{"entity": "researcher", "timestamp": "2026-07-14T03:23:23.218Z", "family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c"}}, "publications": [{"entity": "publication", "iuid": "8846d92f48ef4728b42be2ccbf41fb61", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8846d92f48ef4728b42be2ccbf41fb61.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8846d92f48ef4728b42be2ccbf41fb61"}}, "title": "Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data", "authors": [{"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Yang", "given": "Qiao", "initials": "Q"}, {"family": "Acs", "given": "Balazs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d642b1db48643f497be9a35a71dadde.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d232b4567694b6f80b59ad262e7ff54.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Steen", "given": "Sanna", "initials": "S"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}], "type": "journal-article", "published": "2025-09-09", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "310", "issn-l": null}, "abstract": "Breast cancer is a highly heterogeneous disease with diverse outcomes, and intra-tumoral heterogeneity plays a significant role in both diagnosis and treatment. Despite its importance, the spatial distribution of intra-tumoral heterogeneity is not fully elucidated. Spatial transcriptomics has emerged as a promising tool to study the molecular mechanisms behind many diseases. It offers accurate measurements of RNA abundance, providing powerful tools to correlate the morphologies of cellular neighborhoods with localized gene expression patterns. However, the spot-based spatial transcriptomic tools, including the most widely used platform, Visium, do not achieve single-cell resolution readouts, which hinders data interpretability. In this study, we present a computational pathology image analysis pipeline (i.e., computational tissue annotation, CTA) that utilizes machine learning algorithms to accurately map tumor, stroma, and immune compartments within Visium-assayed tumor sections. Using a cohort of 23 breast tumor sections from four patients, we demonstrate that CTA can provide high-resolution annotations on the hematoxylin-and-eosin-stained images alongside the paired sequencing data, support the evaluation of deconvolution methods, deepen insights into intra-tumoral heterogeneity by increasing data analysis resolution, assist with spatially resolved intrinsic subtyping, and enhance the visualization of lymphocyte clones at single-cell resolution. The proposed pipeline provides valuable insights into the complex spatial architecture of breast cancer, contributing to more personalized diagnostics and treatment strategies.", "doi": "10.1038/s41698-025-01104-3", "pmid": "40925915", "labels": {"Camilla Engblom": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12420830"}, {"db": "pii", "key": "10.1038/s41698-025-01104-3"}], "notes": [], "created": "2025-12-01T15:33:06.973Z", "modified": "2025-12-09T10:34:56.329Z"}, {"entity": "publication", "iuid": "fe9cf0f6d04a4cd6aedfa01c32fc97b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fe9cf0f6d04a4cd6aedfa01c32fc97b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fe9cf0f6d04a4cd6aedfa01c32fc97b9"}}, "title": "Tertiary lymphoid structures in Merkel cell carcinoma facilitate na\u00efve and central memory T-cell infiltration linked to immunotherapy response", "authors": [{"family": "Srinivas", "given": "Nalini", "initials": "N"}, {"family": "Spassova", "given": "Ivelina", "initials": "I"}, {"family": "Lei", "given": "Kuan Cheok", "initials": "KC"}, {"family": "Gao", "given": "Jiwei", "initials": "J"}, {"family": "Pino", "given": "Mar\u00eda Jos\u00e9", "initials": "MJ", "orcid": "0009-0004-0516-6867", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb929c821d834477b1b474d8d1423706.json"}}, {"family": "Giglio", "given": "Giovanni", "initials": "G"}, {"family": "Kitanovski", "given": "Simo", "initials": "S"}, {"family": "Dalkoohi", "given": "Mazdak", "initials": "M"}, {"family": "Livingstone", "given": "Elisabeth", "initials": "E"}, {"family": "Leiter", "given": "Ulrike", "initials": "U"}, {"family": "Mohr", "given": "Peter", "initials": "P"}, {"family": "Gambichler", "given": "Thilo", "initials": "T"}, {"family": "Stoffels", "given": "Ingo", "initials": "I"}, {"family": "Ugurel", "given": "Selma", "initials": "S", "orcid": "0000-0002-9384-6704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd5e687b8ade4fd3901fc5f0488a1127.json"}}, {"family": "Cheung", "given": "Phyllis Fung Yi", "initials": "PFY"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Lui", "given": "Weng Onn", "initials": "WO"}, {"family": "Becker", "given": "J\u00fcrgen Christian", "initials": "JC", "orcid": "0000-0001-9183-653X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7197f45a2a7c4f16a45bb196e9b32fba.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "9", "pages": "e012224", "issn-l": null}, "abstract": "The presence of tertiary lymphoid structures (TLS) in solid tumors, including Merkel cell carcinoma (MCC), is associated with a better prognosis and a better response to immunotherapy with immune checkpoint inhibition (ICI). The detailed mechanisms by which TLS influence antitumor immune responses are only partially understood.\n\nClinically annotated tumor tissues of 27 patients with MCC were obtained prior to ICI therapy. Tumor samples were subjected to transcriptomic and multiplex immuno-visual profiling, T-cell receptor (TCR) clonotype mapping, as well as-in selected cases-spatial transcriptomics to comprehensively characterize the tumor immune microenvironment.\n\nWeighted gene co-expression network analysis (WGCNA) of transcriptomic data in combination with topological overlap measures indicated a higher abundance of TLS in tumors of patients with MCC responding to ICI therapy. This concept was substantiated through immunomorphological analyses, revealing mature B-cell follicle-like structures characterized by high endothelial venules (HEVs). Further supporting HEVs as critical entry points for na\u00efve T cells, the presence of TLS was correlated with a pronounced infiltration of CD4+ and CD8+ T cells, exhibiting both na\u00efve and central memory phenotypes. The TCR repertoire of these infiltrates exhibited enhanced richness and diversity with a pronounced reactivity toward Merkel cell polyomavirus-derived T-cell epitopes. Spatially resolved RNA and V(D)J sequencing revealed the expression of genes associated with T-cell recruitment within TLS, alongside the presence of na\u00efve and central memory T-cell markers. Notably, individual clonally expanded TCR transcripts were detected both within TLS and among tumor-infiltrating lymphocytes. The latter were associated with low expression of memory cell markers and high expression of effector cell markers. Additionally, a spatial gradient in the expression of genes linked to immune stress in MCC cells-such as those involved in the interferon-\u03b3 response and antigen processing and presentation machinery-originated in proximity to the TLS.\n\nOur findings are consistent with a key role of TLS in shaping immune interactions within the MCC microenvironment, driving the recruitment of diverse tumor-reactive T cells. These insights hold promise for advancing immunotherapeutic strategies.", "doi": "10.1136/jitc-2025-012224", "pmid": "40992783", "labels": {"Camilla Engblom": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12458699"}, {"db": "pii", "key": "jitc-2025-012224"}], "notes": [], "created": "2025-12-01T15:32:17.638Z", "modified": "2026-06-30T11:26:30.155Z"}, {"entity": "publication", "iuid": "80625326e9a047959c1d1f617b678ff2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/80625326e9a047959c1d1f617b678ff2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/80625326e9a047959c1d1f617b678ff2"}}, "title": "Putting cancer immunotherapy into spatial context in the clinic.", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "43", "issue": "4", "pages": "471-476", "issn-l": "1087-0156"}, "abstract": null, "doi": "10.1038/s41587-025-02596-x", "pmid": "40229365", "labels": {"Camilla Engblom": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-025-02596-x"}], "notes": [], "created": "2025-12-01T15:30:56.177Z", "modified": "2025-12-01T15:30:56.191Z"}, {"entity": "publication", "iuid": "a8f955e41ebd42daa2b3966499fa8248", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a8f955e41ebd42daa2b3966499fa8248"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "SH", "orcid": "0000-0001-8924-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e49aa3ca14b490eb378dbd956efaffc.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0772d0f35bde4d4ca46b93eaaf7b96cf.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4f921580aec4734ad538c0bc3e70b02.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "982", "issn-l": "2041-1723"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"SciLifeLab Fellow": null, "Camilla Engblom": null}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-06-01T06:49:27.955Z", "modified": "2023-06-01T06:49:28.457Z"}, {"entity": "publication", "iuid": "b01eeb48ff96488a819c96b07c32fdb4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b01eeb48ff96488a819c96b07c32fdb4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b01eeb48ff96488a819c96b07c32fdb4"}}, "title": "Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e39a73daed74f38be122ae9c564810c.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/614fde5d55514a1e8199062647806eec.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d232b4567694b6f80b59ad262e7ff54.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82aebb401f644b2fbd015827dc916078.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Steiner", "given": "Embla", "initials": "E"}, {"family": "Mantovani", "given": "Giulia", "initials": "G"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/642b3b7751434194b4f55f2af8d746a4.json"}}, {"family": "Jangard", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3772-2026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fd4438472764db09961f035401a7d6f.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-6948-7281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b1d4eb97634409a99a53c55e2bdcf86.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Mold", "given": "Jeff", "initials": "J", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3190bb256fcb4a9eb4f4ef06bb99eb5c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}], "type": "posted-content", "published": "2022-11-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.11.22.516865", "pmid": null, "labels": {"SciLifeLab Fellow": null, "Camilla Engblom": null}, "xrefs": [], "notes": [], "created": "2023-06-01T06:50:48.655Z", "modified": "2025-12-04T16:55:39.953Z"}]}