PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40)

PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery

PandaOmics is a cloud-based software platform that applies artificial intelligence and bioinformatics techniques to multimodal omics and biomedical text data for therapeutic target and biomarker discovery. PandaOmics generates novel and repurposed therapeutic target and biomarker hypotheses with the desired properties and is available through licensing or collaboration. Targets and biomarkers generated by the platform were previously validated in both in vitro and in vivo studies. PandaOmics is a core component of Insilico Medicine's Pharma.ai drug discovery suite, which also includes Chemistry42 for the de novo generation of novel small molecules, and inClinico─a data-driven multimodal platform that forecasts a clinical trial's probability of successful transition from phase 2 to phase 3. In this paper, we demonstrate how the PandaOmics platform can efficiently identify novel molecular targets and biomarkers for various diseases.

Novel RICTOR amplification harbouring entities: FISH validation of RICTOR amplification in tumour tissue after next-generation sequencing

Alterations in mTOR signalling molecules, including RICTOR amplification, have been previously described in many cancers, particularly associated with poor prognosis. In this study, RICTOR copy number variation (CNV) results of diagnostic next-generation sequencing (NGS) were analysed in 420 various human malignant tissues. RICTOR amplification was tested by Droplet Digital PCR (ddPCR) and validated using the "gold standard" fluorescence in situ hybridisation (FISH). Additionally, the consequences of Rictor protein expression were also studied by immunohistochemistry. RICTOR amplification was presumed in 37 cases with CNV ≥ 3 by NGS, among these, 16 cases (16/420; 3.8%) could be validated by FISH, however, ddPCR confirmed only 11 RICTOR-amplified cases with lower sensitivity. Based on these, neither NGS nor ddPCR could replace traditional FISH in proof of RICTOR amplification. However, NGS could be beneficial to highlight potential RICTOR-amplified cases. The obtained results of the 14 different tumour types with FISH-validated RICTOR amplification demonstrate the importance of RICTOR amplification in a broad spectrum of tumours. The newly described RICTOR-amplified entities could initiate further collaborative studies with larger cohorts to analyse the prevalence of RICTOR amplification in rare diseases. Finally, our and further work could help to improve and expand future therapeutic opportunities for mTOR-targeted therapies.

Chemistry42: An AI-Driven Platform for Molecular Design and Optimization

Chemistry42 is a software platform for de novo small molecule design and optimization that integrates Artificial Intelligence (AI) techniques with computational and medicinal chemistry methodologies. Chemistry42 efficiently generates novel molecular structures with optimized properties validated in both in vitro and in vivo studies and is available through licensing or collaboration. Chemistry42 is the core component of Insilico Medicine's Pharma.ai drug discovery suite. Pharma.ai also includes PandaOmics for target discovery and multiomics data analysis, and inClinico─a data-driven multimodal forecast of a clinical trial's probability of success (PoS). In this paper, we demonstrate how the platform can be used to efficiently find novel molecular structures against DDR1 and CDK20.

Targeting PRAS40: a novel therapeutic strategy for human diseases

Proline-rich Akt substrate of 40 kD (PRAS40) is not only the substrate of protein kinase B (PKB/Akt), but also the binding protein of 14-3-3 protein. PRAS40 is expressed in a variety of tissues in vivo and has multiple phosphorylation sites, which its activity is closely related to phosphorylation. Studies have shown that PRAS40 is involved in regulating cell growth, cell apoptosis, oxidative stress, autophagy and angiogenesis, as well as various of signalling pathways such as mammalian target of mammalian target rapamycin (mTOR), protein kinase B (PKB/Akt), nuclear factor kappa-B(NF-κB), proto-oncogene serine/threonine-protein kinase PIM-1(PIM1) and pyruvate kinase M2 (PKM2). The interactive roles between PRAS40 and these signal proteins were analysed by bioinformatics in this paper. Moreover, it is of great necessity for analyse the important roles of PRAS40 in some human diseases including cardiovascular disease, ischaemia-reperfusion injury, neurodegenerative disease, cancer, diabetes and other metabolic diseases. Finally, the effects of miRNA on the regulation of PRAS40 function and the occurrence and development of PRAS40-related diseases are also discussed. Overall, PRAS40 is expected to be a drug target and provide a new treatment strategy for human diseases.

The Molecular Landscape and Biological Alterations Induced by PRAS40-Knockout in Head and Neck Squamous Cell Carcinoma

PRAS40 (Prolin-rich Akt substrate of 40 kDa) is a critical protein, which directly connects PI3K/Akt and mTORC1 pathway. It plays an indispensable role in the development of various diseases. However, the relationship between PRAS40 and head and neck squamous cell carcinoma (HNSCC) remains unclear. Here, our study indicated that high expression of PRAS40 mRNA is a favorable prognostic factor in HNSCC patients by analyzing 498 clinical and mRNA data. Moreover, we confirmed that CRISPR/Cas9 induced PRAS40-knockout would promote colony formation, cell migration, and invasion in several HNSCC cell lines. RNA-seq was employed to investigate the further possible mechanisms involving the above regulations by PRAS40 in HNSCC cells. The molecular landscape contributed by 253 differentially expressed mRNA after PRAS40-knockout was enriched in TGF-beta, PI3K-Akt, P53, mTOR, NF-κB signaling pathway. Partial molecular alternations within these pathways were validated by qPCR or Western blotting. Besides, we found that high expression of PRAS40 in HNSC patients would present more CD8⁺ T and T follicular helper cells, but less Th17 cells than the patients with low expression of PRAS40. The altered molecular pathways and tumor-infiltrating immune cells might associate with the mechanism of PRAS40 being a suppressor in HNSCC cells, which would provide a potential prognostic predictor and therapeutic target in HNSCC patients.

High PRAS40 mRNA expression and its role in prognosis of clear cell renal cell carcinoma

Background

Clear cell renal cell carcinoma (ccRCC) is one of the most common type of kidney malignancy. The proline-rich Akt substrate of 40 kDa (PRAS40) plays an important role in tumor growth. The present study aimed to analysis the prognostic value of PRAS40 mRNA expression in ccRCC.

Methods

We analyzed the PRAS40 mRNA expression using the data from TCGA-KIRC cohort. A receiver operating characteristic (ROC) curve was performed to assessed the diagnostic value of PRAS40 mRNA expression in ccRCC. Chi-square test was used to analyzed the correlation between clinical characteristics and PRAS40 mRNA expression. Kaplan-Meier analysis and Cox analysis were performed to determine the prognostic value of PRAS40 mRNA expression in ccRCC. Gene set enrichment analysis (GSEA) was conducted using TCGA database.

Results

Our results revealed that PRAS40 mRNA expression was higher in ccRCC tissues than in normal tissues. PRAS40 presented a moderate diagnostic value in ccRCC. High PRAS40 mRNA expression was correlated with histological grade, clinical stage, T classification, distant metastasis and vital status of ccRCC. High PRAS40 mRNA expression was associated with poor overall survival. Furthermore, Multivariate analysis revealed that PRAS40 was an independent risk factor for ccRCC patients. Myc targets, DNA repair, oxidative phosphorylation, glycolysis, adipogenesis, p53 pathway, reactive oxygen species pathway, myogenesis were differentially enriched in the phenotype that positively correlated with PRAS40.

Conclusions

In conclusion, our results suggest that PRAS40 was a promising diagnostic and prognostic biomarker for ccRCC.

PRAS40 Phosphorylation Correlates with Insulin-Like Growth Factor-1 Receptor-Induced Resistance to Epidermal Growth Factor Receptor Inhibition in Head and Neck Cancer Cells

EGFR inhibitors have shown poor efficacy in head and neck squamous cell carcinoma (HNSCC) with demonstrated involvement of the insulin-like growth factor-1 receptor (IGF1R) in resistance to EGFR inhibition. IGF1R activates the PI3K-Akt pathway, which phosphorylates proline-rich Akt substrate of 40 kDa (PRAS40) to cease mTOR inhibition resulting in increased mTOR signaling. Proliferation assays separated six HNSCC cell lines into two groups: sensitive to EGFR inhibition or resistant; all sensitive cell lines demonstrated reduced sensitivity to EGFR inhibition upon IGF1R activation. Reverse phase protein microarray analysis and immunoblot identified a correlation between increased PRAS40 phosphorylation and IGFR-mediated resistance to EGFR inhibition. In sensitive cell lines, PRAS40 phosphorylation decreased 44%-80% with EGFR inhibition and was restored to 98%-196% of control by IGF1R activation, while phosphorylation was unaffected in resistant cell lines. Possible involvement of mTOR in this resistance mechanism was demonstrated through a similar pattern of p70S6K phosphorylation. However, addition of temsirolimus, an mTORC1 inhibitor, was insufficient to overcome IGF1R-mediated resistance and suggested an alternative mechanism. Forkhead box O3a (FOXO3a), which has been reported to complex with PRAS40 in the cytoplasm, demonstrated a 6-fold increase in nuclear to cytoplasmic ratio upon EGFR inhibition that was eliminated with concurrent IGF1R activation. Transcription of FOXO3a-regulated TRAIL and PTEN-induced putative kinase-1 (PINK1) was increased with EGFR inhibition in sensitive cell lines; this effect was diminished with IGF1R stimulation. IMPLICATIONS: These data suggest PRAS40 may play an important role in IGF1R-based therapeutic resistance to EGFR inhibition, and this likely occurs via inhibition of FOXO3a-mediated proapoptotic gene transcription.

TAB3 upregulates PIM1 expression by directly activating the TAK1-STAT3 complex to promote colorectal cancer growth

Transforming growth factor-β-activated kinase 1 (TAK1)-binding protein 3 (TAB3) and the proviral integration site for Moloney murine leukaemia virus 1 (PIM1) are implicated in cancer development. In this study, we investigated the relationship between TAB3 and PIM1 in colorectal cancer (CRC) and determined the potential role and molecular mechanism of TAB3 in PIM1-mediated CRC growth. We found that TAB3 and PIM1 expression levels were positively correlated in CRC tissues. The knockdown of TAB3 significantly decreased PIM1 expression and inhibited CRC proliferation in vitro and in vivo. The upregulation of PIM1 rescued the decreased cell proliferation induced by TAB3 knockdown, whereas PIM1 knockdown decreased TAB3-enhanced CRC proliferation. Additionally, TAB3 regulates PIM1 expression through the STAT3 signalling pathway and confirmed a positive correlation between TAB3 and phosphorylated-STAT3 expression in CRC tissues. Patients with high expression of TAB3 and phosphorylated-STAT3 had the worst prognosis. Mechanistically, TAB3 regulates PIM1 expression by promoting STAT3 phosphorylation and activation through the formation of the TAB3-TAK1-STAT3 complex. Overall, a novel CRC regulatory circuit involving the TAB3-TAK1-STAT3 complex and PIM1 was identified, the dysfunction of which may contribute to CRC tumorigenesis.

Iron oxide nanoparticles promote vascular endothelial cells survival from oxidative stress by enhancement of autophagy

Dextran-coated superparamagnetic iron oxide nanoparticles (Dex-SPIONs) are excellent magnetic resonance imaging contrast agents for disease diagnosis and therapy. They can be delivered to target tissues mainly though vascular endothelium cells, which are major targets of oxidative stress. In cardiovascular cells, autophagy serves primarily on a pro-survival approach that protects the cells from oxidative stress even some autophagy inducers have been developed for adjuvant therapy of cardiovascular disorders. Our study demonstrated that the nanoparticles could be taken up by human umbilical vein endothelial cells (HUVECs) without causing obvious cytotoxicity but triggering autophagy. Furthermore, our results revealed that Dex-SPIONs could enhance HUVECs survival and reverse the reduction of nitric oxide secretion under the condition of H₂O₂ damage. However, these effects could be diminished by the autophagy inhibitor. In particular, we discovered that Dex-SPIONs evoked autophagy in HUVECs by reducing the phosphorylation of PRAS40, an upstream regulator of autophagy initiation. These results suggested that Dex-SPIONs functions as an autophagic-related antioxidant in HUVECs which may be utilized as an adjuvant therapy to cardiovascular disease associated with oxidative stress.

Gallbladder cancer integrated bioinformatics analysis of protein profile data

AIM

Identifying the critical genes that differentiate gall bladder cancer from a normal gall bladder and the related biological terms was the aim of this study.

BACKGROUND

The molecular mechanism underlying gall bladder cancer (GBC) trigger and development still requires investigations. Potential therapeutic biomarkers can be identified through protein-protein interaction network prediction of proteome as a complementary study.

METHODS

Here, a literature review of proteomics studies of gall bladder cancer from 2010 to 2019 was undertaken to screen differentially expressed proteins in this cancer. A network of 27 differentially expressed proteins (DEPs) via Cytoscape 3.7.1 and its plug-ins was constructed and analyzed.

RESULTS

Ten proteins were introduced as hub-bottlenecks among which four were from DEPs. The gene ontology analysis also indicated that positive regulation of multi-organism process and regulation of response to biotic stimulus are the most disrupted biological processes of GBC considering their relationships with the DEPs.

CONCLUSION

ACTG, ALB, GGH, and DYNC1H1, and relative biological terms were introduced as drug targets and possible diagnostic biomarkers.