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For: Achinger-Kawecka J, Valdes-Mora F, Luu PL, Giles KA, Caldon CE, Qu W, Nair S, Soto S, Locke WJ, Yeo-Teh NS, Gould CM, Du Q, Smith GC, Ramos IR, Fernandez KF, Hoon DS, Gee JMW, Stirzaker C, Clark SJ. Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Nat Commun 2020;11:320. [PMID: 31949157 DOI: 10.1038/s41467-019-14098-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/17/2019] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Zhang Y, Dali R, Blanchette M. RobusTAD: reference panel based annotation of nested topologically associating domains. Genome Biol 2025;26:129. [PMID: 40390127 PMCID: PMC12087246 DOI: 10.1186/s13059-025-03568-9] [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: 09/29/2023] [Accepted: 04/04/2025] [Indexed: 05/21/2025]  Open
2
Playter C, Golloshi R, Garretson JH, Rodriguez Gonzalez A, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering pre-existing and induced 3D genome architecture changes involved in constricted melanoma migration. iScience 2025;28:112346. [PMID: 40292313 PMCID: PMC12032941 DOI: 10.1016/j.isci.2025.112346] [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: 08/22/2024] [Revised: 01/22/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025]  Open
3
Celestra D, Nguyen NNL, Laberthonniere C, Pang KC, Saffery R, Davey RA, Mhlanga M, Cheung AS, Novakovic B. Epigenetic remodeling by sex hormone receptors and implications for gender affirming hormone therapy. Front Immunol 2025;16:1501959. [PMID: 40406098 PMCID: PMC12095348 DOI: 10.3389/fimmu.2025.1501959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 04/17/2025] [Indexed: 05/26/2025]  Open
4
Choppavarapu L, Fang K, Liu T, Ohihoin AG, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue. Cell Rep 2025;44:115450. [PMID: 40112000 PMCID: PMC12103084 DOI: 10.1016/j.celrep.2025.115450] [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: 08/23/2024] [Revised: 01/12/2025] [Accepted: 02/28/2025] [Indexed: 03/22/2025]  Open
5
Yuan L, Cai Y, Wang G, Liu X, Chen B, Zhou D, Wu Y, Qu N, Li X, Zhou W. SGK3 promotes estrogen receptor-positive breast cancer proliferation by activating STAT3/ZMIZ2 pathway to stabilise β-catenin. Br J Pharmacol 2025;182:1856-1875. [PMID: 39876548 DOI: 10.1111/bph.17453] [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: 05/17/2024] [Revised: 12/22/2024] [Accepted: 12/28/2024] [Indexed: 01/30/2025]  Open
6
Zhang R, Jiang WJ, Zhao S, Kang LJ, Wang QS, Feng YM. FOXF2 expression triggered by endocrine therapy orchestrates therapeutic resistance through reorganization of chromatin architecture in breast cancer. Cancer Lett 2025;612:217463. [PMID: 39828125 DOI: 10.1016/j.canlet.2025.217463] [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: 07/03/2024] [Revised: 12/27/2024] [Accepted: 01/11/2025] [Indexed: 01/22/2025]
7
Giles KA, Taberlay PC, Cesare AJ, Jones MJK. Roles for the 3D genome in the cell cycle, DNA replication, and double strand break repair. Front Cell Dev Biol 2025;13:1548946. [PMID: 40083661 PMCID: PMC11903485 DOI: 10.3389/fcell.2025.1548946] [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: 12/20/2024] [Accepted: 02/10/2025] [Indexed: 03/16/2025]  Open
8
de Klein B, Eickhoff N, Zwart W. The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer. Trends Mol Med 2025:S1471-4914(25)00006-1. [PMID: 39934021 DOI: 10.1016/j.molmed.2025.01.006] [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: 11/15/2024] [Revised: 01/10/2025] [Accepted: 01/15/2025] [Indexed: 02/13/2025]
9
Gemma C, Lai CF, Singh AK, Belfiore A, Portman N, Milioli HZ, Periyasamy M, Raafat S, Nicholls AJ, Davies CM, Patel NR, Simmons GM, Fan H, Nguyen VTM, Magnani L, Rakha E, Martin LA, Lim E, Coombes RC, Pruneri G, Buluwela L, Ali S. Induction of the TEAD Coactivator VGLL1 by Estrogen Receptor-Targeted Therapy Drives Resistance in Breast Cancer. Cancer Res 2024;84:4283-4297. [PMID: 39356622 PMCID: PMC7616691 DOI: 10.1158/0008-5472.can-24-0013] [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: 01/03/2024] [Revised: 07/03/2024] [Accepted: 09/25/2024] [Indexed: 10/04/2024]
10
Sun G, Zhao C, Han J, Wu S, Chen Y, Yao J, Li L. Regulatory mechanisms of steroid hormone receptors on gene transcription through chromatin interaction and enhancer reprogramming. Cell Oncol (Dordr) 2024;47:2073-2090. [PMID: 39543064 DOI: 10.1007/s13402-024-01011-y] [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] [Accepted: 10/30/2024] [Indexed: 11/17/2024]  Open
11
Fang K, Ohihoin AG, Liu T, Choppavarapu L, Nosirov B, Wang Q, Yu XZ, Kamaraju S, Leone G, Jin VX. Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer. Genome Med 2024;16:134. [PMID: 39558215 PMCID: PMC11572372 DOI: 10.1186/s13073-024-01407-3] [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: 03/04/2024] [Accepted: 11/07/2024] [Indexed: 11/20/2024]  Open
12
Ankill J, Zhao Z, Tekpli X, Kure EH, Kristensen VN, Mathelier A, Fleischer T. Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. PLoS Comput Biol 2024;20:e1012565. [PMID: 39556603 DOI: 10.1371/journal.pcbi.1012565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 10/16/2024] [Indexed: 11/20/2024]  Open
13
Ded L, Zatecka-Lanska E, Vaculikova E, Frolikova M, Sanovec O, Palenikova V, Simonik O, Dorosh A, Margaryan H, Elzeinova F, Kubatova A, Peknicova J, Paradowska-Dogan A, Steger K, Komrskova K. 17α-Ethynylestradiol alters testicular epigenetic profiles and histone-to-protamine exchange in mice. Reprod Biol Endocrinol 2024;22:135. [PMID: 39491035 PMCID: PMC11533287 DOI: 10.1186/s12958-024-01307-6] [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: 10/25/2023] [Accepted: 10/23/2024] [Indexed: 11/05/2024]  Open
14
Imre L, Nánási P, Benhamza I, Enyedi KN, Mocsár G, Bosire R, Hegedüs É, Niaki EF, Csóti Á, Darula Z, Csősz É, Póliska S, Scholtz B, Mező G, Bacsó Z, Timmers HTM, Kusakabe M, Balázs M, Vámosi G, Ausio J, Cheung P, Tóth K, Tremethick D, Harata M, Szabó G. Epigenetic modulation via the C-terminal tail of H2A.Z. Nat Commun 2024;15:9171. [PMID: 39448645 PMCID: PMC11502880 DOI: 10.1038/s41467-024-53514-9] [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: 07/08/2022] [Accepted: 10/12/2024] [Indexed: 10/26/2024]  Open
15
Jefferson W, Wang T, Padilla-Banks E, Williams C. Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression. Nucleic Acids Res 2024;52:10897-10917. [PMID: 39166489 PMCID: PMC11472041 DOI: 10.1093/nar/gkae714] [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: 01/15/2024] [Revised: 06/27/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]  Open
16
Playter C, Golloshi R, Garretson JH, Gonzalez AR, Olajide TH, Saad A, Benson SJ, McCord RP. Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609017. [PMID: 39229109 PMCID: PMC11370405 DOI: 10.1101/2024.08.21.609017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
17
Chen W, Zeng Y, Achinger-Kawecka J, Campbell E, Jones A, Stewart A, Khoury A, Clark S. Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites. Nucleic Acids Res 2024;52:8086-8099. [PMID: 38950902 PMCID: PMC11317138 DOI: 10.1093/nar/gkae530] [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: 09/29/2023] [Revised: 05/15/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]  Open
18
Cantile M, Belli V, Scognamiglio G, Martorana A, De Pietro G, Tracey M, Budillon A. The role of HOTAIR in the modulation of resistance to anticancer therapy. Front Mol Biosci 2024;11:1414651. [PMID: 38887279 PMCID: PMC11181001 DOI: 10.3389/fmolb.2024.1414651] [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: 04/09/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024]  Open
19
Yadav M, Vaishkiar I, Sharma A, Shukla A, Mohan A, Girdhar M, Kumar A, Malik T, Mohan A. Oestrogen receptor positive breast cancer and its embedded mechanism: breast cancer resistance to conventional drugs and related therapies, a review. Open Biol 2024;14:230272. [PMID: 38889771 DOI: 10.1098/rsob.230272] [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: 08/10/2023] [Accepted: 03/14/2024] [Indexed: 06/20/2024]  Open
20
Trnkova L, Buocikova V, Mego M, Cumova A, Burikova M, Bohac M, Miklikova S, Cihova M, Smolkova B. Epigenetic deregulation in breast cancer microenvironment: Implications for tumor progression and therapeutic strategies. Biomed Pharmacother 2024;174:116559. [PMID: 38603889 DOI: 10.1016/j.biopha.2024.116559] [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: 12/15/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]  Open
21
Toska E. Epigenetic mechanisms of cancer progression and therapy resistance in estrogen-receptor (ER+) breast cancer. Biochim Biophys Acta Rev Cancer 2024;1879:189097. [PMID: 38518961 DOI: 10.1016/j.bbcan.2024.189097] [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: 01/08/2024] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
22
Wang H, Xiong X, Zhang J, Wu M, Gu Y, Chen Y, Gu Y, Wang P. Near-Infrared Light-Driven Nanoparticles for Cancer Photoimmunotherapy by Synergizing Immune Cell Death and Epigenetic Regulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024;20:e2309202. [PMID: 38100237 DOI: 10.1002/smll.202309202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Indexed: 05/25/2024]
23
Kinyamu HK, Bennett BD, Ward JM, Archer TK. Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024;4:1082-1099. [PMID: 38625038 PMCID: PMC11019832 DOI: 10.1158/2767-9764.crc-23-0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
24
Jacob DR, Guiblet WM, Mamayusupova H, Shtumpf M, Ciuta I, Ruje L, Gretton S, Bikova M, Correa C, Dellow E, Agrawal SP, Shafiei N, Drobysevskaja A, Armstrong CM, Lam JDG, Vainshtein Y, Clarkson CT, Thorn GJ, Sohn K, Pradeepa MM, Chandrasekharan S, Brooke GN, Klenova E, Zhurkin VB, Teif VB. Nucleosome reorganisation in breast cancer tissues. Clin Epigenetics 2024;16:50. [PMID: 38561804 PMCID: PMC10986098 DOI: 10.1186/s13148-024-01656-4] [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: 12/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024]  Open
25
Choppavarapu L, Fang K, Liu T, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584872. [PMID: 38559097 PMCID: PMC10979939 DOI: 10.1101/2024.03.13.584872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
26
Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 2024;25:251. [PMID: 38448820 PMCID: PMC10916044 DOI: 10.1186/s12864-024-10027-5] [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: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024]  Open
27
Yang ML, Xu C, Gupte T, Hoffmann TJ, Iribarren C, Zhou X, Ganesh SK. Sex-specific genetic architecture of blood pressure. Nat Med 2024;30:818-828. [PMID: 38459180 PMCID: PMC11797078 DOI: 10.1038/s41591-024-02858-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
28
Achinger-Kawecka J, Stirzaker C, Portman N, Campbell E, Chia KM, Du Q, Laven-Law G, Nair SS, Yong A, Wilkinson A, Clifton S, Milioli HH, Alexandrou S, Caldon CE, Song J, Khoury A, Meyer B, Chen W, Pidsley R, Qu W, Gee JMW, Schmitt A, Wong ES, Hickey TE, Lim E, Clark SJ. The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer. Nat Struct Mol Biol 2024;31:498-512. [PMID: 38182927 PMCID: PMC10948365 DOI: 10.1038/s41594-023-01181-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
29
Terrón-Bautista J, Martínez-Sánchez MDM, López-Hernández L, Vadusevan AA, García-Domínguez M, Williams RS, Aguilera A, Millán-Zambrano G, Cortés-Ledesma F. Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576640. [PMID: 38328138 PMCID: PMC10849543 DOI: 10.1101/2024.01.22.576640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
30
Zhao J, Faryabi RB. Spatial promoter-enhancer hubs in cancer: organization, regulation, and function. Trends Cancer 2023;9:1069-1084. [PMID: 37599153 PMCID: PMC10840977 DOI: 10.1016/j.trecan.2023.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/14/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
31
Pierantoni L, Reis RL, Silva-Correia J, Oliveira JM, Heavey S. Spatial -omics technologies: the new enterprise in 3D breast cancer models. Trends Biotechnol 2023;41:1488-1500. [PMID: 37544843 DOI: 10.1016/j.tibtech.2023.07.003] [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: 01/30/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
32
Kinyamu HK, Bennett BD, Ward JM, Archer T. Proteasome inhibition reprograms chromatin landscape in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562284. [PMID: 37904968 PMCID: PMC10614768 DOI: 10.1101/2023.10.13.562284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
33
Tang S, Roberts RD, Cheng L, Li L. Osteosarcoma Multi-Omics Landscape and Subtypes. Cancers (Basel) 2023;15:4970. [PMID: 37894336 PMCID: PMC10605601 DOI: 10.3390/cancers15204970] [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: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023]  Open
34
Massa C, Seliger B. Combination of multiple omics techniques for a personalized therapy or treatment selection. Front Immunol 2023;14:1258013. [PMID: 37828984 PMCID: PMC10565668 DOI: 10.3389/fimmu.2023.1258013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023]  Open
35
Xu D, Forbes AN, Cohen S, Palladino A, Karadimitriou T, Khurana E. Recapitulation of patient-specific 3D chromatin conformation using machine learning. CELL REPORTS METHODS 2023;3:100578. [PMID: 37673071 PMCID: PMC10545938 DOI: 10.1016/j.crmeth.2023.100578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 04/05/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
36
Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. The EstroGene Database Reveals Diverse Temporal, Context-Dependent, and Bidirectional Estrogen Receptor Regulomes in Breast Cancer. Cancer Res 2023;83:2656-2674. [PMID: 37272757 PMCID: PMC10527051 DOI: 10.1158/0008-5472.can-23-0539] [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: 02/16/2023] [Revised: 04/21/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
37
Santaliz-Casiano A, Mehta D, Danciu OC, Patel H, Banks L, Zaidi A, Buckley J, Rauscher GH, Schulte L, Weller LR, Taiym D, Liko-Hazizi E, Pulliam N, Friedewald SM, Khan S, Kim JJ, Gradishar W, Hegerty S, Frasor J, Hoskins KF, Madak-Erdogan Z. Identification of metabolic pathways contributing to ER+ breast cancer disparities using a machine-learning pipeline. Sci Rep 2023;13:12136. [PMID: 37495653 PMCID: PMC10372029 DOI: 10.1038/s41598-023-39215-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]  Open
38
Zhou J, Zhu M, Wang Q, Deng Y, Liu N, Liu Y, Liu Q. SERPINA3-ANKRD11-HDAC3 pathway induced aromatase inhibitor resistance in breast cancer can be reversed by HDAC3 inhibition. Commun Biol 2023;6:695. [PMID: 37414914 PMCID: PMC10326080 DOI: 10.1038/s42003-023-05065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023]  Open
39
Wang J, Nakato R. Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells. iScience 2023;26:106908. [PMID: 37283809 PMCID: PMC10239702 DOI: 10.1016/j.isci.2023.106908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]  Open
40
Zboril EK, Grible JM, Boyd DC, Hairr NS, Leftwich TJ, Esquivel MF, Duong AK, Turner SA, Ferreira-Gonzalez A, Olex AL, Sartorius CA, Dozmorov MG, Harrell JC. Stratification of Tamoxifen Synergistic Combinations for the Treatment of ER+ Breast Cancer. Cancers (Basel) 2023;15:3179. [PMID: 37370789 PMCID: PMC10296623 DOI: 10.3390/cancers15123179] [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: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023]  Open
41
Liu J, Li P, Sun J, Guo J. LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data. Brief Bioinform 2023;24:7150739. [PMID: 37139561 DOI: 10.1093/bib/bbad165] [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: 01/09/2023] [Revised: 03/06/2023] [Accepted: 04/09/2023] [Indexed: 05/05/2023]  Open
42
Sun G, Wei Y, Zhou B, Wang M, Luan R, Bai Y, Li H, Wang S, Zheng D, Wang C, Wang S, Zeng K, Liu S, Lin L, He M, Zhang Q, Zhao Y. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. Cell Death Differ 2023;30:1260-1278. [PMID: 36828916 PMCID: PMC10154423 DOI: 10.1038/s41418-023-01135-y] [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: 07/15/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]  Open
43
Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023;13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023]  Open
44
Gao S, Zhang W, Ma J, Ni X. PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer. J Transl Med 2023;21:220. [PMID: 36967443 PMCID: PMC10040131 DOI: 10.1186/s12967-023-04031-8] [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: 05/25/2022] [Accepted: 03/01/2023] [Indexed: 03/27/2023]  Open
45
Mortezaee K, Majidpoor J, Najafi S, Tasa D. Bypassing anti-PD-(L)1 therapy: Mechanisms and management strategies. Biomed Pharmacother 2023;158:114150. [PMID: 36577330 DOI: 10.1016/j.biopha.2022.114150] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]  Open
46
Walker RR, Rentia Z, Chiappinelli KB. Epigenetically programmed resistance to chemo- and immuno-therapies. Adv Cancer Res 2023;158:41-71. [PMID: 36990538 PMCID: PMC10184181 DOI: 10.1016/bs.acr.2022.12.001] [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] [Indexed: 01/29/2023]
47
Ferrando L, Vingiani A, Garuti A, Vernieri C, Belfiore A, Agnelli L, Dagrada G, Ivanoiu D, Bonizzi G, Munzone E, Lippolis L, Dameri M, Ravera F, Colleoni M, Viale G, Magnani L, Ballestrero A, Zoppoli G, Pruneri G. ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC). PLoS Genet 2023;19:e1010563. [PMID: 36595552 PMCID: PMC9839248 DOI: 10.1371/journal.pgen.1010563] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/13/2023] [Accepted: 12/08/2022] [Indexed: 01/04/2023]  Open
48
Garcia-Recio S, Hinoue T, Wheeler GL, Kelly BJ, Garrido-Castro AC, Pascual T, De Cubas AA, Xia Y, Felsheim BM, McClure MB, Rajkovic A, Karaesmen E, Smith MA, Fan C, Ericsson PIG, Sanders ME, Creighton CJ, Bowen J, Leraas K, Burns RT, Coppens S, Wheless A, Rezk S, Garrett AL, Parker JS, Foy KK, Shen H, Park BH, Krop I, Anders C, Gastier-Foster J, Rimawi MF, Nanda R, Lin NU, Isaacs C, Marcom PK, Storniolo AM, Couch FJ, Chandran U, Davis M, Silverstein J, Ropelewski A, Liu MC, Hilsenbeck SG, Norton L, Richardson AL, Symmans WF, Wolff AC, Davidson NE, Carey LA, Lee AV, Balko JM, Hoadley KA, Laird PW, Mardis ER, King TA, Perou CM. Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis. NATURE CANCER 2023;4:128-147. [PMID: 36585450 PMCID: PMC9886551 DOI: 10.1038/s43018-022-00491-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/11/2022] [Indexed: 12/31/2022]
49
Sreekar N, Shrestha S. Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1. Bioinform Biol Insights 2023;17:11779322231167971. [PMID: 37124129 PMCID: PMC10134125 DOI: 10.1177/11779322231167971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023]  Open
50
Ng ASN, Zhang S, Mak VCY, Zhou Y, Yuen Y, Sharma R, Lu Y, Zhuang G, Zhao W, Pang HH, Cheung LWT. AKTIP loss is enriched in ERα-positive breast cancer for tumorigenesis and confers endocrine resistance. Cell Rep 2022;41:111821. [PMID: 36516775 PMCID: PMC9837615 DOI: 10.1016/j.celrep.2022.111821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]  Open
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