{"entity": "researcher", "timestamp": "2026-08-20T20:46:18.347Z", "family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "affiliations": ["Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.", "Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd"}}, "publications": [{"entity": "publication", "iuid": "bcacaa65eecd45d197bf8c8c5a452c53", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcacaa65eecd45d197bf8c8c5a452c53.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcacaa65eecd45d197bf8c8c5a452c53"}}, "title": "Tissue-resident microbiota impacts colorectal cancer progression and prognosis.", "authors": [{"family": "Shi", "given": "Zhun", "initials": "Z", "orcid": "0000-0001-9270-8177", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b977a429a79c4cd7af4b0884f3f00b28.json"}}, {"family": "Ren", "given": "Huahui", "initials": "H", "orcid": "0000-0003-1154-9448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/982cd90d91f841cdaeb35901487acc0b.json"}}, {"family": "Lin", "given": "Cong", "initials": "C", "orcid": "0009-0002-1494-4427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4fc57d6657440989fc9882843a05f25.json"}}, {"family": "Li", "given": "Fuqiang", "initials": "F", "orcid": "0000-0002-2085-1457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f35de79205341e1b552af0d9a53c272.json"}}, {"family": "Wu", "given": "Meizhen", "initials": "M", "orcid": "0009-0001-7702-0080", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3347dd4410ee46158b0e71d5fa2cfea2.json"}}, {"family": "Yang", "given": "Fangming", "initials": "F"}, {"family": "Luo", "given": "Tian", "initials": "T"}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Hammarstr\u00f6m", "given": "Klara", "initials": "K"}, {"family": "Zhu", "given": "Ting", "initials": "T"}, {"family": "Zhu", "given": "Shida", "initials": "S"}, {"family": "Zhong", "given": "Yiyi", "initials": "Y"}, {"family": "Ljuslinder", "given": "Ingrid", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Palmqvist", "given": "Richard", "initials": "R", "orcid": "0000-0002-9933-2843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d058745d8b514f589888e8a2a0ccd603.json"}}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Wu", "given": "Kui", "initials": "K", "orcid": "0000-0002-6857-7231", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31d4921301bd47d29263ec562266fb24.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}, {"family": "Zhong", "given": "Huanzi", "initials": "H", "orcid": "0000-0001-9512-1750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b4b088eddb9486db8240a0e37c8a4af.json"}}], "type": "journal article", "published": "2025-12-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "346", "issn-l": "2041-1723"}, "abstract": "To deepen the understanding of tissue-resident microbiota in colorectal cancer (CRC), we analyzed whole-genome and transcriptome data from 937 patients. We identified 249 genera and 361 species commonly present in both tumors and adjacent normal tissues (NATs). Distinct microbial signatures were associated with anatomical location, tumor stages, hypermutation status, mutations in CRC driver and DNA damage repair genes, as well as consensus molecular subtypes (CMSs). Notably, the presence of the pks island and elevated abundance of Enterobacteriaceae were linked to poor prognosis specifically in CMS2 tumors. Finally, microbial risk scores derived from taxa present in tumor or NATs predicted patient prognosis independently of established clinico-molecular factors. Prognostic taxa were strongly associated with tumor transcriptomic pathways related to hypoxia, immune response, and metabolic status. These findings revealed the heterogeneity of tissue-resident microbiota and their critical role in CRC progression, highlighting potential avenues for targeted intervention.", "doi": "10.1038/s41467-025-67047-2", "pmid": "41354681", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12789584"}, {"db": "pii", "key": "10.1038/s41467-025-67047-2"}], "notes": [], "created": "2026-08-20T08:54:26.805Z", "modified": "2026-08-20T08:54:27.156Z"}, {"entity": "publication", "iuid": "58b067a430774262adb4e5c56b520389", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/58b067a430774262adb4e5c56b520389.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/58b067a430774262adb4e5c56b520389"}}, "title": "Prognostic genome and transcriptome signatures in colorectal cancers.", "authors": [{"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}}, {"family": "Li", "given": "Fuqiang", "initials": "F", "orcid": "0000-0002-2085-1457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f35de79205341e1b552af0d9a53c272.json"}}, {"family": "Wu", "given": "Meizhen", "initials": "M"}, {"family": "Luo", "given": "Tian", "initials": "T"}, {"family": "Hammarstr\u00f6m", "given": "Klara", "initials": "K"}, {"family": "Torell", "given": "Emma", "initials": "E"}, {"family": "Ljuslinder", "given": "Ingrid", "initials": "I"}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5219527c2dc6480da474f3c47dff9318.json"}}, {"family": "L\u00f6fgren-Burstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0003-4766-3250", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5309a6a95144a8ebc1afbfde45f3e99.json"}}, {"family": "Zingmark", "given": "Carl", "initials": "C", "orcid": "0000-0002-8627-5739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8f8085f10044c18de0ca94153d34a7.json"}}, {"family": "Edin", "given": "Sofia", "initials": "S"}, {"family": "Larsson", "given": "Chatarina", "initials": "C", "orcid": "0000-0002-5250-3617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8cfd9d2257f4114841bccd38f31dcbd.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Osterman", "given": "Erik", "initials": "E", "orcid": "0000-0003-1621-7872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4943dc1995bf4688b5b1b570ca61f687.json"}}, {"family": "Osterlund", "given": "Emerik", "initials": "E", "orcid": "0000-0003-0973-6332", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e64664f9600b430183f9edfdf10fa2df.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Neves", "given": "In\u00eas", "initials": "I", "orcid": "0000-0002-6459-4237", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2aa37042980f4e358240bde56c1a456e.json"}}, {"family": "Yacoub", "given": "Nicole", "initials": "N"}, {"family": "Gu\u00f0nad\u00f3ttir", "given": "Unnur", "initials": "U"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd2f8ad89196420584d0f79ad24575d3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Palmqvist", "given": "Richard", "initials": "R", "orcid": "0000-0002-9933-2843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d058745d8b514f589888e8a2a0ccd603.json"}}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a6e2e5d236148c7ba386c89941f2d41.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Wu", "given": "Kui", "initials": "K", "orcid": "0000-0002-6857-7231", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31d4921301bd47d29263ec562266fb24.json"}}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Lin", "given": "Cong", "initials": "C", "orcid": "0009-0002-1494-4427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4fc57d6657440989fc9882843a05f25.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "633", "issue": "8028", "pages": "137-146", "issn-l": "0028-0836"}, "abstract": "Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGF\u03b2 pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.", "doi": "10.1038/s41586-024-07769-3", "pmid": "39112715", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11374687"}, {"db": "pii", "key": "10.1038/s41586-024-07769-3"}], "notes": [], "created": "2026-08-20T08:58:59.051Z", "modified": "2026-08-20T08:58:59.424Z"}, {"entity": "publication", "iuid": "78c76a7f70ac4e538725e7fd89e96a16", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/78c76a7f70ac4e538725e7fd89e96a16.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/78c76a7f70ac4e538725e7fd89e96a16"}}, "title": "Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma.", "authors": [{"family": "Sandberg", "given": "Emma", "initials": "E", "orcid": "0009-0003-5681-4417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f583a5882174325974058d4cb3b1a9e.json"}}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/458c07a1748d4ce0ac5cff3d6836f350.json"}}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Edgren", "given": "Tomas", "initials": "T"}, {"family": "Al Nassralla", "given": "Shahed", "initials": "S"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8749cdcda45a43d8bb2df04b0b211f36.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}], "type": "journal article", "published": "2024-01-27", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "3", "issn-l": "2072-6694"}, "abstract": "Mutation analysis of circulating tumor DNA (ctDNA) has applications in monitoring of colorectal cancer (CRC) patients for recurrence. Considering the low tumor fraction of ctDNA in cell-free DNA (cfDNA) isolated from blood plasma, the sensitivity of the detection method is important. Here, plasma DNA collected at diagnosis and follow-up from 25 CRC patients was analyzed using a multiplex superRCA mutation detection assay. The assay was also performed on genomic DNA (gDNA) from tumor and normal tissue from 20 of these patients. The lower limit of detection for most sequence variants was in the range of 10-5, while when analyzing cfDNA from plasma with a typical input of 33 ng, the practical detection limit was ~10-4 or 0.01% mutant allele frequency (MAF). In 17 of 19 patients with identified hotspot mutations in tumor gDNA, at least one hotspot mutation could be detected in plasma DNA at the time of diagnosis. The MAF increased at subsequent time points in four of the patients who experienced a clinical relapse. Multiplex superRCA analysis of the remaining six patients did not reveal any hotspot mutations. In conclusion, multiplex superRCA assays proved suitable for monitoring CRC patients by analyzing hotspot mutations in cfDNA, and dynamic changes in MAF were observed in patients with clinical relapse.", "doi": "10.3390/cancers16030549", "pmid": "38339300", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10854605"}, {"db": "pii", "key": "cancers16030549"}], "notes": [], "created": "2026-08-20T13:40:00.649Z", "modified": "2026-08-20T13:40:00.755Z"}, {"entity": "publication", "iuid": "bd5589a02cc24d7ebdfd569f383e9442", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd5589a02cc24d7ebdfd569f383e9442.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd5589a02cc24d7ebdfd569f383e9442"}}, "title": "Sensitive and Specific Analyses of Colorectal Cancer Recurrence through Multiplex superRCA Mutation Detection in Blood Plasma", "authors": [{"family": "Sandberg", "given": "Emma", "initials": "E", "orcid": "0009-0003-5681-4417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f583a5882174325974058d4cb3b1a9e.json"}}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}}, {"family": "Edqvist", "given": "Per Henrik", "initials": "PH"}, {"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Edgren", "given": "Tomas", "initials": "T"}, {"family": "Al Nassralla", "given": "Shahed", "initials": "S"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a4a4dfe9cc6478baaaae4672181691c.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U", "orcid": "0000-0002-7820-1000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8749cdcda45a43d8bb2df04b0b211f36.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/851b95a56b3244fb9bc7cec8294e7ae7.json"}}], "type": "posted-content", "published": "2024-01-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.20944/preprints202401.0950.v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:56:38.266Z", "modified": "2026-08-20T12:56:38.348Z"}, {"entity": "publication", "iuid": "4169939771554f4689b01d54aee78cfc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4169939771554f4689b01d54aee78cfc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4169939771554f4689b01d54aee78cfc"}}, "title": "Rigorous software pipeline for clinical somatic mutation analyses of solid tumors", "authors": [{"family": "Stoimenov", "given": "Ivaylo", "initials": "I", "orcid": "0000-0002-2133-7396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10ad1a77c6f241418187734e9a47c16c.json"}}, {"family": "Rashyna", "given": "Marina", "initials": "M"}, {"family": "Adlerteg", "given": "Tom", "initials": "T"}, {"family": "Nunes", "given": "Lu\u00eds", "initials": "L", "orcid": "0000-0002-3391-1607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa31ccf1801456bb57744978bd605fd.json"}}, {"family": "Ekstr\u00f6m", "given": "Joakim", "initials": "J", "orcid": "0000-0002-9734-3979", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b217a0aef38c4eb7a84bfc11a90d9d99.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": 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