{"entity": "researcher", "timestamp": "2026-08-15T12:56:59.243Z", "family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "affiliations": ["Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden. tobias.sjoblom@igp.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a"}}, "publications": [{"entity": "publication", "iuid": "823c71158dcd4b9fb085d01e55d13e48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48"}}, "title": "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.", "authors": [{"family": "Yadav", "given": "Ram Prakash", "initials": "RP"}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Xie", "given": "Minglu", "initials": "M"}, {"family": "Salehi", "given": "Maede", "initials": "M"}, {"family": "Torell", "given": "Emma", "initials": "E"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Glimelius", "given": "Ingrid", "initials": "I"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10022", "issn-l": "2041-1723"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.", "doi": "10.1038/s41467-025-66170-4", "pmid": "41238550", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66170-4"}, {"db": "pmc", "key": "PMC12618699"}], "notes": [], "created": "2025-11-17T09:00:46.632Z", "modified": "2025-11-17T09:00:47.092Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Kenrick", "given": "Josefin", "initials": "J", "orcid": "0000-0002-0110-5192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83beb37b7bc4e0aa84106bea7c6e0d0.json"}}, {"family": "Johansson", "given": "Emil", "initials": "E", "orcid": "0009-0003-1250-0678", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d953dd65ab24e8ab08aee7e7f101702.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Akyildiz", "given": "Murat", "initials": "M", "orcid": "0000-0002-2080-7528", "researcher": {"href": "https://publications.scilifelab.se/researcher/439d9835321449e4811478ad27c82a99.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Sk\u00f6ld", "given": "Hilda", "initials": "H", "orcid": "0009-0004-0961-4006", "researcher": {"href": "https://publications.scilifelab.se/researcher/bef5a1edbcab4c3286df2e2652d6f931.json"}}, {"family": "Antonopoulos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0003-2781-3872", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfd9fba645e64087a41f3bc7c3d35239.json"}}, {"family": "Apostolakis", "given": "Emmanouil", "initials": "E", "orcid": "0009-0003-6873-174X", "researcher": {"href": "https://publications.scilifelab.se/researcher/419cb52646134fe2bde5d6d700845708.json"}}, {"family": "Balcioglu", "given": "Yasin Hasan", "initials": "YH", "orcid": "0000-0002-1336-1724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4e7f3fd813e432b9a3e604a2cc26832.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-7981-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70d058e4d5bc49d7a3c958950c9d4e6d.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S"}, {"family": "Brage", "given": "Suzanne Egyhazi", "initials": "SE"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}, {"family": "Cajander", "given": "Sara", "initials": "S", "orcid": "0000-0003-3921-4244", "researcher": {"href": "https://publications.scilifelab.se/researcher/43cda9fcbe7141c9aa28d349176d21c8.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Dayangac", "given": "Murat", "initials": "M", "orcid": "0000-0002-1240-7233", "researcher": {"href": "https://publications.scilifelab.se/researcher/a72ffcb2d31744c3ac1c4e5f2221be09.json"}}, {"family": "Dinler-Doganay", "given": "Gizem", "initials": "G", "orcid": "0000-0002-3586-1287", "researcher": {"href": "https://publications.scilifelab.se/researcher/d505e0932953412683b2e511a503d489.json"}}, {"family": "Do\u011fanay", "given": "Levent", "initials": "L"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Enblad", "given": "Malin", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Falck-Jones", "given": "Sara", "initials": "S"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A", "orcid": "0000-0001-7583-282X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0543fb8f425844bcaf599f48292132a7.json"}}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Gunnarsson", "given": "Karin", "initials": "K", "orcid": "0000-0001-9986-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/943c35b7307848fbbf7ab5312aa0a432.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I", "orcid": "0000-0002-4514-7706", "researcher": {"href": "https://publications.scilifelab.se/researcher/90121ddba7fe4f928c1b121b162c2509.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Holmqvist", "given": "Marie", "initials": "M", "orcid": "0000-0001-8996-5260", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55ea451c3194ac0b5f0d49a096818bb.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B", "orcid": "0000-0003-2241-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/19120340af6c42bd8a359ce39d4a8b99.json"}}, {"family": "Hultgren", "given": "Rebecka", "initials": "R", "orcid": "0000-0002-8869-0493", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b922400ae3f43bfbdd095bc9d897ccf.json"}}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ", "orcid": "0000-0003-4122-1945", "researcher": {"href": "https://publications.scilifelab.se/researcher/adccb07f0a744e648516bd7b672d70be.json"}}, {"family": "Janols", "given": "Helena", "initials": "H", "orcid": "0000-0002-3857-163X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4a90d4b8024c84b65ec6569f21f53a.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Klareskog", "given": "Lars", "initials": "L", "orcid": "0000-0001-9601-6186", "researcher": {"href": "https://publications.scilifelab.se/researcher/c89507c56863420b89f9b417a6f44451.json"}}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications.scilifelab.se/researcher/085cca6e87fb4639b720b0e5c8c1da2a.json"}}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M", "orcid": "0000-0002-4948-8380", "researcher": {"href": "https://publications.scilifelab.se/researcher/24d1313454704814b6f591a63dc5d5cb.json"}}, {"family": "Lautenbach", "given": "Maximilian Julius", "initials": "MJ", "orcid": "0000-0001-5763-6964", "researcher": {"href": "https://publications.scilifelab.se/researcher/6de69bdbf1d5487abf499b72ba038dfb.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H", "orcid": "0000-0002-5871-268X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c5d63f995546049a240cd52052e1df.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Lipcsey", "given": "Miklos", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Meng", "given": "Lingqi", "initials": "L", "orcid": "0000-0001-9986-9205", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2974c70b2ea4ef1b546d1bdc629067b.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "A"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Nguyen", "given": "Mai Thi-Huyen", "initials": "MT", "orcid": "0009-0002-7680-1464", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e89828a6064cc6a99a8944ab6a6a6f.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Norrby-Teglund", "given": "Anna", "initials": "A", "orcid": "0000-0001-9372-1795", "researcher": {"href": "https://publications.scilifelab.se/researcher/25c11b43fc984bbca28fcc5bbf211d58.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A"}, {"family": "Nowak", "given": "Piotr", "initials": "P", "orcid": "0000-0003-2747-0734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c123e0198b6f4a80a9a46e88843c6c6f.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "Padyukov", "given": "Leonid", "initials": "L", "orcid": "0000-0003-2950-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/052dbef663f442f2a72161d634b9ce7d.json"}}, {"family": "Pauksens", "given": "Karlis", "initials": "K", "orcid": "0000-0003-2626-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/22a7a44fa1b94d5a87e561442e905432.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Reepalu", "given": "Anton", "initials": "A", "orcid": "0000-0003-1690-8921", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a2d4fc25964bc48bd8d5b3593aab5a.json"}}, {"family": "Roy", "given": "Joy", "initials": "J", "orcid": "0000-0002-5645-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/d59de368e4784a3cb56dcc634fde37ef.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sen", "given": "Meltem", "initials": "M", "orcid": "0000-0002-6248-7091", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f5b63f920994f81bc6fec1a37105cba.json"}}, {"family": "Siika", "given": "Antti", "initials": "A", "orcid": "0000-0002-2551-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/596e04ba84e54b188f93ed3e3be94ebf.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skoglund", "given": "Lovisa", "initials": "L", "orcid": "0009-0002-7863-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6bab6ea5e824b13ad5b77a6fa08523e.json"}}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K", "orcid": "0000-0003-1585-8475", "researcher": {"href": "https://publications.scilifelab.se/researcher/66bfc091e8784259bfbf0f30a996391e.json"}}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A", "orcid": "0000-0001-8928-3374", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b2d7f254c57489da8329627d49bad87.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0002-8801-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6ffa1185f4142b7ab7c372c0c139df6.json"}}, {"family": "Sund\u00e9n-Cullberg", "given": "Jonas", "initials": "J"}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"family": "Sutantiwanichkul", "given": "Thanadol", "initials": "T", "orcid": "0000-0002-1072-6863", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f33fff56f34d72bb1bbc88608ed914.json"}}, {"family": "Svedman", "given": "Fernanda Costa", "initials": "FC", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b2e407aeb49a88b1ef0f7b1e02ce7.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH", "orcid": "0000-0002-8964-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/a94e99b0020f4ef28c00bb20e1a1c8ac.json"}}, {"family": "T\u00fcrkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Unge", "given": "Christian", "initials": "C"}, {"family": "Venge", "given": "Per", "initials": "P", "orcid": "0000-0001-5863-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1695020d4d724ba8b378c992e28e21b1.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications.scilifelab.se/researcher/18460524ba914a91ad61dd2ec231c3a7.json"}}, {"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Ye\u015filkaya", "given": "Umit Haluk", "initials": "UH"}, {"family": "Yuan", "given": "Meng", "initials": "M", "orcid": "0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "b894c8f51e7b40e7b9e2c3472acdd17e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e"}}, "title": "A novel PML germline variant as a candidate predisposing genetic aberration in familial acute myeloid leukaemia.", "authors": [{"family": "Soussi", "given": "Thierry", "initials": "T", "orcid": "0000-0001-8184-3293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce7c1391f634a9684352a3c49401939.json"}}, {"family": "Kundu", "given": "Snehangshu", "initials": "S", "orcid": "0000-0003-3541-5583", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fa7619cacd842b6a6151964710315d2.json"}}, {"family": "Gerbaud", "given": "Pauline", "initials": "P"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Baskin", "given": "Berivan", "initials": "B"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Delhommeau", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0002-4915-0734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c51994ab468649ffb31f061f2a6f8023.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "207", "issue": "3", "pages": "1118-1121", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.20255", "pmid": "40954117", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12436221"}], "notes": [], "created": "2025-11-26T14:14:25.189Z", "modified": "2025-11-26T14:14:25.660Z"}, {"entity": "publication", "iuid": "8e3c080a6b6f4c1494f64bbfe3ee1dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4"}}, "title": "Identification of a small molecule targeting EPLIN as a novel strategy for the treatment of pediatric neuroblastoma and medulloblastoma.", "authors": [{"family": "Lindell", "given": "Emma", "initials": "E", "orcid": "0009-0001-2785-946X", "researcher": {"href": "https://publications.scilifelab.se/researcher/667fca56e7c74aa7984daf5dac4bbc2e.json"}}, {"family": "Guo", "given": "Jing", "initials": "J", "orcid": "0000-0002-6399-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e778f67395b491daec1b80d805ab6bd.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Lu", "given": "Xi", "initials": "X"}, {"family": "Wacker", "given": "Tabea", "initials": "T"}, {"family": "Zhong", "given": "Lei", "initials": "L"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Svanberg", "given": "Sara", "initials": "S"}, {"family": "Chowdhury", "given": "Azazul I", "initials": "AI"}, {"family": "Bergsten", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Zhang", "given": "Xiaonan", "initials": "X", "orcid": "0000-0003-4359-9079", "researcher": {"href": "https://publications.scilifelab.se/researcher/306b1ef8c6904d6b936e11442b4515f4.json"}}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "issn-l": "2041-4889", "volume": "16", "issue": "1", "pages": "554"}, "abstract": "Amplification of the MYCN proto-oncogene serves as a key marker of aggressive disease and poor treatment outcomes in certain pediatric tumors originating from the nervous system, including neuroblastoma and medulloblastoma. However, the complex nature of the challenging MYCN protein underscores the urgent need for additional targets and therapies to tackle neuroblastoma and medulloblastoma. In this study, with a primary focus on neuroblastoma and the aim of also benefiting children with medulloblastoma, we identified FLIX5, a small compound that exhibits broad cytotoxicity against both neuroblastoma and medulloblastoma cells, primarily by triggering apoptosis. Furthermore, FLIX5 enhances the cholesterol dependency of neuroblastoma cells under conditions where mitochondrial function is impaired. FLIX5 as well shows a synergistic effect when combined with vincristine, a conventional anticancer drug, against neuroblastoma cells and organoids. Through proteome integral solubility alteration, computational molecular docking predictions, and cellular thermal shift assays for target identification and validation, FLIX5 reveals EPLIN (Epithelial Protein Lost In Neoplasm) as a previously unexplored drug target. EPLIN is involved in several cellular processes, including cholesterol uptake and mitochondrial function. The discovery of FLIX5 targeting EPLIN presents new opportunities for treating malignant pediatric tumors, with the potential to target chemoresistant dormant cancer cells and broaden its therapeutic applications to other tumor types.", "doi": "10.1038/s41419-025-07876-7", "pmid": "40701975", "labels": {"NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Chemical Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287531"}, {"db": "pii", "key": "10.1038/s41419-025-07876-7"}], "notes": [], "created": "2025-09-30T09:25:55.225Z", "modified": "2025-11-25T17:06:41.935Z"}, {"entity": "publication", "iuid": "b5cadf33662a43ba963d6e97bfa96d3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5cadf33662a43ba963d6e97bfa96d3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5cadf33662a43ba963d6e97bfa96d3a"}}, "title": "Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare.", "authors": [{"family": "K\u00e4mpe", "given": "Anders", "initials": "A", "orcid": "0000-0002-1829-3855", "researcher": {"href": "https://publications.scilifelab.se/researcher/0785e17b57384962a0ff9bc7ecaa80c8.json"}}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S"}, {"family": "Walsh", "given": "Colum P", "initials": "CP"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}, {"family": "Clareborn", "given": "Anna", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Edsj\u00f6", "given": "Anders", "initials": "A", "orcid": "0000-0001-8783-8284", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fae25d88855440194b9bb11b3d18bf8.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Haag", "given": "Margareta", "initials": "M"}, {"family": "Hagwall", "given": "Anna", "initials": "A"}, {"family": "Johansson Soller", "given": "Maria", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lu", "given": "Yi", "initials": "Y", "orcid": "0000-0001-9933-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a73eafe0b0e4221a77b96800883413d.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Melin", "given": "Beatrice", "initials": "B"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Saal", "given": "Lao H", "initials": "LH", "orcid": "0000-0002-0815-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a1ec17a1d2e46e78f483f8e43f5e5f2.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B", "orcid": "0000-0002-9692-101X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea901d796bc4f3fbc53f930c5021118.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Jacobsson", "given": "Bo", "initials": "B", "orcid": "0000-0001-5079-2374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6968816ded4a50b1029ee3f4afbeed.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Persson", "given": "Bengt", "initials": "B"}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T"}], "type": "letter", "published": "2025-06-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "issn-l": "1078-8956", "volume": "31", "issue": "6", "pages": "1730-1732"}, "abstract": null, "doi": "10.1038/s41591-025-03631-9", "pmid": "40186080", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Clinical Genomics Lund": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-025-03631-9"}], "notes": [], "created": "2025-07-08T13:55:07.435Z", "modified": "2025-11-21T13:21:42.346Z"}, {"entity": "publication", "iuid": "60d83cc8c444462f8cfce90048ed5781", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60d83cc8c444462f8cfce90048ed5781.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60d83cc8c444462f8cfce90048ed5781"}}, "title": "Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer.", "authors": [{"family": "Hammarstr\u00f6m", "given": "Klara", "initials": "K", "orcid": "0000-0002-8271-2241", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e06b1abd3594e3db5eb216271b0b0a4.json"}}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be3293494cd4efe9bab07504cc1fcd0.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f3bfe35ddf41e5beb4312d3408a7ea.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd907ed1df0441b99789d3e045c4d890.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Korsavidou Hult", "given": "Nafsika", "initials": "N", "orcid": "0000-0002-5562-449X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eeafca618c14d40b4bd78b4a08f3774.json"}}, {"family": "Imam", "given": "Israa", "initials": "I", "orcid": "0000-0002-0232-2391", "researcher": {"href": "https://publications.scilifelab.se/researcher/15735120d46649e6ba5cd94c925fd375.json"}}, {"family": "Osterlund", "given": "Emerik", "initials": "E", "orcid": "0000-0003-0973-6332", "researcher": {"href": "https://publications.scilifelab.se/researcher/edf1c930ec4149e59a952cd04ff0a4f8.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}], "type": "journal article", "published": "2024-07-01", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "155", "issue": "1", "pages": "40-53", "issn-l": "0020-7136"}, "abstract": "Rectal cancer poses challenges in preoperative treatment response, with up to 30% achieving a complete response (CR). Personalized treatment relies on accurate identification of responders at diagnosis. This study aimed to unravel CR determinants, overall survival (OS), and time to recurrence (TTR) using clinical and targeted sequencing data. Analyzing 402 patients undergoing preoperative treatment, tumor stage, size, and treatment emerged as robust response predictors. CR rates were higher in smaller, early-stage, and intensively treated tumors. Targeted sequencing analyzed 216 cases, while 120 patients provided hotspot mutation data. KRAS mutation dramatically reduced CR odds by over 50% (odds ratio [OR] = 0.3 in the targeted sequencing and OR = 0.4 hotspot cohorts, respectively). In contrast, SMAD4 and SYNE1 mutations were associated with higher CR rates (OR = 6.0 and 6.8, respectively). Favorable OS was linked to younger age, CR, and low baseline carcinoembryonic antigen levels. Notably, CR and an APC mutation increased TTR, while a BRAF mutation negatively affected TTR. Beyond tumor burden, SMAD4 and SYNE1 mutations significantly influenced CR. KRAS mutations independently correlated with radiotherapy resistance, and BRAF mutations heightened recurrence risk. Intriguingly, non-responding tumors with initially small sizes carried a higher risk of recurrence. The findings, even if limited in addition to the imperfect clinical factors, offer insights into rectal cancer treatment response, guiding personalized therapeutic strategies. By uncovering factors impacting CR, OS, and TTR, this study underscores the importance of tailored approaches for rectal cancer patients. These findings, based on extensive analysis and mutation data, pave the way for personalized interventions, optimizing outcomes in the challenges of rectal cancer preoperative treatment.", "doi": "10.1002/ijc.34880", "pmid": "38376070", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-05T07:25:22.269Z", "modified": "2025-02-28T14:10:15.877Z"}, {"entity": "publication", "iuid": "2fc8ac99f46d428480fbce04b83ee0ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fc8ac99f46d428480fbce04b83ee0ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fc8ac99f46d428480fbce04b83ee0ed"}}, "title": "Loss of CYP2D6 sensitizes hepatocellular carcinomas and neuroblastomas to talazoparib", "authors": [{"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Zhang", "given": "Xiaonan", "initials": "X"}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Zhong", "given": "Lei", "initials": "L"}, {"family": "Rendo", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Nuciforo", "given": "Sandro", "initials": "S", "orcid": "0000-0002-1863-1869", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b482d9fe714486c9d25585c9820e7ee.json"}}, {"family": "Dupuis", "given": "Jordan", "initials": "J"}, {"family": "Azhar", "given": "Muhammad Al", "initials": "MA"}, {"family": "Tsiara", "given": "Ioanna", "initials": "I"}, {"family": "Seeburger", "given": "Pauline", "initials": "P"}, {"family": "Nassralla", "given": "Shahed Al", "initials": "SA"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Heim", "given": "Markus", "initials": "M", "orcid": "0000-0002-7523-4894", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0addc8ca3f3430ba6acd1d56c9fa451.json"}}, {"family": "Globisch", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4526-5788", "researcher": {"href": "https://publications.scilifelab.se/researcher/05ac9b47b0264cafad6fbf8b46bccced.json"}}], "type": "posted-content", "published": "2023-08-21", "journal": {"title": "res sq", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-3254750/v1", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-18T18:47:52.126Z", "modified": "2025-12-22T07:56:27.854Z"}, {"entity": "publication", "iuid": "bd7e4686333d489495edae6e2cb9e54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/978fc6fea7d54f5b81a8b5a87efa083a.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e801966db544e6286fb2b4037980dba.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a52b4426da84787aeb56b8d6232ba87.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4308"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-11-29T19:16:18.991Z", "modified": "2024-01-16T13:48:32.880Z"}, {"entity": "publication", "iuid": "84a78d53a4334fc19fc2291e44e6e963", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a78d53a4334fc19fc2291e44e6e963.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a78d53a4334fc19fc2291e44e6e963"}}, "title": "Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.", "authors": [{"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hedlund-Lindberg", "given": "Julia", "initials": "J"}, {"family": "Svensson", "given": "Johanna", "initials": "J"}, {"family": "Manninen", "given": "Johanna", "initials": "J"}, {"family": "\u00d6st", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Ramsell", "given": "Jon", "initials": "J"}, {"family": "\u00c5slin", "given": "Matilda", "initials": "M", "orcid": "0000-0002-2450-6415", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3f0bf2483a543d689fb6e95804066dd.json"}}, {"family": "Ivansson", "given": "Emma", "initials": "E"}, {"family": "Lomnytska", "given": "Marta", "initials": "M"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-7135-3132", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb40cfcba9154502ad1d530c5e4a8a66.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2022-03-30", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "7", "issn-l": "2072-6694"}, "abstract": "Ovarian cancer is the eighth most common cancer among women and has a 5-year survival of only 30-50%. The survival is close to 90% for patients in stage I but only 20% for patients in stage IV. The presently available biomarkers have insufficient sensitivity and specificity for early detection and there is an urgent need to identify novel biomarkers.\n\nWe employed the Explore PEA technology for high-precision analysis of 1463 plasma proteins and conducted a discovery and replication study using two clinical cohorts of previously untreated patients with benign or malignant ovarian tumours (N = 111 and N = 37).\n\nThe discovery analysis identified 32 proteins that had significantly higher levels in malignant cases as compared to benign diagnoses, and for 28 of these, the association was replicated in the second cohort. Multivariate modelling identified three highly accurate models based on 4 to 7 proteins each for separating benign tumours from early-stage and/or late-stage ovarian cancers, all with AUCs above 0.96 in the replication cohort. We also developed a model for separating the early-stage from the late-stage achieving an AUC of 0.81 in the replication cohort. These models were based on eleven proteins in total (ALPP, CXCL8, DPY30, IL6, IL12, KRT19, PAEP, TSPAN1, SIGLEC5, VTCN1, and WFDC2), notably without MUCIN-16. The majority of the associated proteins have been connected to ovarian cancer but not identified as potential biomarkers.\n\nThe results show the ability of using high-precision proteomics for the identification of novel plasma protein biomarker candidates for the early detection of ovarian cancer.", "doi": "10.3390/cancers14071757", "pmid": "35406529", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8997113"}, {"db": "pii", "key": "cancers14071757"}], "notes": [], "created": "2022-05-06T10:19:41.790Z", "modified": "2022-12-02T08:50:06.321Z"}, {"entity": "publication", "iuid": "a8fd622b15c7467f997c96de28f1a14e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e"}}, "title": "Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.", "authors": [{"family": "Mathioudaki", "given": "Argyri", "initials": "A"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Saksena", "given": "Pushpa", "initials": "P"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "19304", "issn-l": "2045-2322"}, "abstract": "Breast cancer (BC) is a genetically heterogeneous disease with high prevalence in Northern Europe. However, there has been no detailed investigation into the Scandinavian somatic landscape. Here, in a homogeneous Swedish cohort, we describe the somatic events underlying BC, leveraging a targeted next-generation sequencing approach. We designed a 20.5 Mb array targeting coding and regulatory regions of genes with a known role in BC (n = 765). The selected genes were either from human BC studies (n = 294) or from within canine mammary tumor associated regions (n = 471). A set of predominantly estrogen receptor positive tumors (ER + 85%) and their normal tissue counterparts (n = 61) were sequenced to ~ 140 \u00d7 and 85 \u00d7 mean target coverage, respectively. MuTect2 and VarScan2 were employed to detect single nucleotide variants (SNVs) and copy number aberrations (CNAs), while MutSigCV (SNVs) and GISTIC (CNAs) algorithms estimated the significance of recurrent somatic events. The significantly mutated genes (q \u2264 0.01) were PIK3CA (28% of patients), TP53 (21%) and CDH1 (11%). However, histone modifying genes contained the largest number of variants (KMT2C and ARID1A, together 28%). Mutations in KMT2C were mutually exclusive with PI3KCA mutations (p \u2264 0. 001) and half of these affect the formation of a functional PHD domain. The tumor suppressor CDK10 was deleted in 80% of the cohort while the oncogene MDM4 was amplified. Mutational signature analyses pointed towards APOBEC deaminase activity (COSMIC signature 2) and DNA mismatch repair (COSMIC signature 6). We noticed two significantly distinct patterns related to patient age; TP53 being more mutated in the younger group (29% vs 9% of patients) and CDH23 mutations were absent from the older group. The increased somatic mutation prevalence in the histone modifying genes KMT2C and ARID1A distinguishes the Swedish cohort from previous studies. KMT2C regulates enhancer activation and assists tumor proliferation in a hormone-rich environment, possibly pointing to a role in ER + BC, especially in older cases. Finally, age of onset appears to affect the mutational landscape suggesting that a larger age-diverse population incorporating more molecular subtypes should be studied to elucidate the underlying mechanisms.", "doi": "10.1038/s41598-020-74580-1", "pmid": "33168853", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-74580-1"}, {"db": "pmc", "key": "PMC7653953"}], "notes": [], "created": "2020-12-08T23:29:22.318Z", "modified": "2024-01-16T13:48:41.384Z"}, {"entity": "publication", "iuid": "7c8b4a4859ad48729c578fc278db0e40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8b4a4859ad48729c578fc278db0e40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8b4a4859ad48729c578fc278db0e40"}}, "title": "Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression.", "authors": [{"family": "Larsson", "given": "Chatarina", "initials": "C"}, {"family": "Cordeddu", "given": "Lina", "initials": "L"}, {"family": "Siggens", "given": "Lee", "initials": "L"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Ali", "given": "Muhammad Akhtar", "initials": "MA"}, {"family": "Pristov\u0161ek", "given": "Nu\u0161a", "initials": "N"}, {"family": "Hartman", "given": "Karin", "initials": "K"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}], "type": "journal article", "published": "2020-05-29", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "12", "issue": "1", "pages": "74", "issn-l": "1868-7075"}, "abstract": "The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types; however, the effects of mutations on epigenome organization, gene expression, and cell growth are not clear. A frequently recurring mutation in colorectal cancer (CRC) with microsatellite instability is a single nucleotide deletion within the exon 38 poly-A(9) repeat (c.8390delA) which results in frameshift preceding the functional carboxy-terminal SET domain. To study effects of KMT2C expression in CRC cells, we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous c.8390delA mutant.\n\nGene editing resulted in increased KMT2C expression, increased H3K4me1 levels, altered gene expression profiles, and subtle negative effects on cell growth, where higher dependence and stronger effects of KMT2C expression were observed in RKO compared to HCT116 cells. Surprisingly, we found that the two RKO and HCT116 CRC cell lines have distinct baseline H3K4me1 epigenomic profiles. In RKO cells, a flatter genome-wide H3K4me1 profile was associated with more increased H3K4me1 deposition at enhancers, reduced cell growth, and more differential gene expression relative to HCT116 cells when KMT2C was restored. Profiling of H3K4me1 did not indicate a highly specific regulation of gene expression as KMT2C-induced H3K4me1 deposition was found globally and not at a specific enhancer sub-set in the engineered cells. Although we observed variation in differentially regulated gene sets between cell lines and individual clones, differentially expressed genes in both cell lines included genes linked to known cancer signaling pathways, estrogen response, hypoxia response, and aspects of immune system regulation.\n\nHere, KMT2C restoration reduced CRC cell growth and reinforced genome-wide H3K4me1 deposition at enhancers; however, the effects varied depending upon the H3K4me1 status of KMT2C deficient cells. Results indicate that KMT2C inactivation may promote colorectal cancer development through transcriptional dysregulation in several pathways with known cancer relevance.", "doi": "10.1186/s13148-020-00863-z", "pmid": "32471474", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-020-00863-z"}, {"db": "pmc", "key": "PMC7257146"}], "notes": [], "created": "2020-08-25T13:15:07.034Z", "modified": "2024-01-16T13:48:42.473Z"}, {"entity": "publication", "iuid": "f2317acce3bc4c839fb919d77f6e0a01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2317acce3bc4c839fb919d77f6e0a01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2317acce3bc4c839fb919d77f6e0a01"}}, "title": "Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.", "authors": [{"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be3293494cd4efe9bab07504cc1fcd0.json"}}, {"family": "Aaseb\u00f8", "given": "Kristine", "initials": "K", "orcid": "0000-0003-3575-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/d615e45a5b3340a79d3bd16c921c2ce2.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f3bfe35ddf41e5beb4312d3408a7ea.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Dragomir", "given": "Anca", "initials": "A", "orcid": "0000-0003-2777-8114", "researcher": {"href": "https://publications.scilifelab.se/researcher/da4c734efcc240d589dc5c99a433d904.json"}}, {"family": "Pfeiffer", "given": "Per", "initials": "P"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd907ed1df0441b99789d3e045c4d890.json"}}, {"family": "Sorbye", "given": "Halfdan", "initials": "H"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Acta Oncol", "issn": "1651-226X", "volume": "59", "issue": "4", "pages": "417-426", "issn-l": "0284-186X"}, "abstract": "Background: We have reported that BRAF V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations.Material and methods: A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan-Meier estimator and the Cox regression analysis.Results: Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides BRAF V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. BRAF V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the BRAF mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, p = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors.Conclusions: Right-sided tumor location, BRAF V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.", "doi": "10.1080/0284186X.2019.1711169", "pmid": "31924107", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-02-11T10:07:57.408Z", "modified": "2024-01-16T13:48:42.696Z"}, {"entity": "publication", "iuid": "d18a2001ca2a484ea1267aaed4906d19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d18a2001ca2a484ea1267aaed4906d19"}}, "title": "Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.", "authors": [{"family": "Rendo", "given": "Veronica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/d79942eca68f4b2d8c2e72cf258f1213.json"}}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Ng", "given": "Adrian", "initials": "A"}, {"family": "O\u02bcBrien", "given": "Casey", "initials": "C", "orcid": "0000-0002-6572-4881", "researcher": {"href": "https://publications.scilifelab.se/researcher/5782c9d8ce674fe8ad55eba0d514da54.json"}}, {"family": "Giannakis", "given": "Marios", "initials": "M"}, {"family": "Artursson", "given": "Per", "initials": "P", "orcid": "0000-0002-3708-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/31575936c2714e1eb2f35c12df9a65a8.json"}}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Cheong", "given": "Ian", "initials": "I"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}], "type": "journal article", "published": "2020-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1308"}, "abstract": "Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.", "doi": "10.1038/s41467-020-15111-4", "pmid": "32161261", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15111-4"}, {"db": "pmc", "key": "PMC7066191"}], "notes": [], "created": "2020-03-17T11:11:47.766Z", "modified": "2025-10-17T13:05:08.058Z"}, {"entity": "publication", "iuid": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}]}