{"entity": "researcher", "timestamp": "2026-08-09T07:10:38.927Z", "family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "affiliations": ["Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d"}}, "publications": [{"entity": "publication", "iuid": "5736722e01b74b29baf8fe43d4ce6819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819"}}, "title": "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.", "authors": [{"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Alameddine", "given": "Asmaa", "initials": "A"}, {"family": "Sp\u00f6rndly-Nees", "given": "Ellinor", "initials": "E"}, {"family": "Montigny", "given": "Mathilde", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2025-08-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "751", "issn-l": "1471-2164"}, "abstract": "Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes.\n\nThe RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions.\n\nOur findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.", "doi": "10.1186/s12864-025-11814-4", "pmid": "40826322", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12363045"}, {"db": "pii", "key": "10.1186/s12864-025-11814-4"}], "notes": [], "created": "2025-09-08T07:04:42.067Z", "modified": "2025-09-09T13:14:43.091Z"}, {"entity": "publication", "iuid": "da70971f10de48a2a607c9b51dc45c38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38"}}, "title": "Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N", "orcid": "0009-0002-9876-4262", "researcher": {"href": "https://publications.scilifelab.se/researcher/e95627ce396b48f3828f038706cad7ac.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "Han", "given": "Jilong", "initials": "J", "orcid": "0000-0001-9747-8163", "researcher": {"href": "https://publications.scilifelab.se/researcher/6849bbc1472c447a82af373ca5a44e21.json"}}, {"family": "Humblot", "given": "Patrice", "initials": "P", "orcid": "0000-0002-5292-1798", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d74c76f33864331ab7c72614ae855f0.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}], "type": "journal article", "published": "2024-09-11", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "18", "issn-l": null}, "abstract": "Endometritis is an inflammatory disease that negatively influences fertility and is common in milk-producing cows. An in vitro model for bovine endometrial inflammation was used to identify enrichment of cis-acting regulatory elements in differentially methylated regions (DMRs) in the genome of in vitro-cultured primary bovine endometrial epithelial cells (bEECs) before and after treatment with lipopolysaccharide (LPS) from E. coli, a key player in the development of endometritis. The enriched regulatory elements contain binding sites for transcription factors with established roles in inflammation and hypoxia including NFKB and Hif-1\u03b1. We further showed co-localization of certain enriched cis-acting regulatory motifs including ARNT, Hif-1\u03b1, and NRF1. Our results show an intriguing interplay between increased mRNA levels in LPS-treated bEECs of the mRNAs encoding the key transcription factors such as AHR, EGR2, and STAT1, whose binding sites were enriched in the DMRs. Our results demonstrate an extraordinary cis-regulatory complexity in these DMRs having binding sites for both inflammatory and hypoxia-dependent transcription factors. Obtained data using this in vitro model for bacterial-induced endometrial inflammation have provided valuable information regarding key transcription factors relevant for clinical endometritis in both cattle and humans.", "doi": "10.3390/ijms25189832", "pmid": "39337320", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "ijms25189832"}, {"db": "pmc", "key": "PMC11432661"}], "notes": [], "created": "2024-09-30T06:07:03.182Z", "modified": "2024-09-30T06:07:04.535Z"}, {"entity": "publication", "iuid": "eab4268374624f2ab14306ca0d1dd3b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0"}}, "title": "Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).", "authors": [{"family": "Landi", "given": "Michael", "initials": "M", "orcid": "0000-0001-5597-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a48329b81f14ff191ed7a8c8cb562b8.json"}}, {"family": "Shah", "given": "Trushar", "initials": "T", "orcid": "0000-0002-0091-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db73454fcb34150bd72bcc5e850cb5e.json"}}, {"family": "Falquet", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8102-7579", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba0eeebd71e4f6ca50a2751f898fc6a.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Gisel", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7218-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2eb91acead14ec58845e9eda08742fa.json"}}], "type": "dataset", "published": "2023-12-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "887", "issn-l": "2052-4463"}, "abstract": "Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.", "doi": "10.1038/s41597-023-02800-0", "pmid": "38071206", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10710486"}, {"db": "pii", "key": "10.1038/s41597-023-02800-0"}], "notes": [], "created": "2023-12-11T06:42:02.155Z", "modified": "2024-01-05T16:18:41.036Z"}, {"entity": "publication", "iuid": "06e65b3fd65f4c00ac715731fc165702", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06e65b3fd65f4c00ac715731fc165702.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06e65b3fd65f4c00ac715731fc165702"}}, "title": "Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.", "authors": [{"family": "Lindholm Carlstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Etemadikhah", "given": "Mitra", "initials": "M", "orcid": "0000-0001-5795-9085", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e68ca63254a4b5697188bb87087852f.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Feuk", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2021-08-13", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "12", "issue": "8", "pages": null}, "abstract": "Schizophrenia is a genetically complex neuropsychiatric disorder with largely unresolved mechanisms of pathology. Identification of genes and pathways associated with schizophrenia is important for understanding the development, progression and treatment of schizophrenia. In this study, pathways associated with schizophrenia were explored at the level of gene expression. The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex-matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from the prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways. The results were validated with RT-qPCR. Significant differential expression between patient and controls groups was found for 71 genes. Gene ontology analysis of differentially expressed genes revealed an up-regulation of multiple genes in immune response among the patients (corrected p-value = 0.004). Several genes in the category belong to the complement system, including C1R, C1S, C7, FCN3, SERPING1, C4A and CFI. The increased complement expression is primarily driven by a subgroup of patients with increased expression of immune/inflammatory response genes, pointing to important differences in disease etiology within the patient group. Weighted gene co-expression network analysis highlighted networks associated with both synaptic transmission and activation of the immune response. Our results demonstrate the importance of immune-related pathways in schizophrenia and provide evidence for elevated expression of the complement cascade as an important pathway in schizophrenia pathology.", "doi": "10.3390/genes12081242", "pmid": "34440415", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes12081242"}, {"db": "pmc", "key": "PMC8393670"}], "notes": [], "created": "2021-11-24T13:25:18.239Z", "modified": "2024-01-16T13:48:38.753Z"}, {"entity": "publication", "iuid": "65338b6f4c55448b9e4454def5c0cc0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d"}}, "title": "LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Ivanova", "given": "Elena", "initials": "E"}, {"family": "Kelsey", "given": "Gavin", "initials": "G"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2020-06-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "385", "issn-l": "1471-2164"}, "abstract": "Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 \u03bcg/mL LPS for 24 h.\n\nDNA samples extracted at 0 h and 24 h were sequenced using reduced representation bisulfite sequencing (RRBS). When comparing DNA methylation results at 24 h to time 0 h, a larger proportion of hypomethylated regions were identified in the LPS-treated groups, whereas the trend was opposite in controls. When comparing LPS groups to controls at 24 h, a total of 1291 differentially methylated regions (DMRs) were identified (55% hypomethylated and 45% hypermethylated). Integration of DNA methylation data obtained here with our previously published gene expression data obtained from the same samples showed a negative correlation (r = - 0.41 for gene promoter, r = - 0.22 for gene body regions, p < 0.05). Differential methylation analysis revealed that effects of LPS treatment were associated with methylation changes for genes involved in regulation of immune and inflammatory responses, cell adhesion, and external stimuli. Gene ontology and pathway analyses showed that most of the differentially methylated genes (DMGs) were associated with cell proliferation and apoptotic processes; and pathways such as calcium-, oxytocin- and MAPK-signaling pathways with recognized roles in innate immunity. Several DMGs were related to systemic inflammation and tissue re-modelling including HDAC4, IRAK1, AKT1, MAP3K6, Wnt7A and ADAMTS17.\n\nThe present results show that LPS altered the DNA methylation patterns of bovine endometrial epithelial cells. This information, combined with our previously reported changes in gene expression related to endometrial function, confirm that LPS activates pro-inflammatory mechanisms leading to perturbed immune balance and cell adhesion processes in the endometrium.", "doi": "10.1186/s12864-020-06777-7", "pmid": "32493210", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06777-7"}, {"db": "pmc", "key": "PMC7268755"}], "notes": [], "created": "2020-06-09T14:54:11.383Z", "modified": "2024-01-16T13:48:42.410Z"}, {"entity": "publication", "iuid": "8e7d434d65094896b5c0c4f4328ae62e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e"}}, "title": "Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes.", "authors": [{"family": "Etemadikhah", "given": "Mitra", "initials": "M", "orcid": "0000-0001-5795-9085", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e68ca63254a4b5697188bb87087852f.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Wetterberg", "given": "Lennart", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2020-01-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "630", "issn-l": "2045-2322"}, "abstract": "Schizophrenia is a complex neurodevelopmental disorder with high rate of morbidity and mortality. While the heritability rate is high, the precise etiology is still unknown. Although schizophrenia is a central nervous system disorder, studies using peripheral tissues have also been established to search for patient specific biomarkers and to increase understanding of schizophrenia etiology. Among all peripheral tissues, fibroblasts stand out as they are easy to obtain and culture. Furthermore, they keep genetic stability for long period and exhibit molecular similarities to cells from nervous system. Using a unique set of fibroblast samples from a genetically isolated population in northern Sweden, we performed whole transcriptome sequencing to compare differentially expressed genes in seven controls and nine patients. We found differential fibroblast expression between cases and controls for 48 genes, including eight genes previously implicated in schizophrenia or schizophrenia related pathways; HGF, PRRT2, EGR1, EGR3, C11orf87, TLR3, PLEKHH2 and PIK3CD. Weighted gene correlation network analysis identified three differentially co-expressed networks of genes significantly-associated with schizophrenia. All three modules were significantly suppressed in patients compared to control, with one module highly enriched in genes involved in synaptic plasticity, behavior and synaptic transmission. In conclusion, our results support the use of fibroblasts for identification of differentially expressed genes in schizophrenia and highlight dysregulation of synaptic networks as an important mechanism in schizophrenia.", "doi": "10.1038/s41598-020-57467-z", "pmid": "31959813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-57467-z"}, {"db": "pmc", "key": "PMC6971273"}], "notes": [], "created": "2020-07-03T05:23:47.172Z", "modified": "2024-01-16T13:48:43.065Z"}, {"entity": "publication", "iuid": "55e97ce1989c4bb184fae3027bb2bf9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c"}}, "title": "Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.", "authors": [{"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "van Schaik", "given": "Tom", "initials": "T", "orcid": "0000-0001-7850-5074", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ccfcbccc214a7591e33d611edf0e8a.json"}}, {"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Charpigny", "given": "Gilles", "initials": "G"}, {"family": "Valarcher", "given": "Jean Francois", "initials": "JF"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2019-09-05", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "14", "issue": "9", "pages": "e0222081", "issn-l": "1932-6203"}, "abstract": "Lipopolysaccharide (LPS) expressed on the surface of Gram-negative bacteria activates pro-inflammatory pathways, dys-regulates the function of endometrial cells and is a key player in the mechanisms involved in endometritis. This study aimed to investigate the effects of LPS on bovine endometrial epithelial cells (bEEC) from whole transcriptome with a special focus on genes involved in embryo-maternal interactions. Following in vitro culture, bEEC from three cows were exposed to 0, 2, and 8 \u03bcg/mL LPS for 24h. RNA samples extracted at 0 and 24 hours were analyzed by RNA sequencing (RNA-seq). At 24h, 2035 differentially expressed genes (DEGs) were identified between controls and samples treated with 2 \u03bcg/mL LPS. Gene ontology analysis showed that over-expressed DEGs were associated to immune response, response to stress and external stimuli, catalytic activity, and cell cycle. Genes associated with cell membrane and cell adhesion pathways were under-expressed. LPS induced changes in expression of specific genes related to embryo-maternal interactions including under-expression of eight members of the cadherin superfamily, over-expression of six members of the mucin family, and differential expression of a large set of genes binding the above molecules and of more than 20 transcripts coding for cytokines and their receptors. Type I interferon-\u03c4 dependent genes were also over-expressed. From a sub-set of 19 genes, (biological replicates of bEEC from cows taken at time 6 (n = 3), 24 (n = 6) and 48 hours (n = 3), and 2 technical replicates per sample) differential gene expression was confirmed by RT2-qPCR (r2 between fold changes at 24 hours by RT2-qPCR and RNA-seq = 0.97). These results indicate that LPS affects the function of bEEC in many ways by differential transcription, glycolytic metabolism and oxidative stress. Many transcriptomic signatures related to implantation and embryo maternal interactions were strongly affected by LPS. These results pave the way for further studies to investigate the duration of these changes and their possible impact on endometrial function and fertility.", "doi": "10.1371/journal.pone.0222081", "pmid": "31487323", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6728075"}, {"db": "pii", "key": "PONE-D-19-15238"}], "notes": [], "created": "2024-09-30T06:07:45.782Z", "modified": "2024-09-30T06:07:46.035Z"}, {"entity": "publication", "iuid": "ee94eab47af144b0a91add67c1458f35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee94eab47af144b0a91add67c1458f35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee94eab47af144b0a91add67c1458f35"}}, "title": "Expression profiling and in situ screening of circular RNAs in human tissues.", "authors": [{"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Manivannan", "given": "Manimozhi", "initials": "M"}, {"family": "Bramlett", "given": "Kelli", "initials": "K"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2018-11-16", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "16953", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Circular RNAs (circRNAs) were recently discovered as a class of widely expressed noncoding RNA and have been implicated in regulation of gene expression. However, the function of the majority of circRNAs remains unknown. Studies of circRNAs have been hampered by a lack of essential approaches for detection, quantification and visualization. We therefore developed a target-enrichment sequencing method suitable for screening of circRNAs and their linear counterparts in large number of samples. We also applied padlock probes and in situ sequencing to visualize and determine circRNA localization in human brain tissue at subcellular levels. We measured circRNA abundance across different human samples and tissues. Our results highlight the potential of this RNA class to act as a specific diagnostic marker in blood and serum, by detection of circRNAs from genes exclusively expressed in the brain. The powerful and scalable tools we present will enable studies of circRNA function and facilitate screening of circRNA as diagnostic biomarkers.", "doi": "10.1038/s41598-018-35001-6", "pmid": "30446675", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-35001-6"}, {"db": "pmc", "key": "PMC6240052"}], "notes": [], "created": "2018-11-19T13:50:06.813Z", "modified": "2025-10-17T13:02:18.588Z"}]}