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33 results for “Cancer”
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ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing.
bioRxiv : the preprint server for biology · 2026
Chemical proteomics has identified covalent ligands targeting cysteine residues across many hundreds of human proteins. The functional effects of these liganding events, however, remain challenging to assign at scale. Here we describe ESCAPE (Endogenous Site-specific Competition Assays using Prime Editors), …
PMID 42619774 DOI ↗
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Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
RNA (New York, N.Y.) · 2026 · 32(5): 635-653
Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. …
PMID 41535088 DOI ↗
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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
Cell chemical biology · 2026 · 33(2): 256-267.e11
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We previously described a chloroacetamide compound (R)-SKBG-1 that covalently binds …
PMID 41534524 DOI ↗
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Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies, such as triple negative breast cancer (TNBC). Here, we employed both in vitro …
PMID 41411621 DOI ↗
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Imaging Cellular Metabolic Rewiring with SuMMIT-SRS.
bioRxiv : the preprint server for biology · 2025
Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope …
PMID 41279865 DOI ↗
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Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) play important roles in mRNA transcription, processing, and translation. Chemical tools are lacking for RBPs, which has hindered efforts to perturb and understand RBP function in cells. We recently reported a chloroacetamide compound ( <i>R</i> )-SKBG-1 that …
PMID 40661397 DOI ↗
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Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.
bioRxiv : the preprint server for biology · 2025
RNA-binding proteins (RBPs) are important regulators of post-transcriptional gene expression. Understanding which and how RBPs promote cancer progression is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ both <i>in vitro</i> …
PMID 40655003 DOI ↗
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Phenylpyrazoles as Inhibitors of the m<sup>6</sup>A RNA-Binding Protein YTHDF2.
JACS Au · 2025 · 5(2): 618-630
The <i>N</i>6-methyladenosine (m<sup>6</sup>A) modification, which is the most common RNA modification in eukaryotes, is regulated by the "writer" methyltransferases, the "reader" m<sup>6</sup>A binding proteins, and the "eraser" demethylases. m<sup>6</sup>A plays a multifunctional role in physiological and pathological processes, regulating all …
PMID 40017738 DOI ↗
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Steering research on mRNA splicing in cancer towards clinical translation.
Nature reviews. Cancer · 2024 · 24(12): 887-905
Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome …
PMID 39384951 DOI ↗
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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024 · 34(11): 2012-2024
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …
PMID 38906680 DOI ↗
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circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.
bioRxiv : the preprint server for biology · 2024
Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses …
PMID 37745562 DOI ↗
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Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.
Current opinion in biotechnology · 2024 · 85: 103048
Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the …
PMID 38142648 DOI ↗
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A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
Nature communications · 2023 · 14(1): 5195
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that …
PMID 37673892 DOI ↗
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Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology · 2023 · 19(7): 825-836
Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and stereoselectively decrease the expression of transcripts encoding the androgen receptor and its splice variants …
PMID 36864190 DOI ↗
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In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.
Blood cancer discovery · 2023 · 4(3): 180-207
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) …
PMID 36763002 DOI ↗
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Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.
Nature communications · 2023 · 14(1): 551
Regulation of RNA processing contributes profoundly to tissue development and physiology. Here, we report that serine-arginine-rich splicing factor 1 (SRSF1) is essential for hepatocyte function and survival. Although SRSF1 is mainly known for its many roles in mRNA metabolism, it …
PMID 36759613 DOI ↗
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Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology · 2023 · 21(1): e3001983
During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the …
PMID 36716323 DOI ↗
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Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
Nature communications · 2022 · 13(1): 7506
Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains …
PMID 36473869 DOI ↗
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Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery · 2022 · 12(3): 836-855
Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …
PMID 34620690 DOI ↗
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Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis.
Cellular and molecular life sciences : CMLS · 2022 · 79(3): 147
In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we …
PMID 35195778 DOI ↗
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Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
Molecular cell · 2021 · 81(15): 3048-3064.e9
RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in …
PMID 34216543 DOI ↗
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Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
Genome medicine · 2020 · 12(1): 112
Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …
PMID 33287884 DOI ↗
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Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Molecular cell · 2020 · 80(3): 452-469.e9
Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens …
PMID 33157015 DOI ↗
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Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.
Science immunology · 2020 · 5(47)
During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …
PMID 32414833 DOI ↗
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An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.
Nature cancer · 2020 · 1(4): 410-422
Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …
PMID 34109316 DOI ↗
Datasets 25+
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
GPL24676
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC
Homo sapiens · GPL571
A seven-gene signature aggregates a subgroup of stage II colon cancers with stage III.
Homo sapiens · GPL570
Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery
Homo sapiens · GPL13497
Gene Expression Profiles in Stage II and III Colon Cancer. Application of a 128-gene signature
Homo sapiens · GPL570
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)
Homo sapiens · GPL570
Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients
Mus musculus · GPL570
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
RNA-Seq of CD8+ T cell subsets during LCMV infection III
Mus musculus · GPL17021
A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease
Homo sapiens · GPL16791
Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death
Mus musculus · GPL21103
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
MYC ChIP-seq in human pancreatic ductal adenocarcinoma cells
Homo sapiens · GPL16791
Refined molecular taxonomy and treatment remodeling of pancreatic cancer using single-cell resolution
Homo sapiens · GPL20301
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL24676
A Transcriptomic Analysis of the Development of Skeletal Muscle Atrophy in Cancer-Cachexia in Tumor-Bearing Mice
Mus musculus · GPL17021
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer
Homo sapiens · GPL24676
Showing first 25 dataset results.
Analyses 23
GSE280897 · 6 steps · RNA-seq · geo_data_processing
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)
GSE280898 · 5 steps · eCLIP · geo_data_processing
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)
GSE280899 · 6 steps · GSE · code_examples
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)
GSE313324 · 2 steps · geo_data_processing
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. (2025)
GSE114820 · 4 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE143804 · 9 steps · ChIP-Seq · code_examples
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)
GSE154778 · 1 step · RNA-Seq · code_examples
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)
GSE202051 · 5 steps · RNA-Seq · code_examples
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)
GSE234078 · 3 steps · GSE · code_examples
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)
GSE137258 · 2 steps · OTHER · code_examples
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. (2021)
GSE13067 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE133479 · 2 steps · RNA-Seq · code_examples
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. (2020)
GSE133509 · 1 step · RNA-Seq · code_examples
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. (2020)
GSE135300 · 2 steps · RNA-Seq · code_examples
An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. (2020)
GSE14333 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE145984 · 5 steps · RNA-Seq · code_examples
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. (2020)
GSE146726 · 4 steps · RNA-Seq · code_examples
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression. (2020)
GSE17536 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE17538 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE31595 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE33113 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE37892 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE87211 · 1 step · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)