Searching journal content for articles similar to Bilke et al. 23 (11): 1797.

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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...is frequently integrated in HCC and might play a pivotal role in abnormal gene expression, highlighting its potential as a therapeutic target.Primary liver cancer (PLC) is a leading cause of cancer-related mortality in more than 136 countries, and its incidence is projected to increase (Rumgay et al. 2022...
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Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
- Ziyan Rao,
- Min Zhang,
- Shaodong Huang,
- Chenyang Wu,
- Yuheng Zhou,
- Weijie Zhang,
- Xia Lin,
- and Dongyu Zhao
Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
...oncogenic lncRNAs and four tumor-suppressive lncRNAs specifically in prostate cancer.ResultsCancer lncRNAs tend to be coexpressed with and close to cancer driver PCGsWe collected cancer driver PCGs from the Cancer Gene Census (CGC) database v.94 (Sondka et al. 2018) and cancer lncRNAs from Cancer Lnc...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...) and visualized on the WashU Epi Browser (Zhuo et al. 2023). Public ChIP-seq data were sourced from CistromeDB (Zheng et al. 2019) (http://cistrome.org/db/).Sanger sequencingNested PCR gene-specific primers (GSPs) were designed to target the fusion sequence of the predicted LTR7-PLAAT4 isoform 2 and were provided...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...into the potential benefits or drawbacks of glucocorticoid treatments in cancer patients. Further research is also needed to elucidate what additional tumor-suppressive or oncogenic roles GR may play in the prostate (Hiltunen et al. 2024).MethodsCell culture and treatmentsVCaP (ATCC CRL-2876, Research Resource...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...et al. 2016, 2018; Takeda et al. 2018; Morton et al. 2019; Wu et al. 2019; Kim et al. 2020; Liu et al. 2021). In addition, genes within the duplicated regions are not necessarily the actual oncogenic targets of the duplications, as exemplified by duplications of enhancers within the SNCAIP gene...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...of patients, because many gene fusions can be addressed therapeutically with targeted drugs (Schram et al. 2017). The most prominent examples are fusions between BCR and ABL1 in chronic myeloid leukemia and acute lymphoblastic leukemia, which can be treated effectively using imatinib and related drugs (An et...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...unable to detect enrichment over the IgG control (Supplemental Fig. S2E).RUW-associated genes include differentially expressed classical Wnt target genesTo further investigate the potential impact of RUWs, we used GREAT (McLean et al. 2010) to assign the RUW peaks to 431 nearby genes (Supplemental Fig. S...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...2018). miRNAs group into seed families that mostly target the same pool of mRNAs through complementary base pairing of their 7-nt seed region (Lai 2002; Bartel 2009). Each family targets hundreds of mRNAs, and together, miRNAs are considered key post-transcriptional regulators (Friedman et al. 2009).It...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...drive the expression of oncogenes (Jang et al. 2019).In aging, a -wide loss of methylation with age has been observed in human CD4+ T cells and skin keratinocytes (Heyn et al. 2012; Vandiver et al. 2015; Jenkinson et al. 2017). Several early studies analyzing the methylation of repetitive elements...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...tumorigenesis by regulating the expression of oncogenes (via loss of miRNA regulation) and tumor suppressors (via disruption of competing-endogenous RNA cross talk) (Masamha et al. 2014; Li et al. 2015; Chen et al. 2018b; Mitra et al. 2018; Park et al. 2018). The relevance of APA in cancer was established...
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