{"entity": "researcher", "timestamp": "2026-09-25T16:49:08.784Z", "family": "Pyl", "given": "Paul-Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "affiliations": ["Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f"}}, "publications": [{"entity": "publication", "iuid": "49e62d644ebe443aadddfc6ce597ef6f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/49e62d644ebe443aadddfc6ce597ef6f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/49e62d644ebe443aadddfc6ce597ef6f"}}, "title": "The Progression of Mycosis Fungoides During Treatment with Mogamulizumab: A BIO-MUSE Case Study of the Tumor and Immune Response in Peripheral Blood and Tissue.", "authors": [{"family": "Johansson", "given": "Angelica", "initials": "A"}, {"family": "Kalliara", "given": "Eirini", "initials": "E", "orcid": "0000-0001-8772-0729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02b4a571c41c44a39e5c894b6a4cbbd6.json"}}, {"family": "Belfrage", "given": "Emma", "initials": "E", "orcid": "0000-0003-1717-0842", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1bf19d14779e4badb96f96202192b859.json"}}, {"family": "Alling", "given": "Teodor", "initials": "T", "orcid": "0000-0003-1680-5666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3962c279bda542cfaddd73679ab5a756.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f.json"}}, {"family": "Gerdtsson", "given": "Anna Sandstr\u00f6m", "initials": "AS", "orcid": "0000-0003-1932-0365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a421e038391a4e368d9460c7b5867579.json"}}, {"family": "Gullberg", "given": "Urban", "initials": "U"}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Drott", "given": "Kristina", "initials": "K", "orcid": "0000-0002-9350-7016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4a5e6e82f504c509b100c6b7a3b4a29.json"}}, {"family": "Ek", "given": "Sara", "initials": "S", "orcid": "0000-0002-1388-4912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e439837a691847bea96ecaf13c9c4b74.json"}}], "type": "journal article", "published": "2025-01-14", "journal": {"title": "Biomedicines", "issn": "2227-9059", "volume": "13", "issue": "1", "issn-l": null}, "abstract": "Background/objectives: Mycosis fungoides (MF) is a rare malignancy, with an indolent course in the early stages of the disease. However, due to major molecular and clinical heterogeneity, patients at an advanced stage of the disease have variable responses to treatment and considerably reduced life expectancy. Today, there is a lack of specific markers for the progression from early to advanced stages of the disease. To address these challenges, the non-interventional BIO-MUSE trial was initiated. Here, we report on a case study involving one patient, where combined omics analysis of tissue and blood was used to reveal the unique molecular features associated with the progression of the disease. Methods: We applied 10\u00d7 genomics-based single-cell RNA sequencing to CD3+ peripheral T-cells, combined with T-cell receptor sequencing, to samples collected at multiple timepoints during the progression of the disease. In addition, GeoMx-based digital spatial profiling of T-helper (CD3+/CD8-), T-cytotoxic (CD3+/CD8+), and CD163+ cells was performed on skin biopsies. Results. The results pinpoint targets, such as transforming growth factor \u03b21, as some of the mechanisms underlying disease progression, which may have the potential to improve patient prognostication and the development of precision medicine efforts. Conclusions: We propose that in patients with MF, the evolution of the malignant clone and the associated immune response need to be studied jointly to define relevant strategies for intervention.", "doi": "10.3390/biomedicines13010186", "pmid": "39857770", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11761615"}, {"db": "pii", "key": "biomedicines13010186"}], "notes": [], "created": "2026-09-23T13:18:19.123Z", "modified": "2026-09-23T13:18:19.340Z"}, {"entity": "publication", "iuid": "01aa670515c141988687470e44a6762c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/01aa670515c141988687470e44a6762c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/01aa670515c141988687470e44a6762c"}}, "title": "Quantification and Profiling of Early and Late Differentiation Stage T Cells in Mantle Cell Lymphoma Reveals Immunotherapeutic Targets in Subsets of Patients.", "authors": [{"family": "Lokhande", "given": "Lavanya", "initials": "L"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0009-0001-6214-198X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc5bb733433b4d6b8721900739105fb5.json"}}, {"family": "de Matos Rodrigues", "given": "Joana", "initials": "J"}, {"family": "Hassan", "given": "May", "initials": "M"}, {"family": "Olsson", "given": "Lina M", "initials": "LM", "orcid": "0000-0002-1359-0295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/675f08c2d5db4b40bce7fa233b618a3b.json"}}, {"family": "Pyl", "given": "Paul-Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f.json"}}, {"family": "Vasquez", "given": "Louella", "initials": "L"}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Gerdtsson", "given": "Anna Sandstr\u00f6m", "initials": "AS", "orcid": "0000-0003-1932-0365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a421e038391a4e368d9460c7b5867579.json"}}, {"family": "Jerkeman", "given": "Mats", "initials": "M"}, {"family": "Ek", "given": "Sara", "initials": "S", "orcid": "0000-0002-1388-4912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e439837a691847bea96ecaf13c9c4b74.json"}}], "type": "journal article", "published": "2024-06-21", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "13", "issn-l": "2072-6694"}, "abstract": "With the aim to advance the understanding of immune regulation in MCL and to identify targetable T-cell subsets, we set out to combine image analysis and spatial omic technology focused on both early and late differentiation stages of T cells. MCL patient tissue (n = 102) was explored using image analysis and GeoMx spatial omics profiling of 69 proteins and 1812 mRNAs. Tumor cells, T helper (TH) cells and cytotoxic (TC) cells of early (CD57-) and late (CD57+) differentiation stage were analyzed. An image analysis workflow was developed based on fine-tuned Cellpose models for cell segmentation and classification. TC and CD57+ subsets of T cells were enriched in tumor-rich compared to tumor-sparse regions. Tumor-sparse regions had a higher expression of several key immune suppressive proteins, tentatively controlling T-cell expansion in regions close to the tumor. We revealed that T cells in late differentiation stages (CD57+) are enriched among MCL infiltrating T cells and are predictive of an increased expression of immune suppressive markers. CD47, IDO1 and CTLA-4 were identified as potential targets for patients with T-cell-rich MCL TIME, while GITR might be a feasible target for MCL patients with sparse T-cell infiltration. In subgroups of patients with a high degree of CD57+ TC-cell infiltration, several immune checkpoint inhibitors, including TIGIT, PD-L1 and LAG3 were increased, emphasizing the immune-suppressive features of this highly differentiated T-cell subset not previously described in MCL.", "doi": "10.3390/cancers16132289", "pmid": "39001353", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11240320"}, {"db": "pii", "key": "cancers16132289"}], "notes": [], "created": "2026-09-23T12:24:44.119Z", "modified": "2026-09-23T12:24:44.335Z"}, {"entity": "publication", "iuid": "8f3f5c2e49994d55a42fd41d2d9326b4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8f3f5c2e49994d55a42fd41d2d9326b4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8f3f5c2e49994d55a42fd41d2d9326b4"}}, "title": "\u201dEvolution of ipsilateral breast cancer decoded by proteogenomics\u201d", "authors": [{"family": "Marchi", "given": "Tommaso De", "initials": "TD", "orcid": "0000-0002-4845-1084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68502c65e0754c4698a3f4d3c802acc4.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f.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": "Reinsbach", "given": "Susanne Erika", "initials": "SE", "orcid": "0000-0003-0509-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35ebeb793254320982f857ec99fe02a.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9759-2211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbd59f99c568418d82c52fb9e049001a.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Pekar", "given": "Gyula", "initials": "G", "orcid": "0000-0002-0667-0270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef9d9b551a86483d82356c914dbe826c.json"}}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f.json"}}, {"family": "Fredriksson", "given": "Irma", "initials": "I", "orcid": "0000-0001-7811-9317", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75574ec73d974ea7be24724f74f6b0cb.json"}}, {"family": "Malmstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Fern\u00f6", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-2220-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190c0c5f17f4c298855f9b13f9bb16d.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Malmst\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c89da9268a4f47a8a99fd62de451aaa7.json"}}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E", "orcid": "0000-0003-0262-9083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c4af562bc1248ecbbb730a496675571.json"}}], "type": "posted-content", "published": "2022-07-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.07.13.499898", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:19:37.685Z", "modified": "2026-09-23T15:19:37.859Z"}]}