{"entity": "researcher", "timestamp": "2026-10-05T20:39:34.170Z", "family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "affiliations": ["Karolinska Institutet, Stockholm, Sweden.", "University of Helsinki, Helsinki, Finland.", "University of Cambridge, Cambridge, UK."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5"}}, "publications": [{"entity": "publication", "iuid": "a8fbcd4a221c4de2a1151348bd4c9304", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304"}}, "title": "Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.", "authors": [{"family": "Kauko", "given": "Otto", "initials": "O", "orcid": "0000-0001-8948-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5390cad42a0409f8b66f56ab23ca232.json"}}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-9725-6907", "researcher": {"href": "https://publications.scilifelab.se/researcher/1171591a6a724f50a631d34948c6f14a.json"}}, {"family": "H\u00e4kkinen", "given": "Antti", "initials": "A", "orcid": "0000-0002-8081-1588", "researcher": {"href": "https://publications.scilifelab.se/researcher/b00bca666f344d4980a97bbdba20361e.json"}}, {"family": "Queiroz", "given": "Rayner M L", "initials": "RML"}, {"family": "P\u00e4\u00e4kk\u00f6nen", "given": "Mirva", "initials": "M"}, {"family": "Ventel\u00e4", "given": "Sami", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications.scilifelab.se/researcher/916e190e150e465c9e6afc11911bae04.json"}}, {"family": "Murgia", "given": "Antonio", "initials": "A"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B", "orcid": "0000-0001-6576-5440", "researcher": {"href": "https://publications.scilifelab.se/researcher/283b12ad225d4fb2b4e38b7f10c026d4.json"}}, {"family": "Routila", "given": "Johannes", "initials": "J", "orcid": "0000-0001-5385-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/71ee18226e6e4a42ae83b7106ca8b343.json"}}, {"family": "Wei", "given": "Gong-Hong", "initials": "G"}, {"family": "Irjala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-3054-4677", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf759b807e9640aab8fcadbad0c60662.json"}}, {"family": "Griffin", "given": "Julian L", "initials": "JL", "orcid": "0000-0003-1336-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e91146412f4bd2a0bed9331efee8d2.json"}}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS", "orcid": "0000-0003-0594-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b4e7e18a88455199308070d6da7ea3.json"}}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Hautaniemi", "given": "Sampsa", "initials": "S", "orcid": "0000-0002-7749-2694", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29cabf8ec5e4f78b9d14984a60c3e84.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "11", "issue": "34", "pages": "eadt1798"}, "abstract": "Mutations in numerous genes contribute to human cancer, with different oncogenic lesions prevalent in different cancer types. However, the malignant phenotype is simple, characterized by unrestricted cell growth, invasion, and often metastasis. One possible hypothesis explaining this dichotomy is that cancer genes regulate common targets, which then function as master regulators of essential cancer phenotypes. To identify mechanisms that drive the most fundamental feature shared by all tumors-unrestricted cell proliferation-we used a multiomic approach, which identified translation and ribosome biogenesis as common targets of major oncogenic pathways across cancer types. Proteomic analysis of tumors and functional studies of cell cultures established nucleolar and coiled-body phosphoprotein 1 as a key node, whose convergent regulation, both transcriptionally and posttranslationally, is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways regulate the same set of targets for growth control, revealing key downstream nodes that could be targeted for therapy or chemoprevention.", "doi": "10.1126/sciadv.adt1798", "pmid": "40834066", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13155486"}], "notes": [], "created": "2025-11-25T16:41:01.046Z", "modified": "2026-05-25T19:26:02.282Z"}, {"entity": "publication", "iuid": "2c7db473960c4c7fa52c676e6bfc84e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0"}}, "title": "Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer.", "authors": [{"family": "Sur", "given": "Inderpreet", "initials": "I"}, {"family": "Zhao", "given": "Wenshuo", "initials": "W"}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Kling Pilstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Webb", "given": "Anna T", "initials": "AT", "orcid": "0000-0001-6045-415X", "researcher": {"href": "https://publications.scilifelab.se/researcher/909754226aa04eb0824fc87c9efc628a.json"}}, {"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Katajisto", "given": "Pekka", "initials": "P", "orcid": "0000-0002-3033-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/68045c70bad544b68bbe913e7bf0ded8.json"}}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Rannikmae", "given": "Helena", "initials": "H"}, {"family": "de la Roche", "given": "Marc", "initials": "M"}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "8", "issue": "6", "issn-l": "2575-1077"}, "abstract": "Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here, we show that the genomic region upstream of Myc, which carries more cancer susceptibility in humans than any other genomic region, is required for intestinal regeneration after radiation damage. Failure to regenerate is associated with inefficient Ly6a/Sca1+ stem/progenitor cell mobilization, and almost complete failure to re-establish Lgr5+ cell compartment in the intestinal crypts. The Myc upstream region is also critical for growth of adult intestinal cells in 3D organoid culture. We show that culture conditions recapitulating most aspects of adult normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results establish a function for the Myc super-enhancer region as the genetic link between tissue regeneration and tumorigenesis, and demonstrates that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct.2-540", "doi": "10.26508/lsa.202403090", "pmid": "40180576", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969384"}, {"db": "pii", "key": "8/6/e202403090"}], "notes": [], "created": "2025-04-07T08:30:27.159Z", "modified": "2025-04-07T08:30:27.535Z"}, {"entity": "publication", "iuid": "137020d2610745cd87cce59a5abf3c44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/137020d2610745cd87cce59a5abf3c44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/137020d2610745cd87cce59a5abf3c44"}}, "title": "Rapid genome editing by CRISPR-Cas9-POLD3 fusion", "authors": [{"family": "Reint", "given": "Ganna", "initials": "G", "orcid": "0000-0003-4823-5485", "researcher": {"href": "https://publications.scilifelab.se/researcher/8063f0233fce42d2800af0dd8a201543.json"}}, {"family": "Li", "given": "Zhuokun", "initials": "Z", "orcid": "0000-0001-7297-6916", "researcher": {"href": "https://publications.scilifelab.se/researcher/3190ddc72cae4be88cee6bbdfbe5bd9a.json"}}, {"family": "Labun", "given": "Kornel", "initials": "K"}, {"family": "Keskitalo", "given": "Salla", "initials": "S"}, {"family": "Soppa", "given": "Inkeri", "initials": "I"}, {"family": "Mamia", "given": "Katariina", "initials": "K"}, {"family": "Tolo", "given": "Eero", "initials": "E"}, {"family": "Szymanska", "given": "Monika", "initials": "M", "orcid": "0000-0003-0957-9568", "researcher": {"href": "https://publications.scilifelab.se/researcher/a88ceae65ec04e27bfc68f49e2069533.json"}}, {"family": "Meza-Zepeda", "given": "Leonardo A", "initials": "LA"}, {"family": "Lorenz", "given": "Susanne", "initials": "S"}, {"family": "Cieslar-Pobuda", "given": "Artur", "initials": "A"}, {"family": "Hu", "given": "Xian", "initials": "X", "orcid": "0000-0002-3381-7514", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b2d7ac27cb04fbd9dd490821902baf8.json"}}, {"family": "Bordin", "given": "Diana L", "initials": "DL"}, {"family": "Staerk", "given": "Judith", "initials": "J", "orcid": "0000-0001-8698-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f30975ef27407b921667af5549a015.json"}}, {"family": "Valen", "given": "Eivind", "initials": "E"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Varjosalo", "given": "Markku", "initials": "M", "orcid": "0000-0002-1340-9732", "researcher": {"href": "https://publications.scilifelab.se/researcher/631a0a4964d747399c0b1781e546f0ab.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}, {"family": "Haapaniemi", "given": "Emma", "initials": "E", "orcid": "0000-0002-6693-8208", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef52d64bd7f4acfaa50db137d249f3c.json"}}], "type": "journal-article", "published": "2021-12-13", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "10", "issue": null, "pages": null}, "abstract": "Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein - Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.", "doi": "10.7554/elife.75415", "pmid": "34898428", "labels": {"CRISPR Functional Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-08T16:06:42.582Z", "modified": "2023-08-02T09:55:52.753Z"}, {"entity": "publication", "iuid": "a2f4cac8c5a8400dad504a02d294f38f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2f4cac8c5a8400dad504a02d294f38f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2f4cac8c5a8400dad504a02d294f38f"}}, "title": "Reply to \"CRISPR screens are feasible in TP53 wild-type cells\".", "authors": [{"family": "Haapaniemi", "given": "Emma", "initials": "E"}, {"family": "Botla", "given": "Sandeep", "initials": "S", "orcid": "0000-0001-9937-0455", "researcher": {"href": "https://publications.scilifelab.se/researcher/b212bb391c24480bb02eb187a21bd7cc.json"}}, {"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "letter", "published": "2019-08-00", "journal": {"volume": "15", "issn": "1744-4292", "issue": "8", "pages": "e9059", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Haapaniemi et al address the issues raised by Brown et al and discuss several differences between the analyses performed by the two groups.", "doi": "10.15252/msb.20199059", "pmid": "31464368", "labels": {"CRISPR Functional Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6686827"}], "notes": [], "created": "2019-12-15T09:52:16.699Z", "modified": "2021-07-06T14:39:52.728Z"}, {"entity": "publication", "iuid": "2bd73789ab074bedbd1b4bdade0c4cab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bd73789ab074bedbd1b4bdade0c4cab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bd73789ab074bedbd1b4bdade0c4cab"}}, "title": "CRISPR/Cas9 screening using unique molecular identifiers.", "authors": [{"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Botla", "given": "Sandeep K", "initials": "SK", "orcid": "0000-0001-9937-0455", "researcher": {"href": "https://publications.scilifelab.se/researcher/b212bb391c24480bb02eb187a21bd7cc.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2017-10-09", "journal": {"volume": "13", "issn": "1744-4292", "issue": "10", "pages": "945", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Loss-of-function screening by CRISPR/Cas9 gene knockout with pooled, lentiviral guide libraries is a widely applicable method for systematic identification of genes contributing to diverse cellular phenotypes. Here, Random Sequence Labels (RSLs) are incorporated into the guide library, which act as unique molecular identifiers (UMIs) to allow massively parallel lineage tracing and lineage dropout screening. RSLs greatly improve the reproducibility of results by increasing both the precision and the accuracy of screens. They reduce the number of cells needed to reach a set statistical power, or allow a more robust screen using the same number of cells.", "doi": "10.15252/msb.20177834", "pmid": "28993443", "labels": {"CRISPR Functional Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5658704"}], "notes": [], "created": "2017-10-20T10:29:09.604Z", "modified": "2021-07-06T14:41:38.936Z"}]}