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"authors": [{"family": "Borgenvik", "given": "Anna", "initials": "A", "orcid": "0000-0003-4696-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca3b4c4e7b2b4fe4867c4e356957d4c9.json"}}, {"family": "Holmberg", "given": "Karl O", "initials": "KO", "orcid": "0000-0002-4402-0586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/469c34ade5f34855880bd40a0ed93a5b.json"}}, {"family": "Bolin", "given": "Sara", "initials": "S", "orcid": "0000-0003-2835-1518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/144233601c624bcd815822ff601d5e3e.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75b5d6dc5cde46b8aca859fb961bf1de.json"}}, {"family": "Savov", "given": "Vasil", "initials": "V", "orcid": "0000-0003-2347-1975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e70244e16a3478e83abd7072ec7610b.json"}}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G", "orcid": "0000-0002-7762-1468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4bd52a448ba4dae883c2e14cddd2699.json"}}, {"family": "Hutter", "given": "Sonja", "initials": "S", "orcid": "0000-0003-3340-9315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68742a90cc194135a0eb33d52fe8b17a.json"}}, {"family": "Garancher", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-5779-2860", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a08bf535ab73447baf9f6fef6a2a34cd.json"}}, {"family": "Rahmanto", "given": "Aldwin Suryo", "initials": "AS", "orcid": "0000-0002-4593-286X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59328511ffe441f08443f83089cc909b.json"}}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4557-2390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad8f5ab0560d4b7596ddd5e407b96d8f.json"}}, {"family": "Olsen", "given": "Thale Kristin", "initials": "TK", "orcid": "0000-0003-4655-7384", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edb08108179a4b94a69eeca5809df636.json"}}, {"family": "Mainwaring", "given": "Oliver J", "initials": "OJ", "orcid": "0000-0002-7973-9849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29515b9bedc74325aa50a0da62cd299a.json"}}, {"family": "Sattanino", "given": "Damiana", "initials": "D", "orcid": "0000-0002-2747-4842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e621b0c6b77443f083541dd2fd65ab34.json"}}, {"family": "Verbaan", "given": "Annemieke D", "initials": "AD", "orcid": "0000-0001-6793-0577", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/625389e761a746d6b9c65ab0c81d8582.json"}}, {"family": "Rusert", "given": "Jessica M", "initials": "JM", "orcid": "0000-0003-0751-2693", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19ba859c845b4578b0b7fe729033c01a.json"}}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0003-3942-6271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63e6602d2807417684239b93eb065a26.json"}}, {"family": "Bravo", "given": "Mar Ballester", "initials": "MB", "orcid": "0000-0002-1371-6679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fc8169b243f403bbb9d85a2cc51a20a.json"}}, {"family": "Dang", "given": "Yonglong", "initials": "Y", "orcid": "0000-0001-9705-5507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a828f29d1e8f40a69087ea74c89bc32c.json"}}, {"family": "Wenz", "given": "Amelie S", "initials": "AS", "orcid": "0000-0003-1929-382X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/262d770d769340bc8cf743701280a879.json"}}, {"family": "Richardson", "given": "Stacey", "initials": "S", "orcid": "0000-0003-1841-6330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bae77ca73b1845cb94fbae185a0d5d72.json"}}, {"family": "Fotaki", "given": "Grammatiki", "initials": "G", "orcid": "0000-0002-1343-1921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b70b2fd7c1e348668fb7355bec1fcc3b.json"}}, {"family": "Hill", "given": "Rebecca M", "initials": "RM", "orcid": "0000-0001-8405-2219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1259bdc29b04296a844a8e51c538990.json"}}, {"family": "Dubuc", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-3447-6715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/98d65b7575504dd7bc1419885b7c5bdd.json"}}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d630aa01038d4be68a001ae0fd4f3def.json"}}, {"family": "Remke", "given": "Marc", "initials": "M", "orcid": "0000-0002-9404-9993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/975d2595635e45c49b84050b802a9251.json"}}, {"family": "\u010can\u010der", "given": "Matko", "initials": "M", "orcid": "0000-0001-5825-5151", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05cbffef1ba74a4890860f33af1f5719.json"}}, {"family": "Jernberg-Wiklund", "given": "Helena", "initials": "H", "orcid": "0000-0002-9319-7986", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1e229ba71ec4129ac7ca516f90838ef.json"}}, {"family": "Giraud", "given": "G\u00e9raldine", "initials": "G", "orcid": "0000-0002-2771-9889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b71981055bfa4c1180c753e61b5b0919.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffb9d3c94e54fac97be6c78586940eb.json"}}, {"family": "Taylor", "given": "Michael D", "initials": "MD", "orcid": "0000-0001-7009-3466", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/619748747921467fa6c6ec4a973f2d1d.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O", "orcid": "0000-0002-0316-0195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bc4930422a046f69295e2c59a569657.json"}}, {"family": "Clifford", "given": "Steven C", "initials": "SC", "orcid": "0000-0003-4893-2184", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd7e72eebce545f99f8d96a4ead4b395.json"}}, {"family": "Sch\u00fcller", "given": "Ulrich", "initials": "U", "orcid": "0000-0002-8731-1121", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bfed174354240068d313e96bc371611.json"}}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ", "orcid": "0000-0002-7463-8352", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ca40f1c54d43d0af707c509bff1e9a.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H", "orcid": "0000-0002-0364-2709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ae643d4831f469c95c3d5b3955784ea.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e673fa8c86348fb8c1a2ae34ba7ba9a.json"}}], "type": "journal article", "published": "2022-12-16", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "82", "issue": "24", "pages": "4586-4603", "issn-l": "0008-5472"}, "abstract": "Relapse is the leading cause of death in patients with medulloblastoma, the most common malignant pediatric brain tumor. A better understanding of the mechanisms underlying recurrence could lead to more effective therapies for targeting tumor relapses. Here, we observed that SOX9, a transcription factor and stem cell/glial fate marker, is limited to rare, quiescent cells in high-risk medulloblastoma with MYC amplification. In paired primary-recurrent patient samples, SOX9-positive cells accumulated in medulloblastoma relapses. SOX9 expression anti-correlated with MYC expression in murine and human medulloblastoma cells. However, SOX9-positive cells were plastic and could give rise to a MYC high state. To follow relapse at the single-cell level, an inducible dual Tet model of medulloblastoma was developed, in which MYC expression was redirected in vivo from treatment-sensitive bulk cells to dormant SOX9-positive cells using doxycycline treatment. SOX9 was essential for relapse initiation and depended on suppression of MYC activity to promote therapy resistance, epithelial-mesenchymal transition, and immune escape. p53 and DNA repair pathways were downregulated in recurrent tumors, whereas MGMT was upregulated. Recurrent tumor cells were found to be sensitive to treatment with an MGMT inhibitor and doxorubicin. These findings suggest that recurrence-specific targeting coupled with DNA repair inhibition comprises a potential therapeutic strategy in patients affected by medulloblastoma relapse.\n\nSOX9 facilitates therapy escape and recurrence in medulloblastoma via temporal inhibition of MYC/MYCN genes, revealing a strategy to specifically target SOX9-positive cells to prevent tumor relapse.", "doi": "10.1158/0008-5472.CAN-22-2108", "pmid": "36219398", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9755969"}, {"db": "pii", "key": "709709"}], "notes": [], "created": "2026-08-20T12:11:07.388Z", "modified": "2026-08-20T12:11:07.663Z"}, {"entity": "publication", "iuid": "cf3c179176354f60b3454b5d80a14496", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf3c179176354f60b3454b5d80a14496.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf3c179176354f60b3454b5d80a14496"}}, "title": "FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.", "authors": [{"family": "Zhao", "given": "Linxuan", "initials": "L", "orcid": "0000-0002-8883-5656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7578093c7e0c4220a0035bc2ff7a482b.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Polavarapu", "given": "Vamsi Krishna", "initials": "VK"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Valero-Mart\u00ednez", "given": "Blanca", "initials": "B"}, {"family": "Dang", "given": "Yonglong", "initials": "Y"}, {"family": "Maturi", "given": "Nagaprathyusha", "initials": "N"}, {"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Neves", "given": "In\u00eas", "initials": "I"}, {"family": "Yildirim", "given": "Irem", "initials": "I"}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffb9d3c94e54fac97be6c78586940eb.json"}}], "type": "journal article", "published": "2021-12-02", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "21", "pages": "e125", "issn-l": "0305-1048"}, "abstract": "The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing \u223c4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.", "doi": "10.1093/nar/gkab813", "pmid": "34534335", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8643707"}, {"db": "pii", "key": "6371973"}], "notes": [], "created": "2026-08-20T09:49:43.106Z", "modified": "2026-08-20T09:49:43.237Z"}]}