{"entity": "researcher", "timestamp": "2026-08-20T21:36:32.953Z", "family": "Alitalo", "given": "Kari", "initials": "K", "orcid": "0000-0002-7331-0902", "affiliations": ["Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.", "iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.", "Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9a1a31264694e4fba6026b293655ff0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9a1a31264694e4fba6026b293655ff0"}}, "publications": [{"entity": "publication", "iuid": "bcc41ca9b55740199005eb5ade37e808", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc41ca9b55740199005eb5ade37e808.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc41ca9b55740199005eb5ade37e808"}}, "title": "Multi-omics characterization of lymphedema-induced adipose tissue resulting from breast cancer-related surgery.", "authors": [{"family": "Karaman", "given": "Sinem", "initials": "S", "orcid": "0000-0002-0719-1773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53c13db10ca640ac8c09f2f6fff39ab4.json"}}, {"family": "Lehti", "given": "Satu", "initials": "S", "orcid": "0000-0002-9980-6201", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb39a15b84784665a9fe03c0b4f6bfe4.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR", "orcid": "0000-0002-6229-3588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e30b400bf04e4533bc6dea9fcddeec87.json"}}, {"family": "K\u00e4kel\u00e4", "given": "Reijo", "initials": "R", "orcid": "0000-0003-4953-3062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fcacd0a6b6464d4abdcdf5b224fc100b.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Brorson", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-9968-6062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d08f6448ced54397810a1a25d6e0b2d5.json"}}, {"family": "Alitalo", "given": "Kari", "initials": "K", "orcid": "0000-0002-7331-0902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9a1a31264694e4fba6026b293655ff0.json"}}, {"family": "Kivel\u00e4", "given": "Riikka", "initials": "R", "orcid": "0000-0002-2686-8890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a403e2cd104187a27e495f4ee20425.json"}}], "type": "journal article", "published": "2024-10-31", "journal": {"title": "FASEB J.", "issn": "1530-6860", "volume": "38", "issue": "20", "pages": "e70097", "issn-l": "0892-6638"}, "abstract": "Secondary lymphedema (LE) following breast cancer-related surgery is a life-long complication, which currently has no cure. LE induces significant regional adipose tissue deposition, requiring liposuction as a treatment. Here, we aimed to elucidate the transcriptional, metabolomic, and lipidomic signature of the adipose tissue developed due to the surgery-induced LE in short- and long-term LE patients and compared the transcriptomic landscape of LE adipose tissue to the obesity-induced adipose tissue. Adipose tissue biopsies were obtained from breast cancer-operated females with LE from the affected and non-affected arms (n = 20 patients). To decipher the molecular properties of the LE adipose tissue, we performed RNA sequencing, metabolomics, and lipidomics combined with bioinformatics analyses. Differential gene expression data from a cohort of lean and obese patients without LE was used for comparisons. Integrative analysis of functional genomics revealed that inflammatory response, cell chemotaxis, and angiogenesis were upregulated biological processes in the LE arm, indicating a sustained inflammation in the edematous adipose tissue; whereas, epidermal differentiation, cell-cell junction organization, water homeostasis, and neurogenesis were downregulated in the LE arm. Surprisingly, only a few genes were found to be the same in the LE-induced and the obesity-induced adipose tissue expansion, indicating a different type of adipose tissue development in these two conditions. In metabolomics analysis, we found reduced levels of a branched-chain amino acid valine in the LE arm and downregulation of the mRNA levels of its transporter SLC6A15. Lipidomics analyses did not show any significant differences between the LE and non-LE arms, suggesting that other factors affect the lipid composition of the adipose tissue more than the LE in these patients. Our results provide a detailed molecular characterization of adipose tissue in secondary LE after breast cancer-related surgery. We also show distinct differences in transcriptomic signatures between LE-induced adipose tissue and obesity-induced adipose tissue, but only minor differences in metabolome and lipidome between the LE and the non-LE arm.", "doi": "10.1096/fj.202400498RR", "pmid": "39394863", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11580717"}], "notes": [], "created": "2026-08-20T09:52:23.663Z", "modified": "2026-08-20T09:52:23.938Z"}, {"entity": "publication", "iuid": "a2d4d6d4a5c5405aa4e890d419216721", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2d4d6d4a5c5405aa4e890d419216721.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2d4d6d4a5c5405aa4e890d419216721"}}, "title": "Distinct molecular profiles and shared drug vulnerabilities in pancreatic metastases of renal cell carcinoma.", "authors": [{"family": "Roos-Mattila", "given": "Matilda", "initials": "M", "orcid": "0000-0002-2834-3211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9dd8feca623400d8e0c17b2725b6dc7.json"}}, {"family": "Kallio", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-6374-6203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/341466e88f824af587e257b73582d6dd.json"}}, {"family": "Luck", "given": "Tamara J", "initials": "TJ"}, {"family": "Polso", "given": "Minttu", "initials": "M"}, {"family": "Kumari", "given": "Romika", "initials": "R"}, {"family": "Mikkonen", "given": "Piia", "initials": "P"}, {"family": "V\u00e4lim\u00e4ki", "given": "Katja", "initials": "K", "orcid": "0000-0001-9117-7589", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e4948127dec4455803fa8c74fefbde5.json"}}, {"family": "Malmstedt", "given": "Minna", "initials": "M"}, {"family": "Ellonen", "given": "Pekka", "initials": "P"}, {"family": "Pellinen", "given": "Teijo", "initials": "T", "orcid": "0000-0001-9652-7373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e73595c0cc64a68a59cd95772784859.json"}}, {"family": "Heckman", "given": "Caroline A", "initials": "CA", "orcid": "0000-0002-4324-8706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0490f5eb61a4d92a44815d03de84af4.json"}}, {"family": "Mustonen", "given": "Harri", "initials": "H", "orcid": "0000-0001-5632-6796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f009308cd84542ae8c384fbfe87501d2.json"}}, {"family": "Puolakkainen", "given": "Pauli A", "initials": "PA"}, {"family": "Alitalo", "given": "Kari", "initials": "K", "orcid": "0000-0002-7331-0902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9a1a31264694e4fba6026b293655ff0.json"}}, {"family": "Kallioniemi", "given": "Olli", "initials": "O", "orcid": "0000-0002-3231-0332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb8605b07c884323afe4e1f2da37a031.json"}}, {"family": "Mirtti", "given": "Tuomas", "initials": "T", "orcid": "0000-0003-0455-9891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1963bc5086f4b45b9a48cb60115d578.json"}}, {"family": "Rannikko", "given": "Antti S", "initials": "AS"}, {"family": "Pieti\u00e4inen", "given": "Vilja M", "initials": "VM", "orcid": "0000-0003-3125-2406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d24125e51334b94bce4ef70fed1e585.json"}}, {"family": "Sepp\u00e4nen", "given": "Hanna E", "initials": "HE"}], "type": "journal article", "published": "2024-10-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1355", "issn-l": "2399-3642"}, "abstract": "Clear-cell renal cell carcinoma (ccRCC) is the most common origin of pancreatic metastases (PM). Distinct genomic aberrations, favorable prognosis, and clinical observations on high angiogenesis, and succeeding tyrosine kinase inhibitor (TKI) sensitivity have been reported in PM-ccRCC. However, no functional or single-cell studies have been conducted thus far. We recruited five PM-ccRCC patients and investigated the genomic, single-cell transcriptomic, and drug sensitivity profiles of their patient-derived cells (PDCs). The PM depicted both expected and novel genomic alterations. Further, the transcriptomics differed from both primary and metastatic ccRCC, with upregulations of the PI3K/mTOR and - supporting the clinical observations - angiogenesis pathways. Data integration at pathway level showed that transcriptomics explained drug sensitivities the best. Accordingly, PM-ccRCC PDCs shared sensitivity to many PI3K/mTOR inhibitors. Altogether, we show distinct genomic and transcriptomic signatures in PM-ccRCC, highlight the superiority of transcriptomics in interpreting drug sensitivities, and encourage the use of TKIs and PI3K/mTOR inhibitors in PM-ccRCC.", "doi": "10.1038/s42003-024-07004-9", "pmid": "39427059", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11490566"}, {"db": "pii", "key": "10.1038/s42003-024-07004-9"}], "notes": [], "created": "2026-08-20T09:25:17.594Z", "modified": "2026-08-20T09:25:17.901Z"}, {"entity": "publication", "iuid": "1a7b60fbbb744e058e52b6c798e857e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a7b60fbbb744e058e52b6c798e857e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a7b60fbbb744e058e52b6c798e857e4"}}, "title": "Multi-omics characterization of lymphedema-induced adipose tissue from breast cancer patients", "authors": [{"family": "Karaman", "given": "Sinem", "initials": "S", "orcid": "0000-0002-0719-1773", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53c13db10ca640ac8c09f2f6fff39ab4.json"}}, {"family": "Lehti", "given": "Satu", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Taskinen", "given": "Marja Riitta", "initials": "MR", "orcid": "0000-0002-6229-3588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e30b400bf04e4533bc6dea9fcddeec87.json"}}, {"family": "K\u00e4kel\u00e4", "given": "Reijo", "initials": "R"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Brorson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Alitalo", "given": "Kari", "initials": "K", "orcid": "0000-0002-7331-0902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9a1a31264694e4fba6026b293655ff0.json"}}, {"family": "Kivel\u00e4", "given": "Riikka", "initials": "R", "orcid": "0000-0002-2686-8890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0a403e2cd104187a27e495f4ee20425.json"}}], "type": "posted-content", "published": "2023-11-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.11.03.565593", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:48:47.522Z", "modified": "2026-08-20T10:49:20.664Z"}]}