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  • 1. Butler, L. M.
    et al.
    Hallström, Björn Mikael
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pontén, F.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Renné, T.
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome2016In: Cell Systems, ISSN 2405-4712, Vol. 3, no 3, p. 287-301.e3Article in journal (Refereed)
    Abstract [en]

    Endothelial cells line blood vessels and regulate hemostasis, inflammation, and blood pressure. Proteins critical for these specialized functions tend to be predominantly expressed in endothelial cells across vascular beds. Here, we present a systems approach to identify a panel of human endothelial-enriched genes using global, body-wide transcriptomics data from 124 tissue samples from 32 organs. We identified known and unknown endothelial-enriched gene transcripts and used antibody-based profiling to confirm expression across vascular beds. The majority of identified transcripts could be detected in cultured endothelial cells from various vascular beds, and we observed maintenance of relative expression in early passage cells. In summary, we describe a widely applicable method to determine cell-type-specific transcriptome profiles in a whole-organism context, based on differential abundance across tissues. We identify potential vascular drug targets or endothelial biomarkers and highlight candidates for functional studies to increase understanding of the endothelium in health and disease.

  • 2. Carreras-Puigvert, J.
    et al.
    Zitnik, M.
    Jemth, A. -S
    Carter, M.
    Unterlass, J. E.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Loseva, O.
    Karem, Z.
    Calderón-Montanõ, J. M.
    Lindskog, C.
    Edqvist, P. -H
    Matuszewski, D. J.
    Ait Blal, Hammou
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berntsson, R. P. A.
    Häggblad, M.
    Martens, U.
    Studham, M.
    Lundgren, B.
    Wählby, C.
    Sonnhammer, E. L. L.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stenmark, P.
    Zupan, B.
    Helleday, T.
    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 1541Article in journal (Refereed)
    Abstract [en]

    The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.

  • 3. Djureinovic, Dijana
    et al.
    Hallström, Björn M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Horie, Masafumi
    Mattsson, Johanna Sofia Margareta
    La Fleur, Linnea
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brunnstrom, Hans
    Lindskog, Cecilia
    Madjar, Katrin
    Rahnenfuehrer, Joerg
    Ekman, Simon
    Stahle, Elisabeth
    Koyi, Hirsh
    Branden, Eva
    Edlund, Karolina
    Hengstler, Jan G.
    Lambe, Mats
    Saito, Akira
    Botling, Johan
    Ponten, Fredrik
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Micke, Patrick
    Profiling cancer testis antigens in non-small-cell lung cancer2016In: JCI INSIGHT, ISSN 2379-3708, Vol. 1, no 10, article id e86837Article in journal (Refereed)
    Abstract [en]

    Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small-cell lung cancer (NSCLC), we compared RNAseq data from 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the Caner Testis Database (CTdatabase), 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase, thus representing potential new CTAs. Cluster analysis revealed that CTA expression is histology dependent and concurrent expression is common. IHC confirmed tissue-specific protein expression of selected new CTAs (TKTL1, TGIF2LX, VCX, and CXORF67). Furthermore, methylation was identified as a regulatory mechanism of CTA expression based on independent data from The Cancer Genome Atlas. The proposed prognostic impact of CTAs in lung cancer was not confirmed, neither in our RNAseq cohort nor in an independent meta-analysis of 1,117 NSCLC cases. In summary, we defined a set of 90 reliable CTAs, including information on protein expression, methylation, and survival association. The detailed RNAseq catalog can guide biomarker studies and efforts to identify targets for immunotherapeutic strategies.

  • 4.
    Eraslan, Basak
    et al.
    Tech Univ Munich, Dept Informat, Computat Biol, Munich, Germany.;Ludwig Maximilians Univ Munchen, Grad Sch Quantitat Biosci QBM, Munich, Germany..
    Wang, Dongxue
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Gusic, Mirjana
    Tech Univ Munich, Inst Human Genet, Munich, Germany.;Helmholtz Zentrum Munchen, Inst Human Genet, Neuherberg, Germany..
    Prokisch, Holger
    Tech Univ Munich, Inst Human Genet, Munich, Germany.;Helmholtz Zentrum Munchen, Inst Human Genet, Neuherberg, Germany..
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Asplund, Anna
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Ponten, Frederik
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Wieland, Thomas
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Hopf, Thomas
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Hahne, Hannes
    OmicScouts GmbH, Freising Weihenstephan, Germany..
    Kuster, Bernhard
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany.;CIPSM, Munich, Germany..
    Gagneur, Julien
    Tech Univ Munich, Dept Informat, Computat Biol, Munich, Germany..
    Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues2019In: Molecular Systems Biology, ISSN 1744-4292, E-ISSN 1744-4292, Vol. 15, no 2, article id e8513Article in journal (Refereed)
    Abstract [en]

    Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.

  • 5. Fletcher, E.
    et al.
    Feizi, A.
    Bisschops, M. M. M.
    Hallström, Björn M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Khoomrung, S.
    Siewers, V.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Chalmers University of Technology, Sweden.
    Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments2017In: Metabolic engineering, ISSN 1096-7176, E-ISSN 1096-7184, Vol. 39, p. 19-28Article in journal (Refereed)
    Abstract [en]

    Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3 M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.

  • 6. Haglund, Felix
    et al.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Inga-Lena
    Hoog, Anders
    Juhlin, C. Christofer
    Larsson, Catharina
    Inflammatory infiltrates in parathyroid tumors2017In: European Journal of Endocrinology, ISSN 0804-4643, E-ISSN 1479-683X, Vol. 177, no 6, p. 445-453Article in journal (Refereed)
    Abstract [en]

    Context: Inflammatory infiltrates are sometimes present in solid tumors and may be coupled to clinical behavior or etiology. Infectious viruses contribute to tumorigenesis in a significant fraction of human neoplasias. Objective: Characterize inflammatory infiltrates and possible viral transcription in primary hyperparathyroidism. Design: From the period 2007 to 2016, a total of 55 parathyroid tumors (51 adenomas and 4 hyperplasias) with prominent inflammatory infiltrates were identified from more than 2000 parathyroid tumors in the pathology archives, and investigated by immunohistochemistry for CD4, CD8, CD20 and CD45 and scored as +0, +1 or +2. Clinicopathological data were compared to 142 parathyroid adenomas without histological evidence of inflammation. Transcriptome sequencing was performed for 13 parathyroid tumors (four inflammatory, 9 non-inflammatory) to identify potential viral transcripts. Results: Tumors had prominent germinal center-like nodular (+2) lymphocytic infiltrates consisting of T and B lymphocytes (31%) and/or diffuse (+1-2) infiltrates of predominantly CD8+T lymphocytes (84%). In the majority of cases with adjacent normal parathyroid tissue, the normal rim was unaffected by the inflammatory infiltrates (96%). Presence of inflammatory infiltrates was associated with higher levels of serum-PTH (P = 0.007) and oxyphilic differentiation (P = 0.002). Co-existent autoimmune disease was observed in 27% of patients with inflammatory infiltrates, which in turn was associated with oxyphilic differentiation (P = 0.041). Additionally, prescription of anti-inflammatory drugs was associated with lower serum ionized calcium (P = 0.037). Conclusions: No evidence of virus-like sequences in the parathyroid tumors could be found by transcriptome sequencing, suggesting that other factors may contribute to attract the immune system to the parathyroid tumor tissue.

  • 7. Huang, M.
    et al.
    Bao, J.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Petranovic, D.
    Nielsen, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Efficient protein production by yeast requires global tuning of metabolism2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 1131Article in journal (Refereed)
    Abstract [en]

    The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.

  • 8. Palmgren, Michael
    et al.
    Engstrom, Karin
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wahlberg, Karin
    Sondergaard, Dan Ariel
    Sall, Torbjorn
    Vahter, Marie
    Broberg, Karin
    AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 4, article id e0175422Article in journal (Refereed)
    Abstract [en]

    Organisms have evolved the ability to tolerate toxic substances in their environments, often by producing metabolic enzymes that efficiently detoxify the toxicant. Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, metabolise inorganic arsenic to less toxic metabolites. This multistep process produces mono-, di-, and trimethylated arsenic metabolites, which the organism excretes. In humans, arsenite methyltransferase (AS3MT) appears to be the main metabolic enzyme that methylates arsenic. In this study, we examined the evolutionary origin of AS3MT and assessed the ability of different genotypes to produce methylated arsenic metabolites. Phylogenetic analysis suggests that multiple, independent horizontal gene transfers between different bacteria, and from bacteria to eukaryotes, increased tolerance to environmental arsenic during evolution. These findings are supported by the observation that genetic variation in AS3MT correlates with the capacity to methylate arsenic. Adaptation to arsenic thus serves as a model for how organisms evolve to survive under toxic conditions.

  • 9.
    Palmgren, Michael
    et al.
    Univ Copenhagen, Dept Plant & Environm Sci, Copenhagen, Denmark.;Karolinska Inst, Inst Environm Med, Stockholm, Sweden..
    Sorensen, Danny Mollerup
    Univ Copenhagen, Dept Plant & Environm Sci, Copenhagen, Denmark..
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Säll, Torbjörn
    Lund Univ, Dept Biol, Lund, Sweden..
    Broberg, Karin
    Karolinska Inst, Inst Environm Med, Stockholm, Sweden..
    Evolution of P2A and P5A ATPases: ancient gene duplications and the red algal connection to green plants revisited2019In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054Article in journal (Refereed)
    Abstract [en]

    In a search for slowly evolving nuclear genes that may cast light on the deep evolution of plants, we carried out phylogenetic analyses of two well-characterized subfamilies of P-type pumps (P2A and P5A ATPases) from representative branches of the eukaryotic tree of life. Both P-type ATPase genes were duplicated very early in eukaryotic evolution and before the divergence of the present eukaryotic supergroups. Synapomorphies identified in the sequences provide evidence that green plants and red algae are more distantly related than are green plants and eukaryotic supergroups in which secondary or tertiary plastids are common, such as several groups belonging to the clade that includes Stramenopiles, Alveolata, Rhizaria, Cryptophyta and Haptophyta (SAR). We propose that red algae branched off soon after the first photosynthesizing eukaryote had acquired a primary plastid, while in another lineage that led to SAR, the primary plastid was lost but, in some cases, regained as a secondary or tertiary plastid.

  • 10. Pateraki, Irini
    et al.
    Andersen-Ranberg, Johan
    Jensen, Niels Bjerg
    Wubshet, Sileshi Gizachew
    Heskes, Allison Maree
    Forman, Victor
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hamberger, Britta
    Motawia, Mohammed Saddik
    Olsen, Carl Erik
    Staerk, Dan
    Hansen, Jorgen
    Moller, Birger Lindberg
    Hamberger, Bjorn
    Total biosynthesis of the cyclic AMP booster for skolin from Coleus forskohlii2017In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e23001Article in journal (Refereed)
    Abstract [en]

    Forskolin is a unique structurally complex labdane-type diterpenoid used in the treatment of glaucoma and heart failure based on its activity as a cyclic AMP booster. Commercial production of forskolin relies exclusively on extraction from its only known natural source, the plant Coleus forskohlii, in which forskolin accumulates in the root cork. Here, we report the discovery of five cytochrome P450s and two acetyltransferases which catalyze a cascade of reactions converting the forskolin precursor 13R-manoyl oxide into forskolin and a diverse array of additional labdane-type diterpenoids. A minimal set of three P450s in combination with a single acetyl transferase was identified that catalyzes the conversion of 13R-manoyl oxide into forskolin as demonstrated by transient expression in Nicotiana benthamiana. The entire pathway for forskolin production from glucose encompassing expression of nine genes was stably integrated into Saccharomyces cerevisiae and afforded forskolin titers of 40 mg/L.

  • 11. van Wijk, Xander M.
    et al.
    Dohrmann, Simon
    Hallström, Björn M.
    KTH, School of Biotechnology (BIO). Tech Univ Denmark, Denmark.
    Li, Shangzhong
    Voldborg, Bjorn G.
    Meng, Brandon X.
    McKee, Karen K.
    van Kuppevelt, Toin H.
    Yurchenco, Peter D.
    Palsson, Bernhard O.
    Lewis, Nathan E.
    Nizet, Victor
    Esko, Jeffrey D.
    Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion2017In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 8, no 1, article id e02128-16Article in journal (Refereed)
    Abstract [en]

    To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants of Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-cas9) gene targeting. When these mutants were compared to the pgsA745 cell line, a CHO xylosyltransferase mutant generated previously using chemical mutagenesis, an unexpected result was obtained. Bacterial invasion of pgsA745 cells by group B Streptococcus (GBS), group A Streptococcus, and Staphylococcus aureus was markedly reduced compared to the invasion of wild-type cells, but newly generated CRISPR-cas9 mutants were only resistant to GBS. Invasion of pgsA745 cells was not restored by transfection with xylosyltransferase, suggesting that an additional mutation conferring panresistance to multiple bacteria was present in pgsA745 cells. Whole-genome sequencing and transcriptome sequencing (RNA-Seq) uncovered a deletion in the gene encoding the laminin subunit alpha 2 (Lama2) that eliminated much of domain L4a. Silencing of the long Lama2 isoform in wild-type cells strongly reduced bacterial invasion, whereas transfection with human LAMA2 cDNA significantly enhanced invasion in pgsA745 cells. The addition of exogenous laminin-alpha 2 beta 1 gamma 1/laminin-alpha 2 beta 2 gamma 1 strongly increased bacterial invasion in CHO cells, as well as in human alveolar basal epithelial and human brain microvascular endothelial cells. Thus, the L4a domain in laminin alpha 2 is important for cellular invasion by a number of bacterial pathogens. IMPORTANCE Pathogenic bacteria penetrate host cellular barriers by attachment to extracellular matrix molecules, such as proteoglycans, laminins, and collagens, leading to invasion of epithelial and endothelial cells. Here, we show that cellular invasion by the human pathogens group B Streptococcus, group A Streptococcus, and Staphylococcus aureus depends on a specific domain of the laminin alpha 2 subunit. This finding may provide new leads for the molecular pathogenesis of these bacteria and the development of novel antimicrobial drugs.

  • 12.
    Wang, Dongxue
    et al.
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Eraslan, Basak
    Tech Univ Munich, Dept Informat, Computat Biol, Garching, Germany.;Ludwig Maximilians Univ Munchen, Gene Ctr, Dept Biochem, Quantitat Biosci Munich, Munich, Germany..
    Wieland, Thomas
    OmicScouts GmbH, Freising Weihenstephan, Germany..
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hopf, Thomas
    OmicScouts GmbH, Freising Weihenstephan, Germany..
    Zolg, Daniel Paul
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Zecha, Jana
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Asplund, Anna
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Li, Li-hua
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Meng, Chen
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Frejno, Martin
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Schmidt, Tobias
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Schnatbaum, Karsten
    JPT Peptide Technol GmbH, Berlin, Germany..
    Wilhelm, Mathias
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany..
    Ponten, Frederik
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gagneur, Julien
    Tech Univ Munich, Dept Informat, Computat Biol, Garching, Germany..
    Hahne, Hannes
    OmicScouts GmbH, Freising Weihenstephan, Germany..
    Kuster, Bernhard
    Tech Univ Munich, Chair Prote & Bioanalyt, Freising Weihenstephan, Germany.;CIPSM, Munich, Germany..
    A deep proteome and transcriptome abundance atlas of 29 healthy human tissues2019In: Molecular Systems Biology, ISSN 1744-4292, E-ISSN 1744-4292, Vol. 15, no 2, article id e8503Article in journal (Refereed)
    Abstract [en]

    Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.

  • 13.
    Zieba, Agata
    et al.
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75185 Uppsala, Sweden..
    Sjöstedt, Evelina
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Olovsson, Matts
    Uppsala Univ, Dept Womens & Childrens Hlth, S-75185 Uppsala, Sweden..
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oskarsson, Linda
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75185 Uppsala, Sweden..
    Edlund, Karolina
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75185 Uppsala, Sweden..
    Tolf, Anna
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75185 Uppsala, Sweden..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ponten, Fredrik
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75185 Uppsala, Sweden..
    The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling2015In: Omics, ISSN 1536-2310, E-ISSN 1557-8100, Vol. 19, no 11, p. 659-668Article in journal (Refereed)
    Abstract [en]

    The human uterus includes the complex endometrial mucosa, the endometrium that undergoes dynamic, hormone-dependent alterations throughout the life of fertile females. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to analyze gene expression patterns in the normal endometrium. Human endometrial tissues from five women were used for deep sequencing (RNA-Seq). The mRNA and protein expression data from the endometrium were compared to 31 (RNA) and 44 (protein) other normal tissue types, to identify genes with elevated expression in the endometrium and to localize the expression of corresponding proteins at a cellular resolution. Based on the expression levels of transcripts, we could classify all putative human protein coding genes into categories defined by expression patterns and found altogether 101 genes that showed an elevated pattern of expression in the endometrium, with only four genes showing more than five-fold higher expression levels in the endometrium compared to other tissues. In conclusion, our analysis based on transcriptomics and antibody-based protein profiling reports here comprehensive lists of genes with elevated expression levels in the endometrium, providing important starting points for a better molecular understanding of human reproductive biology and disease.

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