{"entity": "researcher", "timestamp": "2026-09-28T11:20:34.442Z", "family": "Mitra", "given": "Shamik", "initials": "S", "orcid": "0000-0001-6995-0600", "affiliations": ["Division of Oncology and Pathology, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d01abe99508473e96316b7a0b8e5832.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d01abe99508473e96316b7a0b8e5832"}}, "publications": [{"entity": "publication", "iuid": "d6b26e8dd4f245feb6adbe0bac2e2c96", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d6b26e8dd4f245feb6adbe0bac2e2c96.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d6b26e8dd4f245feb6adbe0bac2e2c96"}}, "title": "MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.", "authors": [{"family": "Sydow", "given": "Saskia", "initials": "S", "orcid": "0009-0003-0358-8268", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7d695d43b9944e2accb6ba11a71cbda.json"}}, {"family": "Piccinelli", "given": "Paul", "initials": "P"}, {"family": "Mitra", "given": "Shamik", "initials": "S", "orcid": "0000-0001-6995-0600", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d01abe99508473e96316b7a0b8e5832.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P"}, {"family": "Hesla", "given": "Asle", "initials": "A", "orcid": "0000-0001-6205-0773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1c7ec8160e14a59b8e63fb079bab321.json"}}, {"family": "B R De Mattos", "given": "Camila", "initials": "C", "orcid": "0000-0002-5698-6281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5a1fbf356154145bab775fba892c564.json"}}, {"family": "K\u00f6ster", "given": "Jan", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8b8ce05cf7f49aeb3199b5938b9f160.json"}}, {"family": "Wardenaar", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0001-9891-1897", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/177096d8964049b59db4e7acc966ce13.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F", "orcid": "0000-0003-0989-3127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a51813cf7cc5472187e592f79c61e5d2.json"}}, {"family": "Spierings", "given": "Diana", "initials": "D", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bc5511772c742fe85f9c6d8c0510105.json"}}, {"family": "Mertens", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-6278-5232", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0bf9191ab79413690786292b70be3a9.json"}}], "type": "journal article", "published": "2024-05-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "606", "issn-l": "2399-3642"}, "abstract": "Well-differentiated liposarcoma (WDLS) displays amplification of genes on chromosome 12 (Chr12) in supernumerary ring or giant marker chromosomes. These structures have been suggested to develop through chromothripsis, followed by circularization and breakage-fusion-bridge (BFB) cycles. To test this hypothesis, we compared WDLSs with Chr12 amplification in rod-shaped chromosomes with WDLSs with rings. Both types of amplicons share the same spectrum of structural variants (SVs), show higher SV frequencies in Chr12 than in co-amplified segments, have SVs that fuse the telomeric ends of co-amplified chromosomes, and lack interspersed deletions. Combined with the finding of cells with transient rod-shaped structures in tumors with ring chromosomes, this suggests a stepwise process starting with the gain of Chr12 material that, after remodeling which does not fit with classical chromothripsis, forms a dicentric structure with other chromosomes. Depending on if and when telomeres from other chromosomes are captured, circularized or linear gain of 12q sequences will predominate.", "doi": "10.1038/s42003-024-06307-1", "pmid": "38769442", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11106292"}, {"db": "pii", "key": "10.1038/s42003-024-06307-1"}], "notes": [], "created": "2026-09-23T12:24:37.827Z", "modified": "2026-09-23T12:24:38.156Z"}, {"entity": "publication", "iuid": "d801092b7a76424c92c2ff6be90e95e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d801092b7a76424c92c2ff6be90e95e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d801092b7a76424c92c2ff6be90e95e8"}}, "title": "Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.", "authors": [{"family": "Mitra", "given": "Shamik", "initials": "S", "orcid": "0000-0001-6995-0600", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d01abe99508473e96316b7a0b8e5832.json"}}, {"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Cabrita", "given": "Rita", "initials": "R"}, {"family": "Choi", "given": "Jiyeon", "initials": "J"}, {"family": "Zhang", "given": "Tongwu", "initials": "T"}, {"family": "Isaksson", "given": "Karolin", "initials": "K"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Carneiro", "given": "Ana", "initials": "A"}, {"family": "Staaf", "given": "Johan", "initials": "J"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nielsen", "given": "Kari", "initials": "K"}, {"family": "Brown", "given": "Kevin M", "initials": "KM"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-6865-0147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1a508c9b2fc4fe6bb6bdfff9989eb93.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "14", "issue": "5", "pages": "933-950", "issn-l": "1574-7891"}, "abstract": "The presence of immune cells in the tumor microenvironment has been associated with response to immunotherapies across several cancer types, including melanoma. Despite its therapeutic relevance, characterization of the melanoma immune microenvironments remains insufficiently explored. To distinguish the immune microenvironment in a cohort of 180 metastatic melanoma clinical specimens, we developed a method using promoter CpG methylation of immune cell type-specific genes extracted from genome-wide methylation arrays. Unsupervised clustering identified three immune methylation clusters with varying levels of immune CpG methylation that are related to patient survival. Matching protein and gene expression data further corroborated the identified epigenetic characterization. Exploration of the possible immune exclusion mechanisms at play revealed likely dependency on MITF protein level and PTEN loss-of-function events for melanomas unresponsive to immunotherapies (immune-low). To understand whether melanoma tumors resemble other solid tumors in terms of immune methylation characteristics, we explored 15 different solid tumor cohorts from TCGA. Low-dimensional projection based on immune cell type-specific methylation revealed grouping of the solid tumors in line with melanoma immune methylation clusters rather than tumor types. Association of survival outcome with immune cell type-specific methylation differed across tumor and cell types. However, in melanomas immune cell type-specific methylation was associated with inferior patient survival. Exploration of the immune methylation patterns in a pan-cancer context suggested that specific immune microenvironments might occur across the cancer spectrum. Together, our findings underscore the existence of diverse immune microenvironments, which may be informative for future immunotherapeutic applications.", "doi": "10.1002/1878-0261.12663", "pmid": "32147909", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7191190"}], "notes": [], "created": "2026-09-23T08:47:29.042Z", "modified": "2026-09-23T08:47:29.205Z"}]}