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1

Dogan, Senol, Emrulla Spahiu, and Anis Cilic. "Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs." Genes 13, no. 7 (2022): 1152. http://dx.doi.org/10.3390/genes13071152.

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MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing protein alterations in cancer cells by preventing some genes from being translated into proteins. In this research, a structural analysis of 587 miRNAs that are differentially expressed in myeloid cancer was carried out. Length distribution studies revealed a mean and median of 22 nucleotides, with an av
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Ceglia, Nicholas, Maryam Pourmaleki, Alessandro Grande, et al. "Abstract B054: Identification of spatial motifs linked to tumor genotype using graph attention networks." Clinical Cancer Research 31, no. 13_Supplement (2025): B054. https://doi.org/10.1158/1557-3265.aimachine-b054.

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Abstract Spatial analysis of cancer requires computational methods capable of addressing the complexity and heterogeneity characteristic of tumor tissue architectures. Unlike well-organized tissues such as developing organs or the brain, cancer tissues lack easily identifiable spatial motifs, necessitating computational models that model a principled definition of a spatial motif tailored to their unique structure. We present GRAFITI, a graph autoencoder specifically designed to identify spatial motifs within cancer tissues using a formal graph-based definition. GRAFITI employs state of the ar
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Saha, Karani, Grace Nielsen, and Wenfeng An. "Abstract B012: Transcriptional activation of mouse LINE-1 promoter by transcription factor YY1." Cancer Immunology Research 11, no. 12_Supplement (2023): B012. http://dx.doi.org/10.1158/2326-6074.tumimm23-b012.

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Abstract Long interspersed element type 1 (LINE-1) are highly abundant non-LTR retrotransposons in mammalian genomes. LINE-1 hypomethylation and overexpression has been considered as a hallmark of many human cancers. Moreover, active movement of LINE-1 results in insertional mutagenesis and may contribute to cancer initiation or progression. Transcription is the initial and critical regulatory step for active LINE-1 movement. Therefore, investigating LINE-1 transcriptional regulation is important for our understanding of LINE-1’s role in cancer. In human LINE-1, an intact YY1 transcription fac
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Hyun, Jason C., Shun H. Yip, Neeti Swarup, et al. "Abstract LB108: Specific plasma DNA end-motifs distinguish patients with lung adenocarcinoma versus benign nodules." Cancer Research 84, no. 7_Supplement (2024): LB108. http://dx.doi.org/10.1158/1538-7445.am2024-lb108.

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Abstract Background: Recent studies have identified blood plasma DNA as a rich source of biomarkers for non-invasive cancer detection. In particular, analysis of shorter DNA fragments or “fragmentomics” have shown promising results with numerous competing approaches such as those based on mutation calls, length distributions, or preferred fragmentation patterns. In this study, we assessed the potential of fragment end motif distributions in discriminating patients with lung adenocarcinoma versus benign tumors. Methods: Plasma samples from 37 patients (20 benign, 17 malignant) were subject to w
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Alam, Tanvir, Meshari Alazmi, Xin Gao, and Stefan T. Arold. "How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine–aspartic acid (LD) motifs." Biochemical Journal 460, no. 3 (2014): 317–29. http://dx.doi.org/10.1042/bj20140298.

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LD motifs (leucine–aspartic acid motifs) are short helical protein–protein interaction motifs that have emerged as key players in connecting cell adhesion with cell motility and survival. LD motifs are required for embryogenesis, wound healing and the evolution of multicellularity. LD motifs also play roles in disease, such as in cancer metastasis or viral infection. First described in the paxillin family of scaffolding proteins, LD motifs and similar acidic LXXLL interaction motifs have been discovered in several other proteins, whereas 16 proteins have been reported to contain LDBDs (LD moti
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6

Zhang, Jian, Wei Wang, and Yingmei Li. "A characteristic comparison of cell-free DNA isolated from plasma and cerebrospinal fluid in patients with cancer." Journal of Clinical Oncology 41, no. 16_suppl (2023): e14008-e14008. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e14008.

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e14008 Background: Cell-free DNA (cfDNA) from plasma has proved its power as a liquid biopsy analyte in many cancer types, except cancers from central nervous system (CNS). CfDNA from cerebrospinal fluid (CSF) better recapitulates mutations for primary CNS tumors or cancer brain metastasis. The characteristics of cfDNA from plasma, including concentration range, mutation frequency, length, end motif etc. have been thoroughly studied, while the features of cfDNA from CSF are yet to be investigated. Methods: We retrospectively reviewed records since 2021 from a clinical sequencing center, and se
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7

Sahu, Tanishq, and Ruchi Yadav. "Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis." Biomedical and Biotechnology Research Journal 8, no. 4 (2024): 524–31. https://doi.org/10.4103/bbrj.bbrj_338_24.

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Abstract Context: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is an important technology to identify the genome-wide location of DNA-binding proteins such as histones proteins, transcription factors, RNA polymerase, or any protein of interest. ChIP-seq has been used to study the binding sites and efficacy of drugs in cancer cell lines etc. Aims: In current research, breast cancer cell line data have been used to study the effect PADI2 (peptidyl arginine deiminas
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8

Kobayashi, Takahiko, Junich Ishida, Yuichi Shimizu, et al. "Decreased RNA-binding motif 5 expression is associated with tumor progression in gastric cancer." Tumor Biology 39, no. 3 (2017): 101042831769454. http://dx.doi.org/10.1177/1010428317694547.

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RNA-binding motif 5 is a putative tumor suppressor gene that modulates cell cycle arrest and apoptosis. We recently demonstrated that RNA-binding motif 5 inhibits cell growth through the p53 pathway. This study evaluated the clinical significance of RNA-binding motif 5 expression in gastric cancer and the effects of altered RNA-binding motif 5 expression on cancer biology in gastric cancer cells. RNA-binding motif 5 protein expression was evaluated by immunohistochemistry using the surgical specimens of 106 patients with gastric cancer. We analyzed the relationships of RNA-binding motif 5 expr
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9

Schmücker, Anna, Bingkun Lei, Zdravko J. Lorković, et al. "Crosstalk between H2A variant-specific modifications impacts vital cell functions." PLOS Genetics 17, no. 6 (2021): e1009601. http://dx.doi.org/10.1371/journal.pgen.1009601.

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Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phos
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10

Tanne, Antoine, Luciana R. Muniz, Anna Puzio-Kuter, et al. "Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells." Proceedings of the National Academy of Sciences 112, no. 49 (2015): 15154–59. http://dx.doi.org/10.1073/pnas.1517584112.

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Recent studies have demonstrated abundant transcription of a set of noncoding RNAs (ncRNAs) preferentially within tumors as opposed to normal tissue. Using an approach from statistical physics, we quantify global transcriptome-wide motif use for the first time, to our knowledge, in human and murine ncRNAs, determining that most have motif use consistent with the coding genome. However, an outlier subset of tumor-associated ncRNAs, typically of recent evolutionary origin, has motif use that is often indicative of pathogen-associated RNA. For instance, we show that the tumor-associated human rep
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11

Zeng, Huang, Shuangshuang Kang, Yu Zhang, et al. "Synthesis and Biological Evaluation of Oleanolic Acid Derivatives as Selective Vascular Endothelial Growth Factor Promoter i-Motif Ligands." International Journal of Molecular Sciences 22, no. 4 (2021): 1711. http://dx.doi.org/10.3390/ijms22041711.

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Vascular endothelial growth factor (VEGF) is an angiogenic growth factor and plays a key role in tumor progression. The C-rich DNA sequence of VEGF promoter can form i-motif structure, which is a potential target for the development of novel anticancer agents. However, there is a limited number of chemotypes as the selective ligands of VEGF promoter i-motif, which leaves much room for development. Herein, we report the discovery of the natural oleanolic acid scaffold as a novel chemotype for the development of selective ligands of VEGF i-motif. A series of oleanolic acid derivatives as VEGF pr
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12

Lee, Yoonji, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, and Nick V. Grishin. "pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes." Bioinformatics 36, no. 3 (2019): 961–63. http://dx.doi.org/10.1093/bioinformatics/btz657.

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Abstract Motivation The consensus pattern of Nuclear Export Signal (NES) is a short sequence motif that is commonly identified in protein sequences, whether the motif acts as an NES (true positive) or not (false positive). Finding more plausible NES functioning regions among the vast array of consensus-matching segments would provide an interesting resource for further experimental validation. Better defined NES should also allow meaningful mapping of cancer-related mutation positions, leading to plausible explanations for the relationship between nuclear export and disease. Results Possible N
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13

Kim, Yoo-Na, Sangmi Lee, Allen Lynch, Tae Hee Kim, Peter J. Park, and Doga Gulhan. "Abstract PR020: A novel framework for epigenome-dependent multimodal fragment-signature analysis reveals insights into cell-free DNA generation in cancer." Clinical Cancer Research 30, no. 21_Supplement (2024): PR020. http://dx.doi.org/10.1158/1557-3265.liqbiop24-pr020.

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Abstract Background: The genome-wide pattern of cell-free DNA (cfDNA) is influenced by fragmentation enzymes, nucleosome occupancy, and epigenetic factors, as well as cell death mechanisms. Better modeling of these factors and their interactions will be essential for more sensitive detection of tumor-specific features and tissue-of-origin. Methods: To obtain mechanistic insights into cfDNA fragmentation, we developed a fragmentomics signature analysis framework. Our fragmenTopics algorithm (i) decomposes contributions of different fragment lengths and end-motif signatures using topic modeling
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14

Mehra, Navi, Bhavika Patel, Stephanie Allen, et al. "Multispectral imaging to detect immune phenotypes associated with the tumor microenvironment in a multi-tissue study: A full automated 7-color mIF immuno-oncology workflow." Journal of Immunology 208, no. 1_Supplement (2022): 48.15. http://dx.doi.org/10.4049/jimmunol.208.supp.48.15.

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Abstract Immunotherapy and precision medicine are rapidly developing approaches to cancer therapy. Biomarkers that detect the tumor and tumor microenvironment allow for the development of strategies that accelerate the advancement of treatments to enhance a patient’s immune system. Akoya’s MOTiF™ PD-1/PD-L1 Panel is a validated, multiplex immunoassay enabling detection of the 6 most clinically relevant immuno-oncology and spatial biomarkers: PD-1, PD-L1, FoxP3, CD8, CD68, and PanCK. The MOTiF™ PD-1/PD-L1 Panel was used to analyze the tumor microenvironment and specifically assess immune phenot
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15

Ozenberger, Benjamin B., Li Li, and Kevin B. Jones. "Abstract 2356: The epigenomic characterization of clear cell sarcoma." Cancer Research 82, no. 12_Supplement (2022): 2356. http://dx.doi.org/10.1158/1538-7445.am2022-2356.

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Abstract Clear cell sarcoma (CCS) is an aggressive malignancy that affects adolescents and young adults. CCS is a translocation-driven sarcoma subtype meaning a genetic fusion event defines and drives the malignancy. The chromosomal translocation occurring between EWSR1 on chromosome 22 and ATF1 on chromosome 12 results in the EWSR1-ATF1 fusion oncogene (hereafter abbreviated EA1) which drives more than 90% of CCS cases. The EA1 oncoprotein is a transcription factor that reprograms gene expression to drive CCS. However, the target genes of EA1 and how EA1 affects target gene expression levels
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16

Magnussen, Synnøve Norvoll, Jimita Toraskar, Elin Hadler-Olsen, Tonje S. Steigedal, and Gunbjørg Svineng. "Nephronectin as a Matrix Effector in Cancer." Cancers 13, no. 5 (2021): 959. http://dx.doi.org/10.3390/cancers13050959.

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The extracellular matrix protein nephronectin plays an important regulatory role during embryonic development, controlling renal organogenesis through integrin α8β1 association. Nephronectin has three main domains: five N-terminal epidermal growth factor-like domains, a linker region harbouring two integrin-binding motifs (RGD and LFEIFEIER), and a C-terminal MAM domain. In this review, we look into the domain-related functions of nephronectin, and tissue distribution and expression. During the last two decades it has become evident that nephronectin also plays a role during cancer progression
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17

Ogata, Kosuke, Shunsuke Takagi, Naoyuki Sugiyama, and Yasushi Ishihama. "Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors." Cancers 15, no. 1 (2022): 78. http://dx.doi.org/10.3390/cancers15010078.

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We present a motif-targeting phosphoproteome analysis workflow utilizing in vitro kinase reaction to enrich a subset of peptides with specific primary sequence motifs. Phosphopeptides are enriched and dephosphorylated with alkaline phosphatase, followed by in vitro kinase reaction to phosphorylate substrate peptides with specific primary-sequence motifs. These phosphopeptides are enriched again, TMT-labeled, dephosphorylated to enhance MS-detectability, and analyzed by LC/MS/MS. We applied this approach to inhibitor-treated cancer cells, and successfully profiled the inhibitory spectra of mult
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Xue, Zhijing, Weijia Li, Hailing Ding, et al. "Virulence gene polymorphisms in Shandong Helicobacter pylori strains and their relevance to gastric cancer." PLOS ONE 19, no. 9 (2024): e0309844. http://dx.doi.org/10.1371/journal.pone.0309844.

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Background Helicobacter pylori (H. pylori) virulence factors, particularly the cagA and vacA genotypes, play important roles in the pathogenic process of gastrointestinal disease. Methods The cagA and vacA genotypes of 87 H. pylori strains were determined by PCR and sequencing. The EPIYA and CM motif patterns were analyzed and related to clinical outcomes. We examined the associations between the virulence genes of H. pylori and gastrointestinal diseases in Shandong, and the results were analyzed via the chi-square test and logistic regression model. Results Overall, 76 (87.36%) of the strains
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Sara Adel Amin, Emad Abd El Mongy Sadaka, Khalid Ahmed Ismail, Ashraf Fathy Barakat, Ahmed Abdel Aziem Menaisy, and Amr Abd Elmoneim Mahmoud. "Relation between baseline CXCR1 expression and neoadjuvant chemotherapy response in breast cancer patients." Journal of the Pakistan Medical Association 73, no. 4 (2023): S52—S55. http://dx.doi.org/10.47391/jpma.egy-s4-8.

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Objective: To examine the C-X-C Motif Chemokine Receptor 1 expression in breast cancer tissues prior to neo-adjuvant chemotherapy, and its relationship to neo-adjuvant chemotherapy effectiveness and other prognostic variables.Method: The prospective study was conducted at Kafrelsheikh University Hospital, Egypt, from November 2018 to March 2021, and comprised patients with recent histopathologically proven breast cancer cases eligible for chemotherapy. Paraffin blocks of tumour specimens were stained by immunohistochemical stain using concentrating rabbit anti-human C-X-C Motif Chemokine Recep
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Patel, Bhavika, Stephanie Allen, Brittney Boldt, Najiba Mammadova, Agnes Haggerty, and Navi Mehra. "Abstract 2769: Advance understanding of the tumor microenvironment with multiplex immunofluorescence." Cancer Research 82, no. 12_Supplement (2022): 2769. http://dx.doi.org/10.1158/1538-7445.am2022-2769.

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Abstract Immunotherapy and precision medicine are rapidly developing approaches to cancer therapy. Biomarkers that detect the tumor and tumor microenvironment allow for the development of strategies that accelerate the advancement of treatments to enhance a patient’s immune system. Akoya’s MOTiF™ PD-1/PD-L1 Panel is a validated, multiplex immunoassay enabling detection of the 6 most clinically relevant immuno-oncology and spatial biomarkers: PD-1, PD-L1, FoxP3, CD8, CD68, and PanCK. The MOTiF™ PD-1/PD-L1 Panel was used to analyze the tumor microenvironment and specifically assess immune phenot
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Pachathundikandi, Gutiérrez-Escobar, and Tegtmeyer. "Tailor-Made Detection of Individual Phosphorylated and Non-Phosphorylated EPIYA-Motifs of Helicobacter pylori Oncoprotein CagA." Cancers 11, no. 8 (2019): 1163. http://dx.doi.org/10.3390/cancers11081163.

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The gastric pathogen and carcinogen Helicobacter pylori (H. pylori) encodes a type IV secretion system for translocation of the effector protein CagA into host cells. Injected CagA becomes tyrosine-phosphorylated at the five amino acid residue Glutamate-Proline- Isoleucine-Tyrosine-Alanine (EPIYA)-sequence motifs. These phosphorylated EPIYA-sites represent recognition motifs for binding of multiple host factors, which then manipulate signaling pathways to trigger gastric disease. Thus, efficient detection of single phosphorylated EPIYA-motifs in CagA is required. Detection of phospho-CagA is p
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Wei, Chao, Jiongjie Jing, Xiaoyuan Yan, et al. "MIWI N-terminal RG motif promotes efficient pachytene piRNA production and spermatogenesis independent of LINE1 transposon silencing." PLOS Genetics 19, no. 11 (2023): e1011031. http://dx.doi.org/10.1371/journal.pgen.1011031.

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PIWI proteins and their associated piRNAs act to silence transposons and promote gametogenesis. Murine PIWI proteins MIWI, MILI, and MIWI2 have multiple arginine and glycine (RG)-rich motifs at their N-terminal domains. Despite being known as docking sites for the TDRD family proteins, the in vivo regulatory roles for these RG motifs in directing PIWI in piRNA biogenesis and spermatogenesis remain elusive. To investigate the functional significance of RG motifs in mammalian PIWI proteins in vivo, we genetically engineered an arginine to lysine (RK) point mutation of a conserved N-terminal RG m
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Dai, Juncheng, Zhihua Li, Christopher I. Amos, et al. "Systematic analyses of regulatory variants in DNase I hypersensitive sites identified two novel lung cancer susceptibility loci." Carcinogenesis 40, no. 3 (2019): 432–40. http://dx.doi.org/10.1093/carcin/bgy187.

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AbstractDNase I hypersensitive sites (DHS) are abundant in regulatory elements, such as promoter, enhancer and transcription factor binding sites. Many studies have revealed that disease-associated variants were concentrated in DHS-related regions. However, limited studies are available on the roles of DHS-related variants in lung cancer. In this study, we performed a large-scale case–control study with 20 871 lung cancer cases and 15 971 controls to evaluate the associations between regulatory genetic variants in DHS and lung cancer susceptibility. The expression quantitative trait loci (eQTL
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Guan, Guofang, Ranwei Li, Wenfang Tang, et al. "Expression of RNA-binding motif 10 is associated with advanced tumor stage and malignant behaviors of lung adenocarcinoma cancer cells." Tumor Biology 39, no. 3 (2017): 101042831769174. http://dx.doi.org/10.1177/1010428317691740.

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This study assessed RNA-binding motif 10 expression in lung adenocarcinoma tissues and examined the role and mechanism of RNA-binding motif 10 in the regulation of lung adenocarcinoma malignancy. Lung adenocarcinoma and corresponding adjacent non-tumor lung tissues from 41 patients were subjected to reverse transcription-polymerase chain reaction and Western blot assessment to detect RNA-binding motif 10 expression. Recombinant lentivirus carrying RNA-binding motif 10 complementary DNA was used to infect lung adenocarcinoma cell lines, A549 and H1299 cells. Complementary DNA microarray was use
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A. Altimmime, Baqir, and Farah A. Rashid. "CXCL12 as a Metastasis Inducer Chemokine of Breast Cancer." Al-Nahrain Journal of Science 27, no. 5 (2024): 49–57. https://doi.org/10.22401/anjs.27.5.06.

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Breast cancer is a worrying challenge nowadays because it represents the most common type of cancer that has been diagnosed in women. Breast cancer deaths mainly result from metastasis instead of primary tumor. C-X-C motif chemokine ligand 12is a chemokine that belongs to CXC group and has chemot axis property that makes it able to migrate immune cells. Based on several studies, C-X-C motif chemokine ligand 12and its receptor C-X-C chemokine receptor type 4could promote breast cancer metastasis. Breast cancer metastasis is a multistep process in which the C-X-C motif chemokine ligand 12/C-X-C
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Gonzalez Quesada, Yulemi, and Luc DesGroseillers. "A Degradation Motif in STAU1 Defines a Novel Family of Proteins Involved in Inflammation." International Journal of Molecular Sciences 23, no. 19 (2022): 11588. http://dx.doi.org/10.3390/ijms231911588.

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Cancer development is regulated by inflammation. Staufen1 (STAU1) is an RNA-binding protein whose expression level is critical in cancer cells as it is related to cell proliferation or cell death. STAU1 protein levels are downregulated during mitosis due to its degradation by the E3 ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C). In this paper, we map the molecular determinant involved in STAU1 degradation to amino acids 38–50, and by alanine scanning, we shorten the motif to F39PxPxxLxxxxL50 (FPL-motif). Mutation of the FPL-motif prevents STAU1 degradation by APC/C. Interesting
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Kawai, Kenichiro. "Abstract 6561: Specific binding mode of RNA binding protetin FAM120A to lncRNA." Cancer Research 83, no. 7_Supplement (2023): 6561. http://dx.doi.org/10.1158/1538-7445.am2023-6561.

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Abstract Long noncoding RNAs (lncRNAs) are defined as transcripts >200 nucleotides in length with no protein-coding potential. LncRNAs play diverse roles in regulating gene transcription, post-transcription, translation, and epigenetic modification through interaction with RNA binding proteins (RBPs). Here, we analyzed binding motif of a RBP, family with sequence similarity 120A (FAM120A), which is highly expressed in multiple cancer types and associated with poor prognosis. To investigate FAM120A interacting RNAs genome-wide, we conducted cross-linking immunoprecipitation combined with
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TAYLOR, Kathryn M., Helen E. MORGAN, Andrea JOHNSON, Lisa J. HADLEY, and Robert I. NICHOLSON. "Structure–function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters." Biochemical Journal 375, no. 1 (2003): 51–59. http://dx.doi.org/10.1042/bj20030478.

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The LIV-1 gene has been previously associated with oestrogen-positive breast cancer and its metastatic spread to the regional lymph nodes. We have investigated the protein product of this gene as a marker for disease progression of breast cancer. The protein sequence contains a potential metalloprotease motif (HEXPHEXGD), which fits the consensus sequence for the catalytic zinc-binding site motif of the zincin metalloproteases. This motif has identified a new subfamily of ZIP (Zrt-, Irt-like proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc transporters). Expre
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Kashkin, K. N. "Looking for Tumor Specific Promoters In Silico." Russian Journal of Bioorganic Chemistry 48, no. 6 (2022): 1230–39. http://dx.doi.org/10.1134/s1068162022060127.

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Abstract— Previously we demonstrated the tumor-specific activity of several human native and chimeric promoters. Here we have analyzed the DNA sequences of experimentally tested tumor-specific promoters for the presence of recognition matrices of transcription factors and for de novo motif discovery. CiiiDER and MEME Suite software tools were used for this purpose. A number of transcription factor matrices have been identified, which are present more often in tumor-specific promoters than in the promoters of housekeeping genes. New promoter–TF regulatory relationships have been predicted by pa
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Rogozin, Igor, Abiel Roche-Lima, Artem Lada, et al. "Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes." Cancers 11, no. 2 (2019): 211. http://dx.doi.org/10.3390/cancers11020211.

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Cancer genomes accumulate nucleotide sequence variations that number in the tens of thousands per genome. A prominent fraction of these mutations is thought to arise as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases. These enzymes, collectively called activation induced deaminase (AID)/APOBECs, deaminate cytosines located within defined DNA sequence contexts. The resulting changes of the original C:G pair in these contexts (mutational signatures) provide indirect evidence for the participation of specific cytosine deaminases in a given cancer type. The conventi
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Ayyalasomayajula, Ramya, and Mare Cudic. "Targeting Siglec–Sialylated MUC1 Immune Axis in Cancer." Cancers 16, no. 7 (2024): 1334. http://dx.doi.org/10.3390/cancers16071334.

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Siglecs play a key role in mediating cell–cell interactions via the recognition of different sialylated glycoconjugates, including tumor-associated MUC1, which can lead to the activation or inhibition of the immune response. The activation occurs through the signaling of Siglecs with the cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM)-containing proteins, while the inhibition signal is a result of the interaction of intracellular immunoreceptor tyrosine-based inhibition motif (ITIM)-bearing receptors. The interaction of tumor-associated MUC1 sialylated glycans with Siglecs vi
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Ghareyazi, Amin, Amir Mohseni, Hamed Dashti, et al. "Whole-Genome Analysis of De Novo Somatic Point Mutations Reveals Novel Mutational Biomarkers in Pancreatic Cancer." Cancers 13, no. 17 (2021): 4376. http://dx.doi.org/10.3390/cancers13174376.

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It is now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancr
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Elengoe, Asita, Mohammed Abu Naser, and Salehhuddin Hamdan. "A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif." International Journal of Genomics 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/391293.

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Currently, protein interaction ofHomo sapiensnucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simu
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Ozenberger, Benjamin B., Li Li, Emily R. Wilson, Alexander J. Lazar, Jared J. Barrott, and Kevin B. Jones. "EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and a Mouse Genetic Model." Cancers 15, no. 24 (2023): 5750. http://dx.doi.org/10.3390/cancers15245750.

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Clear cell sarcoma (CCS) is a rare, aggressive malignancy that most frequently arises in the soft tissues of the extremities. It is defined and driven by expression of one member of a family of related translocation-generated fusion oncogenes, the most common of which is EWSR1::ATF1. The EWSR1::ATF1 fusion oncoprotein reprograms transcription. However, the binding distribution of EWSR1::ATF1 across the genome and its target genes remain unclear. Here, we interrogated the genomic distribution of V5-tagged EWSR1::ATF1 in tumors it had induced upon expression in mice that also recapitulated the t
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Yanguas, Francisco, and M. Henar Valdivieso. "Analysis of the SNARE Stx8 recycling reveals that the retromer-sorting motif has undergone evolutionary divergence." PLOS Genetics 17, no. 3 (2021): e1009463. http://dx.doi.org/10.1371/journal.pgen.1009463.

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Fsv1/Stx8 is aSchizosaccharomyces pombeprotein similar to mammalian syntaxin 8.stx8Δcells are sensitive to salts, and the prevacuolar endosome (PVE) is altered instx8Δcells. These defects depend on the SNARE domain, data that confirm the conserved function of syntaxin8 and Stx8 in vesicle fusion at the PVE. Stx8 localizes at thetrans-Golgi network (TGN) and the prevacuolar endosome (PVE), and its recycling depends on the retromer component Vps35, and on the sorting nexins Vps5, Vps17, and Snx3. Several experimental approaches demonstrate that Stx8 is a cargo of the Snx3-retromer. Using extensi
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Wang, Mei, Chunping Wu, Yu Guo, Xiaojuan Cao, Wenwei Zheng, and Guo-Kang Fan. "The primary growth of laryngeal squamous cell carcinoma cells in vitro is effectively supported by paired cancer-associated fibroblasts alone." Tumor Biology 39, no. 5 (2017): 101042831770551. http://dx.doi.org/10.1177/1010428317705512.

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Most primarily cultured laryngeal squamous cell carcinoma cells are difficult to propagate in vitro and have a low survival rate. However, in our previous work to establish a laryngeal squamous cell carcinoma cell line, we found that laryngeal cancer-associated fibroblasts appeared to strongly inhibit the apoptosis of primarily cultured laryngeal squamous cell carcinoma cells in vitro. In this study, we investigated whether paired laryngeal cancer-associated fibroblasts alone can effectively support the growth of primarily cultured laryngeal squamous cell carcinoma cells in vitro. In all, 29 l
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PRATAP, ABHAY, SETU TALIYAN, and TIRATHA RAJ SINGH. "NMDB: NETWORK MOTIF DATABASE ENVISAGED AND EXPLICATED FROM HUMAN DISEASE SPECIFIC PATHWAYS." Journal of Biological Systems 22, no. 01 (2014): 89–100. http://dx.doi.org/10.1142/s0218339014500053.

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The study of network motifs for large number of networks can aid us to resolve the functions of complex biological networks. In biology, network motifs that reappear within a network more often than expected in random networks include negative autoregulation, positive autoregulation, single-input modules, feedforward loops, dense overlapping regulons and feedback loops. These network motifs have their different dynamical functions. In this study, our main objective is to examine the enrichment of network motifs in different biological networks of human disease specific pathways. We characteriz
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Ma, Xiao, Dan Li, Yan Gao, and Cheng Liu. "miR-451a Inhibits the Growth and Invasion of Osteosarcoma via Targeting TRIM66." Technology in Cancer Research & Treatment 18 (January 1, 2019): 153303381987020. http://dx.doi.org/10.1177/1533033819870209.

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The importance of microRNAs in regulating osteosarcoma development has been studied in recent years. However, the function of microRNA-451a in osteosarcoma growth is rarely investigated. Here, we explored the expression of microRNA-451a in osteosarcoma cell lines. Bioinformatic software, luciferase activity reporter assay, and Western blot were conducted to determine the association between microRNA-451a and tripartite motif-containing 66. Cell Counting Kit-8 assay and transwell assay were used to explore the regulatory effects of microRNA-451a on osteosarcoma cells. Moreover, we explored whet
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Mitchell, Kelly, Samuel Sprowls, Sajina Shakya, et al. "STEM-24. WDR5 REPRESENTS A THERAPEUTICALLY EXPLOITABLE TARGET FOR CANCER STEM CELLS IN GLIOBLASTOMA." Neuro-Oncology 25, Supplement_5 (2023): v38. http://dx.doi.org/10.1093/neuonc/noad179.0149.

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Abstract Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors that are driven by populations of cancer stem cells (CSCs). In this study, we perform an epigenetic-focused functional genomics screen in GBM organoids and identify WDR5 as an essential epigenetic regulator in the SOX2-enriched, therapy resistant cancer stem cell niche. Despite their importance for tumor growth, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in GBM patient-derived organoids to id
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Baroni, T. E., T. Wang, H. Qian, et al. "A global suppressor motif for p53 cancer mutants." Proceedings of the National Academy of Sciences 101, no. 14 (2004): 4930–35. http://dx.doi.org/10.1073/pnas.0401162101.

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Herrera-León, Claudia, Francisco Ramos-Martín, Hassan El Btaouri, et al. "The Influence of Short Motifs on the Anticancer Activity of HB43 Peptide." Pharmaceutics 14, no. 5 (2022): 1089. http://dx.doi.org/10.3390/pharmaceutics14051089.

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Despite the remarkable similarity in amino acid composition, many anticancer peptides (ACPs) display significant differences in terms of activity. This strongly suggests that particular relative dispositions of amino acids (motifs) play a role in the interaction with their biological target, which is often the cell membrane. To better verify this hypothesis, we intentionally modify HB43, an ACP active against a wide variety of cancers. Sequence alignment of related ACPs by ADAPTABLE web server highlighted the conserved motifs that could be at the origin of the activity. In this study, we show
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Vacher, Sophie, Voreak Suybeng, Elodie Girard, et al. "Genomic Instability Signature of Palindromic Non-Coding Somatic Mutations in Bladder Cancer." Cancers 12, no. 10 (2020): 2882. http://dx.doi.org/10.3390/cancers12102882.

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Numerous pan-genomic studies identified alterations in protein-coding genes and signaling pathways involved in bladder carcinogenesis, while non-coding somatic alterations remain weakly explored. The goal of this study was to identify clinical biomarkers in non-coding regions for bladder cancer patients. We have previously identified in bladder tumors two non-coding mutational hotspots occurring at high frequencies (≥30%). These mutations are located close to the GPR126 and PLEKHS1 genes, at the guanine or the cytosine of a TGAACA core motif flanked, on both sides, by a stretch of palindromic
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Ding, Yi, Yi Lu, Xinjie Xie, Bo Sheng, and Zuopei Wang. "Silencing TRIM37 inhibits the proliferation and migration of non-small cell lung cancer cells." RSC Advances 8, no. 64 (2018): 36852–57. http://dx.doi.org/10.1039/c8ra06391e.

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Hubert, Christopher, Kelly Mitchell, Samuel Sprowls, et al. "361 WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastoma." Journal of Clinical and Translational Science 7, s1 (2023): 107. http://dx.doi.org/10.1017/cts.2023.401.

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OBJECTIVES/GOALS: Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors that are driven by populations of cancer stem cells (CSCs). In this study, we perform an epigenetic-focused functional genomics screen in GBM organoids and identify WDR5 as an essential epigenetic regulator in the SOX2-enriched, therapy resistant cancer stem cell niche. METHODS/STUDY POPULATION: Despite their importance for tumor growth, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in
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Łabędź, Wojciech, Anna Przybyla, Agnieszka Zimna, Mikołaj Dąbrowski, and Łukasz Kubaszewski. "The Role of Cytokines in the Metastasis of Solid Tumors to the Spine: Systematic Review." International Journal of Molecular Sciences 24, no. 4 (2023): 3785. http://dx.doi.org/10.3390/ijms24043785.

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Although many studies have investigated the role of cytokines in bone metastases, our knowledge of their function in spine metastasis is limited. Therefore, we performed a systematic review to map the available evidence on the involvement of cytokines in spine metastasis in solid tumors. A PubMed search identified 211 articles demonstrating a functional link between cytokines/cytokine receptors and bone metastases, including six articles confirming the role of cytokines/cytokine receptors in spine metastases. A total of 68 cytokines/cytokine receptors were identified to mediate bone metastases
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Ladewig, Erik, Abbas Nazir, Christina Leslie, and Charles Sawyers. "Abstract 2048: Mutations in FOXA1 alter chromatin remodeling and cell fate in prostate organoids." Cancer Research 83, no. 7_Supplement (2023): 2048. http://dx.doi.org/10.1158/1538-7445.am2023-2048.

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Abstract Genomic analysis of targeted patient tumor sequencing identified frequent mutations, 41% in prostate cancer (Li, et al., 2020) in the gene FOXA1, a developmentally important pioneer transcription factor (TF) in mammary and prostate tissues. Previous work by our group and others has shown that these FOXA1 mutations alter global chromatin accessibility and promote growth in prostate cells (Adams, 2019), but the underlying molecular details, including the identity of partner TFs, remain unclear. To address this topic, we generated mouse prostate organoids expressing Foxa1 alleles harbori
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Maziarz, Marcin, Stefan Broselid, Vincent DiGiacomo та ін. "A biochemical and genetic discovery pipeline identifies PLCδ4b as a nonreceptor activator of heterotrimeric G-proteins". Journal of Biological Chemistry 293, № 44 (2018): 16964–83. http://dx.doi.org/10.1074/jbc.ra118.003580.

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Recent evidence has revealed that heterotrimeric G-proteins can be activated by cytoplasmic proteins that share an evolutionarily conserved sequence called the Gα-binding-and-activating (GBA) motif. This mechanism provides an alternative to canonical activation by G-protein–coupled receptors (GPCRs) and plays important roles in cell function, and its dysregulation is linked to diseases such as cancer. Here, we describe a discovery pipeline that uses biochemical and genetic approaches to validate GBA candidates identified by sequence similarity. First, putative GBA motifs discovered in bioinfor
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Fu, Chunhong, Ming Yuan, Jie Sun, et al. "RNA-Binding Motif Protein 11 (RBM11) Serves as a Prognostic Biomarker and Promotes Ovarian Cancer Progression." Disease Markers 2021 (August 14, 2021): 1–7. http://dx.doi.org/10.1155/2021/3037337.

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Ovarian cancer is one of the most lethal gynecologic malignancies for women. Due to the lack of efficient target therapy, the overall survival rate for patients with advanced ovarian cancer is still low. Illustrating the molecular mechanisms dictating ovarian cancer progression is critically important to develop novel therapeutic agents. Here, we found that RNA-binding motif protein 11 (RBM11) was highly elevated in ovarian cancer tissues compared with normal ovary, while RBM11 depletion in ovarian cancer cells resulted in impaired cell growth and invasion. Moreover, knockdown of RBM11 also re
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Sun, Hongli, Xianwei Dai, and Bing Han. "TRIM29 as a Novel Biomarker in Pancreatic Adenocarcinoma." Disease Markers 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/317817.

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Background and Aim. Tripartite motif-containing 29 (TRIM29) is structurally a member of the tripartite motif family of proteins and is involved in diverse human cancers. However, its role in pancreatic cancer remains unclear.Methods. The expression pattern of TRIM29 in pancreatic ductal adenocarcinoma was assessed by immunocytochemistry. Multivariate logistic regression analysis was used to investigate the association between TRIM29 and clinical characteristics.In vitroanalyses by scratch wound healing assay and invasion assays were performed using the pancreatic cancer cell lines.Results. Imm
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Lin, Xiaomin, Jiahui Zhang, Jihai Liang, Dongsheng Ji, Zhi-Shu Huang, and Ding Li. "Selective Up-Regulation of Tumor Suppressor Gene Retinoblastoma by Bisacridine Derivative Through Gene Promoter Quadruplex Structures for Cancer Treatment." International Journal of Molecular Sciences 26, no. 4 (2025): 1417. https://doi.org/10.3390/ijms26041417.

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The retinoblastoma (RB) gene is an important tumor suppressor gene with a higher mutation frequency than other tumor suppressor genes. The mutation or inactivation of RB has been found in various cancers. The discovery of small molecules to promote RB expression is an effective anti-cancer strategy. Special DNA secondary structures with G-quadruplex and i-motif on the RB promoter could act as “molecular switches” for gene transcriptional regulation and are potentially important targets for the development of new anti-cancer drugs. After extensive screening, we found that the bisacridine deriva
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