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  • 1.
    Pineau, Charles
    et al.
    Univ Rennes, INSERM, UMR S 1085, EHESP,Irset Inst Rech Sante Environm & Travail, F-35042 Rennes, France;Univ Rennes, Protim, F-35042 Rennes, France.
    Hikmet, Feria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Zhang, Cheng
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, S-17121 Stockholm, Sweden.
    Oksvold, Per
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, S-17121 Stockholm, Sweden.
    Chen, Shuqi
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, S-17121 Stockholm, Sweden.
    Fagerberg, Linn
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, S-17121 Stockholm, Sweden.
    Uhlen, Mathias
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, S-17121 Stockholm, Sweden.
    Lindskog, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics2019In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 18, no 12, p. 4215-4230Article in journal (Refereed)
    Abstract [en]

    One of the most complex organs in the human body is the testis, where spermatogenesis takes place. This physiological process involves thousands of genes and proteins that are activated and repressed, making testis the organ with the highest number of tissue-specific genes. However, the function of a large proportion of the corresponding proteins remains unknown and testis harbors many missing proteins (MPs), defined as products of protein-coding genes that lack experimental mass spectrometry evidence. Here, an integrated omits approach was used for exploring the cell type-specific protein expression of genes with an elevated expression in testis. By combining genome-wide transcriptomics analysis with immunohistochemistry, more than 500 proteins with distinct testicular protein expression patterns were identified, and these were selected for in-depth characterization of their in situ expression in eight different testicular cell types. The cell type-specific protein expression patterns allowed us to identify six distinct clusters of expression at different stages of spermatogenesis. The analysis highlighted numerous poorly characterized proteins in each of these clusters whose expression overlapped with that of known proteins involved in spermatogenesis, including 85 proteins with an unknown function and 60 proteins that previously have been classified as MPs. Furthermore, we were able to characterize the in situ distribution of several proteins that previously lacked spatial information and cell type specific expression within the testis. The testis elevated expression levels both at the RNA and protein levels suggest that these proteins are related to testis-specific functions. In summary, the study demonstrates the power of combining genome-wide transcriptomics analysis with antibody-based protein profiling to explore the cell type-specific expression of both well-known proteins and MPs. The analyzed proteins constitute important targets for further testis-specific research in male reproductive disorders.

  • 2.
    Schuster, Jens
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fatima, Ambrin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sobol, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Noraddin, Feria Hikmet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Laan, Loora
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dahl, Niklas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Generation of three human induced pluripotent stem cell (iPSC) lines from three patients with Dravet syndrome carrying distinct SCN1A gene mutations2019In: Stem Cell Research, ISSN 1873-5061, E-ISSN 1876-7753, Vol. 39, article id 101523Article in journal (Refereed)
    Abstract [en]

    Dravet syndrome (DS) is a childhood epilepsy syndrome caused by heterozygous mutations in the SCN1A gene encoding voltage-gated sodium channel Nav1.1. We generated iPSCs from fibroblasts of three DS patients carrying distinct SCN1A mutations (c.5502-5509dupGCTTGAAC, c.2965G>C and c.651C>G). The iPSC lines were genetically stable and each line retained the SCN1A gene mutation of the donor fibroblasts. Characterization of the iPSC lines confirmed expression of pluripotency markers, absence of exogenous vector expression and trilineage differentiation potential. These iPSC lines offer a useful resource to investigate the molecular mechanisms underlying Nav1.1 haploinsufficiency and for drug development to improve treatment of DS patients.

  • 3.
    Schuster, Jens
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Laan, Loora
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Klar, Joakim
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Jin, Zhe
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Birnir: Molecular Physiology and Neuroscience.
    Huss, Mikael
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Wallenberg Long Term Bioinformat Support, Stockholm, Sweden.
    Korol, Sergiy
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Birnir: Molecular Physiology and Neuroscience.
    Noraddin, Feria Hikmet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sobol, Maria
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Birnir, Bryndis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Birnir: Molecular Physiology and Neuroscience.
    Dahl, Niklas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment2019In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 132, article id 104583Article in journal (Refereed)
    Abstract [en]

    Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the a-subunit of the neuronal sodium channel Na(v)1.1. The syndrome is characterized by age related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Na(v)1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic interneuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Na(v)1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.

  • 4.
    Sjostedt, Evelina
    et al.
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Zhong, Wen
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Fagerberg, Linn
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Karlsson, Max
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Mitsios, Nicholas
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden.
    Adori, Csaba
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden.
    Oksvold, Per
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Edfors, Fredrik
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Limiszewska, Agnieszka
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden.
    Noraddin, Feria Hikmet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Huang, Jinrong
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;BGI Shenzhen, Shenzhen 518083, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark;Univ Copenhagen, Dept Biol, DK-2100 Copenhagen, Denmark.
    Du, Yutao
    BGI Shenzhen, Shenzhen 518083, Peoples R China;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.
    Lin, Lin
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark.
    Dong, Zhanying
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;BGI Shenzhen, Shenzhen 518083, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark.
    Yang, Ling
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;BGI Shenzhen, Shenzhen 518083, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark.
    Liu, Xin
    BGI Shenzhen, Shenzhen 518083, Peoples R China;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.
    Jiang, Hui
    BGI Shenzhen, MGI, Shenzhen 518083, Peoples R China.
    Xu, Xun
    BGI Shenzhen, Shenzhen 518083, Peoples R China;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.
    Wang, Jian
    BGI Shenzhen, Shenzhen 518083, Peoples R China;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.
    Yang, Huanming
    BGI Shenzhen, Shenzhen 518083, Peoples R China;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China.
    Bolund, Lars
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;BGI Shenzhen, Shenzhen 518083, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark.
    Mardinoglu, Adil
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Zhang, Cheng
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    von Feilitzen, Kalle
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Lindskog, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Pontén, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Luo, Yonglun
    BGI Qingdao, Lars Bolund Inst Regenerat Med, Qingdao 266555, Peoples R China;BGI Shenzhen, Shenzhen 518083, Peoples R China;Aarhus Univ, Dept Biomed, DK-80000 Aarhus, Denmark.
    Hokfelt, Tomas
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden.
    Uhlen, Mathias
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Stockholm, Sweden.
    Mulder, Jan
    Karolinska Inst, Dept Neurosci, S-17177 Stockholm, Sweden.
    An atlas of the protein-coding genes in the human, pig, and mouse brain2020In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 367, no 6482, p. 1090-+, article id eaay5947Article in journal (Refereed)
    Abstract [en]

    The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.

  • 5.
    Sjöstedt, Evelina
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden.
    Sivertsson, Åsa
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden.
    Noraddin, Feria Hikmet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Katona, Borbala
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Näsström, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vuu, Jimmy
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kesti, Dennis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Oksvold, Per
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden.
    Edqvist, Per-Henrik D
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Olsson, Ingmarie
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Uhlen, Mathias
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden.
    Lindskog, Cecilia
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues2018In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 12, p. 4127-4137Article in journal (Refereed)
    Abstract [en]

    A large portion of human proteins are referred to as missing proteins, defined as protein-coding genes that lack experimental data on the protein level due to factors such as temporal expression, expression in tissues that are difficult to sample, or they actually do not encode functional proteins. In the present investigation, an integrated omics approach was used for identification and exploration of missing proteins. Transcriptomics data from three different sources-the Human Protein Atlas (HPA), the GTEx consortium, and the FANTOM5 consortium-were used as a starting point to identify genes selectively expressed in specialized tissues. Complementing the analysis with profiling on more specific tissues based on immunohistochemistry allowed for further exploration of cell-type-specific expression patterns. More detailed tissue profiling was performed for >300 genes on complementing tissues. The analysis identified tissue-specific expression of nine proteins previously listed as missing proteins (POU4F1, FRMD1, ARHGEF33, GABRG1, KRTAP2-1, BHLHE22, SPRR4, AVPR1B, and DCLK3), as well as numerous proteins with evidence of existence on the protein level that previously lacked information on spatial resolution and cell-type-specific expression pattern. We here present a comprehensive strategy for identification of missing proteins by combining transcriptomics with antibody-based proteomics. The analyzed proteins provide interesting targets for organ-specific research in health and disease.

1 - 5 of 5
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