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       <jats:title>Background<\/jats:title>\n            <jats:p>Previous studies have suggested that, after acquisition of t(11;14), mantle cell lymphoma (MCL) pathogenesis may proceed via several different genetic second hits, which may shape different mutational profiles of clinically manifest lymphoma. The most prevalent second hit in MCL includes <jats:italic>ATM<\/jats:italic> aberrations, accounting for about half of patients with newly diagnosed MCL. As <jats:italic>ATM<\/jats:italic> and <jats:italic>TP53<\/jats:italic> mutations tend to be exclusive in MCL, we retrospectively analyzed the prognostic role of <jats:italic>ATM<\/jats:italic> deletions and\/or mutations in patients with newly diagnosed MCL, both in the entire cohort and in a subcohort of patients with wild-type <jats:italic>TP53<\/jats:italic>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>To investigate deletions and mutations of <jats:italic>ATM<\/jats:italic> and <jats:italic>TP53<\/jats:italic> in newly diagnosed MCL, we used fluorescence in situ hybridization and next-generation sequencing. To assess relationships between variables, non-parametric (Spearman) and chi-square tests were used. The Kruskal\u2013Wallis test was used to analyze differences in continuous variables between two groups of patients. For survival analyses, the standard Kaplan\u2013Meier estimator and log-rank test were employed. Univariate and multivariate Cox proportional hazard models were used to examine the prognostic value of various factors on patient survival.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We analyzed 187 patients with MCL (a median follow-up of 3.6 years). Eighty-one (43%) and 75 (40%) patients had <jats:italic>ATM<\/jats:italic> and <jats:italic>TP53<\/jats:italic> aberrations, respectively. Of note, three (9%) patients with mutated <jats:italic>ATM<\/jats:italic> harbored a germline mutation. Patients with <jats:italic>TP53<\/jats:italic> aberration had shorter survival rates. Although <jats:italic>ATM<\/jats:italic> deletion did not correlate with progression-free survival (PFS) in the entire cohort, it was associated with shorter PFS (hazard ratio 2.25, <jats:italic>p<\/jats:italic>\u2009=\u20090.01) in patients with wild-type <jats:italic>TP53<\/jats:italic>. A higher frequency of <jats:italic>ATM<\/jats:italic> deletion correlated with shorter PFS. Patients with <jats:italic>ATM<\/jats:italic> mutation (and wild-type <jats:italic>TP53<\/jats:italic>) had a trend toward better PFS (albeit not statistically significant). Moreover, patients with a higher variant allele frequency of <jats:italic>ATM<\/jats:italic> mutation tended to have longer PFS.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>\n              <jats:italic>ATM<\/jats:italic> deletion is an important predictor of prognosis in MCL patients and should be routinely examined, especially in those with wild-type <jats:italic>TP53<\/jats:italic>. In contrast, an isolated <jats:italic>ATM<\/jats:italic> mutation may predict a better prognosis in the context of standard immunochemotherapy.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s10020-025-01376-2","type":"journal-article","created":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T16:43:58Z","timestamp":1759164238000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Fundamental prognostic difference of ATM gene mutation and deletion in newly diagnosed mantle cell lymphoma"],"prefix":"10.1186","volume":"31","author":[{"given":"Ales","family":"Obr","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Malarikova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Kriegova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Urbankova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuzana","family":"Zemanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jirina","family":"Manakova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Petrackova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michaela","family":"Vatolikova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adela","family":"Berkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina","family":"Forsterova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomas","family":"Furst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Hruskova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrik","family":"Flodr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Hanackova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vit","family":"Prochazka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomas","family":"Papajik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Trneny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel","family":"Klener","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,9,29]]},"reference":[{"issue":"36","key":"1376_CR1","doi-asserted-by":"publisher","first-page":"58638","DOI":"10.18632\/oncotarget.10716","volume":"7","author":"M Ahmed","year":"2016","unstructured":"Ahmed M, Zhang L, Nomie K, Lam L, Wang M. 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