{"entity": "researcher", "timestamp": "2026-07-19T06:58:08.437Z", "family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "affiliations": ["Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.", "Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af"}}, "publications": [{"entity": "publication", "iuid": "d424cf3383cb4f00b90f3c15f327aeae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d424cf3383cb4f00b90f3c15f327aeae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d424cf3383cb4f00b90f3c15f327aeae"}}, "title": "Dual-Color Expansion Microscopy of Membrane Proteins Using Bioorthogonal Labeling", "authors": [{"family": "Edwards", "given": "Steven", "initials": "S", "orcid": "0000-0001-7930-7977", "researcher": {"href": "https://publications.scilifelab.se/researcher/899ddd1ca8b148f696e5d30f30d762b1.json"}}, {"family": "Meineke", "given": "Birthe", "initials": "B", "orcid": "0000-0002-8912-0783", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cc783424be4fe2b41d82bba5c2a412.json"}}, {"family": "Bauer", "given": "Sebastian", "initials": "S", "orcid": "0009-0009-7265-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eb06fbcd1476b8d55bd823a46a19c.json"}}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Els\u00e4sser", "given": "Simon", "initials": "S", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal-article", "published": "2026-02-04", "journal": {"title": "Nano Lett.", "issn": "1530-6984", "volume": "26", "issue": "4", "pages": "1321-1326", "issn-l": null}, "abstract": "With recent advances in fluorescence microscopy, resolution is often limited by the size of the label and the resulting linkage error, rather than the microscope itself. Site-specific incorporation of noncanonical amino acids (ncAAs) combined with bioorthogonal click chemistry provides a powerful tool for fluorescent protein labeling, overcoming the spatial uncertainty inherent to antibody-based probes. Here, we present a method to further improve labeling precision by combining ncAA labeling with expansion microscopy (ExM) for dual-color super-resolution imaging. After optimizing labeling procedures and fluorophore selection, we visualize and resolve the nanoscale distribution of Na,K-ATPase \u03b11 and \u03b21 subunits in expanded HEK 293T cells. We validate our approach by super-resolution STED imaging of the ncAA labeled \u03b21 subunit in unexpanded cells. This work presents a strong framework for multiplexed, high-resolution imaging, suggesting that ncAA labeling combined with ExM enables biological imaging at the nanometer scale.", "doi": "10.1021/acs.nanolett.5c05301", "pmid": "41571281", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12879918"}], "notes": [], "created": "2026-01-24T20:15:09.343Z", "modified": "2026-02-11T12:54:50.277Z"}, {"entity": "publication", "iuid": "ead989ea22be400abf08c96a2de3f6c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ead989ea22be400abf08c96a2de3f6c0"}}, "title": "RNA transcripts regulate G-quadruplex landscapes through G-loop formation.", "authors": [{"family": "Sato", "given": "Koichi", "initials": "K", "orcid": "0000-0002-0574-774X", "researcher": {"href": "https://publications.scilifelab.se/researcher/419db8b1c9a142d8994dc12727020ed4.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "van den Berg", "given": "Jeroen", "initials": "J", "orcid": "0000-0002-9430-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81ddd6ecb4e4654aef53c4388448204.json"}}, {"family": "Braat", "given": "Diana", "initials": "D", "orcid": "0009-0003-1086-7185", "researcher": {"href": "https://publications.scilifelab.se/researcher/8028609fa976407c9f756fa4640b9012.json"}}, {"family": "Cruz", "given": "Victoria M", "initials": "VM", "orcid": "0000-0001-5385-1472", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8d30dbce78446cc8b327a0df98ce69c.json"}}, {"family": "Navarro Luz\u00f3n", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Schimmel", "given": "Joost", "initials": "J", "orcid": "0000-0002-2620-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a37bb4f3de34d3c8c9fffab2d3a6d0c.json"}}, {"family": "Esteban-Jurado", "given": "Clara", "initials": "C"}, {"family": "Alemany", "given": "Ma\u00eblys", "initials": "M", "orcid": "0009-0004-3277-6206", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc9d305d46084a598ff3eeb47127d700.json"}}, {"family": "Dreyer", "given": "Jan", "initials": "J"}, {"family": "Hendrikx", "given": "Aiko", "initials": "A"}, {"family": "Mattiroli", "given": "Francesca", "initials": "F", "orcid": "0000-0002-1574-7217", "researcher": {"href": "https://publications.scilifelab.se/researcher/0afa3a260bfb4e49b2ed1ef9b3af3357.json"}}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A", "orcid": "0000-0002-9442-3551", "researcher": {"href": "https://publications.scilifelab.se/researcher/86e54078e6ea45949e7468b2653601d9.json"}}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Knipscheer", "given": "Puck", "initials": "P", "orcid": "0000-0003-4198-0132", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b1d8281b234a30b7e450f2759559c2.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6752", "pages": "1225-1231", "issn-l": "0036-8075"}, "abstract": "G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics are controlled remains poorly understood. Here, we report that RNA transcripts govern G4 landscapes through coordinated G-loop assembly and disassembly. G-loop assembly involves activation of the ATM and ATR kinases, followed by homology-directed invasion of RNA opposite the G4 strand mediated by BRCA2 and RAD51. Disassembly of the G-loop resolves the G4 structure through DHX36-FANCJ-mediated G4 unwinding, which triggers nucleolytic incision and subsequent hybrid strand renewal by DNA synthesis. Inhibition of G-loop disassembly causes global G4 and R-loop accumulation, leading to transcriptome dysregulation, replication stress, and genome instability. These findings establish an intricate G-loop assembly-disassembly mechanism that controls G4 landscapes and is essential for cellular homeostasis and survival.", "doi": "10.1126/science.adr0493", "pmid": "40504899", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-28T10:51:58.676Z", "modified": "2025-11-28T10:51:59.081Z"}, {"entity": "publication", "iuid": "6821d1cd51294efd9c8abd81faf7a73a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a"}}, "title": "Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.", "authors": [{"family": "Kumar", "given": "Banushree", "initials": "B", "orcid": "0000-0001-9200-6773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd7494dc4ea43d9b493fd6a099fc675.json"}}, {"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Yung", "given": "Philip Yuk Kwong", "initials": "PYK", "orcid": "0000-0003-2926-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/97f9b0c8cf5a4f3ab22629842c2b08dd.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "Salazar Mantero", "given": "Angelo", "initials": "A"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Hannah", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2024-10-03", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.", "doi": "10.1038/s41596-024-01058-z", "pmid": "39363107", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-024-01058-z"}], "notes": [], "created": "2025-02-28T14:15:54.627Z", "modified": "2025-11-28T20:16:06.367Z"}, {"entity": "publication", "iuid": "39e2c1f3099449c48d370ab641fe8b90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39e2c1f3099449c48d370ab641fe8b90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39e2c1f3099449c48d370ab641fe8b90"}}, "title": "Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress.", "authors": [{"family": "Larsen", "given": "Brian D", "initials": "BD", "orcid": "0000-0002-6169-2317", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ae5a4d242243ef9c06c9eb9aa0d8eb.json"}}, {"family": "Benada", "given": "Jan", "initials": "J", "orcid": "0000-0001-5863-0513", "researcher": {"href": "https://publications.scilifelab.se/researcher/e455ed441daa4747b0cfb17eb92d15d8.json"}}, {"family": "Yung", "given": "Philip Yuk Kwong", "initials": "PYK", "orcid": "0000-0003-2926-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/97f9b0c8cf5a4f3ab22629842c2b08dd.json"}}, {"family": "Bell", "given": "Ryan A V", "initials": "RAV"}, {"family": "Pappas", "given": "George", "initials": "G"}, {"family": "Urban", "given": "Vaclav", "initials": "V"}, {"family": "Ahlskog", "given": "Johanna K", "initials": "JK"}, {"family": "Kuo", "given": "Tia T", "initials": "TT", "orcid": "0000-0002-3532-2718", "researcher": {"href": "https://publications.scilifelab.se/researcher/101f25cabf1540fe9f7e14074c8f78c5.json"}}, {"family": "Janscak", "given": "Pavel", "initials": "P"}, {"family": "Megeney", "given": "Lynn A", "initials": "LA", "orcid": "0000-0002-6824-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8661ae775cf4c3ca050da7b8b1a41f1.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}, {"family": "S\u00f8rensen", "given": "Claus S", "initials": "CS", "orcid": "0000-0001-6022-9710", "researcher": {"href": "https://publications.scilifelab.se/researcher/383102b1b30543169e973c3998256320.json"}}], "type": "journal article", "published": "2022-04-29", "journal": {"title": "Science", "issn": "1095-9203", "volume": "376", "issue": "6592", "pages": "476-483", "issn-l": "0036-8075"}, "abstract": "Genotoxic therapy such as radiation serves as a frontline cancer treatment, yet acquired resistance that leads to tumor reoccurrence is frequent. We found that cancer cells maintain viability during irradiation by reversibly increasing genome-wide DNA breaks, thereby limiting premature mitotic progression. We identify caspase-activated DNase (CAD) as the nuclease inflicting these de novo DNA lesions at defined loci, which are in proximity to chromatin-modifying CCCTC-binding factor (CTCF) sites. CAD nuclease activity is governed through phosphorylation by DNA damage response kinases, independent of caspase activity. In turn, loss of CAD activity impairs cell fate decisions, rendering cancer cells vulnerable to radiation-induced DNA double-strand breaks. Our observations highlight a cancer-selective survival adaptation, whereby tumor cells deploy regulated DNA breaks to delimit the detrimental effects of therapy-evoked DNA damage.", "doi": "10.1126/science.abi6378", "pmid": "35482866", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-09T15:46:15.480Z", "modified": "2024-01-16T13:48:36.960Z"}, {"entity": "publication", "iuid": "f262bf6310d1438b9abbf94866a09252", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f262bf6310d1438b9abbf94866a09252.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f262bf6310d1438b9abbf94866a09252"}}, "title": "Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids.", "authors": [{"family": "van Husen", "given": "Lea S", "initials": "LS", "orcid": "0000-0002-6737-3835", "researcher": {"href": "https://publications.scilifelab.se/researcher/381bac34b83f47bdb09fa6b78914cc5c.json"}}, {"family": "Katsori", "given": "Anna-Maria", "initials": "A", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Meineke", "given": "Birthe", "initials": "B"}, {"family": "Tjernberg", "given": "Lars O", "initials": "LO", "orcid": "0000-0001-6889-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/35d7bd25361f4e08a7223926311b399a.json"}}, {"family": "Schedin-Weiss", "given": "Sophia", "initials": "S"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "ChemBioChem", "issn": "1439-7633", "issn-l": "1439-4227", "volume": "22", "issue": "22", "pages": "3208-3213"}, "abstract": "Human induced pluripotent stem cell (hiPSC) technology has revolutionized studies on human biology. A wide range of cell types and tissue models can be derived from hiPSCs to study complex human diseases. Here, we use PiggyBac-mediated transgenesis to engineer hiPSCs with an expanded genetic code. We demonstrate that genomic integration of expression cassettes for a pyrrolysyl-tRNA synthetase (PylRS), pyrrolysyl-tRNA (PylT) and the target protein of interest enables site-specific incorporation of a non-canonical amino acid (ncAA) in response to an amber stop codon. Neural stem cells, neurons and brain organoids derived from the engineered hiPSCs continue to express the amber suppression machinery and produce ncAA-bearing reporter. The incorporated ncAA can serve as a minimal bioorthogonal handle for further modifications by labeling with fluorescent dyes. Site-directed ncAA mutagenesis will open a wide range of applications to probe and manipulate proteins in brain organoids and other hiPSC-derived cell types and complex tissue models.", "doi": "10.1002/cbic.202100399", "pmid": "34431592", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2021-11-17T13:17:12.910Z", "modified": "2023-06-19T11:42:30.795Z"}, {"entity": "publication", "iuid": "f18d7672bbbb4e5dbcd524fde4fbc995", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995"}}, "title": "The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.", "authors": [{"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Zisi", "given": "Asimina", "initials": "A", "orcid": "0000-0002-4253-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf82380ca6e4cd1985bc9dd23789539.json"}}, {"family": "Sakkas", "given": "Elpidoforos", "initials": "E"}, {"family": "Bartkova", "given": "Jirina", "initials": "J"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af59464d2c74c27af7a43fb5d1a670e.json"}}, {"family": "Dyrskj\u00f8t", "given": "Lars", "initials": "L"}, {"family": "Broholm", "given": "Helle", "initials": "H", "orcid": "0000-0002-6029-822X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6d1ef8a71f24d1694aee57b47c22198.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "32", "issn-l": "2375-2548"}, "abstract": "Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.", "doi": "10.1126/sciadv.abf7561", "pmid": "34348895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "7/32/eabf7561"}, {"db": "pmc", "key": "PMC8336962"}], "notes": [], "created": "2021-10-01T09:03:24.915Z", "modified": "2023-06-19T11:42:22.695Z"}, {"entity": "publication", "iuid": "48993691f2c64543b650f3b600450b73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73"}}, "title": "Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.", "authors": [{"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Christian", "given": "Murray", "initials": "M"}, {"family": "Meineke", "given": "Birthe", "initials": "B"}, {"family": "Els\u00e4sser", "given": "Simon", "initials": "S", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Andr\u00e9ll", "given": "Juni", "initials": "J"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Dillner", "given": "Joakim", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "McInerney", "given": "Gerald", "initials": "G", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2021-06-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3695"}, "abstract": "Serological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%-14.7%). This includes 5.4% of the samples being IgG+IgM+ against several SARS-CoV-2 proteins, as well as 2.1% being IgG-IgM+ and 5.0% being IgG+IgM- for the virus' S protein. Subjects classified as IgG+ for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG+ for only the S protein (OR = 6.1; p < 0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus.", "doi": "10.1038/s41467-021-23893-4", "pmid": "34140485", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23893-4"}, {"db": "pmc", "key": "PMC8211676"}], "notes": [], "created": "2021-10-05T16:26:34.397Z", "modified": "2021-12-06T07:43:55.459Z"}, {"entity": "publication", "iuid": "e980f00b87dd45d3ab9ceb6c3c4cca0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e980f00b87dd45d3ab9ceb6c3c4cca0c"}}, "title": "An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.", "authors": [{"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J", "orcid": "0000-0001-9529-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbe28157081c49debba23f0b9ebd9c74.json"}}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Caridha", "given": "Rozina", "initials": "R"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2020-10-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5095", "issn-l": "2041-1723"}, "abstract": "Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.", "doi": "10.1038/s41467-020-18863-1", "pmid": "33037201", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7547087"}, {"db": "pii", "key": "10.1038/s41467-020-18863-1"}], "notes": [], "created": "2024-04-03T14:21:34.373Z", "modified": "2024-04-03T14:22:37.597Z"}]}