{"doi":"10.1098/rsob.220068","title":"Integrative analysis of genomic and transcriptomic alterations of\n                    <i>AGR2</i>\n                    and\n                    <i>AGR3</i>\n                    in cancer","abstract":"<jats:p>\n                    The\n                    <jats:italic>AGR2</jats:italic>\n                    and\n                    <jats:italic>AGR3</jats:italic>\n                    genes have been shown by numerous groups to be functionally associated with adenocarcinoma progression and metastasis. In this paper, we explore the data available in databases concerning genomic and transcriptomic features of these two genes: the NCBI dbSNP database was used to explore the presence and roles of constitutional SNPs, and the NCI, Cancer Cell Line Encyclopedia (CCLE) and TCGA databases were used to explore somatic mutations and copy number variations (CNVs), as well as mRNA expression of these genes in human cancer cell lines and tumours. Relationships of\n                    <jats:italic>AGR2</jats:italic>\n                    /\n                    <jats:italic>3</jats:italic>\n                    expression with whole-genome mRNA expression and cancer features (i.e. mutations and CNVs of oncogenes and tumour suppressor genes (TSG)) were established using the CCLE and TCGA databases. In addition, the CCLE data concerning CRISPR gene extinction screens (Achilles project) of these two genes and a panel of oncogenes and TSG were explored. We observed that no functional polymorphism or recurrent mutation could be detected in\n                    <jats:italic>AGR2</jats:italic>\n                    or\n                    <jats:italic>AGR3</jats:italic>\n                    . The expression of these genes was positively correlated with the expression of epithelial genes and inversely correlated with that of mesenchymal genes. It was also significantly associated with several cancer features, such as\n                    <jats:italic>TP53</jats:italic>\n                    or\n                    <jats:italic>SMAD4</jats:italic>\n                    mutations, depending on the gene and the cancer type. In addition, the CRISPR screens revealed the absence of cell fitness modification upon gene extinction, in contrast with oncogenes (cell fitness decrease) and TSG (cell fitness increase). Overall, these explorations revealed that AGR2 and AGR3 proteins appear as common non-genetic evolutionary factors in the process of human tumorigenesis.\n                  </jats:p>","journal":"Open Biology","year":2022,"id":618724,"datarank":0.37273599746820013,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.0,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1596381,"name":"Ines Villamor","orcid":null,"position":1,"is_corresponding":false},{"id":749810,"name":"Éric Chevet","orcid":"0000-0001-5855-4522","position":2,"is_corresponding":false},{"id":1596382,"name":"Frederic Delom","orcid":"0000-0002-4600-7633","position":3,"is_corresponding":false},{"id":241965,"name":"Jacques Robert","orcid":"0000-0003-4380-1476","position":4,"is_corresponding":false},{"id":1596380,"name":"Delphine Fessart","orcid":"0000-0001-7566-5670","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Integrative analysis of genomic and transcriptomic alterations of\n                    <i>AGR2</i>\n                    and\n                    <i>AGR3</i>\n                    in cancer","abstract":"<jats:p>\n                    The\n                    <jats:italic>AGR2</jats:italic>\n                    and\n                    <jats:italic>AGR3</jats:italic>\n                    genes have been shown by numerous groups to be functionally associated with adenocarcinoma progression and metastasis. In this paper, we explore the data available in databases concerning genomic and transcriptomic features of these two genes: the NCBI dbSNP database was used to explore the presence and roles of constitutional SNPs, and the NCI, Cancer Cell Line Encyclopedia (CCLE) and TCGA databases were used to explore somatic mutations and copy number variations (CNVs), as well as mRNA expression of these genes in human cancer cell lines and tumours. Relationships of\n                    <jats:italic>AGR2</jats:italic>\n                    /\n                    <jats:italic>3</jats:italic>\n                    expression with whole-genome mRNA expression and cancer features (i.e. mutations and CNVs of oncogenes and tumour suppressor genes (TSG)) were established using the CCLE and TCGA databases. In addition, the CCLE data concerning CRISPR gene extinction screens (Achilles project) of these two genes and a panel of oncogenes and TSG were explored. We observed that no functional polymorphism or recurrent mutation could be detected in\n                    <jats:italic>AGR2</jats:italic>\n                    or\n                    <jats:italic>AGR3</jats:italic>\n                    . The expression of these genes was positively correlated with the expression of epithelial genes and inversely correlated with that of mesenchymal genes. It was also significantly associated with several cancer features, such as\n                    <jats:italic>TP53</jats:italic>\n                    or\n                    <jats:italic>SMAD4</jats:italic>\n                    mutations, depending on the gene and the cancer type. In addition, the CRISPR screens revealed the absence of cell fitness modification upon gene extinction, in contrast with oncogenes (cell fitness decrease) and TSG (cell fitness increase). Overall, these explorations revealed that AGR2 and AGR3 proteins appear as common non-genetic evolutionary factors in the process of human tumorigenesis.\n                  </jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35857928","pmcid":"PMC9277299","openalex_id":null,"authors":[],"funders":[{"funder_name":"Agence Nationale de la Recherche","grant_id":"N/A","title":null},{"funder_name":"Fondation pour la Recherche Médicale","grant_id":"DEQ20180339169","title":null},{"funder_name":"Fondation ARC pour la Recherche sur le Cancer","grant_id":"PJA 20181207750","title":null},{"funder_name":"Institut National du Cancer","grant_id":"unidentified","title":"unidentified"}],"total_grants":4,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"gold","license":"Royal Society Data Sharing and Accessibility","oa_locations":[{"url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.220068","host_type":"publisher"},{"url":"https://royalsocietypublishing.org/doi/full-xml/10.1098/rsob.220068","host_type":"publisher"},{"url":"https://doi.org/10.1098/rsob.220068","host_type":"Unpaywall"},{"url":"https://europepmc.org/articles/PMC9277299","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9277299?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1101/2022.03.08.483441","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/35857928","host_type":""},{"url":"http://dx.doi.org/10.1098/rsob.220068","host_type":""},{"url":"https://doaj.org/article/2c54ffa3206f43e58d32b3f1a1f46ac1","host_type":""},{"url":"https://hal.science/hal-03777236v1","host_type":""},{"url":"https://hal.science/hal-03777236v1/document","host_type":""}],"fields_of_study":["03 medical and health sciences","0302 clinical medicine"],"mesh_terms":["Humans","Adenocarcinoma","Carrier Proteins","Mucoproteins","Neoplasm Proteins","Oncogene Proteins","RNA, Messenger","Genomics","Gene Expression Regulation, Neoplastic","DNA Copy Number Variations","Transcriptome"],"keywords":["Cancer","Genomic","Transcriptomic","Agr3","Agr2","Oncogene Proteins","DNA Copy Number Variations","QH301-705.5","Research","Genomics","Adenocarcinoma","Neoplasm Proteins","Gene Expression Regulation, Neoplastic","Mucoproteins","[SDV.CAN] Life Sciences [q-bio]/Cancer","Humans","RNA, Messenger","Biology (General)","Carrier Proteins","Transcriptome"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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