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  • 1.
    Alharbi, Adel F.
    et al.
    Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom; Medina Regional Laboratory, General Directorate of Health Affairs, Ministry of Health, Medina, Saudi Arabia.
    Sheng, Nongfei
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi.
    Nicol, Katie
    Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
    Strömberg, Nicklas
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi.
    Hollox, Edward J.
    Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
    Balancing selection at the human salivary agglutinin gene (DMBT1) driven by host-microbe interactions2022Inngår i: iScience, E-ISSN 2589-0042 , Vol. 25, nr 5, artikkel-id 104189Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Discovering loci under balancing selection in humans can identify loci with alleles that affect response to the environment and disease. Genome variation data have identified the 5′ region of the DMBT1 gene as undergoing balancing selection in humans. DMBT1 encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340, or salivary agglutinin. DMBT1 binds to a variety of pathogens through a tandemly arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of domains polymorphic in humans. We show that the signal of balancing selection is driven by one haplotype usually carrying a shorter SRCR repeat and another usually carrying a longer SRCR repeat. DMBT1 encoded by a shorter SRCR repeat allele does not bind a cariogenic and invasive Streptococcus mutans strain, in contrast to the long SRCR allele that shows binding. Our results suggest that balancing selection at DMBT1 is due to host-microbe interactions of encoded SRCR tandem repeat alleles.

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  • 2. Devoy, Anny
    et al.
    Price, Georgia
    De Giorgio, Francesca
    Bunton-Stasyshyn, Rosie
    Thompson, David
    Gasco, Samanta
    Allan, Alasdair
    Codner, Gemma F.
    Nair, Remya R.
    Tibbit, Charlotte
    McLeod, Ross
    Ali, Zeinab
    Noda, Judith
    Marrero-Gagliardi, Alessandro
    Brito-Armas, José M.
    Williams, Chloe
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Öztürk, Muhammet M.
    Simon, Michelle
    O'Neill, Edward
    Bryce-Smith, Sam
    Harrison, Jackie
    Atkins, Gemma
    Corrochano, Silvia
    Stewart, Michelle
    Gilthorpe, Jonathan D.
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Teboul, Lydia
    Acevedo-Arozena, Abraham
    Fisher, Elizabeth M. C.
    Cunningham, Thomas J.
    Generation and analysis of innovative genomically humanized knockin SOD1, TARDBP (TDP-43), and FUS mouse models2021Inngår i: iScience, E-ISSN 2589-0042 , Vol. 24, nr 12, artikkel-id 103463Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) is a fatal neurodegenerative disorder, and continued innovation is needed for improved understanding and for developing therapeutics. We have created next-generation genomically humanized knockin mouse models, by replacing the mouse genomic region of Sod1, Tardbp (TDP-43), and Fus, with their human orthologs, preserving human protein biochemistry and splicing with exons and introns intact. We establish a new standard of large knockin allele quality control, demonstrating the utility of indirect capture for enrichment of a genomic region of interest followed by Oxford Nanopore sequencing. Extensive analysis shows that homozygous humanized animals only express human protein at endogenous levels. Characterization of humanized FUS animals showed that they are phenotypically normal throughout their lifespan. These humanized strains are vital for preclinical assessment of interventions and serve as templates for the addition of coding or non-coding human ALS/FTD mutations to dissect disease pathomechanisms, in a physiological context.

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  • 3.
    Gineste, Charlotte
    et al.
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Youhanna, Sonia
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Vorrink, Sabine U.
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Henriksson, Sara
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hernández, Andrés
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Cheng, Arthur J.
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Chaillou, Thomas
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Buttgereit, Andreas
    Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
    Schneidereit, Dominik
    Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
    Friedrich, Oliver
    Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
    Hultenby, Kjell
    Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden.
    Bruton, Joseph D.
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Ivarsson, Niklas
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Sandblad, Linda
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lauschke, Volker M.
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tübingen, Tübingen, Germany.
    Westerblad, Håkan
    Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Enzymatically dissociated muscle fibers display rapid dedifferentiation and impaired mitochondrial calcium control2022Inngår i: iScience, E-ISSN 2589-0042 , Vol. 25, nr 12, artikkel-id 105654Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cells rapidly lose their physiological phenotype upon disruption of their extracellular matrix (ECM)-intracellular cytoskeleton interactions. By comparing adult mouse skeletal muscle fibers, isolated either by mechanical dissection or by collagenase-induced ECM digestion, we investigated acute effects of ECM disruption on cellular and mitochondrial morphology, transcriptomic signatures, and Ca2+ handling. RNA-sequencing showed striking differences in gene expression patterns between the two isolation methods with enzymatically dissociated fibers resembling myopathic phenotypes. Mitochondrial appearance was grossly similar in the two groups, but 3D electron microscopy revealed shorter and less branched mitochondria following enzymatic dissociation. Repeated contractions resulted in a prolonged mitochondrial Ca2+ accumulation in enzymatically dissociated fibers, which was partially prevented by cyclophilin inhibitors. Of importance, muscle fibers of mice with severe mitochondrial myopathy show pathognomonic mitochondrial Ca2+ accumulation during repeated contractions and this accumulation was concealed with enzymatic dissociation, making this an ambiguous method in studies of native intracellular Ca2+ fluxes.

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  • 4. Hoepfner, Dorothea
    et al.
    Fauser, Joel
    Kaspers, Marietta S.
    Pett, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hedberg, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Itzen, Aymelt
    Monoclonal Anti-AMP Antibodies Are Sensitive and Valuable Tools for Detecting Patterns of AMPylation2020Inngår i: iScience, E-ISSN 2589-0042 , Vol. 23, nr 12, artikkel-id 101800Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    AMPylation is a post-translational modification that modifies amino acid side chains with adenosine monophosphate (AMP). Recently, a role of AMPylation as a universal regulatory mechanism in infection and cellular homeostasis has emerged, driving the demand for universal tools to study this modification. Here, we describe three monoclonal anti-AMP antibodies (mAbs) from mouse that are capable of protein backbone-independent recognition of AMPylation, in denatured (western blot) as well as native (ELISA, IP) applications, thereby outperforming previously reported tools. These antibodies are highly sensitive and specific for AMP modifications, highlighting their potential as tools for new target identification, as well as for validation of known targets. Interestingly, applying the anti-AMP mAbs to various cancer cell lines reveals a previously undescribed broad and diverse AMPylation pattern. In conclusion, these anti-AMP mABs will further advance the current understanding of AMPylation and the spectrum of modified targets.

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  • 5.
    Lorenzon, Paolo
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Antos, Kamil
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Tripathi, Anushree
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Vedin, Viktoria
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Berghard, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Medini, Paolo
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    In vivo spontaneous activity and coital-evoked inhibition of mouse accessory olfactory bulb output neurons2023Inngår i: iScience, E-ISSN 2589-0042 , Vol. 26, nr 9, artikkel-id 107545Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Little is known about estrous effects on brain microcircuits. We examined the accessory olfactory bulb (AOB) in vivo, in anesthetized naturally cycling females, as model microcircuit receiving coital somatosensory information. Whole-cell recordings demonstrate that output neurons are relatively hyperpolarized in estrus and unexpectedly fire high frequency bursts of action potentials. To mimic coitus, a calibrated artificial vagino-cervical stimulation (aVCS) protocol was devised. aVCS evoked stimulus-locked local field responses in the interneuron layer independent of estrous stage. The response is sensitive to α1-adrenergic receptor blockade, as expected since aVCS increases norepinephrine release in AOB. Intriguingly, only in estrus does aVCS inhibit AOB spike output. Estrus-specific output reduction coincides with prolonged aVCS activation of inhibitory interneurons. Accordingly, in estrus the AOB microcircuit sets the stage for coital stimulation to inhibit the output neurons, possibly via high frequency bursting-dependent enhancement of reciprocal synapse efficacy between inter- and output neurons.

    Fulltekst (pdf)
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  • 6. Saccon, Elisa
    et al.
    Chen, Xi
    Mikaeloff, Flora
    Rodriguez, Jimmy Esneider
    Szekely, Laszlo
    Vinhas, Beatriz Sa
    Krishnan, Shuba
    Byrareddy, Siddappa N.
    Frisan, Teresa
    Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Vegvari, Akos
    Mirazimi, Ali
    Neogi, Ujjwal
    Gupta, Soham
    Cell-type-resolved quantitative proteomics map of interferon response against SARS-CoV-22021Inngår i: iScience, E-ISSN 2589-0042 , Vol. 24, nr 5, artikkel-id 102420Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The commonly used laboratory cell lines are the first line of experimental models to study the pathogenicity and performing antiviral assays for emerging viruses. Here, we assessed the tropism and cytopathogenicity of the first Swedish isolate of SARS-CoV-2 in six different human cell lines, compared their growth characteristics, and performed quantitative proteomics for the susceptible cell lines. Overall, Calu-3, Caco2, Huh7, and 293FT cell lines showed a high-to-moderate level of susceptibility to SARS-CoV-2. In Caco2 cells, the virus can achieve high titers in the absence of any prominent cytopathic effect. The protein abundance profile during SARS-CoV-2 infection revealed cell-type-specific regulation of cellular pathways. Type-I interferon signaling was identified as the common dysregulated cellular response in Caco2, Calu-3, and Huh7 cells. Together, our data show cell-type specific variability for cytopathogenicity, susceptibility, and cellular response to SARS-CoV-2 and provide important clues to guide future studies.

    Fulltekst (pdf)
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  • 7.
    Thakur, Noopur
    et al.
    Uppsala University.
    Hamidi, Anahita
    Uppsala University.
    Song, Jie
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Itoh, Susumu
    Showa Pharmaceutical University, Tokyo, Japan.
    Bergh, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Heldin, Carl-Henrik
    Uppsala University.
    Landström, Maréne
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi. Uppsala University.
    Smad7 Enhances TGF-β-Induced Transcription of c-Jun and HDAC6 Promoting Invasion of Prostate Cancer Cells2020Inngår i: iScience, E-ISSN 2589-0042 , Vol. 23, nr 9, artikkel-id 101470Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transforming growth factor β (TGF-β) enhances migration and invasion of cancer cells, causing life-threatening metastasis. Smad7 expression is induced by TGF-β to control TGF-β signaling in a negative feedback manner. Here we report an additional function of Smad7, i.e., to enhance TGF-β induction of c-Jun and HDAC6 via binding to their regulatory regions, promoting migration and invasion of prostate cancer cells. Lysine 102 in Smad7 is crucial for binding to specific consensus sites in c-Jun and HDAC6, even when endogenous Smad2, 3, and 4 were silenced by siRNA. A correlation between the mRNA expression of Smad7 and HDAC6, Smad7 and c-Jun, and c-Jun and HDAC6 was found in public databases from analyses of prostate cancer tissues. High expression of Smad7, HDAC6, and c-Jun correlated with poor prognosis for patients with prostate cancer. The knowledge that Smad7 can activate transcription of proinvasive genes leading to prostate cancer progression provides clinically relevant information. 

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  • 8.
    Štrancar, Vida
    et al.
    Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    van Midden, Katarina P.
    Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Krahn, Daniel
    The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, United Kingdom; Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute or Antimicrobial Research, University of Oxford, Mansfield Road, Oxford, United Kingdom.
    Morimoto, Kyoko
    The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, United Kingdom.
    Novinec, Marko
    Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Stael, Simon
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
    Schofield, Christopher J.
    Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute or Antimicrobial Research, University of Oxford, Mansfield Road, Oxford, United Kingdom.
    Klemenčič, Marina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    van der Hoorn, Renier A.L.
    The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, United Kingdom.
    Activity-based probes trap early active intermediates during metacaspase activation2022Inngår i: iScience, E-ISSN 2589-0042 , Vol. 25, nr 11, artikkel-id 105247Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Metacaspases are essential cysteine proteases present in plants, fungi, and protists that are regulated by calcium binding and proteolytic maturation through mechanisms not yet understood. Here, we developed and validated activity-based probes for the three main metacaspase types, and used them to study calcium-mediated activation of metacaspases from their precursors in vitro. By combining substrate-inspired tetrapeptide probes containing an acyloxymethylketone (AOMK) reactive group, with purified representatives of type-I, type-II, and type-III metacaspases, we were able to demonstrate that labeling of mature metacaspases is strictly dependent on calcium. The probe with the highest affinity for all metacaspases also labels higher molecular weight proteoforms of all three metacaspases only in the presence of calcium, displaying the active, unprocessed metacaspase intermediates. Our data suggest that metacaspase activation proceeds through previously unknown active intermediates that are formed upon calcium binding, before precursor processing.

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