{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T04:51:47Z","timestamp":1793681507004,"version":"4.5.1"},"reference-count":95,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T00:00:00Z","timestamp":1762300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T00:00:00Z","timestamp":1762300800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000982","name":"Conquer Cancer Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000982","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/s41467-025-64666-7","type":"journal-article","created":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T13:06:57Z","timestamp":1762348017000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Functional genomics and tumor microenvironment analysis reveal prognostic biological subtypes in Mantle cell lymphoma"],"prefix":"10.1038","volume":"16","author":[{"given":"Sunandini","family":"Sharma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roshia","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1324-6678","authenticated-orcid":false,"given":"Alyssa","family":"Bouska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2750-6741","authenticated-orcid":false,"given":"Dylan","family":"Jochum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meghana","family":"Kesireddy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simeon","family":"Mahov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Lownik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waseem","family":"Lone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahfuza Afroz","family":"Soma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Gamboa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vaishnavi","family":"Devarakonda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1083-8283","authenticated-orcid":false,"given":"Dalia","family":"El-Gamal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atqiya","family":"Fariha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adnan","family":"Mansoor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian K.","family":"Link","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranjana H.","family":"Advani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul M.","family":"Barr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre H.","family":"Goy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amitkumar","family":"Mehta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manali","family":"Kamdar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah M.","family":"Stephens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Bachanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynette","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2932-7800","authenticated-orcid":false,"given":"Ryan","family":"Morin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3945-3552","authenticated-orcid":false,"given":"Prasath","family":"Pararajalingam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew A.","family":"Lunning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Weisenburger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6243-6008","authenticated-orcid":false,"given":"Wing C.","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2621-3584","authenticated-orcid":false,"given":"Joseph","family":"Khoury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy C.","family":"Greiner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1015-7434","authenticated-orcid":false,"given":"Julie M.","family":"Vose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7472-822X","authenticated-orcid":false,"given":"Akil","family":"Merchant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5375-7515","authenticated-orcid":false,"given":"Chengfeng","family":"Bi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3668-0629","authenticated-orcid":false,"given":"Javeed","family":"Iqbal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"On behalf of the North American Mantle Cell Lymphoma Project (NAMCLP)","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,5]]},"reference":[{"key":"64666_CR1","unstructured":"Swerdlow, S. et al. WHO Classification of Tumors of Haematopoietic and Lymphoid Tissues. 4, revised edn, (International Agency for Research on Cancer, 2017)."},{"key":"64666_CR2","doi-asserted-by":"publisher","first-page":"4315","DOI":"10.1182\/blood-2005-04-1753","volume":"106","author":"K Fu","year":"2005","unstructured":"Fu, K. et al. Cyclin D1-negative mantle cell lymphoma: a clinicopathologic study based on gene expression profiling. Blood 106, 4315\u20134321 (2005).","journal-title":"Blood"},{"key":"64666_CR3","doi-asserted-by":"publisher","first-page":"1488","DOI":"10.3324\/haematol.2009.013359","volume":"94","author":"SA Pileri","year":"2009","unstructured":"Pileri, S. A. & Falini, B. Mantle cell lymphoma. Haematologica 94, 1488\u20131492 (2009).","journal-title":"Haematologica"},{"key":"64666_CR4","doi-asserted-by":"publisher","first-page":"2495","DOI":"10.1056\/NEJMra2202672","volume":"386","author":"JO Armitage","year":"2022","unstructured":"Armitage, J. O. & Longo, D. L. Mantle-Cell Lymphoma. N. Engl. J. Med. 386, 2495\u20132506 (2022).","journal-title":"N. Engl. J. Med."},{"key":"64666_CR5","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1111\/bjh.18597","volume":"201","author":"M Harmanen","year":"2023","unstructured":"Harmanen, M. et al. Survival of patients with mantle cell lymphoma in the rituximab era: Retrospective binational analysis between 2000 and 2020. Br. J. Haematol. 201, 64\u201374 (2023).","journal-title":"Br. J. Haematol."},{"key":"64666_CR6","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S1535-6108(03)00028-X","volume":"3","author":"A Rosenwald","year":"2003","unstructured":"Rosenwald, A. et al. The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. Cancer Cell 3, 185\u2013197 (2003).","journal-title":"Cancer Cell"},{"key":"64666_CR7","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1158\/0008-5472.CAN-09-3419","volume":"70","author":"V Fernandez","year":"2010","unstructured":"Fernandez, V. et al. Genomic and gene expression profiling defines indolent forms of mantle cell lymphoma. Cancer Res. 70, 1408\u20131418 (2010).","journal-title":"Cancer Res."},{"key":"64666_CR8","doi-asserted-by":"publisher","first-page":"4939","DOI":"10.1182\/blood-2011-07-370122","volume":"119","author":"J Iqbal","year":"2012","unstructured":"Iqbal, J. et al. Genome-wide miRNA profiling of mantle cell lymphoma reveals a distinct subgroup with poor prognosis. Blood 119, 4939\u20134948 (2012).","journal-title":"Blood"},{"key":"64666_CR9","doi-asserted-by":"publisher","first-page":"3121","DOI":"10.1158\/1078-0432.CCR-12-3077","volume":"19","author":"A Navarro","year":"2013","unstructured":"Navarro, A. et al. microRNA expression profiles identify subtypes of mantle cell lymphoma with different clinicobiological characteristics. Clin. Cancer Res. 19, 3121\u20133129 (2013).","journal-title":"Clin. Cancer Res."},{"key":"64666_CR10","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1182\/blood-2010-01-263806","volume":"116","author":"EM Hartmann","year":"2010","unstructured":"Hartmann, E. M. et al. Pathway discovery in mantle cell lymphoma by integrated analysis of high-resolution gene expression and copy number profiling. Blood 116, 953\u2013961 (2010).","journal-title":"Blood"},{"key":"64666_CR11","doi-asserted-by":"publisher","first-page":"806","DOI":"10.1016\/j.ccell.2016.09.014","volume":"30","author":"AC Queiros","year":"2016","unstructured":"Queiros, A. C. et al. Decoding the DNA methylome of mantle cell Lymphoma in the light of the entire B cell lineage. Cancer Cell 30, 806\u2013821 (2016).","journal-title":"Cancer Cell"},{"key":"64666_CR12","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1182\/blood.2020005289","volume":"136","author":"F Nadeu","year":"2020","unstructured":"Nadeu, F. et al. Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood 136, 1419\u20131432 (2020).","journal-title":"Blood"},{"key":"64666_CR13","doi-asserted-by":"publisher","unstructured":"Yi, S. et al. Genomic and transcriptomic profiling reveals distinct molecular subsets associated with outcomes in mantle cell lymphoma. J. Clin. Invest. 132, https:\/\/doi.org\/10.1172\/jci153283 (2022).","DOI":"10.1172\/jci153283"},{"key":"64666_CR14","doi-asserted-by":"publisher","first-page":"2761","DOI":"10.1002\/ijc.29326","volume":"136","author":"S Bernard","year":"2015","unstructured":"Bernard, S. et al. Inhibitors of BCR signalling interrupt the survival signal mediated by the micro-environment in mantle cell lymphoma. Int. J. Cancer 136, 2761\u20132774 (2015).","journal-title":"Int. J. Cancer"},{"key":"64666_CR15","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1182\/blood-2017-04-776740","volume":"130","author":"P Balsas","year":"2017","unstructured":"Balsas, P. et al. SOX11 promotes tumor protective microenvironment interactions through CXCR4 and FAK regulation in mantle cell lymphoma. Blood 130, 501\u2013513 (2017).","journal-title":"Blood"},{"key":"64666_CR16","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13045-023-01520-7","volume":"16","author":"JM Vose","year":"2023","unstructured":"Vose, J. M. et al. Integrative analysis of clinicopathological features defines novel prognostic models for mantle cell lymphoma in the immunochemotherapy era: a report from The North American Mantle Cell Lymphoma Consortium. J. Hematol. Oncol. 16, 122 (2023).","journal-title":"J. Hematol. Oncol."},{"key":"64666_CR17","doi-asserted-by":"publisher","first-page":"690","DOI":"10.3324\/haematol.2020.274258","volume":"107","author":"MCJ Ma","year":"2022","unstructured":"Ma, M. C. J. et al. Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma. Haematologica 107, 690\u2013701 (2022).","journal-title":"Haematologica"},{"key":"64666_CR18","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-4-r41","volume":"12","author":"CH Mermel","year":"2011","unstructured":"Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).","journal-title":"Genome Biol."},{"key":"64666_CR19","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1438-2","volume":"18","author":"YP Lai","year":"2017","unstructured":"Lai, Y. P. et al. iGC-an integrated analysis package of gene expression and copy number alteration. BMC Bioinform. 18, 35 (2017).","journal-title":"BMC Bioinform."},{"key":"64666_CR20","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","volume":"162","author":"JH Levine","year":"2015","unstructured":"Levine, J. H. et al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184\u2013197 (2015).","journal-title":"Cell"},{"key":"64666_CR21","doi-asserted-by":"publisher","first-page":"1731","DOI":"10.3389\/fimmu.2020.01731","volume":"11","author":"K Wu","year":"2020","unstructured":"Wu, K. et al. Redefining tumor-associated macrophage subpopulations and functions in the tumor microenvironment. Front. Immunol. 11, 1731 (2020).","journal-title":"Front. Immunol."},{"key":"64666_CR22","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/s41392-023-01452-1","volume":"8","author":"S Chen","year":"2023","unstructured":"Chen, S. et al. Macrophages in immunoregulation and therapeutics. Signal Transduct. Target Ther. 8, 207 (2023).","journal-title":"Signal Transduct. Target Ther."},{"key":"64666_CR23","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1126\/science.aad5227","volume":"351","author":"IM Slaymaker","year":"2016","unstructured":"Slaymaker, I. M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84\u201388 (2016).","journal-title":"Science"},{"key":"64666_CR24","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1038\/nbt.4172","volume":"36","author":"LW Koblan","year":"2018","unstructured":"Koblan, L. W. et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol. 36, 843\u2013846 (2018).","journal-title":"Nat. Biotechnol."},{"key":"64666_CR25","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1126\/science.aba8853","volume":"368","author":"RT Walton","year":"2020","unstructured":"Walton, R. T., Christie, K. A., Whittaker, M. N. & Kleinstiver, B. P. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368, 290\u2013296 (2020).","journal-title":"Science"},{"key":"64666_CR26","doi-asserted-by":"publisher","first-page":"e211","DOI":"10.3324\/haematol.2018.205229","volume":"104","author":"S Rule","year":"2019","unstructured":"Rule, S. et al. Ibrutinib for the treatment of relapsed\/refractory mantle cell lymphoma: extended 3.5-year follow up from a pooled analysis. Haematologica 104, e211\u2013e214 (2019).","journal-title":"Haematologica"},{"key":"64666_CR27","doi-asserted-by":"publisher","first-page":"E137","DOI":"10.1002\/ajh.26109","volume":"96","author":"P Jain","year":"2021","unstructured":"Jain, P. et al. Outcomes of relapsed mantle cell lymphoma patients after discontinuing acalabrutinib. Am. J. Hematol. 96, E137\u2013E140 (2021).","journal-title":"Am. J. Hematol."},{"key":"64666_CR28","doi-asserted-by":"publisher","first-page":"2482","DOI":"10.1056\/NEJMoa2201817","volume":"386","author":"ML Wang","year":"2022","unstructured":"Wang, M. L. et al. Ibrutinib plus bendamustine and rituximab in untreated mantle-cell Lymphoma. N. Engl. J. Med. 386, 2482\u20132494 (2022).","journal-title":"N. Engl. J. Med."},{"key":"64666_CR29","doi-asserted-by":"publisher","first-page":"2927","DOI":"10.1182\/bloodadvances.2019001350","volume":"4","author":"HA Hill","year":"2020","unstructured":"Hill, H. A. et al. Genetic mutations and features of mantle cell lymphoma: a systematic review and meta-analysis. Blood Adv. 4, 2927\u20132938 (2020).","journal-title":"Blood Adv."},{"key":"64666_CR30","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1182\/blood-2015-11-681460","volume":"128","author":"NS Saba","year":"2016","unstructured":"Saba, N. S. et al. Pathogenic role of B-cell receptor signaling and canonical NF-kappaB activation in mantle cell lymphoma. Blood 128, 82\u201392 (2016).","journal-title":"Blood"},{"key":"64666_CR31","doi-asserted-by":"publisher","first-page":"4215","DOI":"10.1182\/blood-2011-12-400580","volume":"119","author":"L Nygren","year":"2012","unstructured":"Nygren, L. et al. Prognostic role of SOX11 in a population-based cohort of mantle cell lymphoma. Blood 119, 4215\u20134223 (2012).","journal-title":"Blood"},{"key":"64666_CR32","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1111\/bjh.12854","volume":"166","author":"L Nordstrom","year":"2014","unstructured":"Nordstrom, L. et al. SOX11 and TP53 add prognostic information to MIPI in a homogenously treated cohort of mantle cell lymphoma-a Nordic Lymphoma Group study. Br. J. Haematol. 166, 98\u2013108 (2014).","journal-title":"Br. J. Haematol."},{"key":"64666_CR33","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1007\/s12185-017-2236-y","volume":"106","author":"W Yang","year":"2017","unstructured":"Yang, W. et al. SOX11 regulates the pro-apoptosis signal pathway and predicts a favorable prognosis of mantle cell lymphoma. Int. J. Hematol. 106, 212\u2013220 (2017).","journal-title":"Int. J. Hematol."},{"key":"64666_CR34","doi-asserted-by":"publisher","first-page":"2247","DOI":"10.1182\/blood-2018-02-832535","volume":"131","author":"PY Kuo","year":"2018","unstructured":"Kuo, P. Y. et al. SOX11 augments BCR signaling to drive MCL-like tumor development. Blood 131, 2247\u20132255 (2018).","journal-title":"Blood"},{"key":"64666_CR35","doi-asserted-by":"publisher","first-page":"18250","DOI":"10.1073\/pnas.1314608110","volume":"110","author":"S Bea","year":"2013","unstructured":"Bea, S. et al. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc. Natl. Acad. Sci. USA 110, 18250\u201318255 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"64666_CR36","doi-asserted-by":"publisher","first-page":"2988","DOI":"10.1182\/blood-2013-07-517177","volume":"123","author":"J Zhang","year":"2014","unstructured":"Zhang, J. et al. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood 123, 2988\u20132996 (2014).","journal-title":"Blood"},{"key":"64666_CR37","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1182\/blood.2019002385","volume":"136","author":"P Pararajalingam","year":"2020","unstructured":"Pararajalingam, P. et al. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood 136, 572\u2013584 (2020).","journal-title":"Blood"},{"key":"64666_CR38","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1080\/10428194.2018.1542144","volume":"60","author":"A Mareckova","year":"2019","unstructured":"Mareckova, A. et al. ATM and TP53 mutations show mutual exclusivity but distinct clinical impact in mantle cell lymphoma patients. Leuk. Lymphoma 60, 1420\u20131428 (2019).","journal-title":"Leuk. Lymphoma"},{"key":"64666_CR39","doi-asserted-by":"publisher","first-page":"73558","DOI":"10.18632\/oncotarget.12434","volume":"7","author":"A Mohanty","year":"2016","unstructured":"Mohanty, A. et al. CCND1 mutations increase protein stability and promote ibrutinib resistance in mantle cell lymphoma. Oncotarget 7, 73558\u201373572 (2016).","journal-title":"Oncotarget"},{"key":"64666_CR40","doi-asserted-by":"publisher","first-page":"4599","DOI":"10.1182\/blood-2006-08-039859","volume":"109","author":"A Wiestner","year":"2007","unstructured":"Wiestner, A. et al. Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. Blood 109, 4599\u20134606 (2007).","journal-title":"Blood"},{"key":"64666_CR41","doi-asserted-by":"publisher","first-page":"3592","DOI":"10.4161\/cc.8.21.9993","volume":"8","author":"A Deshpande","year":"2009","unstructured":"Deshpande, A. et al. 3\u2019UTR mediated regulation of the cyclin D1 proto-oncogene. Cell Cycle 8, 3592\u20133600 (2009).","journal-title":"Cell Cycle"},{"key":"64666_CR42","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1200\/JCO.2016.70.7901","volume":"35","author":"DW Scott","year":"2017","unstructured":"Scott, D. W. et al. New molecular assay for the proliferation signature in mantle cell lymphoma applicable to formalin-fixed paraffin-embedded biopsies. J. Clin. Oncol. 35, 1668\u20131677 (2017).","journal-title":"J. Clin. Oncol."},{"key":"64666_CR43","doi-asserted-by":"publisher","first-page":"1386","DOI":"10.1200\/JCO.2015.63.8387","volume":"34","author":"E Hoster","year":"2016","unstructured":"Hoster, E. et al. Prognostic value of Ki-67 index, cytology, and growth pattern in mantle-cell lymphoma: results from randomized trials of the European mantle cell lymphoma network. J. Clin. Oncol. 34, 1386\u20131394 (2016).","journal-title":"J. Clin. Oncol."},{"key":"64666_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41408-023-00927-2","volume":"13","author":"P Jain","year":"2023","unstructured":"Jain, P. et al. Immune-depleted tumor microenvironment is associated with poor outcomes and BTK inhibitor resistance in mantle cell lymphoma. Blood Cancer J. 13, 156 (2023).","journal-title":"Blood Cancer J."},{"key":"64666_CR45","doi-asserted-by":"publisher","first-page":"2698","DOI":"10.1200\/JCO.2015.65.9789","volume":"34","author":"AM Lesokhin","year":"2016","unstructured":"Lesokhin, A. M. et al. Nivolumab in patients with relapsed or refractory hematologic malignancy: preliminary results of a phase Ib study. J. Clin. Oncol. 34, 2698\u20132704 (2016).","journal-title":"J. Clin. Oncol."},{"key":"64666_CR46","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1016\/j.celrep.2019.12.028","volume":"30","author":"J Blagih","year":"2020","unstructured":"Blagih, J. et al. Cancer-specific loss of p53 leads to a modulation of myeloid and T cell responses. Cell Rep. 30, 481\u2013496 (2020).","journal-title":"Cell Rep."},{"key":"64666_CR47","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/s41388-023-02886-1","volume":"43","author":"X Dong","year":"2024","unstructured":"Dong, X. et al. Regulated secretion of mutant p53 negatively affects T lymphocytes in the tumor microenvironment. Oncogene 43, 92\u2013105 (2024).","journal-title":"Oncogene"},{"key":"64666_CR48","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.1016\/j.cell.2009.11.026","volume":"139","author":"PA Muller","year":"2009","unstructured":"Muller, P. A. et al. Mutant p53 drives invasion by promoting integrin recycling. Cell 139, 1327\u20131341 (2009).","journal-title":"Cell"},{"key":"64666_CR49","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-022-09803-x","volume":"22","author":"F Ameli","year":"2022","unstructured":"Ameli, F., Shajareh, E., Mokhtari, M. & Kosari, F. Expression of PD1 and PDL1 as immune-checkpoint inhibitors in mantle cell lymphoma. BMC Cancer 22, 848 (2022).","journal-title":"BMC Cancer"},{"key":"64666_CR50","doi-asserted-by":"publisher","first-page":"3943","DOI":"10.1038\/onc.2016.502","volume":"36","author":"M Fischer","year":"2017","unstructured":"Fischer, M. Census and evaluation of p53 target genes. Oncogene 36, 3943\u20133956 (2017).","journal-title":"Oncogene"},{"key":"64666_CR51","doi-asserted-by":"publisher","first-page":"36409","DOI":"10.18632\/oncotarget.26376","volume":"9","author":"K Cerna","year":"2018","unstructured":"Cerna, K. & Mraz, M. p53 limits B cell receptor (BCR) signalling: a new role for miR-34a and FOXP1. Oncotarget 9, 36409\u201336410 (2018).","journal-title":"Oncotarget"},{"key":"64666_CR52","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1158\/2159-8290.CD-14-0098","volume":"4","author":"D Chiron","year":"2014","unstructured":"Chiron, D. et al. Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma. Cancer Discov. 4, 1022\u20131035 (2014).","journal-title":"Cancer Discov."},{"key":"64666_CR53","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14920","volume":"8","author":"X Zhao","year":"2017","unstructured":"Zhao, X. et al. Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma. Nat. Commun. 8, 14920 (2017).","journal-title":"Nat. Commun."},{"key":"64666_CR54","doi-asserted-by":"crossref","unstructured":"George, B. et al. Ibrutinib Resistance Mechanisms and Treatment Strategies for B-Cell lymphomas. Cancers 12, 1328 (2020).","DOI":"10.3390\/cancers12051328"},{"key":"64666_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-52000-3","volume":"9","author":"MJ McCabe","year":"2019","unstructured":"McCabe, M. J. et al. Development and validation of a targeted gene sequencing panel for application to disparate cancers. Sci. Rep. 9, 17052 (2019).","journal-title":"Sci. Rep."},{"key":"64666_CR56","doi-asserted-by":"publisher","first-page":"851","DOI":"10.3389\/fonc.2019.00851","volume":"9","author":"A Petrackova","year":"2019","unstructured":"Petrackova, A. et al. Standardization of sequencing coverage depth in NGS: recommendation for detection of clonal and subclonal mutations in cancer diagnostics. Front. Oncol. 9, 851 (2019).","journal-title":"Front. Oncol."},{"key":"64666_CR57","doi-asserted-by":"publisher","first-page":"2787","DOI":"10.1128\/AAC.48.8.2787-2792.2004","volume":"48","author":"SL Spruance","year":"2004","unstructured":"Spruance, S. L., Reid, J. E., Grace, M. & Samore, M. Hazard ratio in clinical trials. Antimicrob. Agents Chemother. 48, 2787\u20132792 (2004).","journal-title":"Antimicrob. Agents Chemother."},{"key":"64666_CR58","doi-asserted-by":"publisher","first-page":"3","DOI":"10.20892\/j.issn.2095-3941.2016.0004","volume":"13","author":"SP Strom","year":"2016","unstructured":"Strom, S. P. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol. Med 13, 3\u201311 (2016).","journal-title":"Cancer Biol. Med"},{"key":"64666_CR59","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"64666_CR60","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1279-z","volume":"17","author":"S Tian","year":"2016","unstructured":"Tian, S., Yan, H., Kalmbach, M. & Slager, S. L. Impact of post-alignment processing in variant discovery from whole exome data. BMC Bioinform. 17, 403 (2016).","journal-title":"BMC Bioinform."},{"key":"64666_CR61","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.129684.111","volume":"22","author":"DC Koboldt","year":"2012","unstructured":"Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568\u2013576 (2012).","journal-title":"Genome Res."},{"key":"64666_CR62","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-017-0309-7","volume":"10","author":"C Shyr","year":"2017","unstructured":"Shyr, C. et al. Correction to: FLAGS, frequently mutated genes in public exomes. BMC Med. Genom. 10, 69 (2017).","journal-title":"BMC Med. Genom."},{"key":"64666_CR63","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1101\/gr.239244.118","volume":"28","author":"A Mayakonda","year":"2018","unstructured":"Mayakonda, A., Lin, D. C., Assenov, Y., Plass, C. & Koeffler, H. P. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome. Res. 28, 1747\u20131756 (2018).","journal-title":"Genome. Res."},{"key":"64666_CR64","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"64666_CR65","doi-asserted-by":"crossref","unstructured":"Dobin, A. & Gingeras, T. R. Mapping RNA-seq Reads with STAR. Curr. Protoc. Bioinform. 51, 11 14 11\u201311 14 19 (2015).","DOI":"10.1002\/0471250953.bi1114s51"},{"key":"64666_CR66","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166\u2013169 (2015).","journal-title":"Bioinformatics"},{"key":"64666_CR67","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"64666_CR68","doi-asserted-by":"publisher","first-page":"D623","DOI":"10.1093\/nar\/gkn698","volume":"37","author":"A Kamburov","year":"2009","unstructured":"Kamburov, A., Wierling, C., Lehrach, H. & Herwig, R. ConsensusPathDB-a database for integrating human functional interaction networks. Nucleic Acids Res. 37, D623\u2013D628 (2009).","journal-title":"Nucleic Acids Res."},{"key":"64666_CR69","doi-asserted-by":"publisher","first-page":"D712","DOI":"10.1093\/nar\/gkq1156","volume":"39","author":"A Kamburov","year":"2011","unstructured":"Kamburov, A. et al. ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res. 39, D712\u2013D717 (2011).","journal-title":"Nucleic Acids Res."},{"key":"64666_CR70","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).","journal-title":"Nucleic Acids Res."},{"key":"64666_CR71","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","volume":"37","author":"AM Newman","year":"2019","unstructured":"Newman, A. M. et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 37, 773\u2013782 (2019).","journal-title":"Nat. Biotechnol."},{"key":"64666_CR72","doi-asserted-by":"publisher","first-page":"251","DOI":"10.4103\/ijd.IJD_201_17","volume":"62","author":"A Hazra","year":"2017","unstructured":"Hazra, A. & Gogtay, N. Biostatistics Series Module 9: Survival Analysis. Indian J. Dermatol 62, 251\u2013257 (2017).","journal-title":"Indian J. Dermatol"},{"key":"64666_CR73","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0617-1","volume":"16","author":"T Kuilman","year":"2015","unstructured":"Kuilman, T. et al. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol. 16, 49 (2015).","journal-title":"Genome Biol."},{"key":"64666_CR74","doi-asserted-by":"publisher","unstructured":"Franch-Exposito, S. et al. CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications. Elife 9, https:\/\/doi.org\/10.7554\/elife.50267 (2020).","DOI":"10.7554\/elife.50267"},{"key":"64666_CR75","doi-asserted-by":"publisher","first-page":"3012","DOI":"10.1093\/bioinformatics\/btw325","volume":"32","author":"ZL Skidmore","year":"2016","unstructured":"Skidmore, Z. L. et al. GenVisR: genomic visualizations in R. Bioinformatics 32, 3012\u20133014 (2016).","journal-title":"Bioinformatics"},{"key":"64666_CR76","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41591-018-0016-8","volume":"24","author":"B Chapuy","year":"2018","unstructured":"Chapuy, B. et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat. Med. 24, 679\u2013690 (2018).","journal-title":"Nat. Med."},{"key":"64666_CR77","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847\u20132849 (2016).","journal-title":"Bioinformatics"},{"key":"64666_CR78","doi-asserted-by":"publisher","first-page":"6813","DOI":"10.1021\/ac901049w","volume":"81","author":"DR Bandura","year":"2009","unstructured":"Bandura, D. R. et al. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal. Chem. 81, 6813\u20136822 (2009).","journal-title":"Anal. Chem."},{"key":"64666_CR79","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.2869","volume":"11","author":"C Giesen","year":"2014","unstructured":"Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat. Methods 11, 417\u2013422 (2014).","journal-title":"Nat. Methods"},{"key":"64666_CR80","doi-asserted-by":"publisher","first-page":"10107","DOI":"10.1021\/ac400996x","volume":"85","author":"HA Wang","year":"2013","unstructured":"Wang, H. A. et al. Fast chemical imaging at high spatial resolution by laser ablation inductively coupled plasma mass spectrometry. Anal. Chem. 85, 10107\u201310116 (2013).","journal-title":"Anal. Chem."},{"key":"64666_CR81","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41587-021-01094-0","volume":"40","author":"NF Greenwald","year":"2022","unstructured":"Greenwald, N. F. et al. Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat. Biotechnol. 40, 555\u2013565 (2022).","journal-title":"Nat. Biotechnol."},{"key":"64666_CR82","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29383-5","volume":"13","author":"CB Pedersen","year":"2022","unstructured":"Pedersen, C. B. et al. cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies. Nat. Commun. 13, 1698 (2022).","journal-title":"Nat. Commun."},{"key":"64666_CR83","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1146\/annurev-biodatasci-020422-050255","volume":"6","author":"SM Guldberg","year":"2023","unstructured":"Guldberg, S. M., Okholm, T. L. H., McCarthy, E. E. & Spitzer, M. H. Computational methods for single-cell proteomics. Annu. Rev. Biomed. Data Sci. 6, 47\u201371 (2023).","journal-title":"Annu. Rev. Biomed. Data Sci."},{"key":"64666_CR84","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-41695-z","volume":"9","author":"VA Traag","year":"2019","unstructured":"Traag, V. A., Waltman, L. & van Eck, N. J. From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 9, 5233 (2019).","journal-title":"Sci. Rep."},{"key":"64666_CR85","doi-asserted-by":"crossref","unstructured":"M\u00fcllner, D. fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python. J. Stat. Softw. 53, 1\u201318 (2013).","DOI":"10.18637\/jss.v053.i09"},{"key":"64666_CR86","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03489-7","volume":"26","author":"N Muller-Botticher","year":"2025","unstructured":"Muller-Botticher, N., Sahay, S., Eils, R. & Ishaque, N. SpatialLeiden: spatially aware Leiden clustering. Genome Biol. 26, 24 (2025).","journal-title":"Genome Biol."},{"key":"64666_CR87","doi-asserted-by":"publisher","unstructured":"Henikoff, S., Henikoff, J. G., Kaya-Okur, H. S. & Ahmad, K. Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation. Elife 9, https:\/\/doi.org\/10.7554\/elife.63274 (2020).","DOI":"10.7554\/elife.63274"},{"key":"64666_CR88","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s13072-019-0287-4","volume":"12","author":"MP Meers","year":"2019","unstructured":"Meers, M. P., Tenenbaum, D. & Henikoff, S. Peak calling by sparse enrichment analysis for CUT&RUN chromatin profiling. Epigenetics Chromatin 12, 42 (2019).","journal-title":"Epigenetics Chromatin"},{"key":"64666_CR89","doi-asserted-by":"publisher","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","volume":"9","author":"M Lawrence","year":"2013","unstructured":"Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).","journal-title":"PLoS Comput. Biol."},{"key":"64666_CR90","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gku365","volume":"42","author":"F Ramirez","year":"2014","unstructured":"Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187\u2013W191 (2014).","journal-title":"Nucleic Acids Res."},{"key":"64666_CR91","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"},{"key":"64666_CR92","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"64666_CR93","doi-asserted-by":"publisher","first-page":"2943","DOI":"10.1093\/bioinformatics\/btac166","volume":"38","author":"GH Putri","year":"2022","unstructured":"Putri, G. H., Anders, S., Pyl, P. T., Pimanda, J. E. & Zanini, F. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics 38, 2943\u20132945 (2022).","journal-title":"Bioinformatics"},{"key":"64666_CR94","doi-asserted-by":"crossref","unstructured":"Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).","DOI":"10.1186\/gb-2010-11-3-r25"},{"key":"64666_CR95","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545\u201315550 (2005).","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64666-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64666-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64666-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T14:06:28Z","timestamp":1762351588000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64666-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,5]]},"references-count":95,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["64666"],"URL":"https:\/\/doi.org\/10.1038\/s41467-025-64666-7","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,5]]},"assertion":[{"value":"12 June 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"9762"}}