Omics A Journal of Integrative Biology最新文献

Right open reading frame kinase 1 (RIOK1) is an atypical kinase involved in ribosome biogenesis, cell cycle progression, and chromosome organization. Its overexpression is linked to tumor progression, metastasis, and chemoresistance, while its absence alters protein phosphorylation across various biological processes. Although the oncogenic role of RIOK1 is recognized, its phospho-regulatory network and the functional relevance of its phosphorylation sites remain unknown. Here, we present the first large-scale phosphoproteomic analysis of RIOK1. Through a systematic assembly of 671 mass spectrometry-based datasets and 157 datasets that quantified RIOK1 phosphopeptides in different experimental conditions, we compiled 13 RIOK1 phosphorylation sites. Notably, phosphorylation at S21 and S22 was predominant, observed in 83% of phosphoproteomics datasets, highlighting their functional significance, and these sites may have a role in RIOK1's interaction with the protein arginine methyltransferase 5 complex. We identified co-differentially regulated phosphorylation events in potential upstream kinases and experimentally validated interactors, providing insights into RIOK1's broader signaling context. The phosphorylation sites in five potential upstream kinases (eukaryotic translation initiation factor 2 alpha kinase 4, ataxia telangiectasia mutated protein kinase, B-Raf proto-oncogene, mitogen-activated protein kinase kinase kinase 3, and polo-like kinase 1) co-differentially regulated with RIOK1 were identified, which regulate their activity in concert with RIOK1 in cancers. Together, this study represents the first comprehensive map to date of RIOK1 phosphorylation and its regulatory associations, highlighting its potential as a therapeutic target in cancers.

Cancer signaling networks play key roles in cancer pathogenesis and drug discovery. The RAS/RAF/MAPK pathway has a crucial role in cell biology and cancer progression, with Raf-1 proto-oncogene, serine/threonine kinase (RAF1) serving as a key regulatory protein in this pathway. This study presents a comprehensive analysis of site-specific phosphorylation of RAF1 and its potential implications in cancer development and therapeutics. Through comprehensive analysis of human cellular phosphoproteomic datasets (769 qualitatively profiled and 196 quantitatively differentially expressed), we identified 63 phosphorylation sites on RAF1. Among these, 29 sites demonstrated distinct regulatory effects in various contexts, including cancer, infections, and signaling-related studies. Notably, our analysis revealed that the most prevalent phosphorylation sites, S259, S621, S642, S296, S301, and S43 primarily regulate kinase-independent RAF1 signaling. This observation suggests a complex interplay between phosphorylation events and RAF1 function, beyond its canonical kinase activity. By elucidating these regulatory mechanisms, our study provides valuable insights into the intricate regulation of RAF1 and its potential impact on cancer-related signaling pathways. These findings not only advance the current understanding of RAF1 regulation but also open new possibilities for the development of targeted therapeutic interventions for cancer treatment. Further investigation of these phosphorylation sites and their functional consequences may lead to novel strategies for cancer treatment innovation by modulating RAF1 activity in cancer cells.

Hepatitis C virus (HCV) is a major global health burden affecting millions worldwide. A deeper understanding of and theories on the mechanisms of HCV replication and pathogenesis would bode well for diagnostics and therapeutics innovation. For example, HCV is known to modulate the host genes (e.g., human hepatocytes) for its efficient viral replication. These host genes are, therefore, among the major targets for treatment of HCV infection. We report here a systematic computational study that involved biocuration of published biomedical literature and data and subsequent network analyses to identify the potential microRNA-based therapeutics targeting HCV replication. We identified 539 HCV induced unidirectionally differential regulated miRNAs and assembled 115 genes that are positively/negatively associated with HCV replication. Furthermore, interaction networks by viral proteins were constructed to reveal the regulation of these microRNA (miRNA)-modulated genes. We found hsa-miR-191-5p and choline kinase alpha (CHKA) as a significant microRNA-gene pair with relevance in glycerophospholipid metabolism, as validated by microarray expression profiles with temporal datasets. Altogether, these results provide comprehensive outline of the emerging data and hypotheses on the complex interplay between HCV and the host cells in modulating cellular miRNAs for viral proliferation. Our findings pave the way for the hypotheses that the induction of hsa-miR-191-5p or its delivery into hepatocytes or the inhibition of CHKA activity could be a potential therapeutic strategy to combat HCV-associated pathologies in the future.

Acute myeloid leukemia (AML) is a heterogeneous malignancy with diverse genetic mutations and oncogenic pathways influencing treatment response. Despite therapeutic advances, relapse and resistance remain persistent issues. This study integrates genomic and transcriptomic profiling to identify biomarkers of high-risk AML, informing personalized medicine strategies. Nonnegative matrix factorization was applied to RNA sequencing data from the BeatAML cohort (N = 462) for patient subtyping, with survival analysis using the Kaplan-Meier method. Immune profiling via xCell and Gene Set Variation Analysis assessed the tumor microenvironment, with findings validated in the Cancer Genome Atlas AML cohort (N = 173). Using a random forest machine learning model, we developed a 20-gene signature identifying a high-risk subgroup comprising approximately 20% of patients with AML. The high-risk AML subtype was enriched for recurrent FLT3, NPM1, and DNMT3A mutations, activation of PI3K/AKT/mTOR, and complement pathways. Immune profiling revealed an immunosuppressive microenvironment with increased M2 macrophages and mesenchymal stem cells. The 20-gene signature predicted high-risk AML with high accuracy (area under the curve = 0.995, F1 = 0.89). AML cell lines representing high- and low-risk phenotypes identified using the 20-gene signature were tested for drug sensitivity, including the standard-of-care cytarabine, and two targeted therapies, the PI3K inhibitor LY294002 and the MAPK inhibitor selumetinib, selected based on enriched pathways in high-risk AML. High-risk AML cell lines exhibited reduced cytarabine sensitivity but greater responsiveness to PI3K and MAPK/ERK inhibitors, consistent with pathway enrichment results. These findings support molecular stratification and predictive signatures as tools to guide therapy in high-risk AML. Further clinical validation is warranted.

Ferroptosis, an iron-dependent form of oxidative cell death, plays a critical role in cancer progression and immune regulation. However, the functional connections of ferroptosis with specific immune cell types remain poorly defined, limiting the future possibilities to harness ferroptosis for cancer biology, diagnosis, and treatment. To address this knowledge gap, we conducted an integrated transcriptomic analysis to investigate ferroptosis-related immune dynamics in gastric cancer (GC). We utilized GC datasets from The Cancer Genome Atlas-stomach adenocarcinoma (n = 412) and the GSE66229 (n = 300) that were clustered into three GC immune subtypes based on single-sample Gene Set Enrichment Analysis scores of 29 immune gene sets. Bulk RNA-seq analysis revealed that the immune-inflamed subtype (HIS) of tumor samples in both GC datasets exhibited the highest ferroptosis enrichment and showed a positive correlation with activated mast cells and neutrophils. Given the regulatory role of mast cells in the tumor microenvironment (TME), particularly in recruiting neutrophils, we further examined their link to ferroptosis. In a fibroblast-mast cell coculture RNA-seq data (GSE223179), fibroblasts exhibited increased ferroptosis enrichment, supporting a mast cell-mediated influence. Single-cell RNA-seq data confirmed stronger interactions between mast cells and fibroblasts in GC compared to normal tissues. Specifically, they revealed a positive correlation between mast cell activity and ferroptosis enrichment in tumor-associated fibroblasts. In conclusion, these findings suggest that mast cells may promote ferroptosis in the TME through paracrine signaling, possibly via annexin and cyclophilin A. By uncovering this novel pathophysiological axis, our study reveals a previously unrecognized role of mast cells in regulating ferroptosis within the TME. The findings call for translational and experimental medical research and have potential implications for innovation toward GC diagnostics and therapeutics.

Conventional pharmacological interventions for erectile dysfunction (ED) primarily rely on the phosphodiesterase-5 (PDE5) inhibitors such as sildenafil, tadalafil, vardenafil, and avanafil that have side effects despite their therapeutic effects. PDE5 is the primary cyclic guanosine monophosphate-degrading enzyme located in the smooth muscles of the corpus cavernosum in the penile tissue that helps in relieving erection. Natural products and phytochemicals are viable sources of molecular leads for drug discovery and development and, thus, offer prospects for innovation in ED treatment. This in silico study reports the screening of phytochemicals from the plant Tribulus terrestris with an eye to identify molecular candidates that inhibit PDE5. Natural products-based compounds that selectively target PDE5 are poised to be useful in clinical management of ED, and potentially with lesser side effects. The following top three phytochemicals identified from T. terrestris showed higher negative binding affinities for the PDE5 enzyme: diosgenin,dehydro (-11.1 kcal/mol), ruscogenin (-11.1 kcal/mol), and hecogenin (-10.3 kcal/mol) compared with the control drug sildenafil (-8.8 kcal/mol). Hydrogen bonds and Van der Waals interactions were the predominant forces influencing the interactions formed in the protein-ligand complexes. The ΔG_bind binding free energies for these top three phytochemicals, diosgenin,dehydro, ruscogenin, and hecogenin, were -19.99 ± 5.99 kcal/mol, -9.05 ± 5.16 kcal/mol, and -14.11 ± 5.33 kcal/mol, respectively. Importantly, diosgenin,dehydro, a saponin obtained from T. terrestris, was identified as a particularly promising candidate for PDE5 inhibition by virtue of its higher negative binding affinity and, therefore, displaying a potential in drug discovery and development for ED. In addition, in silico pharmacokinetic analysis and toxicity assessments support the prospects of these T. terrestris-derived phytochemicals for future in vitro and in vivo research for innovation in ED therapeutics.

Head and neck squamous cell carcinoma (HNSCC) displays significant molecular heterogeneity, which hinders effective and safe treatments and clinical outcomes. This predicament also points to the need for an individually tailored personalized/precision medicine approach in HNSCC that includes the oral, hypopharyngeal, nasopharyngeal, and laryngeal subtypes. This study, with the overarching aim of personalized/precision medicine, attempted to identify (1) a molecular target shared by the HNSCC subtypes and (2) screen for potential anticancer drugs for repurposing that may work across the HNSCC subtypes. The National Center for Biotechnology Information-Gene Expression Omnibus database was used to select the datasets (GSE127165, GSE2379, GSE37991, and GSE12452) for the analyses of differentially expressed genes in HNSCC subtypes. Our transcriptome analyses of the HNSCC subtypes revealed 305 upregulated genes. Subsequently, protein network construction with 305 genes showed three closely interconnected high-risk HNSCC prognostic clusters. Importantly, COL1A1 was identified as the pivotal target regulating the pathogenic cluster protein implicated in cancer pathways. Molecular docking with 1040 anticancer drugs identified bleomycin as a potential candidate, exhibiting a binding affinity of -12.425 kcal/mol and a favorable binding free energy of -92.05 kcal/mol. The dynamic simulations confirmed the stability of the system, with stable interactions over 200 ns. Quantum calculations provided insights into bleomycin's chemical and electronic properties, revealing crucial interactions with COL1A1. In conclusion, our study proposes COL1A1 as a promising potential therapeutic target among HNSCC subtypes, with bleomycin demonstrating notable repurposing potential for HNSCC.

Phytophthora meadii is a polyphagous oomycete causing fatal diseases in economically important cash crops such as rubber, arecanut, cardamom, and other crops and plants of economic significance. Although information on the proteogenomic and proteomic analysis is available for several Phytophthora species, no information on the proteome repertoire of P. meadii is available. In the present study, a gel-free protein annotation was performed using liquid chromatography with tandem mass spectrometry analysis of the P. meadii hyphae, followed by bioinformatics analysis. The results were compared with a global Phytophthora proteome database-based search and an in-house P. meadii genome database, along with RefSeq proteome databases of other selected species of Phytophthora. A total of 7725 and 3979 proteins were exclusively matched with global and in-house databases, respectively. Basic Local Alignment Search Tool analysis showed 209 unique peptide sequences belonging to 85 proteins of P. meadii. Gene Ontology-based functional analysis of the P. meadii mycelial proteome categorized the proteins based on their role in cellular components, molecular functions, and biological processes. Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein network analysis further revealed the role of these proteins in growth and development functions. In addition, proteins potentially involved in virulence, infections in the host system, and several signaling mechanisms were deduced. The current study is the first report on the P. meadii mycelial proteins under optimum growth conditions. These omics data also have socioeconomic implications since Phytophthora causes disease in a wide range of economically noteworthy crops and forest ecosystems.