Proteogenomics

Mechanism of membrane-tethered mitochondrial protein synthesis

Itoh Y, Andréll J, Choi A, ..., Battersby BJ, Amunts A

Science 371 (6531) 846-849 [2021-02-19; online 2021-02-18]

ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.

Mühleip A, Kock Flygaard R, Ovciarikova J, ..., Sheiner L, Amunts A

pii: 10.1038/s41467-020-20381-z

Nat Commun 12 (1) 120 [2021-01-05; online 2021-01-05]

Year 2020

Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses.

Tampere M, Pettke A, Salata C, ..., Jafari R, Puumalainen MR

pii: v12121423 pmc: PMC7762994

Viruses 12 (12) - [2020-12-10; online 2020-12-10]

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi

Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A

Nat Commun 11 (1) 5187 [2020-12-00; online 2020-10-14]

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard RK, Mühleip A, Tobiasson V, Amunts A

pii: 10.1038/s41467-020-18993-6

Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity.

Lytrivi M, Ghaddar K, Lopes M, ..., Eizirik DL, Cnop M

pii: 10.1186/s12864-020-07003-0 pmc: PMC7448506

BMC Genomics 21 (1) 590 [2020-08-26; online 2020-08-26]

Structural basis of mitochondrial translation

Aibara S, Singh V, Modelska A, Amunts A

Elife 9 (-) 1-17 [2020-08-19; online 2020-08-19]

Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.

Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J

pii: 10.1038/s41591-020-0969-2

Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Collaborative] Proteogenomics [Technology development]

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation

Tobiasson V, Amunts A

Elife 9 (-) 1-15 [2020-06-18; online 2020-06-18]

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.

Zhu Y, Orre LM, Zhou Tran Y, ..., Anders S, Lehtiö J

pii: TIR119.001646 pmc: PMC7261819

Mol. Cell Proteomics 19 (6) 1047-1057 [2020-06-00; online 2020-03-23]

Proteogenomics [Technology development]

Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics.

Herr P, Boström J, Rullman E, ..., Maddalo G, Altun M

pii: RA120.001938 pmc: PMC7124475

Mol. Cell Proteomics 19 (4) 608-623 [2020-04-00; online 2020-02-12]

Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly

Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A

NPLANTS 6 (3) 314-320 [2020-03-09; online 2020-03-09]

PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.

Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L

Circ. Res. 126 (5) 571-585 [2020-01-02; online 2020-01-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.

Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S

pii: RA119.001737

Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]

Year 2019

A Mitochondrial LYR Protein Is Required for Complex I Assembly.

Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW

pii: pp.19.00822 pmc: PMC6878026

Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K

Nat Commun 10 (1) - [2019-12-00; online 2019-04-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Proteogenomics [Technology development]

Breast cancer quantitative proteome and proteogenomic landscape

Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]

Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.

Ross JM, Coppotelli G, Branca RM, ..., Sinclair DA, Olson L

pmc: PMC6826127

Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells

Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M

Front Immunol 10 (-) - [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cell Profiling [Collaborative] Proteogenomics [Technology development]

MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.

Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M

pii: S2589-0042(19)30399-2 pmc: PMC6889365

iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]

Structure of a mitochondrial ATP synthase with bound native cardiolipin

Mühleip A, McComas SE, Amunts A

Elife 8 (-) - [2019-11-18; online 2019-11-18]

Myc-dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF receptor-2

Testini C, Smith RO, Jin Y, ..., Hellström M, Claesson‐Welsh L

EMBO rep 20 (11) - [2019-11-05; online 2019-09-23]

Considerations and Implications in the Purification of Extracellular Vesicles – A Cautionary Tale

Lee YXF, Johansson H, Wood MJA, El Andaloussi S

Front. Neurosci. 13 (-) - [2019-10-18; online 2019-10-18]

Bioinformatics Compute and Storage [Service] Proteogenomics [Service]

Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats

Heinrich K, Leslie DJ, Morlock M, Bertilsson S, Jonas K

MBio 10 (4) - [2019-08-20; online 2019-08-20]

Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival

Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A

The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM

pii: 10.1038/s41598-019-43552-5 pmc: PMC6554399

Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]

Autoimmunity and Serology Profiling [Technology development] Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development] Translational Plasma Profiling [Technology development]

The viral protein corona directs viral pathogenesis and amyloid aggregation.

Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S

pii: 10.1038/s41467-019-10192-2 pmc: PMC6536551

Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]

Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Ultrasensitive immunoprofiling of plasma extracellular vesicles identifies syndecan-1 as a potential tool for minimally invasive diagnosis of glioma.

Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M

pii: 1078-0432.CCR-18-2946

Clin. Cancer Res. - (-) - [2019-01-24; online 2019-01-24]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development] Targeted and Structural Proteomics [Service]

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J

Molecular Cell 73 (1) 166-182.e7 [2019-01-00; online 2019-01-00]

Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Year 2018

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J

EBI: PXD006291 EBI: E-MTAB-5285 EBI: E-MTAB-2836

Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J

BMC Biol. 16 (1) - [2018-12-00; online 2018-05-07]

Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin

Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A

jPOSTrepo: JPST000288

Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Proteogenomics [Collaborative]

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome

Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S

BioProject: PRJNA408072 SRA: SRP118970

Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]

Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens

Srinivas V, Lebrette H, Lundin D, ..., Sjöberg BM, Högbom M

Nature 563 (7731) 416-420 [2018-11-00; online 2018-10-31]

Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.

Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL

pii: 10.1038/s41598-018-33960-4 pmc: PMC6203749

Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]

Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment

Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R

Cell Death Dis 9 (9) - [2018-09-00; online 2018-08-28]

Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.

Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U

pii: S2452-302X(18)30096-2 pmc: PMC6115646

JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative] Translational Plasma Profiling [Collaborative]

A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

Wei B, Jolma A, Sahu B, ..., Taipale M, Taipale J

Nat Biotechnol 36 (6) 521-529 [2018-05-21; online 2018-05-21]

MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling

Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M

Proc Natl Acad Sci USA 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]

A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts

Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF

Molecular Plant 11 (2) 342-345 [2018-02-00; online 2018-02-00]

Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome

Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG

PLoS Pathog. 14 (1) e1006852 [2018-01-22; online 2018-01-22]

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

Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R

pii: 10.1038/s41598-017-18985-5 pmc: PMC5765118

Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]

Year 2017

An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus

Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K

PLoS Genet. 13 (12) e1007148 [2017-12-27; online 2017-12-27]

Mechanism of peptide binding and cleavage by the human mitochondrial peptidase neurolysin.

Teixeira PF, Masuyer G, Pinho CM, ..., Stenmark P, Glaser E

pii: S0022-2836(17)30561-2

J. Mol. Biol. - (-) - [2017-11-25; online 2017-11-25]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Normalization of mass spectrometry data (NOMAD).

Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O

pii: S2212-4926(17)30174-4

Adv Biol Regul - (-) - [2017-11-20; online 2017-11-20]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.

Egaña I, Kaito H, Nitzsche A, ..., Hellström M, German Mouse Clinic Consortium

pii: 10.1038/s41598-017-14894-9 pmc: PMC5684320

Sci Rep 7 (1) 15453 [2017-11-13; online 2017-11-13]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Collaborative]

Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia

Moisseiev E, Anderson JD, Oltjen S, ..., Nolta JA, Park SS

Current Eye Research 42 (10) 1358-1367 [2017-10-03; online 2017-06-21]

Molecular profiles of oxyphilic and chief cell parathyroid adenoma.

Lu M, Kjellin H, Fotouhi O, ..., Lehtiö J, Larsson C

pii: S0303-7207(17)30521-X

Mol. Cell. Endocrinol. - (-) - [2017-10-03; online 2017-10-03]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization.

Zhao M, Spiess M, Johansson HJ, ..., Lehtiö J, Strömblad S

pii: 20352 pmc: PMC5652764

Oncotarget 8 (44) 77061-77074 [2017-09-29; online 2017-08-18]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells.

Reithmeier A, Panizza E, Krumpel M, ..., Ek-Rylander B, Andersson G

pii: 10.1186/s12885-017-3616-7 pmc: PMC5602878

BMC Cancer 17 (1) 650 [2017-09-15; online 2017-09-15]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.

Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S

pii: cddis2017406 pmc: PMC5596587 ProteomXchange: PXD001682

Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]

Clinical Proteomics Mass spectrometry [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Proteogenomics [Service]

Tuning Metabolome Coverage in Reversed Phase LC–MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition

Lindahl A, Sääf S, Lehtiö J, Nordström A

Anal. Chem. 89 (14) 7356-7364 [2017-07-18; online 2017-06-28]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Technology development]

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J

pii: 10.1038/s41598-017-04798-z pmc: PMC5495806

Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service]

Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.

Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M

pii: nmicrobiol201768

Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]

Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics

Lindahl A, Heuchel R, Forshed J, ..., Löhr M, Nordström A

Metabolomics 13 (5) - [2017-05-00; online 2017-04-01]

Clinical Proteomics Mass spectrometry [Service] Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J

pii: gkx006 pmc: PMC5389616 ENA: PRJEB13283 ArrayExpress: E-MTAB-4589 PRIDE: PXD003773

Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative] Proteogenomics [Technology development]

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts

Teixeira PF, Kmiec B, Branca RMM, ..., Lehtiö J, Glaser E

Nat Chem Biol 13 (1) 15-17 [2017-01-00; online 2016-10-31]

Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Year 2016

Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.

Maleki S, Kjellqvist S, Paloschi V, ..., Eriksson P, Björck HM

pii: srep35712 pmc: PMC5078843

Sci Rep 6 (-) 35712 [2016-10-25; online 2016-10-25]

Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative]

Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.

Perisic Matic L, Rykaczewska U, Razuvaev A, ..., Hamsten A, Hedin U

pii: ATVBAHA.116.307893

Arterioscler. Thromb. Vasc. Biol. 36 (9) 1947-1961 [2016-09-00; online 2016-07-28]

Clinical Proteomics Mass spectrometry [Collaborative] Proteogenomics [Collaborative]