{"entity": "researcher", "timestamp": "2026-07-11T14:37:16.010Z", "family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971"}}, "publications": [{"entity": "publication", "iuid": "62515568135543558aea5335722cb034", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034"}}, "title": "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.", "authors": [{"family": "Shafighi", "given": "Shadi", "initials": "S"}, {"family": "Geras", "given": "Agnieszka", "initials": "A"}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Sahaf Naeini", "given": "Alireza", "initials": "A"}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "Ra Czkowska", "given": "Alicja", "initials": "A"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications.scilifelab.se/researcher/7645c7bdbd1b436bbb1c218b8e0ce355.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e13fee16a84747a22b438ce26facf7.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca6b8a8caa7494aaec1b0cab3270a31.json"}}], "type": "journal article", "published": "2024-10-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9343", "issn-l": "2041-1723"}, "abstract": "Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.", "doi": "10.1038/s41467-024-53374-3", "pmid": "39472583", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11522407"}, {"db": "pii", "key": "10.1038/s41467-024-53374-3"}], "notes": [], "created": "2024-10-31T12:37:56.764Z", "modified": "2025-02-28T14:14:34.895Z"}, {"entity": "publication", "iuid": "aa7e2fd0de904b36aabb562ce819de11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa7e2fd0de904b36aabb562ce819de11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa7e2fd0de904b36aabb562ce819de11"}}, "title": "Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications.scilifelab.se/researcher/d10a182a9f0a4ec68ff809d1ac5a13a0.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e483b7a04bd44d0ad31e15569ea7ea9.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H", "orcid": "0000-0002-5525-4724", "researcher": {"href": "https://publications.scilifelab.se/researcher/1024be99666a46cd97c75f9220f5b931.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Steiner", "given": "Embla", "initials": "E"}, {"family": "Lu", "given": "Chang", "initials": "C", "orcid": "0000-0001-6304-2820", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0204945479c4066896ba3643fa4229a.json"}}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f8e781842747bb91bdb07e9d5c0cd8.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "Jangard", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3772-2026", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dafcc3cdede495aabccee445306fac1.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba167f912244d879746ed60a3c19568.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "382", "issue": "6675", "pages": "eadf8486"}, "abstract": "The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.", "doi": "10.1126/science.adf8486", "pmid": "38060664", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-09T11:23:39.309Z", "modified": "2024-01-16T13:48:31.521Z"}, {"entity": "publication", "iuid": "972a9d48ef104e73a8766b8630ade5af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "S"}, {"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.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications.scilifelab.se/researcher/8665401549d749ea8c1ab814dbfe5061.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d6b9360321440ca1bc9199a42b624a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "982"}, "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": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-03-06T13:47:42.947Z", "modified": "2023-11-29T11:39:09.375Z"}, {"entity": "publication", "iuid": "f5829319dbfb49ad8137f41b82951481", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5829319dbfb49ad8137f41b82951481.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5829319dbfb49ad8137f41b82951481"}}, "title": "Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.", "authors": [{"family": "Classon", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0392-7605", "researcher": {"href": "https://publications.scilifelab.se/researcher/641cf9db52e64f9fb8eee60a977a88be.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f196173b40b4819a5fcd11bf76a4e6e.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f8e781842747bb91bdb07e9d5c0cd8.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6015314c4c04ee08d7e4358cfb55b9f.json"}}, {"family": "Nkulikiyimfura", "given": "Dieudonn\u00e9", "initials": "D", "orcid": "0000-0002-6981-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/6af6961b78de4d0b96b011009cccc14c.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba167f912244d879746ed60a3c19568.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "16", "issue": "19", "pages": "3452-3464", "issn-l": "1574-7891"}, "abstract": "Prostate cancer is a heterogeneous disease with a need for new prognostic biomarkers. Human leukocyte antigen (HLA) genes are highly polymorphic genes central to antigen presentation to T-cells. Two alleles, HLA-A*02:01 and HLA-A*24:02, have been associated with prognosis in patients diagnosed with de novo metastatic prostate cancer. We leveraged the next-generation sequenced cohorts CPC-GENE and TCGA-PRAD to examine HLA alleles, antiviral T-cell receptors and prostate cancer disease recurrence after prostatectomy. Carrying HLA-A*02:01 (111/229; 48% of patients) was independently associated with disease recurrence in patients with low-intermediate risk prostate cancer. HLA-A*11 (carried by 42/441; 10% of patients) was independently associated with rapid disease recurrence in patients with high-risk prostate cancer. Moreover, HLA-A*02:01 carriers in which anti-cytomegalovirus T-cell receptors (CMV-TCR) were identified in tumors (13/144; 10% of all patients in the cohort) had a higher risk of disease recurrence than CMV-TCR-negative patients. These findings suggest that HLA-type and CMV immunity may be valuable biomarkers for prostate cancer progression.", "doi": "10.1002/1878-0261.13273", "pmid": "35712787", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9533687"}, {"db": "RefSeq", "key": "NC_006273.2"}], "notes": [], "created": "2022-11-09T15:51:53.564Z", "modified": "2024-01-16T13:48:34.865Z"}, {"entity": "publication", "iuid": "ec581b66240c426ca45bd1ab1951a61a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a"}}, "title": "The spatial transcriptomic landscape of the healing mouse intestine following damage.", "authors": [{"family": "Parigi", "given": "Sara M", "initials": "SM"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO", "orcid": "0000-0003-0087-371X", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f01d7b57044e628850bb9705e03ed0.json"}}, {"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Diaz", "given": "Oscar E", "initials": "OE", "orcid": "0000-0001-7622-7832", "researcher": {"href": "https://publications.scilifelab.se/researcher/9aae40d7294841989eee4629596395d3.json"}}, {"family": "Selin", "given": "Katja", "initials": "K", "orcid": "0000-0002-8888-0529", "researcher": {"href": "https://publications.scilifelab.se/researcher/64550a7d2143443dbf3f1575ab3f870d.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications.scilifelab.se/researcher/61802da2579446d5b2a73c4f06b9969e.json"}}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Gagliani", "given": "Nicola", "initials": "N", "orcid": "0000-0001-8514-1395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cc11473c8944eebc0974780d1c6919.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "828"}, "abstract": "The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.", "doi": "10.1038/s41467-022-28497-0", "pmid": "35149721", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-28497-0"}, {"db": "pmc", "key": "PMC8837647"}], "notes": [], "created": "2022-03-29T13:47:22.254Z", "modified": "2022-08-19T09:06:40.669Z"}, {"entity": "publication", "iuid": "06cb8c44cb724e169b03c31f68350a39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39"}}, "title": "Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.", "authors": [{"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4393e30947441519e7ab28fccb9bc3a.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Ehinger", "given": "Anna", "initials": "A", "orcid": "0000-0001-9225-7396", "researcher": {"href": "https://publications.scilifelab.se/researcher/f500d5e3ba094e208ea53b4c42e44ce8.json"}}, {"family": "Wu", "given": "Sunny Z", "initials": "SZ", "orcid": "0000-0002-6153-0449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b354bd9c024e0d9fae3b77b5f7ca3a.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G", "orcid": "0000-0002-1137-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d06a9f413f04f7490b1724c375537c0.json"}}, {"family": "Roden", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2393-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee5b95b08b243e49af7a837ab9f9d39.json"}}, {"family": "Swarbrick", "given": "Alex", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d712c54077427abf4a5ac7cbe2b5a6.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2021-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "6012", "issn-l": "2041-1723"}, "abstract": "In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.", "doi": "10.1038/s41467-021-26271-2", "pmid": "34650042", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8516894"}, {"db": "pii", "key": "10.1038/s41467-021-26271-2"}], "notes": [], "created": "2021-12-06T13:49:12.030Z", "modified": "2024-01-16T13:48:38.238Z"}]}