DNA protein binding motif prediction based on fusion of expectation pooling and LSTM

Author(s):  
Zhaofeng Li ◽  
Shunfang Wang
1995 ◽  
Vol 15 (1) ◽  
pp. 476-487 ◽  
Author(s):  
X Guo ◽  
Y P Zhang ◽  
D A Mitchell ◽  
D T Denhardt ◽  
A F Chambers

The role of RAS in transducing signals from an activated receptor into altered gene expression is becoming clear, though some links in the chain are still missing. Cells possessing activated RAS express higher levels of osteopontin (OPN), an alpha v beta 3 integrin-binding secreted phosphoprotein implicated in a number of developmental, physiological, and pathological processes. We report that in T24 H-ras-transformed NIH 3T3 cells enhanced transcription contributes to the increased expression of OPN. Transient transfection studies, DNA-protein binding assays, and methylation protection experiments have identified a novel ras-activated enhancer, distinct from known ras response elements, that appears responsible for part of the increase in OPN transcription in cells with an activated RAS. In electrophoretic mobility shift assays, the protein-binding motif GGAGGCAGG was found to be essential for the formation of several complexes, one of which (complex A) was generated at elevated levels by cell lines that are metastatic. Southwestern blotting and UV light cross-linking studies indicated the presence of several proteins able to interact with this sequence. The proteins that form these complexes have molecular masses estimated at approximately 16, 28, 32, 45, 80, and 100 kDa. Because the approximately 16-kDa protein was responsible for complex A formation, we have designated it MATF for metastasis-associated transcription factor. The GGANNNAGG motif is also found in some other promoters, suggesting that they may be similarly controlled by MATF.


Cell Reports ◽  
2017 ◽  
Vol 21 (12) ◽  
pp. 3524-3535 ◽  
Author(s):  
Olivier Goupille ◽  
Tipparat Penglong ◽  
Zahra Kadri ◽  
Marine Granger-Locatelli ◽  
Raphaël Denis ◽  
...  

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii224-ii224
Author(s):  
Apeng Chen ◽  
Yinan Jiang ◽  
Zhengwei Li ◽  
Han Zou ◽  
Ulises Santiago ◽  
...  

Abstract Glioblastoma (GBM), the most common and lethal brain tumor, remains incurable despite intensive multimodal treatment. While immunotherapies have been highly effective in some types of cancer, the disappointing results from clinical trials for GBM immunotherapy represent continued challenges. GBM is highly immunosuppressive and resistant to immunotherapy because of glioma cells escaping from immune surveillance by reprograming the tumor microenvironment (TME). However, understanding the mechanisms of immune evasion by GBM remains elusive. Here, we found that Chitinase-3-like-1 (CHI3L1) is highly expressed in GBM and associated with a poor clinical outcome. CHI3L1, also known as human homolog YKL-40, plays a role in tissue remodeling, inflammation and cancer. Interestingly, we found that genetic knockdown (KD) of Chi3l1 in syngeneic immunocompetent mouse GBM models resulted in increased tumor-infiltrating lymphocytes, tumor size reduction, and improved animal survival. Surprisingly, the parallel loss-of-function experiment revealed that Chi3l1 KD did not repress tumor progression in the orthotopic immunodeficient mice with deficient T and B cells. These results suggest the predominant role of CHI3L1 in regulating the GBM immune TME, rather than in tumor cells per se. Mechanistically, we discovered that Galectin-3 (Gal-3) and Galectin-3 binding protein (Gal-3BP) interact competitively with the same binding motif on CHI3L1, leading to selective migration of protumor M2-like versus antitumor M1-like bone marrow-derived macrophages (BMDMs) and resident microglia (MG). Transcriptomic analysis revealed that pro-inflammatory signature and T cell mediated immunity and cytotoxicity signaling are significantly enriched in tumor associated macrophages/microglia (TAMs) composed of BMDMs and MG, which were isolated from tumors with Chi3l1 KD versus wild type. In vitro validations suggest that CHI3L1-Gal-3, but not CHI3L1-Gal-3BP protein binding complex, activates PI3K/AKT/mTOR signaling to control the TAM switch of immune suppression and immune stimulation. Together, these results shed light on molecular mechanism of GBM immune evasion and potential new immunotherapeutic strategies for GBM treatment.


Aging ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 2430-2446 ◽  
Author(s):  
Yingcheng Wu ◽  
Hao Chen ◽  
Yuyan Chen ◽  
Lishuai Qu ◽  
Erhao Zhang ◽  
...  

2011 ◽  
Vol 286 (46) ◽  
pp. 39829-39835 ◽  
Author(s):  
William J. Placzek ◽  
Mattia Sturlese ◽  
Bainan Wu ◽  
Jason F. Cellitti ◽  
Jun Wei ◽  
...  

Cancers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 4022
Author(s):  
Donatella Treppiedi ◽  
Anna Maria Barbieri ◽  
Genesio Di Muro ◽  
Giusy Marra ◽  
Federica Mangili ◽  
...  

Cushing’s Disease (CD) is a rare condition characterized by an overproduction of ACTH by an ACTH-secreting pituitary tumor, resulting in an excess of cortisol release by the adrenal glands. Somatic mutations in the deubiquitinases USP8 and USP48, and in BRAF genes, have been reported in a subset of patients affected by CD. The aim of this study was to characterize the genetic profile of a cohort of 60 patients with ACTH-secreting tumors, searching for somatic mutations in USP8, USP48, and BRAF hotspot regions. Seven patients were found to carry USP8 somatic mutations in the well-characterized 14-3-3 protein binding motif (n = 5 P720R, n = 1 P720Q, n = 1 S718del); 2 patients were mutated in USP48 (M415I); no mutation was identified in BRAF. In addition, a novel USP8 variant, G664R, located in exon 14, upstream of the 14-3-3 protein binding motif, was identified in 1 patient. Functional characterization of USP8 G664R variant was performed in murine corticotroph tumor AtT-20 cells. Transient transfection with the USP8 G664R variant resulted in a significant increase of ACTH release and cell proliferation (+114.5 ± 53.6% and +28.3 ± 2.6% vs. empty vector transfected cells, p < 0.05, respectively). Notably, USP8 proteolytic cleavage was enhanced in AtT-20 cells transfected with G664R USP8 (1.86 ± 0.58–fold increase of N-terminal USP8 fragment, vs. WT USP8, p < 0.05). Surprisingly, in situ Proximity Ligation Assay (PLA) experiments showed a significant reduction of PLA positive spots, indicating USP8/14-3-3 proteins colocalization, in G664R USP8 transfected cells with respect to WT USP8 transfected cells (−47.9 ± 6.6%, vs. WT USP8, p < 0.001). No significant difference in terms of ACTH secretion, cell proliferation and USP8 proteolytic cleavage, and 14-3-3 proteins interaction was observed between G664R USP8 and S718del USP8 transfected cells. Immunofluorescence experiments showed that, contrary to S718del USP8 but similarly to WT USP8 and other USP8 mutants, G664R USP8 displays an exclusive cytoplasmic localization. In conclusion, somatic mutations were found in USP8 (13.3% vs. 36.5% incidence of all published mutations) and USP48 (3.3% vs. 13.3% incidence) hotspot regions. A novel USP8 variant was identified in a CD patient, and in vitro functional studies in AtT-20 cells suggested that this somatic variant might be clinically relevant in ACTH-secreting tumor pathogenesis, expanding the characterization of USP8 functional domains.


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