SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "WFRF:(Orre Lukas M.) "

Sökning: WFRF:(Orre Lukas M.)

  • Resultat 1-10 av 13
  • [1]2Nästa
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Branca, Rui M. M., et al. (författare)
  • HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics
  • 2014
  • Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:1, s. 59-
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>We present a liquid chromatography-mass spectrometry (LC-MSMS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.</p>
  •  
2.
  • Johansson, Henrik J., et al. (författare)
  • Breast cancer quantitative proteome and proteogenomic landscape
  • 2019
  • Ingår i: Nature Communications. - NATURE PUBLISHING GROUP. - 2041-1723 .- 2041-1723. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.</p>
  •  
3.
  • Johansson, Henrik J., et al. (författare)
  • Breast cancer quantitative proteome and proteogenomic landscape
  • 2019
  • Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.</p>
  •  
4.
  • Johansson, Henrik J., et al. (författare)
  • Breast cancer quantitative proteome and proteogenomic landscape
  • 2019
  • Ingår i: Nature Communications. - NATURE PUBLISHING GROUP. - 2041-1723 .- 2041-1723. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.</p>
5.
  •  
6.
  • Zhu, Yafeng, et al. (författare)
  • Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
  • 2018
  • Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3-10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.</p>
  •  
7.
  • Eriksson, Hanna, et al. (författare)
  • Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms
  • 2008
  • Ingår i: Proteomics. - 1615-9853 .- 1615-9861. ; 8:15, s. 3008-3018
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Drug resistance is often associated with upregulation of membrane-associated drug-efflux systems, and thus global membrane proteomics methods are valuable tools in the search for novel components of drug resistance phenotypes. Herein we have compared the microsomal proteome from the lung cancer cell line H69 and its isogenic Doxorubicin-resistant subcell line H69AR. The method used includes microsome preparation, iTRAQ labeling followed by narrow range peptide IEF in an immobilized pH-gradient (IPG-IEF) and LC-MS/MS analysis. We demonstrate that the microsomal preparation and iTRAQ labeling is reproducible regarding protein content and composition. The rationale using narrow range peptide IPG-IEF separation is demonstrated by its ability to: (i) lowering the complexity of the sample by two-thirds while keeping high proteome coverage (96%), (ii) providing high separation efficiency, and (iii) allowing for peptide validation and possibly identifications of post-transcriptional modifications. After analyzing one-fifth of the IEF fractions (effective pH range of 4.0-4.5), a total of 3704 proteins were identified, among which 527 were predicted to be membrane proteins. One of the proteins found to be differentially expressed was Serca 2, a calcium pump located in the ER membrane that potentially could result in changes of apoptotic response toward Doxorubicin.</p>
  •  
8.
  • Fotouhi, Omid, et al. (författare)
  • Proteomics identifies neddylation as a potential therapy target in small intestinal neuroendocrine tumors
  • 2019
  • Ingår i: Oncogene. - NATURE PUBLISHING GROUP. - 0950-9232 .- 1476-5594. ; 38:43, s. 6881-6897
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Patients with small intestinal neuroendocrine tumors (SI-NETs) frequently develop spread disease; however, the underlying molecular mechanisms of disease progression are not known and effective preventive treatment strategies are lacking. Here, protein expression profiling was performed by HiRIEF-LC-MS in 14 primary SI-NETs from patients with and without liver metastases detected at the time of surgery and initial treatment. Among differentially expressed proteins, overexpression of the ubiquitin-like protein NEDD8 was identified in samples from patients with liver metastasis. Further, NEDD8 correlation analysis indicated co-expression with RBX1, a key component in cullin-RING ubiquitin ligases (CRLs). In vitro inhibition of neddylation with the therapeutic agent pevonedistat (MLN4924) resulted in a dramatic decrease of proliferation in SI-NET cell lines. Subsequent mass spectrometry-based proteomics analysis of pevonedistat effects and effects of the proteasome inhibitor bortezomib revealed stabilization of multiple targets of CRLs including p27, an established tumor suppressor in SI-NET. Silencing of NEDD8 and RBX1 using siRNA resulted in a stabilization of p27, suggesting that the cellular levels of NEDD8 and RBX1 affect CRL activity. Inhibition of CRL activity, by either NEDD8/RBX1 silencing or pevonedistat treatment of cells resulted in induction of apoptosis that could be partially rescued by siRNA-based silencing of p27. Differential expression of both p27 and NEDD8 was confirmed in a second cohort of SI-NET using immunohistochemistry. Collectively, these findings suggest a role for CRLs and the ubiquitin proteasome system in suppression of p27 in SI-NET, and inhibition of neddylation as a putative therapeutic strategy in SI-NET.</p>
9.
  • Fotouhi, Omid, et al. (författare)
  • Proteomics identifies neddylation as a potential therapy target in small intestinal neuroendocrine tumors
  • 2019
  • Ingår i: Oncogene. - NATURE PUBLISHING GROUP. - 0950-9232 .- 1476-5594. ; 38:43, s. 6881-6897
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Patients with small intestinal neuroendocrine tumors (SI-NETs) frequently develop spread disease; however, the underlying molecular mechanisms of disease progression are not known and effective preventive treatment strategies are lacking. Here, protein expression profiling was performed by HiRIEF-LC-MS in 14 primary SI-NETs from patients with and without liver metastases detected at the time of surgery and initial treatment. Among differentially expressed proteins, overexpression of the ubiquitin-like protein NEDD8 was identified in samples from patients with liver metastasis. Further, NEDD8 correlation analysis indicated co-expression with RBX1, a key component in cullin-RING ubiquitin ligases (CRLs). In vitro inhibition of neddylation with the therapeutic agent pevonedistat (MLN4924) resulted in a dramatic decrease of proliferation in SI-NET cell lines. Subsequent mass spectrometry-based proteomics analysis of pevonedistat effects and effects of the proteasome inhibitor bortezomib revealed stabilization of multiple targets of CRLs including p27, an established tumor suppressor in SI-NET. Silencing of NEDD8 and RBX1 using siRNA resulted in a stabilization of p27, suggesting that the cellular levels of NEDD8 and RBX1 affect CRL activity. Inhibition of CRL activity, by either NEDD8/RBX1 silencing or pevonedistat treatment of cells resulted in induction of apoptosis that could be partially rescued by siRNA-based silencing of p27. Differential expression of both p27 and NEDD8 was confirmed in a second cohort of SI-NET using immunohistochemistry. Collectively, these findings suggest a role for CRLs and the ubiquitin proteasome system in suppression of p27 in SI-NET, and inhibition of neddylation as a putative therapeutic strategy in SI-NET.</p>
10.
  • Orre, Lukas M., et al. (författare)
  • FUNCTIONAL STUDIES OF S100A6 USING PROTEOMICS
  • 2008
  • Ingår i: Anticancer Research. - INT INST ANTICANCER RESEARCH. - 0250-7005 .- 1791-7530. ; 28:5C, s. 3430-3431
  • Tidskriftsartikel (övrigt vetenskapligt)
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-10 av 13
  • [1]2Nästa
Åtkomst
fritt online (3)
Typ av publikation
tidskriftsartikel (13)
Typ av innehåll
refereegranskat (11)
övrigt vetenskapligt (2)
Författare/redaktör
Orre, Lukas M. (12)
Vesterlund, Mattias (6)
Lehtio, Janne (6)
Huss, Mikael (5)
Johansson, Henrik J. ... (5)
Lehtiö, Janne, (4)
visa fler...
Boekel, Jorrit (4)
Fernandez-Woodbridge ... (4)
Zhu, Yafeng, (4)
Brismar, Hjalmar, (3)
Zhao, Wei, (3)
Sennblad, Bengt, (3)
Bathen, Tone F (3)
Fredlund, Erik, (3)
Hofvind, Solveig (3)
Mills, Gordon B (3)
Maelandsmo, Gunhild ... (3)
Haugen, Mads H. (3)
Nord, Silje (3)
Kristensen, Vessela ... (3)
Sahlberg, Kristine K ... (3)
Schlichting, Ellen, (3)
Branca, Rui M., (3)
Socciarelli, Fabio, (3)
Vacanti, Nathaniel M ... (3)
Siavelis, Ioannis, (3)
Aure, Miriam R., (3)
Beraki, Elsa, (3)
Larsson, Catharina (2)
Zedenius, Jan (2)
Caramuta, Stefano (2)
Lengqvist, Johan, (2)
Borresen-Dale, Anne- ... (2)
Kharaziha, Pedram, (2)
Lewensohn, Rolf (2)
Granholm, Viktor, (2)
Ghaderi, Mehran (2)
Sorlie, Therese (2)
Branca, Rui M. M. (2)
Juhlin, C Christofer (2)
Karesen, Rolf, (2)
Engebraten, Olav, (2)
Naume, Bjorn, (2)
Geisler, Juergen, (2)
Kjellman, Magnus, (2)
Fotouhi, Omid (2)
Kjellin, Hanna, (2)
Pan, Yanbo, (2)
Yousef, Abdelhamid, (2)
Andersson-Sand, Hill ... (2)
visa färre...
Lärosäte
Kungliga Tekniska Högskolan (4)
Uppsala universitet (3)
Stockholms universitet (3)
Linköpings universitet (2)
Umeå universitet (1)
Språk
Engelska (13)
Forskningsämne (UKÄ/SCB)
Medicin och hälsovetenskap (11)
Naturvetenskap (2)

År

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy