{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:09:30Z","timestamp":1753891770447,"version":"3.41.2"},"reference-count":48,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T00:00:00Z","timestamp":1638316800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Oncol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Mounting studies have sought to identify novel mutation biomarkers having diagnostic and prognostic potentials. Nevertheless, the understanding of the mutated pathways related to development and prognosis of B-cell lymphoma is still lacking. We aimed to comprehensively analyze the mutation alterations in genes of canonical signaling pathways and their impacts on the clinic outcomes of patients with B-cell lymphoma.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Circulating cell-free DNA (cfDNA) samples from 79 patients with B-cell lymphomas were used for targeted sequencing with a 560-gene panel for depicting mutation landscapes and identifying gene fusion events. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses of mutated genes were performed. The associations of mutation status of genes and seven canonical oncogenic pathways with progression-free survival (PFS) were assessed using Kaplan-Meier test and multivariate Cox analysis. The variant allele frequencies (VAFs) of genes in TP53 and Hippo pathways in paired baseline and post-treatment samples from 18 B-cell lymphoma patients were compared. Finally, the associations of identified fusion genes, mutated genes, and pathways with treatment response were evaluated based on objective response rates (ORRs) comparisons of groups.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We identified 666 mutations from 262 genes in baseline cfDNAs from 79 B-cell lymphoma patients, and found some genes were preferentially mutated in our cohort such as <jats:italic>GNAQ<\/jats:italic>, <jats:italic>GNAS<\/jats:italic>, <jats:italic>H3F3A<\/jats:italic>, <jats:italic>DNMT3A<\/jats:italic>, <jats:italic>HLA-A<\/jats:italic>, and <jats:italic>HLA-B<\/jats:italic>. These frequently mutated genes were significantly associated with negative \u201cregulation of gene expression, epigenetic\u201d and virus infections such as cytomegalovirus, Epstein-Barr virus, human immunodeficiency virus 1 infections. We detected five fusion genes in at least two patients with B-cell lymphoma, and among them, <jats:italic>TCF7L2<\/jats:italic>_<jats:italic>WT1<\/jats:italic> gene fusion was most frequently detected in 30.4% of patients (24 of 79 cases). <jats:italic>SEPT6<\/jats:italic>_<jats:italic>TRIM33<\/jats:italic> gene fusion, mutated TP53 and Hippo pathways were significantly associated with poor PFS, and <jats:italic>SEPT6<\/jats:italic>_<jats:italic>TRIM33<\/jats:italic> fusion gene and mutated TP53 pathway were independent prognostic factors for B-cell lymphoma. A decreased VAF of <jats:italic>TP53<\/jats:italic> p.Y88C and <jats:italic>LATS2<\/jats:italic> p.F972L was detected in patients with complete response to treatments. Moreover, a significant difference in ORR was observed in patients with NPM1_NR4A3 and SEPT6_TRIM33 fusions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p><jats:italic>SEPT6<\/jats:italic>_<jats:italic>TRIM33<\/jats:italic> gene fusion and mutated TP53 and Hippo pathways may serve as prognostic makers for B-cell lymphoma patients.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fonc.2021.765544","type":"journal-article","created":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T22:31:02Z","timestamp":1638397862000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["SEPT6_TRIM33 Gene Fusion and Mutated TP53 Pathway Associate With Unfavorable Prognosis in Patients With B-Cell Lymphomas"],"prefix":"10.3389","volume":"11","author":[{"given":"Haiying","family":"Fu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huarong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanyan","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianfei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiming","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongping","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenxi","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianzhen","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tingbo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,12,1]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.canlet.2017.07.020","article-title":"MiRNAs in B-Cell Lymphoma: Molecular Mechanisms and Biomarker Potential","volume":"405","author":"Sol\u00e9","year":"2017","journal-title":"Cancer Lett"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1038\/modpathol.2017.58","article-title":"Clinical Utility of Recently Identified Diagnostic, Prognostic, and Predictive Molecular Biomarkers in Mature B-Cell Neoplasms","volume":"30","author":"Onaindia","year":"2017","journal-title":"Mod Pathol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1111\/joim.12633","article-title":"Genetic Landscape and Deregulated Pathways in B-Cell Lymphoid Malignancies","volume":"282","author":"Rosenquist","year":"2017","journal-title":"J Intern Med"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3322\/caac.21660","article-title":"Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J Clin"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1016\/j.beha.2018.07.004","article-title":"Monitoring Clinical Outcomes in Aggressive B-Cell Lymphoma: From Imaging Studies to Circulating Tumor DNA","volume":"31","author":"Melani","year":"2018","journal-title":"Best Pract Res Clin Haematol"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1007\/s11899-018-0468-4","article-title":"Updates on Circulating Tumor DNA Assessment in Lymphoma","volume":"13","author":"Darrah","year":"2018","journal-title":"Curr Hematol Malig Rep"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2015-05-647602","article-title":"MYC-IG Rearrangements Are Negative Predictors of Survival in DLBCL Patients Treated With Immunochemotherapy: A GELA\/LYSA Study","volume":"126","author":"Copie-Bergman","year":"2015","journal-title":"Blood"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1200\/jco.19.00743","article-title":"Prognostic Significance of MYC Rearrangement and Translocation Partner in Diffuse Large B-Cell Lymphoma: A Study by the Lunenburg Lymphoma Biomarker Consortium","volume":"37","author":"Rosenwald","year":"2019","journal-title":"J Clin Oncol"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13045-017-0438-7","article-title":"a. 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