{"entity": "researcher", "timestamp": "2026-04-13T05:42:54.257Z", "family": "Zhou", "given": "Stanley", "initials": "S", "orcid": "0000-0001-8187-0128", "affiliations": ["Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.", "Department of Medical Biophysics, University of Toronto, Toronto, Canada."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383"}}, "publications": [{"entity": "publication", "iuid": "2749014de2334181bacad583b927535e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2749014de2334181bacad583b927535e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2749014de2334181bacad583b927535e"}}, "title": "An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.", "authors": [{"family": "Shrestha", "given": "Raunak", "initials": "R", "orcid": "0000-0002-1144-1413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8056667cd46ecbec79e2789ae8029.json"}}, {"family": "Chesner", "given": "Lisa N", "initials": "LN", "orcid": "0009-0007-2779-8824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ee8b85578474244893baffac823a58c.json"}}, {"family": "Zhang", "given": "Meng", "initials": "M", "orcid": "0000-0003-1042-6294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d24c6c51c024ac0b27a5162c4c2fa91.json"}}, {"family": "Zhou", "given": "Stanley", "initials": "S", "orcid": "0000-0001-8187-0128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e22a4caa4fe04b2bbf6af8d5149f0383.json"}}, {"family": "Foye", "given": "Adam", "initials": "A", "orcid": "0000-0002-9910-9836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c8c402b4a243ab95b9d20ecc43d4b9.json"}}, {"family": "Lundberg", "given": "Arian", "initials": "A", "orcid": "0000-0002-6630-2787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa2c7c8963840bfb6a22d7c5cfe35f9.json"}}, {"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": "Zhu", "given": "Xiaolin", "initials": "X", "orcid": "0000-0002-3221-595X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30d1c66f02ef4b5abc414a110705ccf9.json"}}, {"family": "Moreno-Rodriguez", "given": "Thaidy", "initials": "T", "orcid": "0000-0003-3588-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9adfae1d354f85a76d66de8bc08cba.json"}}, {"family": "Li", "given": "Haolong", "initials": "H", "orcid": "0000-0002-8628-9698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc2d2abba854008b56d417e6083614c.json"}}, {"family": "SU2C/PCF West Coast Prostate Cancer Dream Team", "given": "", "initials": ""}, {"family": "Alumkal", "given": "Joshi J", "initials": "JJ", "orcid": "0000-0003-1278-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92169d39d28f4819959b032eff1b1b80.json"}}, {"family": "Aggarwal", "given": "Rahul", "initials": "R", "orcid": "0000-0001-7003-7982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6eb510bedd42bbb6f57e03e724efba.json"}}, {"family": "Small", "given": "Eric J", "initials": "EJ", "orcid": "0000-0003-3191-6268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5a6d3bacede42059d6bf0f2cbfe0fec.json"}}, {"family": "Lupien", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-0929-9478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1967a3e4d1ff43998c93ea10d874cd01.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": "2024-09-16", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "84", "issue": "18", "pages": "3086-3100", "issn-l": "0008-5472"}, "abstract": "Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease that resists therapy targeting androgen signaling, the primary driver of prostate cancer. mCRPC resists androgen receptor (AR) inhibitors by amplifying AR signaling or by evolving into therapy-resistant subtypes that do not depend on AR. Elucidation of the epigenetic underpinnings of these subtypes could provide important insights into the drivers of therapy resistance. In this study, we produced chromatin accessibility maps linked to the binding of lineage-specific transcription factors (TF) by performing assay for transposase-accessible chromatin sequencing on 70 mCRPC tissue biopsies integrated with transcriptome and whole-genome sequencing. mCRPC had a distinct global chromatin accessibility profile linked to AR function. Analysis of TF occupancy across accessible chromatin revealed 203 TFs associated with mCRPC subtypes. Notably, ZNF263 was identified as a putative prostate cancer TF with a significant impact on gene activity in the double-negative subtype (AR- neuroendocrine-), potentially activating MYC targets. Overall, this analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during progression to mCRPC. Significance: Integration of a large cohort of transcriptome, whole-genome, and ATAC sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.", "doi": "10.1158/0008-5472.CAN-24-0890", "pmid": "38990734", "labels": {"DDLS Fellow": null, "Arian Lundberg": null}, "xrefs": [{"db": "mid", "key": "NIHMS2049608"}, {"db": "pmc", "key": "PMC12248187"}, {"db": "pii", "key": "746391"}], "notes": [], "created": "2025-11-14T07:49:57.398Z", "modified": "2025-11-14T07:49:57.837Z"}, {"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"}]}