{"entity": "researcher", "timestamp": "2026-08-15T06:25:28.691Z", "family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "affiliations": ["Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy.", "Department of Medical Sciences, University of Turin, Turin, Italy."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60"}}, "publications": [{"entity": "publication", "iuid": "8acfeb033c3c459a9cff10bf8bb576c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9"}}, "title": "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.", "authors": [{"family": "Zhang", "given": "Ning", "initials": "N"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Bellomo", "given": "Sara E", "initials": "SE"}, {"family": "Longo", "given": "Gabriel M C", "initials": "GMC", "orcid": "0000-0003-2028-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/2afe47a108d0451ebaf8269a0f18eb84.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Su", "given": "Peng", "initials": "P"}, {"family": "Han", "given": "Bo", "initials": "B"}, {"family": "Wang", "given": "Wanzhong", "initials": "W"}, {"family": "Onorato", "given": "Sofia", "initials": "S"}, {"family": "Grassini", "given": "Dora", "initials": "D"}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Giordano", "given": "Silvia", "initials": "S", "orcid": "0000-0003-1854-1086", "researcher": {"href": "https://publications.scilifelab.se/researcher/7072fc7ce1d44d0392b4ba3da82a16fb.json"}}, {"family": "Yang", "given": "Qifeng", "initials": "Q"}, {"family": "Sapino", "given": "Anna", "initials": "A", "orcid": "0000-0003-3542-9571", "researcher": {"href": "https://publications.scilifelab.se/researcher/b77045e1832b4267b330df154cbe80db.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Roukos", "given": "Vassilis", "initials": "V", "orcid": "0000-0002-5065-3937", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5da3165b15741ff967e77618bd96cc1.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3475", "issn-l": "2041-1723"}, "abstract": "Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.", "doi": "10.1038/s41467-024-47664-z", "pmid": "38658552", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11043350"}, {"db": "pii", "key": "10.1038/s41467-024-47664-z"}], "notes": [], "created": "2024-05-17T09:16:39.558Z", "modified": "2024-11-25T10:16:43.449Z"}, {"entity": "publication", "iuid": "80c75635458e45f883e80acd6b1c4fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1"}}, "title": "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.", "authors": [{"family": "Chen", "given": "Jinxin Phaedo", "initials": "JP", "orcid": "0000-0002-0729-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/25fca568763f4476b53bdf7297689a2e.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wu", "given": "Honggui", "initials": "H", "orcid": "0000-0001-7880-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9697e391fe493ab4b26d2c40e7565f.json"}}, {"family": "Chen", "given": "Chong", "initials": "C", "orcid": "0000-0002-6787-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8a6778068124d7cb3dd1aca6e7cc0ec.json"}}, {"family": "Della Chiara", "given": "Giulia", "initials": "G", "orcid": "0000-0001-5211-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/3410a95b5b674fa69d2c83b479d345a8.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Georgiadis", "given": "Konstantinos L", "initials": "KL"}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM"}, {"family": "Virdi", "given": "Mohit", "initials": "M"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Bellomo", "given": "Sara Erika", "initials": "SE"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1768", "issn-l": "2041-1723"}, "abstract": "Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.", "doi": "10.1038/s41467-024-45972-y", "pmid": "38409079", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10897160"}, {"db": "pii", "key": "10.1038/s41467-024-45972-y"}], "notes": [], "created": "2024-03-14T11:05:03.191Z", "modified": "2024-04-26T09:08:57.780Z"}]}