniques we have purchased a Proximity Extension Assay- based proteomics technology, namely OLINK Signature, to PCF in December 2022. This technology is especially suitable for clinical samples like blood and serum, which still pose challenges for mass spectrometry analysis. Further, we got funding for a new MS instrument from UiO instrument call for research infrastructure (decision Dec 2022). This will give us possibility to further broaden our possibilities for advanced proteomics analysis in 2023. PCF services have an important role for top-level research in HSØ region; this is reflected in the number of users as well as strong publication record. We also play an important role in the research activities of many local research centres like ‘CanCell’ Centre of Excellence and K.G. Jebsen Coeliac Disease Research Centre. In 2022, we have invested in several new, advanced proteomic techniques in PCF, which will later be added to our service portfolio. This will further increase our value to research in the HSØ region.
2021
The Proteomics Core Facility (PCF) at Oslo University Hospital/University of Oslo provides advanced mass spectrometry-based proteomic services to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to meet the growing demand for proteomic technologies in life sciences research today.Proteomics is of fundamental importance to modern life science research. Proteome level information is needed to elucidate disease mechanisms, find new drug targets, and develop personalized medicine, and is integral to numerous other research fields with potential societal benefits. PCF provides a range of proteomics services to our users, with specialist knowledge in protein identification and quantification, as well as the analysis of proteins’ post-translational modifications and protein interactions. The unit has strong expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. PCF personnel include leader of the unit, Dr Tuula Nyman, and head engineers Dr Maria Stensland and Dr Sachin Kumar Singh. All personnel are highly experienced with different proteomics methods and mass spectrometry (MS)-instruments, and all have direct contact with our users to provide advice on experimental set-up, sample preparation and discuss the results of experiments. Proteomics is a constantly evolving field, with new methods, techniques, and instruments developed on a regular basis. PCF is equipped with two advanced MS instruments; one purchased in 2014 (with a major upgrade in 2020, funded with core facility user income), the other installed in 2021. This second instrument, the timsTOF fleX from Bruker, represents the latest state-of-the-art proteomic technology available worldwide today, and will give our users access to cutting-edge analytical techniques not previously available in Norway. We have also set-up and optimized several sample preparation methods to enable more thorough proteome analysis from diverse starting materials which can benefit many PCF users. These include an efficient method to enrich for phosphopeptides from smaller amounts of starting material than previously possible. PCF leader Tuula Nyman is the Project Manager for the National Network for Advanced Proteomics Infrastructure (NAPI, https://www.napi.uio.no/) funded by Research Council of Norway in the end of 2019. NAPI’s main office is located at PCF, where both Dr Nyman and the NAPI Administrative Manager, Dr Joseph Robertson, are based. This positions PCF as a central hub in Norwegian proteomics research. The timsTOF flex instrument mentioned above was funded by NAPI, OUS MTU funds and with PCF user income. In summary, there has been a substantial improvement in the proteomic capabilities of PCF in 2021, and our value to research in the HSØ region is reflected in the number of users (e.g. 55 from UiO/OUS and 13 from abroad in 2021), as well as strong publication record. We play an important role in the research activities of many local research centres like ‘CanCell’ Centre of Excellence (where Dr Nyman is an associate member) and K.G. Jebsen Coeliac Disease Research Centre. In 2021 we have also contributed to COVID research as part of a project published in the European Heart Journal.
2020
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet and University of Oslo provides advanced mass spectrometry-based proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis.Proteomics is an essential part of modern life science research. Proteome level information is needed to elucidate disease mechanisms, to find new drug targets, and to develop personalized medicine. The main areas of expertise of PCF are in protein identification and quantification, and in the analysis of proteins’ post-translational modifications and protein interactions. The unit has special expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. Proteomics methods, techniques, and instruments are under very active development world-wide. The development of high-resolution mass spectrometry (MS) instruments during the last decade has made it possible to perform deeper and faster proteome characterization than has ever been possible before. PCF is equipped with two high-resolution nano LC-MS/MS instruments purchased in 2012 and 2014; latter having major upgrade in the beginning of 2020 funded with core facility user income. PCF leader Tuula Nyman is the project manager for National Network for advanced Proteomics Infrastructure (NAPI) funded by Research Council of Norway in 2019 with official launch of NAPI in 2020. We have hired an administrative manager, Dr Joe Robertson to PCF from August 2020 to coordinate NAPI activities, and launched NAPI web-pages https://www.napi.uio.no/ and twitter account https://twitter.com/napi_norway to make NAPI known in Norwegian proteomics community. NAPI funding will secure new, up-to-date instruments to proteomics core facilities in Norway and closer collaboration and sharing of knowledge between the units. In 2020 we evaluated the possible new LC-MS/MS instruments to PCF, and decided to purchase a new instrument, timsTOF fleX from Bruker. This will be funded through NAPI and additional contribution from OUS to the new nanoLC to be included in the purchase. The new instrument will arrive and be installed to PCF in early 2021. PCF personnel include leader of the unit, Dr Tuula Nyman and head engineers, Dr Maria Stensland and Dr Sachin Singh Kumar, and NAPI admin manager Dr Joe Robertson. All PCF personnel are highly experienced with different proteomics methods and MS-instruments; they have complementary areas of expertise with Dr Stensland having main responsibility for LC-MS/MS instruments and Dr Singh specializing in advanced proteomic data analysis. They share the responsibility for sample preparation and running samples in LC-MS/MS, and both have direct contact with our users and provide advice on experimental set-up, sample preparation and discuss the results of the experiments. Dr Robertson coordinates NAPI activities which directly benefit all PCF users and the whole Norwegian proteomics community. Our highly qualified personnel and the described updates and renewal of LC-MS/MS instruments ensures that PCF is able to provide more advanced proteomics analysis than before to its’ customers and collaborators. The COVID pandemic in 2020 has slowed down many of our users’ research projects, and thus we have analyzed slightly less samples than we had expected, but overall the pandemic has not had a major effect in our activities.
2019
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet and University of Oslo provides advanced mass spectrometry-based proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis.Proteomics is an essential part of modern life science research. Proteome level information is needed to elucidate disease mechanisms, to find new drug targets, and to develop personalized medicine. The main areas of expertise of PCF are in protein identification and quantification, and in the analysis of proteins’ post-translational modifications and protein interactions. The unit has special expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. Proteomics methods, techniques, and instruments are under very active development world-wide. PCF is collaborating actively with several research groups locally and internationally to develop and set-up new proteomics techniques that can be later on taken into the list of services provided by the unit. Proteomics research relies heavily on expensive instrumentation operated by expert users. The development of high-resolution mass spectrometry (MS) instruments during the last decade has made it possible to perform deeper and faster proteome characterization than has ever been possible before. PCF is equipped with two high-resolution nano LC-MS/MS instruments (purchased in 2012 and 2014), and there is urgent need to have new instruments to the unit to keep it up-to-date and to be able to provide most advanced proteomic analysis to the users. PCF leader Tuula Nyman has been active in funding applications to upgrade the current instruments as well as to purchase new instruments to PCF, and in 2019 PCF was able to get significant funding for this. We bought a novel type of nanoLC, EvoSep One with funding from UiO/Faculty of Medicine ‘vitenskapelig utstyr kl. II; kr. 200.000 – 1 mill’. EvosepOne is a novel LC-concept making sample separation 10 times faster and 100 times more robust than todays’ alternatives. This is especially important for clinical proteomics applications but also for all other main proteomics fields where large sample sets need to be efficiently analyzed. In September 2019 the whole proteomics community in Norway got positive news from the Research Council of Norway that the National Network for advanced Proteomics Infrastructure (in short NAPI) coordinated by PCF leader Tuula Nyman will be funded. This funding will make it possible to purchase latest generation LC-MS/MS instruments to most of the proteomics core facilities in Norway in 2020-2021, and it will also make it possible to have closer co-operation and sharing of expertise and instruments between the facilities. Further, with funding from the core facility service fees PCF was able to purchase an upgrade to the QEPlus mass spectrometer purchased in 2014 into a newer generation QE HF-instrument in the end of 2019. PCF personnel include leader of the unit, Dr Tuula Nyman and head engineer, Dr Maria Stensland. Starting from October 2019 we hired another head engineer, Dr Sachin Singh Kumar to PCF. More personnel and the described updates and renewal of LC-MS/MS instruments ensures that PCF is able to provide more advanced proteomics analysis than before to its’ customers and collaborators.
2018
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet and University of Oslo provides advanced mass spectrometry-based proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis.Proteomics is an essential part of modern life science research. Proteome level information is needed to elucidate disease mechanisms, to find new drug targets, and to develop personalized medicine. Proteomics research relies heavily on expensive instrumentation operated by expert users. The development of high-resolution mass spectrometry (MS) instruments during the last decade has made it possible to perform deeper and faster proteome characterization than has ever been possible before. PCF is equipped with two high-resolution nano LC-MS/MS instruments (purchased in 2012 and 2014) and one MALDI-TOF/TOF instrument (purchased in 2005). The unit also has off-line liquid chromatography instrument for protein and peptide separation as well as equipment for protein separation by gel electrophoresis. The main areas of expertise of PCF are in protein identification and quantification, and in the analysis of proteins’ post-translational modifications and protein interactions. The unit has special expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. Proteomics methods, techniques, and instruments are under very active development world-wide. PCF is collaborating actively with several research groups locally and internationally to develop and set-up new proteomics techniques that can be later on taken into the list of services provided by the unit. PCF’s activity is well documented by its services, collaborations and by publications with essential proteomics and mass spectrometry contributions. 55 different research groups have used the core facility during 2016-2018, and the scientific collaborations resulted in authorship in 11 publications in 2018.
2017
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet provides proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis. New techniques and expertise are made available as service regularly.Proteomics is an essential part of modern life science research. Proteome level information is needed to elucidate disease mechanisms, to find new drug targets, and to develop personalized medicine. Proteomics research relies heavily on expensive instrumentation operated by expert users. The development of high-resolution mass spectrometry (MS) instruments during the last decade has made it possible to perform deeper and faster proteome characterization than has ever been possible before. The main areas of expertise of PCF are in protein identification and quantification, and in the analysis of proteins’ post-translational modifications and protein interactions. The unit has special expertise with proteomics applied to immunology and cell signaling research, as well as in clinical proteomics applications. Proteomics methods, techniques, and instruments are under very active development world-wide. PCF is collaborating actively with several research groups locally and internationally to develop and set-up new proteomics techniques that can be later on taken into the list of services provided by the unit. The PCF’s activity is well documented by its services, collaborations and by publications with essential proteomics and mass spectrometry contributions. In 2017 PCF provided services for more than 30 local research groups from UiO and OUS, and for two regional research groups from Akershus and Bærum. In addition, PCF had several international users from research groups from University of Helsinki (Finland), University of Salerno (Italy) and Unversidade Federal do Rio Grande do Norte (Brazil). Further, PCF provided analytical services for one local company. The scientific collaborations resulted in authorship in 17 publications in 2017. At present, the PCF personnel consist of the facility leader Tuula Nyman and head engineer Maria Stensland. PCF is equipped with two high-resolution mass spectrometers coupled to online liquid chromatrography from 2012 and 2014, and an older MALDI-TOF/TOF instrument. The unit also has off-line liquid chromatography instrument for protein and peptide separation as well as equipment for protein separation by gel electrophoresis. For MS data analysis the unit has ProteomeDiscoverer, Mascot, MaxQuant and Perseus softwares. In the future more personnel and new instruments are necessary to develop the proteomics services further. More personnel are needed to ensure enough capacity to assist users in proteomics experimental design, sample preparation and in proteomics data analysis. The Norwegian proteomics core facilities submitted a joint national infrastructure application coordinated by Head of PCF, Tuula Nyman to the Research Council of Norway in October 2016 to upgrade the existing MS instrumentation in the units and to bring in the latest proteomics techniques into the scientific community in Norway. The results from that call came in mid-2017; the proteomics application was graded 7/7 (Exceptional) but unfortunately the Research Council did not fund it. In future PCF will be active in applying more funding both for personnel as well as for new instruments to keep the PCF services at an internationally competitive level.
2016
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet provides proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis. New techniques and expertise are made available as service regularly. The unit is equipped with two high-resolution mass spectrometers coupled to online liquid chromatrography fractionation of peptides (purchased in 2012 and 2014) and one older MALDI-TOF/TOF instrument. The unit also has off-line liquid chromatography instrument for protein and peptide separation as well as equipment for protein separation by gel electrophoresis. PCF personnel consist of the facility leader Tuula Nyman (as of May 1st 2016) and engineer Maria Stensland. The former head Gustavo de Souza left the unit in December 2015 and to ensure that there was minimal effect on the services provided by the core facility Gustavo de Souza acted as consultant assisting the PCF engineer before Nyman took up the position as the PCF head. The new Head of Core Facility, Tuula Nyman has a strong track of record in proteomics research, teaching, and core facility work which will help to develop PCF further. New software tools (ProteomeDiscoverer and Mascot) and computers needed to enable novel possibilities for advanced data analysis have already been purchased and are in use. PCF has also participated in the purchase of a new a preparative liquid chromatography system intended for fast, high-quality protein separations together with other groups in Department of Immunology. This will increase the possibilities of PCF for advanced protein and peptide separation from small sample amounts. It is also critically important to promote education in proteomics and biological mass spectrometry, and the new possibilities these techniques can offer to researchers. Therefore the new core facility leader will take an active role in this and participate in teaching at all levels in her areas of expertise. The proximity of PCF’ know-how and instrumentation to users has ensured an efficient transfer of competence and facilitated the implementation of proteomics into numerous research projects. The PCF’s activity is well documented by its collaborations and by publications with essential proteomics and mass spectrometry contributions. In 2016 the PCF analyzed more than 1250 individual samples (3750 LC-MS/MS runs) from 38 different users. At present, there are no long queues for sample analyses in PCF. However, we have a need for more sensitive new instrument capable of performing most advanced proteomic analyses. This is the case for other proteomics core facilities in Norway also, and to address this, the proteomics core facilities submitted a joint national infrastructure application coordinated by PCF to the Research Council of Norway in October 2016. PCF is also in need for more personnel to assist users in proteomics experimental design, sample preparation and most critically, in proteomics data analysis. Future developments in PCF will include implementing new methods for the analysis of proteins’ post-translational modifications and targeted proteomics. We will also be active in exploring the possibilities for setting up imaging mass spectrometry techniques in collaboration with local research groups interested in this as well as with Nyman’s collaborators in University of Helsinki. Imaging mass spectrometry represents a methodology that is still in its early development within basic and clinical research. It will be especially important in clinical proteomics and biomarker discovery. Correlation of histological phenomena with mass spectrometry-based molecular images will provide a new dimension in medical diagnostics and molecular understanding of health and disease. We believe that this method in the future will supplement immunohistochemistry in routine laboratory diagnostics with the possibility to generate data for individual therapies.
2015
The Proteomics Core Facility (PCF) at Oslo University Hospital – Rikshospitalet provides proteomic service to all research groups in the HSØ region in need of it. We are constantly expanding our service portfolio to serve the increasing demands for such analysis. New techniques and expertise are made available as service regularly. Demands for service in 2015 had increased slightly, once again demonstrating that the level of acceptance of the PCF and data feedback to users has been excellent. As reported on the previous year, during 2014 the PCF was granted funds to acquire a new high resolution instrument through an UiO Infrastructure call. A new QExactive Plus was installed at PCF in late November 2014. This had a direct and positive impact in waiting times for PCF users during 2015. While the 1st semester still had periods of waiting queues reaching 3-4 weeks due to instrument downtime, the 2nd semester had instruments up and running for most of the time meaning waiting was for most period only 1 or 2 weeks. By December 2015 both instruments had run approximately 3000 sample injections each. Failures in the nano-LC system coupled to all instruments as usual have been our major bottleneck; while in the previous report we had indicated that was our utmost priority to acquire a backup LC system to reduce downtime, this was not done in 2015. Additional bottleneck that appeared once two instruments were installed regards to PCF engineer time management. The tasks for sample preparation in addition to maintenance of now three instruments is becoming overwhelming for a engineer at a 100% position. The PCF manager had indicated the Dept. of Immunology and the clinic (KDI) that in the near future the recruitment of an additional engineer at a 50% position might become urgent. All objectives set for projects supporting the application were achieved and publications are being prepared by the collaborators with support from PCF. Finally, early 2015 the current manager, Gustavo de Souza, had decided to resign his position and return to his home country, which happened in last December. The Dept. and KDI are since the 2nd semester of 2015 actively recruiting a new PCF manager. While the new manager is not hired and does not assume the lab, Dr. de Souza is acting as a consultant to PCF to guarantee a smooth transition and to offer any support that the PCF engineer might need while keeping PCF running.
Vitenskapelige artikler
Cypryk W, Czernek L, Horodecka K, Chrzanowski J, Stanczak M, Nurmi K, Bilicka M, Gadzinowski M, Walczak-Drzewiecka A, Stensland M, Eklund K, Fendler W, Nyman TA, Matikainen S

Lipopolysaccharide Primes Human Macrophages for Noncanonical Inflammasome-Induced Extracellular Vesicle Secretion.

J Immunol 2023 Feb 01;210(3):322.

PMID: 36525001

Dahlberg D, Holm S, Sagen EML, Michelsen AE, Stensland M, de Souza GA, Müller EG, Connelly JP, Revheim ME, Halvorsen B, Hassel B

Bacterial Brain Abscesses Expand Despite Effective Antibiotic Treatment: A Process Powered by Osmosis Due to Neutrophil Cell Death.

Neurosurgery 2023 Dec 12. Epub 2023 des 12

PMID: 38084989

Frerker N, Karlsen TA, Stensland M, Nyman TA, Rayner S, Brinchmann JE

Comparison between articular chondrocytes and mesenchymal stromal cells for the production of articular cartilage implants.

Front Bioeng Biotechnol 2023;11():1116513. Epub 2023 feb 21

PMID: 36896010

Gorski K, Jackson CB, Nyman TA, Rezov V, Battersby BJ, Lehesjoki AE

Progressive mitochondrial dysfunction in cerebellar synaptosomes of cystatin B-deficient mice.

Front Mol Neurosci 2023;16():1175851. Epub 2023 mai 12

PMID: 37251643

Hammarén MM, Luukinen H, Sillanpää A, Remans K, Lapouge K, Custódio T, Löw C, Myllymäki H, Montonen T, Seeger M, Robertson J, Nyman TA, Savijoki K, Parikka M

and

mSystems 2023 Jun 29;8(3):e0107322. Epub 2023 mai 15

PMID: 37184670

Harrison SP, Siller R, Tanaka Y, Chollet ME, de la Morena-Barrio ME, Xiang Y, Patterson B, Andersen E, Bravo-Pérez C, Kempf H, Åsrud KS, Lunov O, Dejneka A, Mowinckel MC, Stavik B, Sandset PM, Melum E, Baumgarten S, Bonanini F, Kurek D, Mathapati S, Almaas R, Sharma K, Wilson SR, Skottvoll FS, Boger IC, Bogen IL, Nyman TA, Wu JJ, Bezrouk A, Cizkova D, Corral J, Mokry J, Zweigerdt R, Park IH, Sullivan GJ

Scalable production of tissue-like vascularized liver organoids from human PSCs.

Exp Mol Med 2023 Sep;55(9):2005. Epub 2023 sep 1

PMID: 37653039

Kangas P, Nyman TA, Metsähonkala L, Burns C, Tempest R, Williams T, Karttunen J, Jokinen TS

Towards optimised extracellular vesicle proteomics from cerebrospinal fluid.

Sci Rep 2023 Jun 12;13(1):9564. Epub 2023 jun 12

PMID: 37308520

Krapf SA, Lund J, Bakke HG, Nyman TA, Bartesaghi S, Peng XR, Rustan AC, Thoresen GH, Kase ET

SENP2 knockdown in human adipocytes reduces glucose metabolism and lipid accumulation, while increases lipid oxidation.

Metabol Open 2023 Jun;18():100234. Epub 2023 feb 10

PMID: 37013149

Lunde NN, Osoble NMM, Fernandez AD, Antobreh AS, Jafari A, Singh S, Nyman TA, Rustan AC, Solberg R, Thoresen GH

Interplay between Cultured Human Osteoblastic and Skeletal Muscle Cells: Effects of Conditioned Media on Glucose and Fatty Acid Metabolism.

Biomedicines 2023 Oct 27;11(11). Epub 2023 okt 27

PMID: 38001909

Misceo D, Lirussi L, Strømme P, Sumathipala D, Guerin A, Wolf NI, Server A, Stensland M, Dalhus B, Tolun A, Kroes HY, Nyman TA, Nilsen HL, Frengen E

A homozygous POLR1A variant causes leukodystrophy and affects protein homeostasis.

Brain 2023 Aug 01;146(8):3513.

PMID: 36917474

Ueland T, Äikäs LAO, Dahl TB, Gregersen I, Olsen MB, Michelsen A, Schanke Y, Holopainen M, Ruhanen H, Singh S, , Tveita AA, Finbråten AK, Heggelund L, Trøseid M, Dyrhol-Riise AM, Nyman TA, Holven KB, Öörni K, Aukrust P, Halvorsen B

Low-density lipoprotein particles carrying proinflammatory proteins with altered aggregation pattern detected in COVID-19 patients 3 months after hospitalization.

J Infect 2023 May;86(5):489. Epub 2023 feb 21

PMID: 36822413

Aas V, Øvstebø R, Brusletto BS, Aspelin T, Trøseid AS, Qureshi S, Eid DSO, Olstad OK, Nyman TA, Haug KBF

Distinct microRNA and protein profiles of extracellular vesicles secreted from myotubes from morbidly obese donors with type 2 diabetes in response to electrical pulse stimulation.

Front Physiol 2023;14():1143966. Epub 2023 mar 30

PMID: 37064893

Berge-Seidl S, Nielsen NV, Rodriguez Alfonso AA, Etscheid M, Kandanur SPS, Haug BE, Stensland M, Thiede B, Karacan M, Preising N, Wiese S, Ständker L, Declerck PJ, Løset GÅ, Kanse SM

Identification of a Phage Display-Derived Peptide Interacting with the N-Terminal Region of Factor VII Activating Protease (FSAP) Enables Characterization of Zymogen Activation.

ACS Chem Biol 2022 Sep 16;17(9):2631. Epub 2022 sep 7

PMID: 36070465

Dahlberg D, Rummel J, Distante S, de Souza GA, Stensland ME, Mariussen E, Rootwelt H, Voie Ø, Hassel B

Glioblastoma microenvironment contains multiple hormonal and non-hormonal growth-stimulating factors.

Fluids Barriers CNS 2022 Jun 04;19(1):45. Epub 2022 jun 4

PMID: 35659255

Hautala K, Pursiainen J, Näreaho A, Nyman T, Varmanen P, Sukura A, Nielsen MK, Savijoki K

Label-free quantitative proteomics and immunoblotting identifies immunoreactive and other excretory-secretory (E/S) proteins of

Front Immunol 2022;13():1045468. Epub 2022 nov 16

PMID: 36466892

Høyer H, Busk ØL, Esbensen QY, Røsby O, Hilmarsen HT, Russell MB, Nyman TA, Braathen GJ, Nilsen HL

Clinical characteristics and proteome modifications in two Charcot-Marie-Tooth families with the AARS1 Arg326Trp mutation.

BMC Neurol 2022 Aug 15;22(1):299. Epub 2022 aug 15

PMID: 35971119

Mengeste AM, Nikolic N, Dalmao Fernandez A, Feng YZ, Nyman TA, Kersten S, Haugen F, Kase ET, Aas V, Rustan AC, Thoresen GH

Insight Into the Metabolic Adaptations of Electrically Pulse-Stimulated Human Myotubes Using Global Analysis of the Transcriptome and Proteome.

Front Physiol 2022;13():928195. Epub 2022 jul 6

PMID: 35874526

Salvati A, Melone V, Sellitto A, Rizzo F, Tarallo R, Nyman TA, Giurato G, Nassa G, Weisz A

Combinatorial targeting of a chromatin complex comprising Dot1L, menin and the tyrosine kinase BAZ1B reveals a new therapeutic vulnerability of endocrine therapy-resistant breast cancer.

Breast Cancer Res 2022 Jul 18;24(1):52. Epub 2022 jul 18

PMID: 35850772

Aarsund M, Nyman TA, Stensland ME, Wu Y, Inngjerdingen M

Isolation of a cytolytic subpopulation of extracellular vesicles derived from NK cells containing NKG7 and cytolytic proteins.

Front Immunol 2022;13():977353. Epub 2022 sep 15

PMID: 36189227

Snapkov I, Chernigovskaya M, Sinitcyn P, Lê Quý K, Nyman TA, Greiff V

Progress and challenges in mass spectrometry-based analysis of antibody repertoires.

Trends Biotechnol 2022 Apr;40(4):463. Epub 2021 sep 14

PMID: 34535228

Ng MYW, Charsou C, Lapao A, Singh S, Trachsel-Moncho L, Schultz SW, Nakken S, Munson MJ, Simonsen A

The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics.

Nat Commun 2022 Oct 21;13(1):6283. Epub 2022 okt 21

PMID: 36270994

Katare PB, Dalmao-Fernandez A, Mengeste AM, Hamarsland H, Ellefsen S, Bakke HG, Kase ET, Thoresen GH, Rustan AC

Energy metabolism in skeletal muscle cells from donors with different body mass index.

Front Physiol 2022;13():982842. Epub 2022 nov 17

PMID: 36467688

Kaivola J, Nyman TA, Matikainen S

Inflammasomes and SARS-CoV-2 Infection.

Viruses 2021 12 14;13(12). Epub 2021 des 14

PMID: 34960782

Skagen C, Nyman TA, Peng XR, O'Mahony G, Kase ET, Rustan AC, Thoresen GH

Chronic treatment with terbutaline increases glucose and oleic acid oxidation and protein synthesis in cultured human myotubes.

Curr Res Pharmacol Drug Discov 2021;2():100039. Epub 2021 jun 11

PMID: 34909668

Vestad B, Nyman TA, Hove-Skovsgaard M, Stensland M, Hoel H, Trøseid AS, Aspelin T, Aass HCD, Puhka M, Hov JR, Nielsen SD, Øvstebø R, Trøseid M

Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk.

Sci Rep 2021 11 09;11(1):21936. Epub 2021 nov 9

PMID: 34754007

Mirlashari MR, Vetlesen A, Nissen-Meyer LSH, Stensland ME, Singh SK, Nyman TA, Hetland G

Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients.

Proteomics Clin Appl 2021 Nov;15(6):e2100022. Epub 2021 sep 22

PMID: 34510746

Røberg-Larsen H, Lundanes E, Nyman TA, Berven FS, Wilson SR

Liquid chromatography, a key tool for the advancement of single-cell omics analysis.

Anal Chim Acta 2021 Sep 15;1178():338551. Epub 2021 apr 22

PMID: 34482862

Holm S, Kared H, Michelsen AE, Kong XY, Dahl TB, Schultz NH, Nyman TA, Fladeby C, Seljeflot I, Ueland T, Stensland M, Mjaaland S, Goll GL, Nissen-Meyer LS, Aukrust P, Skagen K, Gregersen I, Skjelland M, Holme PA, Munthe LA, Halvorsen B

Immune complexes, innate immunity, and NETosis in ChAdOx1 vaccine-induced thrombocytopenia.

Eur Heart J 2021 10 14;42(39):4064-4072.

PMID: 34405870

Borowicz P, Sundvold V, Chan H, Abrahamsen G, Kjelstrup H, Nyman TA, Spurkland A

Tyr

J Immunol 2021 08 15;207(4):1128-1137. Epub 2021 jul 28

PMID: 34321230

Reigada I, San-Martin-Galindo P, Gilbert-Girard S, Chiaro J, Cerullo V, Savijoki K, Nyman TA, Fallarero A, Miettinen I

Surfaceome and Exoproteome Dynamics in Dual-Species

Front Microbiol 2021;12():672975. Epub 2021 jun 25

PMID: 34248881

Wanichawan P, Skogestad J, Lunde M, Støle TP, Stensland M, Nyman TA, Sjaastad I, Sejersted OM, Aronsen Jm, Carlson CR

Design of a Proteolytically Stable Sodium-Calcium Exchanger 1 Activator Peptide for

Front Pharmacol 2021;12():638646. Epub 2021 jun 7

PMID: 34163352

Savijoki K, Myllymäki H, Luukinen H, Paulamäki L, Vanha-Aho LM, Svorjova A, Miettinen I, Fallarero A, Ihalainen TO, Yli-Kauhaluoma J, Nyman TA, Parikka M

Surface-Shaving Proteomics of Mycobacterium marinum Identifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance, and Persistence.

mSystems 2021 Jun 29;6(3):e0050021. Epub 2021 jun 22

PMID: 34156290

Quiles-Jiménez A, Gregersen I, Segers FM, Skarpengland T, Kroustallaki P, Yang K, Kong XY, Lauritzen KH, Olsen MB, Karlsen TR, Nyman TA, Sagen EL, Bjerkeli V, Suganthan R, Nygård S, Scheffler K, Prins J, Van der Veer E, Øgaard JD, Fløisand Y, Jørgensen HF, Holven KB, Biessen EA, Nilsen H, Dahl TB, Holm S, Bennett MR, Aukrust P, Bjørås M, Halvorsen B

DNA glycosylase Neil3 regulates vascular smooth muscle cell biology during atherosclerosis development.

Atherosclerosis 2021 05;324():123-132. Epub 2021 feb 23

PMID: 33714552

Stamnaes J, Stray D, Stensland M, Sarna VK, Nyman TA, Lundin KEA, Sollid LM

In Well-Treated Celiac Patients Low-Level Mucosal Inflammation Predicts Response to 14-day Gluten Challenge.

Adv Sci (Weinh) 2021 Feb;8(4):2003526. Epub 2021 jan 4

PMID: 33643806

Ramberg H, Richardsen E, de Souza GA, Rakaee M, Stensland ME, Braadland PR, Nygård S, Ögren O, Guldvik IJ, Berge V, Svindland A, Taskén KA, Andersen S

Proteomic analyses identify major vault protein as a prognostic biomarker for fatal prostate cancer.

Carcinogenesis 2021 05 28;42(5):685-693.

PMID: 33609362

Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A

GAK and PRKCD are positive regulators of PRKN-independent mitophagy.

Nat Commun 2021 10 20;12(1):6101. Epub 2021 okt 20

PMID: 34671015

Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A

Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer.

Mol Cell Proteomics 2020 Feb;19(2):245-260. Epub 2020 des 2

PMID: 33451386

Louwe MC, Olsen MB, Kaasbøll OJ, Yang K, Fosshaug LE, Alfsnes K, Øgaard JDS, Rashidi A, Skulberg VM, Yang M, de Miranda Fonseca D, Sharma A, Aronsen Jm, Schrumpf E, Ahmed MS, Dahl CP, Nyman TA, Ueland T, Melum E, Halvorsen BE, Bjørås M, Attramadal H, Sjaastad I, Aukrust P, Yndestad A

Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction.

JACC Basic Transl Sci 2020 Dec;5(12):1210-1224. Epub 2020 des 9

PMID: 33426377

Gorski K, Spoljaric A, Nyman TA, Kaila K, Battersby BJ, Lehesjoki AE

Quantitative Changes in the Mitochondrial Proteome of Cerebellar Synaptosomes From Preclinical Cystatin B-Deficient Mice.

Front Mol Neurosci 2020;13():570640. Epub 2020 nov 13

PMID: 33281550

Eieland AK, Normann KR, Sundaram AYM, Nyman TA, Øystese KAB, Lekva T, Berg JP, Bollerslev J, Olarescu NC

Distinct Pattern of Endoplasmic Reticulum Protein Processing and Extracellular Matrix Proteins in Functioning and Silent Corticotroph Pituitary Adenomas.

Cancers (Basel) 2020 Oct 14;12(10). Epub 2020 okt 14

PMID: 33066652

Mathiesen SB, Lunde M, Stensland M, Martinsen M, Nyman TA, Christensen G, Carlson CR

The Cardiac Syndecan-2 Interactome.

Front Cell Dev Biol 2020;8():792. Epub 2020 aug 28

PMID: 32984315

Matikainen S, Nyman TA, Cypryk W

Inflammasomes: Exosomal miRNAs loaded for action.

J Cell Biol 2020 Oct 05;219(10).

PMID: 32970793

Gigantino V, Salvati A, Giurato G, Palumbo D, Strianese O, Rizzo F, Tarallo R, Nyman TA, Weisz A, Nassa G

Identification of Antiestrogen-Bound Estrogen Receptor α Interactomes in Hormone-Responsive Human Breast Cancer Cell Nuclei.

Proteomics 2020 10;20(19-20):e2000135. Epub 2020 sep 16

PMID: 32865868

Matikainen S, Nyman TA, Cypryk W

Function and Regulation of Noncanonical Caspase-4/5/11 Inflammasome.

J Immunol 2020 Jun 15;204(12):3063-3069.

PMID: 32513874

Krapf SA, Lund J, Lundkvist M, Dale MG, Nyman TA, Thoresen GH, Kase ET

Pancreatic cancer cells show lower oleic acid oxidation and their conditioned medium inhibits oleic acid oxidation in human myotubes.

Pancreatology 2020 Jun;20(4):676-682. Epub 2020 apr 22

PMID: 32360002

Szibor M, Schreckenberg R, Gizatullina Z, Dufour E, Wiesnet M, Dhandapani PK, Debska-Vielhaber G, Heidler J, Wittig I, Nyman TA, Gärtner U, Hall AR, Pell V, Viscomi C, Krieg T, Murphy MP, Braun T, Gellerich FN, Schlüter KD, Jacobs HT

Respiratory chain signalling is essential for adaptive remodelling following cardiac ischaemia.

J Cell Mol Med 2020 03;24(6):3534-3548. Epub 2020 feb 10

PMID: 32040259

Savijoki K, Miettinen I, Nyman TA, Kortesoja M, Hanski L, Varmanen P, Fallarero A

Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of

Microorganisms 2020 Jan 12;8(1). Epub 2020 jan 12

PMID: 31940921

Lunde NN, Gregersen I, Ueland T, Shetelig C, Holm S, Kong XY, Michelsen AE, Otterdal K, Yndestad A, Broch K, Gullestad L, Nyman TA, Bendz B, Eritsland J, Hoffmann P, Skagen K, Gonçalves I, Nilsson J, Grenegård M, Poreba M, Drag M, Seljeflot I, Sporsheim B, Espevik T, Skjelland M, Johansen HT, Solberg R, Aukrust P, Björkbacka H, Andersen GØ, Halvorsen B

Legumain is upregulated in acute cardiovascular events and associated with improved outcome - potentially related to anti-inflammatory effects on macrophages.

Atherosclerosis 2020 03;296():74-82. Epub 2019 des 14

PMID: 31870625

Alexandrova E, Giurato G, Saggese P, Pecoraro G, Lamberti J, Ravo M, Rizzo F, Rocco D, Tarallo R, Nyman TA, Collina F, Cantile M, Di Bonito M, Botti G, Nassa G, Weisz A

Interaction Proteomics Identifies ERbeta Association with Chromatin Repressive Complexes to Inhibit Cholesterol Biosynthesis and Exert An Oncosuppressive Role in Triple-negative Breast Cancer.

Mol Cell Proteomics 2020 02;19(2):245-260. Epub 2019 des 2

PMID: 31792072

Nilsen J, Trabjerg E, Grevys A, Azevedo C, Brennan SO, Stensland M, Wilson J, Sand KMK, Bern M, Dalhus B, Roopenian DC, Sandlie I, Rand KD, Andersen JT

An intact C-terminal end of albumin is required for its long half-life in humans.

Commun Biol 2020 04 20;3(1):181. Epub 2020 apr 20

PMID: 32313072

Amrutkar M, Larsen EK, Aasrum M, Finstadsveen AV, Andresen PA, Verbeke CS, Gladhaug IP

Establishment and Characterization of Paired Primary Cultures of Human Pancreatic Cancer Cells and Stellate Cells Derived from the Same Tumor.

Cells 2020 01 16;9(1). Epub 2020 jan 16

PMID: 31963309

Mathiesen SB, Lunde M, Aronsen Jm, Romaine A, Kaupang A, Martinsen M, de Souza GA, Nyman TA, Sjaastad I, Christensen G, Carlson CR

The cardiac syndecan-4 interactome reveals a role for syndecan-4 in nuclear translocation of muscle LIM protein (MLP).

J Biol Chem 2019 05 31;294(22):8717-8731. Epub 2019 apr 9

PMID: 30967474

Tomescu-Baciu A, Johansen JN, Holmøy T, Greiff V, Stensland M, de Souza GA, Vartdal F, Lossius A

Persistence of intrathecal oligoclonal B cells and IgG in multiple sclerosis.

J Neuroimmunol 2019 Aug 15;333():576966. Epub 2019 mai 16

PMID: 31153015

Hiltunen AK, Savijoki K, Nyman TA, Miettinen I, Ihalainen P, Peltonen J, Fallarero A

Structural and Functional Dynamics of

Microorganisms 2019 Nov 20;7(12). Epub 2019 nov 20

PMID: 31756969

Nassa G, Giurato G, Salvati A, Gigantino V, Pecoraro G, Lamberti J, Rizzo F, Nyman TA, Tarallo R, Weisz A

The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei.

Sci Data 2019 09 16;6(1):173. Epub 2019 sep 16

PMID: 31527615

Yang K, Lauritzen KH, Olsen MB, Dahl TB, Ranheim T, Ahmed MS, Attramadal H, Aukrust P, Halvorsen B, Nyman TA, Sandanger Ø, Yndestad A

Low Cellular NAD

J Immunol 2019 Sep 15;203(6):1598-1608. Epub 2019 aug 19

PMID: 31427442

Savijoki K, Nyman TA, Kainulainen V, Miettinen I, Siljamäki P, Fallarero A, Sandholm J, Satokari R, Varmanen P

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of

Front Microbiol 2019;10():1272. Epub 2019 jun 5

PMID: 31231350

Nassa G, Salvati A, Tarallo R, Gigantino V, Alexandrova E, Memoli D, Sellitto A, Rizzo F, Malanga D, Mirante T, Morelli E, Nees M, Åkerfelt M, Kangaspeska S, Nyman TA, Milanesi L, Giurato G, Weisz A

Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells.

Sci Adv 2019 02;5(2):eaav5590. Epub 2019 feb 6

PMID: 30775443

Richter U, Ng KY, Suomi F, Marttinen P, Turunen T, Jackson C, Suomalainen A, Vihinen H, Jokitalo E, Nyman TA, Isokallio MA, Stewart JB, Mancini C, Brusco A, Seneca S, Lombès A, Taylor RW, Battersby BJ

Mitochondrial stress response triggered by defects in protein synthesis quality control.

Life Sci Alliance 2019 02;2(1). Epub 2019 jan 25

PMID: 30683687

Lie-Jensen A, Ivanauskiene K, Malerød L, Jain A, Tan KW, Laerdahl JK, Liestøl K, Stenmark H, Haglund K

Centralspindlin Recruits ALIX to the Midbody during Cytokinetic Abscission in Drosophila via a Mechanism Analogous to Virus Budding.

Curr Biol 2019 Oct 21;29(20):3538-3548.e7. Epub 2019 okt 10

PMID: 31607533

Sneeggen M, Pedersen NM, Campsteijn C, Haugsten EM, Stenmark H, Schink KO

WDFY2 restrains matrix metalloproteinase secretion and cell invasion by controlling VAMP3-dependent recycling.

Nat Commun 2019 06 28;10(1):2850. Epub 2019 jun 28

PMID: 31253801

Nguéa P A, Robertson J, Herrera MC, Chymkowitch P, Enserink JM

Desumoylation of RNA polymerase III lies at the core of the Sumo stress response in yeast.

J Biol Chem 2019 Dec 06;294(49):18784-18795. Epub 2019 nov 1

PMID: 31676685

Sikorski K, Mehta A, Inngjerdingen M, Thakor F, Kling S, Kalina T, Nyman TA, Stensland ME, Zhou W, de Souza GA, Holden L, Stuchly J, Templin M, Lund-Johansen F

A high-throughput pipeline for validation of antibodies.

Nat Methods 2018 Nov;15(11):909-912. Epub 2018 okt 30

PMID: 30377371

Cypryk W, Nyman TA, Matikainen S

From Inflammasome to Exosome-Does Extracellular Vesicle Secretion Constitute an Inflammasome-Dependent Immune Response?

Front Immunol 2018;9():2188. Epub 2018 sep 25

PMID: 30319640

Giurato G, Nassa G, Salvati A, Alexandrova E, Rizzo F, Nyman TA, Weisz A, Tarallo R

Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells.

Sci Data 2018 03 06;5():180031. Epub 2018 mar 6

PMID: 29509190

Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains.

Microb Biotechnol 2018 05;11(3):510-526. Epub 2018 feb 28

PMID: 29488359

Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Sci Rep 2018 01 11;8(1):498. Epub 2018 jan 11

PMID: 29323256

Nyman TA, Matikainen S

Proteomics to study macrophage response to viral infection.

J Proteomics 2018 May 30;180():99-107. Epub 2017 jun 21

PMID: 28647517

Hassel B, de Souza GA, Stensland ME, Ivanovic J, Voie Ø, Dahlberg D

The proteome of pus from human brain abscesses: host-derived neurotoxic proteins and the cell-type diversity of CNS pus.

J Neurosurg 2018 Sep;129(3):829-837. Epub 2017 okt 20

PMID: 29053067

Kostas M, Haugsten EM, Zhen Y, Sørensen V, Szybowska P, Fiorito E, Lorenz S, Jones N, de Souza GA, Wiedlocha A, Wesche J

Protein Tyrosine Phosphatase Receptor Type G (PTPRG) Controls Fibroblast Growth Factor Receptor (FGFR) 1 Activity and Influences Sensitivity to FGFR Kinase Inhibitors.

Mol Cell Proteomics 2018 May;17(5):850-870. Epub 2018 jan 25

PMID: 29371290

Gravina F, Sanchuki HS, Rodrigues TE, Gerhardt ECM, Pedrosa FO, Souza EM, Valdameri G, de Souza GA, Huergo LF

Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes.

J Proteomics 2018 Mar 01;174():28-35. Epub 2017 des 21

PMID: 29274402

Tutturen AEV, Dørum S, Clancy T, Reims HM, Christophersen A, Lundin KEA, Sollid LM, de Souza GA, Stamnaes J

Characterization of the Small Intestinal Lesion in Celiac Disease by Label-Free Quantitative Mass Spectrometry.

Am J Pathol 2018 Jul;188(7):1563-1579. Epub 2018 apr 22

PMID: 29684362

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E

The SysteMHC Atlas project.

Nucleic Acids Res 2018 Jan 04;46(D1):D1237-D1247.

PMID: 28985418

Iversen R, Snir O, Stensland M, Kroll JE, Steinsbø Ø, Korponay-Szabó IR, Lundin KEA, de Souza GA, Sollid LM

Strong Clonal Relatedness between Serum and Gut IgA despite Different Plasma Cell Origins.

Cell Rep 2017 Sep 05;20(10):2357-2367.

PMID: 28877470

Lubelwana Hafver T, Wanichawan P, Manfra O, de Souza GA, Lunde M, Martinsen M, Louch WE, Sejersted OM, Carlson CR

Mapping the in vitro interactome of cardiac sodium (Na+ )-calcium (Ca2+ ) exchanger 1 (NCX1).

Proteomics 2017 Sep;17(17-18).

PMID: 28755400

Kroll JE, da Silva VL, de Souza SJ, de Souza GA

A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer: PV: A genome browser-like tool, which includes MS data visualization and peptide identification parameters.

Bioessays 2017 Jul;39(7). Epub 2017 jun 5

PMID: 28582591

Sanchuki HB, Gravina F, Rodrigues TE, Gerhardt EC, Pedrosa FO, Souza EM, Raittz RT, Valdameri G, de Souza GA, Huergo LF

Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase.

Biochim Biophys Acta 2017 03;1865(3):344-352. Epub 2016 des 8

PMID: 27939605

Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

Genome Biol 2017 Oct 06;18(1):189. Epub 2017 okt 6

PMID: 29017520

Bulanova D, Ianevski A, Bugai A, Akimov Y, Kuivanen S, Paavilainen H, Kakkola L, Nandania J, Turunen L, Ohman T, Ala-Hongisto H, Pesonen HM, Kuisma MS, Honkimaa A, Walton EL, Oksenych V, Lorey MB, Guschin D, Shim J, Kim J, Than TT, Chang SY, Hukkanen V, Kulesskiy E, Marjomaki VS, Julkunen I, Nyman TA, Matikainen S, Saarela JS, Sane F, Hober D, Gabriel G, De Brabander JK, Martikainen M, Windisch MP, Min JY, Bruzzone R, Aittokallio T, Vähä-Koskela M, Vapalahti O, Pulk A, Velagapudi V, Kainov DE

Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins.

Viruses 2017 Sep 25;9(10). Epub 2017 sep 25

PMID: 28946654

Aittomäki S, Valanne S, Lehtinen T, Matikainen S, Nyman TA, Rämet M, Pesu M

Proprotein convertase Furin1 expression in the Drosophila fat body is essential for a normal antimicrobial peptide response and bacterial host defense.

FASEB J 2017 Nov;31(11):4770-4782. Epub 2017 jul 13

PMID: 28705811

Dumont V, Tolvanen TA, Kuusela S, Wang H, Nyman TA, Lindfors S, Tienari J, Nisen H, Suetsugu S, Plomann M, Kawachi H, Lehtonen S

PACSIN2 accelerates nephrin trafficking and is up-regulated in diabetic kidney disease.

FASEB J 2017 Sep;31(9):3978-3990. Epub 2017 mai 26

PMID: 28550045

Nyman TA, Lorey MB, Cypryk W, Matikainen S

Mass spectrometry-based proteomic exploration of the human immune system: focus on the inflammasome, global protein secretion, and T cells.

Expert Rev Proteomics 2017 May;14(5):395-407. Epub 2017 apr 24

PMID: 28406322

Deptula P, Chamlagain B, Edelmann M, Sangsuwan P, Nyman TA, Savijoki K, Piironen V, Varmanen P

Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation.

Front Microbiol 2017;8():368. Epub 2017 mar 8

PMID: 28337185

Lorey MB, Rossi K, Eklund KK, Nyman TA, Matikainen S

Global Characterization of Protein Secretion from Human Macrophages Following Non-canonical Caspase-4/5 Inflammasome Activation.

Mol Cell Proteomics 2017 Apr;16(4 suppl 1):S187-S199. Epub 2017 feb 14

PMID: 28196878

Wasik AA, Dumont V, Tienari J, Nyman TA, Fogarty CL, Forsblom C, Lehto M, Lehtonen E, Groop PH, Lehtonen S

Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion.

Exp Cell Res 2017 Jan 15;350(2):336-348. Epub 2016 des 20

PMID: 28011197

Gaelings L, Söderholm S, Bugai A, Fu Y, Nandania J, Schepens B, Lorey MB, Tynell J, Vande Ginste L, Le Goffic R, Miller MS, Kuisma M, Marjomäki V, De Brabander J, Matikainen S, Nyman TA, Bamford DH, Saelens X, Julkunen I, Paavilainen H, Hukkanen V, Velagapudi V, Kainov DE

Regulation of kynurenine biosynthesis during influenza virus infection.

FEBS J 2017 01;284(2):222-236. Epub 2016 des 14

PMID: 27860276

Cypryk W, Lorey M, Puustinen A, Nyman TA, Matikainen S

Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection.

J Proteome Res 2017 Jan 06;16(1):217-227. Epub 2016 nov 15

PMID: 27723984

Bober J, Olsnes S, Kostas M, Bogacz M, Zakrzewska M, Otlewski J

Identification of new FGF1 binding partners-Implications for its intracellular function.

IUBMB Life 2016 Mar;68(3):242-51. Epub 2016 feb 2

PMID: 26840910

Haugsten EM, Sørensen V, Kunova Bosakova M, de Souza GA, Krejci P, Wiedlocha A, Wesche J

Proximity Labeling Reveals Molecular Determinants of FGFR4 Endosomal Transport.

J Proteome Res 2016 Oct 07;15(10):3841-3855. Epub 2016 sep 26

PMID: 27615514

Lund-Johansen F, de la Rosa Carrillo D, Mehta A, Sikorski K, Inngjerdingen M, Kalina T, Røysland K, de Souza GA, Bradbury AR, Lecrevisse Q, Stuchly J

MetaMass, a tool for meta-analysis of subcellular proteomics data.

Nat Methods 2016 Oct;13(10):837-40. Epub 2016 aug 29

PMID: 27571551

Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM

Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes.

Sci Rep 2016 May 05;6():25565. Epub 2016 mai 5

PMID: 27146306

Riaz T, Sollid LM, Olsen I, de Souza GA

Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells.

Mol Cell Proteomics 2016 Mar;15(3):1007-16. Epub 2015 des 4

PMID: 26637539

Kalayou S, Granum C, Berntsen HF, Groseth PK, Verhaegen S, Connolly L, Brandt I, de Souza GA, Ropstad E

Label-free based quantitative proteomics analysis of primary neonatal porcine Leydig cells exposed to the persistent contaminant 3-methylsulfonyl-DDE.

J Proteomics 2016 Mar 30;137():68-82. Epub 2015 des 9

PMID: 26691841

Paiva AL, Oliveira JT, de Souza GA, Vasconcelos IM

Label-free Proteomic Reveals that Cowpea Severe Mosaic Virus Transiently Suppresses the Host Leaf Protein Accumulation During the Compatible Interaction with Cowpea (Vigna unguiculata [L.] Walp.).

J Proteome Res 2016 Dec 02;15(12):4208-4220. Epub 2016 nov 16

PMID: 27934294

Vasilevska J, de Souza GA, Stensland M, Skrastina D, Zhulenvovs D, Paplausks R, Kurena B, Kozlovska T, Zajakina A

Comparative protein profiling of B16 mouse melanoma cells susceptible and non-susceptible to alphavirus infection: Effect of the tumor microenvironment.

Cancer Biol Ther 2016 Aug 11. Epub 2016 aug 11

PMID: 27636533

Karlsen TA, de Souza GA, Ødegaard B, Engebretsen L, Brinchmann JE

microRNA-140 Inhibits Inflammation and Stimulates Chondrogenesis in a Model of Interleukin 1ß-induced Osteoarthritis.

Mol Ther Nucleic Acids 2016 Oct 11;5(10):e373. Epub 2016 okt 11

PMID: 27727249

Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA

Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages.

Mol Cell Proteomics 2016 Oct;15(10):3203-3219. Epub 2016 aug 2

PMID: 27486199

Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE

Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction.

Viruses 2016 Sep 29;8(10). Epub 2016 sep 29

PMID: 27690086

Tveita AA, Schjesvold F, Haabeth OA, Fauskanger M, Bogen B

Tumors Escape CD4+ T-cell-Mediated Immunosurveillance by Impairing the Ability of Infiltrating Macrophages to Indirectly Present Tumor Antigens.

Cancer Res 2015 Aug 15;75(16):3268-78. Epub 2015 jun 2

PMID: 26038231

Bergseng E, Dørum S, Arntzen MØ, Nielsen M, Nygård S, Buus S, de Souza GA, Sollid LM

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires.

Immunogenetics 2015 Feb;67(2):73-84. Epub 2014 des 12

PMID: 25502872

Johansen JN, Vartdal F, Desmarais C, Tutturen AE, de Souza GA, Lossius A, Holmøy T

Intrathecal BCR transcriptome in multiple sclerosis versus other neuroinflammation: Equally diverse and compartmentalized, but more mutated, biased and overlapping with the proteome.

Clin Immunol 2015 Oct;160(2):211-25. Epub 2015 jun 6

PMID: 26055752

Rogeberg M, Wettergreen M, Nilsson LN, Fladby T

Identification of amyloid beta mid-domain fragments in human cerebrospinal fluid.

Biochimie 2015 Jun;113():86-92. Epub 2015 apr 10

PMID: 25866191

Øverbye A, Skotland T, Koehler CJ, Thiede B, Seierstad T, Berge V, Sandvig K, Llorente A

Identification of prostate cancer biomarkers in urinary exosomes.

Oncotarget 2015 Oct 6;6(30):30357-76.

PMID: 26196085

Fortuin S, Tomazella GG, Nagaraj N, Sampson SL, Gey van Pittius NC, Soares NC, Wiker HG, de Souza GA, Warren RM

Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: expanding the mycobacterial phosphoproteome catalog.

Front Microbiol 2015;6():6. Epub 2015 feb 10

PMID: 25713560

Camassa LM, Lunde LK, Hoddevik EH, Stensland M, Boldt HB, de Souza GA, Ottersen OP, Amiry-Moghaddam M

Mechanisms underlying AQP4 accumulation in astrocyte endfeet.

Glia 2015 Jun 29. Epub 2015 jun 29

PMID: 26119521

Stamnaes J, Iversen R, du Pré MF, Chen X, Sollid LM

Enhanced B-Cell Receptor Recognition of the Autoantigen Transglutaminase 2 by Efficient Catalytic Self-Multimerization.

PLoS One 2015;10(8):e0134922. Epub 2015 aug 5

PMID: 26244572

Steinsbø Ø, Dørum S, Lundin KE, Sollid LM

Serologic Assay for Diagnosis of Celiac Disease Based on a Patient-Derived Monoclonal Antigliadin Antibody.

Gastroenterology 2015 Nov;149(6):1530-1540.e3. Epub 2015 jul 21

PMID: 26208894

Cypryk W, Lorey M, Puustinen A, Nyman TA, Matikainen S

Proteomic and Bioinformatic Characterization of EVs Released from Human Macrophages upon Influenza A Virus Infection

J Proteome Res. 2016 Oct 11. [Epub ahead of print]

Deltagere
  • Jorunn Stamnæs Prosjektdeltaker
  • Joseph Robertson Prosjektdeltaker
  • Maria Stensland Prosjektdeltaker
  • Tuula Anneli Nyman Prosjektleder
  • Sachin Kumar Singh Prosjektdeltaker
  • Gustavo Antonio De Souza Prosjektleder

eRapport er utarbeidet av Sølvi Lerfald og Reidar Thorstensen, Regionalt kompetansesenter for klinisk forskning, Helse Vest RHF, og videreutvikles av de fire RHF-ene i fellesskap, med støtte fra Helse Vest IKT

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