{"entity": "researcher", "timestamp": "2026-05-12T22:15:41.615Z", "family": "He", "given": "Hansen H", "initials": "HH", "orcid": "0000-0003-2898-3363", "affiliations": ["Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.", "Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98"}}, "publications": [{"entity": "publication", "iuid": "468d8c3dab1c48d889d35d3e63b16ac1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/468d8c3dab1c48d889d35d3e63b16ac1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/468d8c3dab1c48d889d35d3e63b16ac1"}}, "title": "Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer.", "authors": [{"family": "Zhao", "given": "Shuang G", "initials": "SG", "orcid": "0000-0002-9166-6507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7d9e7e456be4376adb63a3e5ab895a7.json"}}, {"family": "Bootsma", "given": "Matthew", "initials": "M"}, {"family": "Zhou", "given": "Stanley", "initials": "S", "orcid": "0000-0001-8187-0128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383.json"}}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Pan", "given": "Chu", "initials": "C"}, {"family": "Arlidge", "given": "Christopher", "initials": "C"}, {"family": "Hawley", "given": "James R", "initials": "JR"}, {"family": "Foye", "given": "Adam", "initials": "A"}, {"family": "Weinstein", "given": "Alana S", "initials": "AS", "orcid": "0000-0002-1563-9072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e16ba4d459704a96adc34a85197bab05.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Li", "given": "Haolong", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "Chesner", "given": "Lisa N", "initials": "LN"}, {"family": "Rydzewski", "given": "Nicholas R", "initials": "NR"}, {"family": "Helzer", "given": "Kyle T", "initials": "KT", "orcid": "0000-0003-3853-5564", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7011e2b72c254794baf945f716d3372d.json"}}, {"family": "Shi", "given": "Yue", "initials": "Y", "orcid": "0000-0002-2860-2666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6128013110c14fedaef6e2ad9924006c.json"}}, {"family": "West Coast Dream Team Consortium", "given": "", "initials": ""}, {"family": "Lynch", "given": "Molly", "initials": "M"}, {"family": "Dehm", "given": "Scott M", "initials": "SM", "orcid": "0000-0002-7827-5579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb947d721b424bb190ddf41a808a2cb0.json"}}, {"family": "Lang", "given": "Joshua M", "initials": "JM", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "He", "given": "Hansen H", "initials": "HH", "orcid": "0000-0003-2898-3363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98.json"}}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Zwart", "given": "Wilbert", "initials": "W", "orcid": "0000-0002-9823-7289", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014603af06df4629b83fb3e7aa17710a.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M"}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "56", "issue": "8", "pages": "1689-1700", "issn-l": "1061-4036"}, "abstract": "The impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2-ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.", "doi": "10.1038/s41588-024-01826-3", "pmid": "39020220", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC11319208"}, {"db": "pii", "key": "10.1038/s41588-024-01826-3"}], "notes": [], "created": "2025-11-14T07:50:01.698Z", "modified": "2025-11-14T07:50:01.999Z"}, {"entity": "publication", "iuid": "995c9d0360cd4a8697f31e6faee4eef6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/995c9d0360cd4a8697f31e6faee4eef6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/995c9d0360cd4a8697f31e6faee4eef6"}}, "title": "The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.", "authors": [{"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Zhao", "given": "Shuang G", "initials": "SG"}, {"family": "Levy", "given": "Samuel", "initials": "S", "orcid": "0000-0002-4444-5103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d205805d1cfb4e71ace25822afb039cb.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Ning", "given": "Yuhong", "initials": "Y"}, {"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"family": "Herberts", "given": "Cameron", "initials": "C", "orcid": "0000-0002-9929-8374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/951e9991fa8a46708c499649d1b6da59.json"}}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Hua", "given": "Junjie T", "initials": "JT", "orcid": "0000-0002-1197-1174", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac6c246ec5104f86a2eae545eb2a8155.json"}}, {"family": "Li", "given": "Haolong", "initials": "H"}, {"family": "Bergamaschi", "given": "Anna", "initials": "A", "orcid": "0000-0001-8709-1766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e4bf75e08ef47cda746d7ef8d563b78.json"}}, {"family": "Maurice-Dror", "given": "Corinne", "initials": "C", "orcid": "0000-0003-4455-4497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e527b177e77f42188e783b702851d298.json"}}, {"family": "Maheshwari", "given": "Ashutosh", "initials": "A"}, {"family": "Chen", "given": "Sujun", "initials": "S"}, {"family": "Ng", "given": "Sarah W S", "initials": "SWS", "orcid": "0000-0002-7647-6940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d889d4ea89443ef9898994e886fab85.json"}}, {"family": "Ye", "given": "Wenbin", "initials": "W", "orcid": "0000-0002-9303-9363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b717fa60edd4b7aa6e7dc899bff0767.json"}}, {"family": "Petricca", "given": "Jessica", "initials": "J"}, {"family": "Fraser", "given": "Michael", "initials": "M"}, {"family": "Chesner", "given": "Lisa", "initials": "L"}, {"family": "Perry", "given": "Marc D", "initials": "MD", "orcid": "0000-0001-6476-2942", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78f79ccc14c042b49c4b223887c717ed.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Chen", "given": "William S", "initials": "WS"}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Chou", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-1258-0391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a72f7d3b2d4f72a8ebfc23f36f3714.json"}}, {"family": "Morgans", "given": "Alicia K", "initials": "AK"}, {"family": "Beer", "given": "Tomasz M", "initials": "TM", "orcid": "0000-0001-5600-9993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c828b8adf0944e72aaacab129733f181.json"}}, {"family": "Thomas", "given": "George V", "initials": "GV"}, {"family": "Gleave", "given": "Martin", "initials": "M"}, {"family": "Lloyd", "given": "Paul", "initials": "P", "orcid": "0000-0003-3508-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96da8d6dbf344cf9a2e36a864ad8ab57.json"}}, {"family": "Phillips", "given": "Tierney", "initials": "T"}, {"family": "McCarthy", "given": "Erin", "initials": "E", "orcid": "0000-0002-3845-4142", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/122a0753d84d47649be4060eb51e8a4d.json"}}, {"family": "Haffner", "given": "Michael C", "initials": "MC", "orcid": "0000-0003-0809-6425", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce395fe9a8b4fcdaec08d5d1cb37dde.json"}}, {"family": "Zoubeidi", "given": "Amina", "initials": "A", "orcid": "0000-0002-0498-142X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a96ebc9e3f464db8b25305742981ed8d.json"}}, {"family": "Annala", "given": "Matti", "initials": "M"}, {"family": "Reiter", "given": "Robert E", "initials": "RE", "orcid": "0000-0002-7962-3985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a81ac4aa295d40d6825364129548f95d.json"}}, {"family": "Rettig", "given": "Matthew B", "initials": "MB", "orcid": "0000-0002-7394-3056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df1dd288962643beb53cce332f615144.json"}}, {"family": "Witte", "given": "Owen N", "initials": "ON", "orcid": "0000-0003-4461-4533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/435dcbfb32af474a9027576c7dc49ec6.json"}}, {"family": "Fong", "given": "Lawrence", "initials": "L", "orcid": "0000-0002-6428-428X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0124854879b543d8b9653fd99cce332c.json"}}, {"family": "Bose", "given": "Rohit", "initials": "R", "orcid": "0000-0002-6785-0697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af6c55d3791a4419813918497eef18b3.json"}}, {"family": "Huang", "given": "Franklin W", "initials": "FW"}, {"family": "Luo", "given": "Jianhua", "initials": "J", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Lang", "given": "Joshua M", "initials": "JM", "orcid": "0000-0002-0943-8872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d37a2599fa044894abc8642baa80e00b.json"}}, {"family": "Mahajan", "given": "Nupam P", "initials": "NP", "orcid": "0000-0002-4150-602X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7e3a532024d413585c0b943b37de3e5.json"}}, {"family": "Lara", "given": "Primo N", "initials": "PN"}, {"family": "Evans", "given": "Christopher P", "initials": "CP", "orcid": "0000-0001-5626-8901", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8a9ee6f18f94c9ea82f34401edc3467.json"}}, {"family": "Tran", "given": "Phuoc T", "initials": "PT", "orcid": "0000-0002-0147-0376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa2bdba7d34d48b89dd173cd0af631f1.json"}}, {"family": "Posadas", "given": "Edwin M", "initials": "EM", "orcid": "0000-0001-8649-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ac1885a27d499b863843697d82d870.json"}}, {"family": "He", "given": "Chuan", "initials": "C"}, {"family": "Cui", "given": "Xiao-Long", "initials": "XL"}, {"family": "Huang", "given": "Jiaoti", "initials": "J"}, {"family": "Zwart", "given": "Wilbert", "initials": "W", "orcid": "0000-0002-9823-7289", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014603af06df4629b83fb3e7aa17710a.json"}}, {"family": "Gilbert", "given": "Luke A", "initials": "LA"}, {"family": "Maher", "given": "Christopher A", "initials": "CA", "orcid": "0000-0002-9035-603X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d6e57151d8f42b3af517e57cd09baa0.json"}}, {"family": "Boutros", "given": "Paul C", "initials": "PC", "orcid": "0000-0003-0553-7520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8dbb2a0bed664b03b96b34bd73d65993.json"}}, {"family": "Chi", "given": "Kim N", "initials": "KN", "orcid": "0000-0002-3782-7226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ee7573962f6411688894c17260e1095.json"}}, {"family": "Ashworth", "given": "Alan", "initials": "A", "orcid": "0000-0003-1446-7878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/217e8097b1a14deba9247b30c1b978a7.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ"}, {"family": "He", "given": "Housheng H", "initials": "HH", "orcid": "0000-0003-2898-3363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/487cb044249647b2a1608be1a33dff98.json"}}, {"family": "Wyatt", "given": "Alexander W", "initials": "AW", "orcid": "0000-0003-2399-0329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41e8ef800a344c68be341f0691438260.json"}}, {"family": "Quigley", "given": "David A", "initials": "DA", "orcid": "0000-0002-4726-1473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7672a24a905407c8b5f9d1e28deea02.json"}}, {"family": "Feng", "given": "Felix Y", "initials": "FY", "orcid": "0000-0002-0963-7687", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5af5c0e774941ac97890f17640a339e.json"}}], "type": "journal article", "published": "2022-11-02", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "82", "issue": "21", "pages": "3888-3902", "issn-l": "0008-5472"}, "abstract": "Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease.\n\nIn prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.", "doi": "10.1158/0008-5472.CAN-22-1123", "pmid": "36251389", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "pmc", "key": "PMC9627125"}, {"db": "pii", "key": "709960"}], "notes": [], "created": "2025-11-14T07:51:45.135Z", "modified": "2025-11-14T07:51:46.107Z"}]}