{"entity": "researcher", "timestamp": "2026-07-15T16:54:09.254Z", "family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "affiliations": ["Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.", "Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae"}}, "publications": [{"entity": "publication", "iuid": "6f6a5bd19f4d4a459ee0ff3a82fc3eef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f6a5bd19f4d4a459ee0ff3a82fc3eef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f6a5bd19f4d4a459ee0ff3a82fc3eef"}}, "title": "Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.", "authors": [{"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Pourbozorgi", "given": "Parham", "initials": "P", "orcid": "0000-0002-5957-627X", "researcher": {"href": "https://publications.scilifelab.se/researcher/520886f23ef54f008bff773ebb86f7b1.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2026-05-22", "journal": {"title": "Life (Basel)", "issn": "2075-1729", "volume": "16", "issue": "6", "issn-l": null}, "abstract": "Precision medicine is increasingly applied in the cancer clinic, adapting treatment to genomic alterations of the tumor. However, whether alterations disrupt the function of a protein can depend on if both alleles of a gene are altered. While massively parallel sequencing technologies can identify sequence aberrations, they are limited in resolving the corresponding haplotype information. In this proof-of-concept case study, we applied the linked-read droplet barcode sequencing (DBS) technology to resolve the haplotype complexity of colorectal cancer genomes on paired tumor and normal samples. Several cancer-related genes carried multiple mutations in either one or both haplotypes. Additionally, a number of haplotype-resolved large structural variants and copy number alterations were detected and phased with short somatic variants. Nearly all characterized oncogenic pathways harbored some of the identified short somatic variants. The study demonstrates that linked-read DBS technology can characterize complex genetic variations in a haplotype context and may provide essential information for personalized approaches.", "doi": "10.3390/life16060874", "pmid": "42355402", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "life16060874"}, {"db": "pmc", "key": "PMC13301505"}], "notes": [], "created": "2026-07-14T17:34:48.527Z", "modified": "2026-07-14T17:34:48.921Z"}, {"entity": "publication", "iuid": "92139d604e30428c85b0f16ddccb99c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8"}}, "title": "Spatial profiling of the mouse colonic immune landscape associated with colitis and sex.", "authors": [{"family": "Holm", "given": "Matilda", "initials": "M"}, {"family": "Stepanauskait\u0117", "given": "Lina", "initials": "L", "orcid": "0000-0003-4173-6009", "researcher": {"href": "https://publications.scilifelab.se/researcher/429f33fed9a44ff4b70ff88d5af917d9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2024-11-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "7", "issue": "1", "pages": "1595"}, "abstract": "Inflammatory intestinal conditions are a major disease burden. Numerous factors shape the distribution of immune cells in the colon, but a spatial characterization of the homeostatic and inflamed colonic immune microenvironment is lacking. Here, we use the COMET platform for multiplex immunofluorescence to profile the infiltration of nine immune cell populations in mice of both sexes (N = 16) with full spatial context, including in regions of squamous metaplasia. Unsupervised clustering, neighborhood analysis, and manual quantification along the proximal-distal axis characterized the colonic immune landscape, quantified cell-cell interactions, and revealed sex differences. The distal colon was the most affected region during colitis, which was pronounced in males, who exhibited a sex-dependent increase of B cells and reduction of M2-like macrophages. Regions of squamous metaplasia exhibited strong infiltration of numerous immune cell populations, especially in males. Females exhibited more helper T cells and neutrophils at homeostasis and increased M2-like macrophage infiltration in the mid-colon upon colitis. Sex differences were corroborated by plasma cytokine profiles. Our results provide a foundation for future studies of inflammatory intestinal conditions.", "doi": "10.1038/s42003-024-07276-1", "pmid": "39613949", "labels": {"Affinity Proteomics Stockholm": "Service", "Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11606951"}, {"db": "pii", "key": "10.1038/s42003-024-07276-1"}], "notes": [], "created": "2024-12-04T20:14:13.972Z", "modified": "2025-02-17T09:58:33.843Z"}, {"entity": "publication", "iuid": "f278321a964942c58d8fad97a3a8e229", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f278321a964942c58d8fad97a3a8e229.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f278321a964942c58d8fad97a3a8e229"}}, "title": "Ovarian ER\u03b2 cistrome and transcriptome reveal chromatin interaction with LRH-1.", "authors": [{"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R"}, {"family": "Lindquist", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Stepanauskaite", "given": "Lina", "initials": "L"}, {"family": "Luo", "given": "Qing", "initials": "Q"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Archer", "given": "Amena", "initials": "A"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2023-11-29", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "21", "issue": "1", "pages": "277", "issn-l": "1741-7007"}, "abstract": "Estrogen receptor beta (ER\u03b2, Esr2) plays a pivotal role in folliculogenesis and ovulation, yet its exact mechanism of action is mainly uncharacterized.\n\nWe here performed ER\u03b2 ChIP-sequencing of mouse ovaries followed by complementary RNA-sequencing of wild-type and ER\u03b2 knockout ovaries. By integrating the ER\u03b2 cistrome and transcriptome, we identified its direct target genes and enriched biological functions in the ovary. This demonstrated its strong impact on genes regulating organism development, cell migration, lipid metabolism, response to hypoxia, and response to estrogen. Cell-type deconvolution analysis of the bulk RNA-seq data revealed a decrease in luteal cells and an increased proportion of theca cells and a specific type of cumulus cells upon ER\u03b2 loss. Moreover, we identified a significant overlap with the gene regulatory network of liver receptor homolog 1 (LRH-1, Nr5a2) and showed that ER\u03b2 and LRH-1 extensively bound to the same chromatin locations in granulosa cells. Using ChIP-reChIP, we corroborated simultaneous ER\u03b2 and LRH-1 co-binding at the ER\u03b2-repressed gene Greb1 but not at the ER\u03b2-upregulated genes Cyp11a1 and Fkbp5. Transactivation assay experimentation further showed that ER\u03b2 and LRH-1 can inhibit their respective transcriptional activity at classical response elements.\n\nBy characterizing the genome-wide endogenous ER\u03b2 chromatin binding, gene regulations, and extensive crosstalk between ER\u03b2 and LRH-1, along with experimental corroborations, our data offer genome-wide mechanistic underpinnings of ovarian physiology and fertility.", "doi": "10.1186/s12915-023-01773-1", "pmid": "38031019", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10688478"}, {"db": "pii", "key": "10.1186/s12915-023-01773-1"}], "notes": [], "created": "2024-01-02T13:30:47.361Z", "modified": "2024-01-16T13:48:31.622Z"}, {"entity": "publication", "iuid": "24debc4b98554ac381461a8be3ba5b25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24debc4b98554ac381461a8be3ba5b25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24debc4b98554ac381461a8be3ba5b25"}}, "title": "Estrogen receptor activation remodelsTEAD1gene expression to alleviate nonalcoholic fatty liver disease", "authors": [{"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ", "orcid": "0000-0002-6086-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d80ebf009104cae8aaf56f9ad998c3b.json"}}, {"family": "Savva", "given": "Christina", "initials": "C", "orcid": "0000-0002-8019-1104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4ce68039184f35922fe3dd337f0ced.json"}}, {"family": "Hases", "given": "Linnea", "initials": "L", "orcid": "0000-0001-6741-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb5e09b88e94ab59a6ca9f8c457c5f4.json"}}, {"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Shen", "given": "Joanne X", "initials": "JX", "orcid": "0009-0008-0322-5615", "researcher": {"href": "https://publications.scilifelab.se/researcher/519a2d0afb6747c6ad3cf2b12c4d0bf3.json"}}, {"family": "Carravilla", "given": "Pablo", "initials": "P", "orcid": "0000-0001-6592-7630", "researcher": {"href": "https://publications.scilifelab.se/researcher/b791a8068a724c179b731f0446b1737a.json"}}, {"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0ce637276ce4cb0b81f9f039d261c61.json"}}, {"family": "N\u00f8rskov S\u00f8ndergaard", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0125f039a4949d8a22b9048d7f6b7d8.json"}}, {"family": "Ferrer-Aumatell", "given": "Cl\u00e0udia", "initials": "C", "orcid": "0009-0008-9828-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/a492fadc2d4e41028a5d103a87e214aa.json"}}, {"family": "Mercier", "given": "Gr\u00e9goire", "initials": "G", "orcid": "0009-0002-9966-9910", "researcher": {"href": "https://publications.scilifelab.se/researcher/b363ed8d40cd4bfdae8783c85922036b.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Korach-Andr\u00e9", "given": "Marion", "initials": "M", "orcid": "0000-0003-3292-9124", "researcher": {"href": "https://publications.scilifelab.se/researcher/407729e3f36742a890a54a8bac2e9662.json"}}, {"family": "Petersson", "given": "Carl", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Hannes", "initials": "H", "orcid": "0000-0002-8474-1759", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e5d3927690e4563a049c1703ecc4034.json"}}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "posted-content", "published": "2023-09-08", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.09.07.556687", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-10T11:47:13.965Z", "modified": "2025-12-18T19:46:10.899Z"}, {"entity": "publication", "iuid": "923e09636e01418bba0d80b842c05813", "links": {"self": {"href": "https://publications.scilifelab.se/publication/923e09636e01418bba0d80b842c05813.json"}, "display": {"href": "https://publications.scilifelab.se/publication/923e09636e01418bba0d80b842c05813"}}, "title": "High-fat diet and estrogen modulate the gut microbiota in a sex-dependent manner in mice.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L", "orcid": "0000-0001-6741-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb5e09b88e94ab59a6ca9f8c457c5f4.json"}}, {"family": "Stepanauskaite", "given": "Lina", "initials": "L", "orcid": "0000-0003-4173-6009", "researcher": {"href": "https://publications.scilifelab.se/researcher/429f33fed9a44ff4b70ff88d5af917d9.json"}}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Brusselaers", "given": "Nele", "initials": "N"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2023-01-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "20", "issn-l": "2399-3642"}, "abstract": "A high-fat diet can lead to gut microbiota dysbiosis, chronic intestinal inflammation, and metabolic syndrome. Notably, resulting phenotypes, such as glucose and insulin levels, colonic crypt cell proliferation, and macrophage infiltration, exhibit sex differences, and females are less affected. This is, in part, attributed to sex hormones. To investigate if there are sex differences in the microbiota and if estrogenic ligands can attenuate high-fat diet-induced dysbiosis, we used whole-genome shotgun sequencing to characterize the impact of diet, sex, and estrogenic ligands on the microbial composition of the cecal content of mice. We here report clear host sex differences along with remarkably sex-dependent responses to high-fat diet. Females, specifically, exhibited increased abundance of Blautia hansenii, and its levels correlated negatively with insulin levels in both sexes. Estrogen treatment had a modest impact on the microbiota diversity but altered a few important species in males. This included Collinsella aerofaciens F, which we show correlated with colonic macrophage infiltration. In conclusion, male and female mice exhibit clear differences in their cecal microbial composition and in how diet and estrogens impact the composition. Further, specific microbial strains are significantly correlated with metabolic parameters.", "doi": "10.1038/s42003-022-04406-5", "pmid": "36624306", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9829864"}, {"db": "pii", "key": "10.1038/s42003-022-04406-5"}], "notes": [], "created": "2023-11-27T21:49:55.417Z", "modified": "2024-01-16T13:48:34.180Z"}, {"entity": "publication", "iuid": "df3618d6438546bdbd1578a94586afc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df3618d6438546bdbd1578a94586afc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df3618d6438546bdbd1578a94586afc8"}}, "title": "Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "23", "issue": "18", "pages": null}, "abstract": "There are significant sex differences in colorectal cancer (CRC), including in incidence, onset, and molecular characteristics. Further, while inflammatory bowel disease (IBD) is a risk factor for CRC in both sexes, men with IBD have a 60% higher risk of developing CRC compared to women. In this study, we investigated sex differences during colitis-associated CRC (CAC) using a chemically induced CAC mouse model. The mice were treated with azoxymethane (AOM) and dextran sodium sulfate (DSS) and followed for 9 and 15 weeks. We performed RNA-sequencing of colon samples from males (n = 15) and females (n = 15) to study different stages of inflammation and identify corresponding transcriptomic sex differences in non-tumor colon tissue. We found a significant transcriptome response to AOM/DSS treatment in both sexes, including in pathways related to inflammation and cell proliferation. Notably, we found a stronger response in males and that male-specific differentially expressed genes were involved in NF\u03baB signaling and circadian rhythm. Further, an overrepresented proportion of male-specific gene regulations were predicted to be targets of Stat3, whereas for females, targets of the glucocorticoid receptor (Gr/Nr3c1) were overrepresented. At 15 weeks, the most apparent sex difference involved genes with functions in T cell proliferation, followed by the regulation of demethylases. The majority of sex differences were thus related to inflammation and the immune system. Our novel data, profiling the transcriptomic response to chemically induced colitis and CAC, indicate clear sex differences in CRC initiation and progression.", "doi": "10.3390/ijms231810408", "pmid": "36142324", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9499483"}, {"db": "pii", "key": "ijms231810408"}], "notes": [], "created": "2022-12-19T10:36:01.618Z", "modified": "2023-10-16T12:40:09.780Z"}, {"entity": "publication", "iuid": "a0c7031690744d69bd94427f6d63b73c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c7031690744d69bd94427f6d63b73c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c7031690744d69bd94427f6d63b73c"}}, "title": "Genome-wide estrogen receptor \u03b2 chromatin binding in human colon cancer cells reveals its tumor suppressor activity.", "authors": [{"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Jafferali", "given": "Mohammed Hakim", "initials": "MH"}, {"family": "Song", "given": "Dandan", "initials": "D"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Zhao", "given": "Chunyan", "initials": "C"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2021-08-01", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "149", "issue": "3", "pages": "692-706", "issn-l": "0020-7136"}, "abstract": "Colorectal cancer (CRC) is the third leading cause of cancer death in the western world. In women, menopausal hormone therapy has been shown to reduce CRC incidence by 20%. Studies demonstrate that estrogen activating estrogen receptor beta (ER\u03b2) protects against CRC. ER\u03b2 is a nuclear receptor that regulates gene expression through interactions with the chromatin. This molecular mechanism is, however, not well characterized in colon. Here, we present for the first time, the cistrome of ER\u03b2 in different colon cancer cell lines. We use cell lines engineered to express ER\u03b2, optimize and validate an ER\u03b2 antibody for chromatin-immunoprecipitation (ChIP), and perform ChIP-Seq. We identify key binding motifs, including ERE, AP-1, and TCF sites, and we determine enrichment of binding to cis-regulatory chromatin sites of genes involved in tumor development, cell migration, cell adhesion, apoptosis, and Wnt signaling pathways. We compare the corresponding cistromes of colon and breast cancer and find that they are conserved for about a third of genes, including GREB1, but that ER\u03b2 tethering to TCF and KLF family motifs is characteristic for colon. We exemplify upregulation of putative CRC tumor suppressor gene CST5 where ER\u03b2 in colon cells binds to cis-regulatory regions nearby (-351 bp) the transcriptional start site. Our work provides a foundation for understanding the mechanism of action of ER\u03b2 in CRC prevention.", "doi": "10.1002/ijc.33573", "pmid": "33754337", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-06-09T12:16:18.247Z", "modified": "2024-01-16T13:48:38.912Z"}, {"entity": "publication", "iuid": "8d23fe4a3c0b49a69a66baaa4811acc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d23fe4a3c0b49a69a66baaa4811acc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d23fe4a3c0b49a69a66baaa4811acc2"}}, "title": "The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Ibrahim", "given": "Ahmed", "initials": "A"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Liu", "given": "Yanghong", "initials": "Y"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2021-01-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "3", "pages": "1354", "issn-l": null}, "abstract": "Colorectal cancer (CRC) is the third leading cause of cancer deaths. Advances within bioinformatics, such as machine learning, can improve biomarker discovery and ultimately improve CRC survival rates. There are clear sex differences in CRC characteristics, but the impact of sex has not been considered with regards to CRC biomarkers. Our aim here was to investigate sex differences in the transcriptome of a normal colon and CRC, and between paired normal and tumor tissue. Next, we attempted to identify CRC diagnostic and prognostic biomarkers and investigate if they are sex-specific. We collected paired normal and tumor tissue, performed RNA-seq, and applied feature selection in combination with machine learning to identify the top CRC diagnostic biomarkers. We used The Cancer Genome Atlas (TCGA) data to identify sex-specific CRC diagnostic biomarkers and performed an overall survival analysis to identify sex-specific prognostic biomarkers. We found transcriptomic sex differences in both the normal colon tissue and in CRC. Forty-four of the top-ranked biomarkers were sex-specific and 20 biomarkers showed a sex-specific prognostic value. Our data show the importance of sex in the discovery of CRC biomarkers. We propose 20 sex-specific CRC prognostic biomarkers, including ESM1, GUCA2A, and VWA2 for males and CLDN1 and FUT1 for females.", "doi": "10.3390/ijms22031354", "pmid": "33572952", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijms22031354"}, {"db": "pmc", "key": "PMC7866425"}], "notes": [], "created": "2021-06-09T12:16:19.522Z", "modified": "2024-01-16T13:48:40.906Z"}]}