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For: Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 2018;173:291-304.e6. [PMID: 29625048 PMCID: PMC5957518 DOI: 10.1016/j.cell.2018.03.022] [Citation(s) in RCA: 1548] [Impact Index Per Article: 221.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/12/2018] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Sahu VK, Sur S, Agarwal S, Madhyastha H, Ranjan A, Basu S. Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions. Biophys Chem 2025;322:107421. [PMID: 40048894 DOI: 10.1016/j.bpc.2025.107421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 09/02/2024] [Accepted: 03/01/2025] [Indexed: 04/27/2025]
2
Kim G, Cha Y, Baek SH. Identification of KANK1 as a tumor suppressor gene in pancreatic ductal adenocarcinoma. Biochem Biophys Res Commun 2025;766:151885. [PMID: 40288262 DOI: 10.1016/j.bbrc.2025.151885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2025] [Accepted: 04/23/2025] [Indexed: 04/29/2025]
3
Ma L, Mao JH, Barcellos-Hoff MH. Systemic inflammation in response to radiation drives the genesis of an immunosuppressed tumor microenvironment. Neoplasia 2025;64:101164. [PMID: 40184664 PMCID: PMC11999686 DOI: 10.1016/j.neo.2025.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 03/24/2025] [Accepted: 03/27/2025] [Indexed: 04/07/2025]
4
Alvarado-Ortiz E, Castañeda-Patlán MC, Moreno-Londoño AP, Tinajero-Rodríguez JM, Briseño-Díaz P, Sarabia-Sánchez MA, Vargas M, Ortiz-Sánchez E, Robles-Flores M. Non-canonical Wnt co-receptors ROR1/ROR2 are differentially regulated by hypoxia in colon cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2025;1872:119968. [PMID: 40268059 DOI: 10.1016/j.bbamcr.2025.119968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 04/25/2025]
5
Smith SC, Diaz-Perez JA, Mochel MC, Billings SD, Fernandez L, Poklepovic AS. A High-grade PML::JAK1 Fusion Sarcoma. Am J Surg Pathol 2025;49:633-635. [PMID: 39494835 DOI: 10.1097/pas.0000000000002326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2024]
6
Ellington CN, Lengerich BJ, Watkins TBK, Yang J, Adduri AK, Mahbub S, Xiao H, Kellis M, Xing EP. Learning to estimate sample-specific transcriptional networks for 7,000 tumors. Proc Natl Acad Sci U S A 2025;122:e2411930122. [PMID: 40408406 DOI: 10.1073/pnas.2411930122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 04/06/2025] [Indexed: 05/25/2025]  Open
7
Schiele P, Japp AS, Stark R, Sattelberg JJ, Nikolaou C, Kornhuber G, Abbasi P, Ding N, Rosnev S, Meinke S, Mühle K, Loyal L, Braun J, Dingeldey M, Durlanik S, Matzmohr N, Ponikwicka-Tyszko D, Wolczynski S, Rahman NA, Taniuchi I, Schlickeiser S, Giesecke-Thiel C, Blankenstein T, Na IK, Thiel A, Frentsch M. CD8+ T cell-derived CD40L mediates noncanonical cytotoxicity in CD40-expressing cancer cells. SCIENCE ADVANCES 2025;11:eadr9331. [PMID: 40397730 DOI: 10.1126/sciadv.adr9331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 04/17/2025] [Indexed: 05/23/2025]
8
Tyutyunyk-Massey L, Chen Z, Liu X, Kawakami M, Harned A, Ng Y, Luke B, Okpechi SC, Ogunlade B, Alfaro Y, Weigert R, Narayan K, Liu X, Dmitrovsky E. CDK2 inhibition produces a persistent population of polyploid cancer cells. JCI Insight 2025;10:e189901. [PMID: 40232858 DOI: 10.1172/jci.insight.189901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/09/2025] [Indexed: 04/17/2025]  Open
9
Wu J, Chen S, Xu R, Chen Y, Guo J, Li J, Zeng X, Wang B, Zhu X. Multidimensional investigation of thyroid hormones and prostate cancer: insights from NHANES, Mendelian randomization, genetic markers, and bioinformatics analyses. Discov Oncol 2025;16:843. [PMID: 40397285 PMCID: PMC12095733 DOI: 10.1007/s12672-025-02672-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 05/12/2025] [Indexed: 05/22/2025]  Open
10
Shankar K, Walker SE. Analysis of divergent gene expression between HPV + and HPV- head and neck squamous cell carcinoma patients. Infect Agent Cancer 2025;20:31. [PMID: 40400005 PMCID: PMC12096591 DOI: 10.1186/s13027-025-00663-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2025] [Accepted: 05/13/2025] [Indexed: 05/23/2025]  Open
11
Chen F, Zhang Y, Li W, Sedlazeck FJ, Shen L, Creighton CJ. Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors. Nat Commun 2025;16:4713. [PMID: 40399292 PMCID: PMC12095544 DOI: 10.1038/s41467-025-60110-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 05/13/2025] [Indexed: 05/23/2025]  Open
12
Meng C, Lin K, Shi W, Teng H, Wan X, DeBruine A, Wang Y, Liang X, Leo J, Chen F, Gu Q, Zhang J, Van V, Maldonado KL, Gan B, Ma L, Lu Y, Zhao D. Histone methyltransferase ASH1L primes metastases and metabolic reprogramming of macrophages in the bone niche. Nat Commun 2025;16:4681. [PMID: 40394007 PMCID: PMC12092585 DOI: 10.1038/s41467-025-59381-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 04/22/2025] [Indexed: 05/22/2025]  Open
13
Akita Y, Velaga R, Iwase M, Shimada S, Kikumori T, Takeuchi D, Takano Y, Ichikawa T, Ebata T, Masuda N. Prognostici of ER-staining patterns and heterogeneity of ER positive HER2 negative breast cancer. Breast Cancer 2025:10.1007/s12282-025-01716-4. [PMID: 40382758 DOI: 10.1007/s12282-025-01716-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/30/2025] [Indexed: 05/20/2025]
14
Chen F, Li H, Wang Y, Tang X, Lin K, Li Q, Meng C, Shi W, Leo J, Liang X, Zhang J, Van V, Mahmud I, Wei B, Lorenzi PL, Raso MG, Aparicio A, Lu Y, Frigo DE, Gan B, Zhao D. CHD1 loss reprograms SREBP2-driven cholesterol synthesis to fuel androgen-responsive growth and castration resistance in SPOP-mutated prostate tumors. NATURE CANCER 2025:10.1038/s43018-025-00952-z. [PMID: 40360905 DOI: 10.1038/s43018-025-00952-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2025] [Indexed: 05/15/2025]
15
Moufarrij S, Dopeso H, Brown DN, Green H, Gill K, Tengelin J, Brodeur MN, Zammarrelli WA, Varice N, Wu M, Jungbluth A, Zhu Y, Chen X, Da Cruz Paula A, Basili T, de Stanchina E, Abu-Rustum NR, Aghajanian C, Ellenson LH, Chui MH, Weigelt B. TROP2 expression and therapeutic targeting in uterine carcinosarcoma. Gynecol Oncol 2025;197:129-138. [PMID: 40344963 DOI: 10.1016/j.ygyno.2025.04.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/22/2025] [Accepted: 04/25/2025] [Indexed: 05/11/2025]
16
Nadendla EK, Tweedell RE, Kasof G, Kanneganti TD. Caspases: structural and molecular mechanisms and functions in cell death, innate immunity, and disease. Cell Discov 2025;11:42. [PMID: 40325022 PMCID: PMC12052993 DOI: 10.1038/s41421-025-00791-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 03/05/2025] [Indexed: 05/07/2025]  Open
17
Iyer AR, Gurumurthy A, Chu SCA, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rosa J, Gupta J, Emmanuel A, Hall CN, Runge JS, Owczarczyk AB, Cho JW, Weiss MB, Anyoha R, Sikkink K, Gemus S, Fulco CP, Perry AM, Schmitt AD, Engreitz JM, Brown NA, Cieslik MP, Ryan RJ. Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. Blood Cancer Discov 2025;6:233-253. [PMID: 40067173 PMCID: PMC12050968 DOI: 10.1158/2643-3230.bcd-24-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 12/28/2024] [Accepted: 03/10/2025] [Indexed: 03/15/2025]  Open
18
Haferssas D, Dubuissez M, Barrera-Chimal J, Messmer C, Affar EB, Larrivée B, Liu XS, Gerarduzzi C. FLT4 activation promotes acute lymphoid leukemia survival through stabilization of MDM2/MDMX and inactivation of p53. Oncogenesis 2025;14:14. [PMID: 40316529 PMCID: PMC12048674 DOI: 10.1038/s41389-025-00552-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 02/21/2025] [Accepted: 03/20/2025] [Indexed: 05/04/2025]  Open
19
Yost KE, Zhao Y, Hung KL, Zhu K, Xu D, Corces MR, Shams S, Louie BH, Sarmashghi S, Sundaram L, Luebeck J, Clarke S, Doane AS, Granja JM, Choudhry H, Imieliński M, Cherniack AD, Khurana E, Bafna V, Felau I, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. Three-dimensional genome landscape of primary human cancers. Nat Genet 2025;57:1189-1200. [PMID: 40355593 DOI: 10.1038/s41588-025-02188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/02/2025] [Indexed: 05/14/2025]
20
Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025;68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
21
Choudalakis S, Kastis GA, Dikaios N. Intra-clustering analysis reveals tissue-specific mutational patterns. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2025;263:108681. [PMID: 40050208 DOI: 10.1016/j.cmpb.2025.108681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 02/06/2025] [Accepted: 02/18/2025] [Indexed: 03/14/2025]
22
Finger AM, Hendley AM, Figueroa D, Gonzalez H, Weaver VM. Tissue mechanics in tumor heterogeneity and aggression. Trends Cancer 2025:S2405-8033(25)00096-2. [PMID: 40307158 DOI: 10.1016/j.trecan.2025.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 03/10/2025] [Accepted: 04/04/2025] [Indexed: 05/02/2025]
23
Kyuno D, Asano H, Okumura R, Takasawa K, Takasawa A, Konno T, Nakamori Y, Magara K, Ono Y, Imamura M, Kimura Y, Kojima T, Osanai M. The Role of Claudin-1 in Enhancing Pancreatic Cancer Aggressiveness and Drug Resistance via Metabolic Pathway Modulation. Cancers (Basel) 2025;17:1469. [PMID: 40361399 PMCID: PMC12070999 DOI: 10.3390/cancers17091469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2025] [Revised: 04/17/2025] [Accepted: 04/24/2025] [Indexed: 05/15/2025]  Open
24
Emmerich PB, Qyli T, Johnson KA, Chaudhuri S, Clark KM, Verhagen NB, Depke MG, Clipson L, Pasch CA, Papadas A, Burkard ME, Wisinski KB, McGregor SM, Asimakopoulos F, Deming DA. Stromal Versican Accumulation and Proteolysis Regulate the Infiltration of CD8+ T Cells in Breast Cancer. Cancers (Basel) 2025;17:1435. [PMID: 40361362 PMCID: PMC12070914 DOI: 10.3390/cancers17091435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/28/2025] [Accepted: 04/18/2025] [Indexed: 05/15/2025]  Open
25
Yan Y, Wang Y, Tang J, Liu X, Wang J, Song G, Li H. Comprehensive Analysis of Oncogenic Somatic Alterations of Mismatch Repair Gene in Breast Cancer Patients. Bioengineering (Basel) 2025;12:426. [PMID: 40281786 PMCID: PMC12025084 DOI: 10.3390/bioengineering12040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 03/12/2025] [Accepted: 03/19/2025] [Indexed: 04/29/2025]  Open
26
Pepe G, Notturno Granieri C, Appierdo R, Ausiello G, Helmer-Citterich M, Gherardini PF. PANDA: PAN Cancer Data Analysis Web Tool. J Mol Biol 2025:169158. [PMID: 40250704 DOI: 10.1016/j.jmb.2025.169158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 03/05/2025] [Accepted: 04/10/2025] [Indexed: 04/20/2025]
27
Espinoza-Ferrao S, Echeverría-Garcés G, Rivera-Orellana S, Bueno-Miño J, Castellanos-Molina E, Benítez-Núñez M, López-Cortés A. Global analysis of actionable genomic alterations in thyroid cancer and precision-based pharmacogenomic strategies. Front Pharmacol 2025;16:1524623. [PMID: 40297138 PMCID: PMC12034932 DOI: 10.3389/fphar.2025.1524623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 04/01/2025] [Indexed: 04/30/2025]  Open
28
Chen LT, Jager M, Rebergen D, Brink GJ, van den Ende T, Vanderlinden W, Kolbeck P, Pagès-Gallego M, van der Pol Y, Besselink N, Moldovan N, Hami N, Kloosterman WP, van Laarhoven H, Mouliere F, Zweemer R, Lipfert J, Derks S, Marcozzi A, de Ridder J. Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling. Genome Res 2025;35:886-899. [PMID: 39805703 PMCID: PMC12047234 DOI: 10.1101/gr.279144.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 01/06/2025] [Indexed: 01/16/2025]
29
Lv X, Liu J, Islam K, Ruan J, He C, Chen P, Huang C, Wang H, Dhar A, Moness M, Shi D, Murphy S, Zhao X, Yang S, Montoute I, Polakkattil A, Chung A, Ruiz E, Carbajal B, Padavala A, Chen L, Hua G, Chen X, Davis JS, Wang C. Hyperactivated YAP1 is essential for sustainable progression of renal clear cell carcinoma. Oncogene 2025:10.1038/s41388-025-03354-8. [PMID: 40210757 DOI: 10.1038/s41388-025-03354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 02/12/2025] [Accepted: 03/17/2025] [Indexed: 04/12/2025]
30
Vivalda F, Gatti M, Manfredi L, Dogan H, Porro A, Collotta G, Ceppi I, von Aesch C, van Ackeren V, Wild S, Steger M, Canovas B, Cubillos-Rojas M, Riera A, Cejka P, Nebreda A, Dibitetto D, Rottenberg S, Sartori A. The PIN1-p38-CtIP signalling axis protects stalled replication forks from deleterious degradation. Nucleic Acids Res 2025;53:gkaf278. [PMID: 40207632 PMCID: PMC11983131 DOI: 10.1093/nar/gkaf278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 03/20/2025] [Accepted: 03/26/2025] [Indexed: 04/11/2025]  Open
31
Bates BA, Bates KE, Boris SA, Wessman C, Stone D, Bryan J, Davis MF, Bailey MH. Intersection of rare pathogenic variants from TCGA in the All of Us Research Program v6. HGG ADVANCES 2025;6:100405. [PMID: 39799398 PMCID: PMC11830373 DOI: 10.1016/j.xhgg.2025.100405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 01/09/2025] [Accepted: 01/08/2025] [Indexed: 01/15/2025]  Open
32
Wala J, Dalin S, Webster S, Shapira O, Busanovich J, Sarmashghi S, Beroukhim R, Bandopadhayay P, Rendo V. Recurrent breakpoints in the BRD4 locus reduce toxicity associated with gene amplification. CELL GENOMICS 2025;5:100815. [PMID: 40112818 PMCID: PMC12008804 DOI: 10.1016/j.xgen.2025.100815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 12/09/2024] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
33
Golas MM, Gunawan B, Gutenberg A, Danner BC, Gerdes JS, Stadelmann C, Füzesi L, Liersch T, Sander B. Cytogenetic signatures favoring metastatic organotropism in colorectal cancer. Nat Commun 2025;16:3261. [PMID: 40188208 PMCID: PMC11972295 DOI: 10.1038/s41467-025-58413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/21/2025] [Indexed: 04/07/2025]  Open
34
Kou Z, Zhu S, Zhu J, Wang S, Zheng Y, Zhou S, Si Z, Zhu H. Multi-omics analysis identifies DLX4 as a novel biomarker for diagnosis, prognosis, and immune infiltration: from pan-cancer to renal cancer. Discov Oncol 2025;16:467. [PMID: 40186710 PMCID: PMC11972278 DOI: 10.1007/s12672-025-02258-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 03/28/2025] [Indexed: 04/07/2025]  Open
35
Pulice JL, Meyerson M. Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma. Mol Cell 2025;85:1311-1329.e16. [PMID: 40139189 DOI: 10.1016/j.molcel.2025.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/17/2024] [Accepted: 03/03/2025] [Indexed: 03/29/2025]
36
Llorente A, Arora GK, Murad R, Emerling BM. Phosphoinositide kinases in cancer: from molecular mechanisms to therapeutic opportunities. Nat Rev Cancer 2025:10.1038/s41568-025-00810-1. [PMID: 40181165 DOI: 10.1038/s41568-025-00810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2025] [Indexed: 04/05/2025]
37
Cron KR, Sivan A, Aquino-Michaels K, Ziblat A, Higgs EF, Sweis RF, Tonea R, Lee S, Gajewski TF. PKCδ Germline Variants and Genetic Deletion in Mice Augment Antitumor Immunity through Regulation of Myeloid Cells. Cancer Immunol Res 2025;13:547-559. [PMID: 39808445 DOI: 10.1158/2326-6066.cir-23-0999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 07/04/2024] [Accepted: 01/10/2025] [Indexed: 01/16/2025]
38
Somes LK, Lei JT, Yi X, Chamorro DF, Shafer P, Gad AZ, Dobrolecki LE, Madaras E, Ahmed N, Lewis MT, Zhang B, Hoyos V. ZP4: A novel target for CAR-T cell therapy in triple negative breast cancer. Mol Ther 2025;33:1621-1641. [PMID: 39980195 PMCID: PMC11997509 DOI: 10.1016/j.ymthe.2025.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 01/24/2025] [Accepted: 02/17/2025] [Indexed: 02/22/2025]  Open
39
Keller P, Dawood M, Chohan BS, Minhas FUAA. HistoKernel: Whole slide image level Maximum Mean Discrepancy kernels for pan-cancer predictive modelling. Med Image Anal 2025;101:103491. [PMID: 39938344 DOI: 10.1016/j.media.2025.103491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 01/27/2025] [Accepted: 01/31/2025] [Indexed: 02/14/2025]
40
Blaszczyk MB, Boukhar SA, Zhou Z, Berim L, Ganesan S, Riedlinger GM. Occult collision tumor of the gastroesophageal junction comprising adenocarcinomas with distinct molecular profiles. Cancer Genet 2025;292-293:27-34. [PMID: 39805155 DOI: 10.1016/j.cancergen.2025.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 12/30/2024] [Accepted: 01/03/2025] [Indexed: 01/16/2025]
41
Yang L, Feng Y, Liu X, Zhang Q, Liu Y, Zhang X, Li P, Chen D. DYNC2H1 mutation as a potential predictive biomarker for immune checkpoint inhibitor efficacy in NSCLC and melanoma. Invest New Drugs 2025;43:199-213. [PMID: 39934438 DOI: 10.1007/s10637-024-01495-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 12/19/2024] [Indexed: 02/13/2025]
42
Kong S, Pan H, Zhang YW, Wang F, Chen J, Dong J, Yin C, Wu J, Zhou D, Peng J, Ma J, Zhou J, Ge D, Lu Y, Wei DD, Fang J, Han W, Shen C, Koeffler HP, Wang B, Jiang Y, Jiang YY. Targeting aldehyde dehydrogenase ALDH3A1 increases ferroptosis vulnerability in squamous cancer. Oncogene 2025;44:1037-1050. [PMID: 39863749 DOI: 10.1038/s41388-025-03277-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 12/15/2024] [Accepted: 01/14/2025] [Indexed: 01/27/2025]
43
Krause MJ, Sinkala M, Ramesar R. Distinct dysregulated pathways in sporadic and Lynch syndrome-associated colorectal cancer offer insights for targeted treatment. FEBS Lett 2025;599:1006-1028. [PMID: 39973357 PMCID: PMC11995676 DOI: 10.1002/1873-3468.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 01/22/2025] [Accepted: 01/28/2025] [Indexed: 02/21/2025]
44
Varney SD, Erkes DA, Mersky GL, Mustafa MU, Chua V, Chervoneva I, Purwin TJ, Alnemri E, Aplin AE. Metabolic Inhibition Induces Pyroptosis in Uveal Melanoma. Mol Cancer Res 2025;23:350-362. [PMID: 39670827 PMCID: PMC11961327 DOI: 10.1158/1541-7786.mcr-24-0508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 11/02/2024] [Accepted: 12/11/2024] [Indexed: 12/14/2024]
45
Pinto R, Vedeld HM, Lind GE, Jeanmougin M. Unraveling epigenetic heterogeneity across gastrointestinal adenocarcinomas through a standardized analytical framework. Mol Oncol 2025;19:1117-1131. [PMID: 39696831 PMCID: PMC11977639 DOI: 10.1002/1878-0261.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 09/30/2024] [Accepted: 10/31/2024] [Indexed: 12/20/2024]  Open
46
Liu Y, Dantas E, Ferrer M, Miao T, Qadiri M, Liu Y, Comjean A, Davidson EE, Perrier T, Ahmed T, Hu Y, Goncalves MD, Janowitz T, Perrimon N. Hepatic gluconeogenesis and PDK3 upregulation drive cancer cachexia in flies and mice. Nat Metab 2025;7:823-841. [PMID: 40275022 PMCID: PMC12021660 DOI: 10.1038/s42255-025-01265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/06/2025] [Indexed: 04/26/2025]
47
Liu P, Page D, Ahlquist P, Ong IM, Gitter A. MPAC: a computational framework for inferring pathway activities from multi-omic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.15.599113. [PMID: 38948762 PMCID: PMC11212914 DOI: 10.1101/2024.06.15.599113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
48
Ohshima H, Kobayashi E, Inaba M, Nakazawa R, Hirai N, Ueno T, Nakanishi Y, Endo K, Kondo S, Moriyama-Kita M, Sugimoto H, Yoshizaki T. HRAS Mutations in Head and Neck Carcinomas in Japanese Patients: Clinical Significance, Prognosis, and Therapeutic Potential. Int J Mol Sci 2025;26:3093. [PMID: 40243851 PMCID: PMC11988887 DOI: 10.3390/ijms26073093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 03/22/2025] [Accepted: 03/25/2025] [Indexed: 04/18/2025]  Open
49
Walter DM, Cho K, Sivakumar S, Lee ITH, Dohlman AB, Shurberg E, Jiang KX, Gupta AA, Frampton GM, Meyerson M. U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.21.644128. [PMID: 40196662 PMCID: PMC11974705 DOI: 10.1101/2025.03.21.644128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
50
Zhang Q, Cui K, Kong Y, Yu J, Luo Z, Yang X, Gong L, Xie Y, Lin J, Liu C, Zhang Z, Liu Y, Liu B, Liang D, Zeng W, He Z, Lan P. Targeting both the enzymatic and non-enzymatic functions of DHODH as a therapeutic vulnerability in c-Myc-driven cancer. Cell Rep 2025;44:115327. [PMID: 39977268 DOI: 10.1016/j.celrep.2025.115327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 12/08/2024] [Accepted: 01/28/2025] [Indexed: 02/22/2025]  Open
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