{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T12:17:42Z","timestamp":1790511462587,"version":"4.1.0"},"reference-count":68,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2018,10,25]],"date-time":"2018-10-25T00:00:00Z","timestamp":1540425600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004622","name":"KWF Kankerbestrijding","doi-asserted-by":"publisher","award":["UL2013\u20106104"],"award-info":[{"award-number":["UL2013\u20106104"]}],"id":[{"id":"10.13039\/501100004622","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Genes Chromosomes &amp; Cancer"],"published-print":{"date-parts":[[2018,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Mycosis fungoides (MF) is the most common cutaneous T\u2010cell lymphoma (CTCL). Causative genetic alterations in MF are unknown. The low recurrence of pathogenic small\u2010scale mutations (ie, nucleotide substitutions, indels) in the disease, calls for the study of additional aspects of MF genetics. Here, we investigated structural genomic alterations in tumor\u2010stage MF by integrating whole\u2010genome sequencing and RNA\u2010sequencing. Multiple genes with roles in cell physiology (<jats:italic>n =<\/jats:italic> 113) and metabolism (<jats:italic>n =<\/jats:italic> 92) were found to be impacted by genomic rearrangements, including 47 genes currently implicated in cancer. Fusion transcripts involving genes of interest such as <jats:italic>DOT1L<\/jats:italic>, <jats:italic>KDM6A<\/jats:italic>, <jats:italic>LIFR<\/jats:italic>, <jats:italic>TP53<\/jats:italic>, and <jats:italic>TP63<\/jats:italic> were also observed. Additionally, we identified recurrent deletions of genes involved in cell cycle control, chromatin regulation, the JAK\u2010STAT pathway, and the PI\u20103\u2010K pathway. Remarkably, many of these deletions result from genomic rearrangements. Deletion of tumor suppressors <jats:italic>HNRNPK<\/jats:italic> and <jats:italic>SOCS1<\/jats:italic> were the most frequent genetic alterations in MF after deletion of <jats:italic>CDKN2A<\/jats:italic>. Notably, <jats:italic>SOCS1<\/jats:italic> deletion could be detected in early\u2010stage MF. In agreement with the observed genomic alterations, transcriptome analysis revealed up\u2010regulation of the cell cycle, JAK\u2010STAT, PI\u20103\u2010K and developmental pathways. Our results position inactivation of <jats:italic>HNRNPK<\/jats:italic> and <jats:italic>SOCS1<\/jats:italic> as potential driver events in MF development.<\/jats:p>","DOI":"10.1002\/gcc.22679","type":"journal-article","created":{"date-parts":[[2018,8,25]],"date-time":"2018-08-25T07:53:36Z","timestamp":1535183616000},"page":"653-664","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["Genomic analysis reveals recurrent deletion of JAK\u2010STAT signaling inhibitors <i>HNRNPK<\/i> and <i>SOCS1<\/i> in mycosis fungoides"],"prefix":"10.1002","volume":"57","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1579-917X","authenticated-orcid":false,"given":"Armando N.","family":"Bastidas Torres","sequence":"first","affiliation":[{"name":"Department of Dermatology Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davy","family":"Cats","sequence":"additional","affiliation":[{"name":"Sequencing Analysis Support Core Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailiang","family":"Mei","sequence":"additional","affiliation":[{"name":"Sequencing Analysis Support Core Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karoly","family":"Szuhai","sequence":"additional","affiliation":[{"name":"Department of Cell and Chemical Biology Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rein","family":"Willemze","sequence":"additional","affiliation":[{"name":"Department of Dermatology Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maarten 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