Machine Learning Approaches for Predicting Virus-Human Protein-Protein Interactions: An Evaluation of Retroviral Interaction Networks DOI Open Access
Omid Mahmoudi,

Somayye Taghvaei,

Shirin Salehi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Abstract Virus-human protein-protein interactions (VHPPI) are key to understanding how viruses manipulate host cellular functions. This study constructed a retroviral-human PPI network by integrating multiple public databases, resulting in 1,387 between 29 retroviral and 1,026 human genes. Using minimal sequence similarity, we generated pseudo-negative dataset for model reliability. Five machine learning models—Logistic Regression (LR), Support Vector Machine (SVM), Naive Bayes (NB), Decision Tree (DT), Random Forest (RF)—were evaluated using accuracy, sensitivity, specificity, PPV, NPV. LR KNN models demonstrated the strongest predictive performance, with sensitivities up 77% specificities of 52%. Feature importance analysis identified GC content semantic similarity as influential predictors. Models trained on selected features showed enhanced accuracy reduced complexity. Our approach highlights potential computational VHPPI predictions, offering valuable insights into viral-host interaction networks guiding therapeutic target identification. Significance addresses crucial gap antiviral research focusing prediction virus-host retroviruses, which linked serious diseases, including certain cancers autoimmune disorders. By leveraging models, essential host-pathogen that underlie survival pathogenesis. These were optimized predict accurately, complex mechanisms retroviruses use processes. viral proteins, such ENV_HV1H2 CD4, play pivotal roles infection persistence. Targeting these specific can potentially disrupt lifecycle while minimizing toxicity cells. thus opens avenues development selective strategies, contributing more effective targeted interventions fewer side effects, marking significant step forward virology drug discovery.

Language: Английский

Interactions between oxidative stress and senescence in cancer: Mechanisms, therapeutic implications, and future perspectives DOI Creative Commons
Dengxiong Li, Qingxin Yu,

Ruicheng Wu

et al.

Redox Biology, Journal Year: 2024, Volume and Issue: 73, P. 103208 - 103208

Published: May 24, 2024

Recently, numerous studies have reported the interaction between senescence and oxidative stress in cancer. However, there is a lack of comprehensive understanding precise mechanisms involved.

Language: Английский

Citations

25
Metabolite signature of human malignant thyroid tissue: A systematic review and meta‐analysis DOI Creative Commons
S. Adeleh Razavi, Babak Khorsand, Pouya Salehipour

et al.

Cancer Medicine, Journal Year: 2024, Volume and Issue: 13(8)

Published: April 1, 2024

Abstract Background Thyroid cancer (TC) is the predominant malignancy within endocrine system. However, standard method for TC diagnosis lacks capability to identify pathological condition of all thyroid lesions. The metabolomics approach has potential manage this problem by identifying differential metabolites. Aims This study conducted a systematic review and meta‐analysis NMR‐based studies in order significant altered metabolites associated with TC. Methods A search published literature any language three databases including Embase, PubMed, Scopus was conducted. Out 353 primary articles, 12 met criteria inclusion review. Among these, five reports belonging articles were eligible meta‐analysis. correlation coefficient orthogonal partial least squares discriminant analysis, popular model multivariate statistical analysis metabolomic data, chosen based on fact that they had been found at studies. Results In total, 49 compounds identified, 40 which increased lesions compared normal samples included lactate, taurine, alanine, glutamic acid, glutamine, leucine, lysine, phenylalanine, serine, tyrosine, valine, choline, glycine, isoleucine. Lipids decreased Lactate alanine malignant versus benign lesions, while, myo‐inositol, scyllo‐inositol, citrate, phosphocholine be decreased. yielded results citrate specimens. Discussion study, we provided concise summary studies, making it easier future researchers compare their prior findings. Conclusion It appears field will experience notable advancement, leading discovery trustworthy diagnostic prognostic biomarkers.

Language: Английский

Citations

11
The E3 ligase TRIM22 functions as a tumor suppressor in breast cancer by targeting CCS for proteasomal degradation to inhibit STAT3 signaling DOI Creative Commons
Yunkai Yang,

Xinhui Hao,

Jingyao Zhang

et al.

Cancer Letters, Journal Year: 2024, Volume and Issue: 600, P. 217157 - 217157

Published: Aug. 8, 2024

Deregulation of E3 ubiquitin ligases drives the proliferation and metastasis various cancers; however, underlying mechanisms remain unknown. This study aimed to investigate role tripartite motif-containing 22 (TRIM22), a poorly investigated ligase in TRIM family, as tumor suppressor breast cancer. High expression TRIM22 cancer correlated with better prognosis. Functional experiments demonstrated that significantly inhibited invasion cells. Label-free proteomics biochemical analyses revealed copper chaperone for superoxide dismutase (CCS), an oncoprotein is upregulated promotes growth cells, was target degradation via K27-linked ubiquitination. Notably, ability coiled-coil domain-defective mutants induce CCS ubiquitination diminished, lysine 76 serving site. Moreover, TRIM22-mediated inhibition cells restored by ectopic expression. RNA-sequencing using Gene Set Enrichment Analysis involved JAK-STAT signaling pathway. overexpression also improved reactive oxygen species levels STAT3 phosphorylation, which or N-acetyl-l-cysteine treatment. Chromatin immunoprecipitation-quantitative polymerase chain reaction results showed decreased enrichment phosphorylated FN1, VIM JARID2 promoters. Clinically, low high survival rates patients upregulation associated prognosis who received classical therapy. downregulated many types, including colon, kidney, lung, prostate cancers. To best our knowledge, first reported inhibits through degradation. potential prognostic biomarker

Language: Английский

Citations

5
Probing the interaction of hesperidin showing antiproliferative activity in colorectal cancer cells and human hemoglobin DOI

Ruiming Deng,

Yanfang Liu, Xiangyu Wu

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 281, P. 136078 - 136078

Published: Sept. 26, 2024

Language: Английский

Citations

4
SHP2-mediated ROS activation induces chondrocyte paraptosis in osteoarthritis and is attenuated by low-intensity pulsed ultrasound DOI Creative Commons
Wenjie Hou,

Xingru Shang,

Xiaoxia Hao

et al.

Journal of Orthopaedic Translation, Journal Year: 2025, Volume and Issue: 52, P. 233 - 248

Published: April 25, 2025

Language: Английский

Citations

0
Novel Strategies for Tumor Treatment: Harnessing ROS-Inducing Active Ingredients from Traditional Chinese Medicine Through Multifunctional Nanoformulations DOI Creative Commons
Zhengguang Zhang, M. Y. Li,

Xiaolong Zhang

et al.

International Journal of Nanomedicine, Journal Year: 2024, Volume and Issue: Volume 19, P. 9659 - 9688

Published: Sept. 1, 2024

Reactive oxygen species (ROS) encompass a diverse group of chemically reactive molecules or ions distinguished by their substantial oxidative potential. Empirical studies have shown that the targeted administration high toxic concentrations ROS can effectively induce tumor cell death in various types. Numerous bioactive ingredients derived from traditional Chinese medicine (TCM), recognized for ROS-inducing properties, demonstrated significant anti-tumor activity. Nonetheless, clinical application has been hindered challenges such as low solubility, limited bioavailability, and poor selectivity. Multifunctional nanoformulations possess potential to overcome these enhance anticancer efficacy active compounds. Through extensive searches academic databases thorough review screening relevant literature, this study aims systematically summarize generalize multiple TCM generation, along with multifunctional nanoformulations, perspectives. The objective is provide new insights references fundamental cancer research treatments. Furthermore, we acknowledge although numerous potentials, potentially offering novel strategies therapy, underlying mechanisms require further comprehensive investigation.

Language: Английский

Citations

3
Paraptosis—A Distinct Pathway to Cell Death DOI Open Access

C Kunst,

Deniz Tümen,

Martha Ernst

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(21), P. 11478 - 11478

Published: Oct. 25, 2024

Cell death is a critical biological process necessary for development, tissue maintenance, and defense against diseases. To date, more than 20 forms of cell have been identified, each defined by unique molecular pathways. Understanding these different essential investigating the pathogenesis diseases such as cancer, neurodegenerative disorders, autoimmune conditions developing appropriate therapies. Paraptosis distinct form regulated characterized cytoplasmic vacuolation dilatation cellular organelles like mitochondria endoplasmic reticulum (ER). It several signaling pathways, instance, those associated with ER stress, calcium overload, oxidative specific cascades insulin-like growth factor I receptor (IGF-IR) its downstream pathways comprising mitogen-activated protein kinases (MAPKs) Jun N-terminal kinase (JNK). has observed in diverse contexts, including development stress responses neuronal, retinal, endothelial, muscle cells. The induction paraptosis increasingly important anticancer therapy, it targets non-apoptotic tumor cells, which can be utilized to induce death. This approach enhances treatment efficacy addresses drug resistance, particularly cases where cancer cells are resistant apoptosis. Combining paraptosis-inducing agents traditional therapies holds promise enhancing overcoming suggesting valuable strategy therapy.

Language: Английский

Citations

3
Soloxolone para-methylanilide effectively suppresses aggressive phenotype of glioblastoma cells including TGF-β1-induced glial-mesenchymal transition in vitro and inhibits growth of U87 glioblastoma xenografts in mice DOI Creative Commons
Kirill V. Odarenko,

Aleksandra V. Sen’kova,

Oksana V. Salomatina

et al.

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 15

Published: July 29, 2024

Soloxolone amides are semisynthetic triterpenoids that can cross the blood-brain barrier and inhibit glioblastoma growth both in vitro vivo . Here we investigate impact of these compounds on processes associated with invasiveness therapy resistance. Screening soloxolone against cells revealed ability compound 7 (soloxolone para -methylanilide) to transforming factor-beta 1 (TGF-β1)-induced glial-mesenchymal transition Compound inhibited morphological changes, wound healing, transwell migration, expression mesenchymal markers (N-cadherin, fibronectin, Slug) TGF-β1-induced U87 U118 cells, while restoring their adhesiveness. Confocal microscopy molecular docking showed reduced SMAD2/3 nuclear translocation probably by direct interaction TGF-β type I II receptors (TβRI/II). In addition, suppressed stemness as evidenced inhibition colony forming ability, spheroid growth, aldehyde dehydrogenase (ALDH) activity. Furthermore, exhibited a synergistic effect temozolomide (TMZ) cell viability. Using N-acetyl-L-cysteine (NAC) flow cytometry analysis Annexin V-FITC-, propidium iodide-, DCFDA-stained was found synergize cytotoxicity TMZ inducing ROS-dependent apoptosis. Further studies , alone or combination TMZ, effectively xenograft tumors mice. Thus, demonstrated promising potential component for glioblastoma, reducing its increasing sensitivity chemotherapy.

Language: Английский

Citations

2
Bunium persicum Seeds Extract in Combination with Vincristine Mediates Apoptosis in MCF-7 Cells through Regulation of Involved Genes and Proteins Expression DOI

Mohammad Rasoul Samandari-Bahraseman,

Ahmad Ismaili, Saeed Esmaeili‐Mahani

et al.

Anti-Cancer Agents in Medicinal Chemistry, Journal Year: 2023, Volume and Issue: 24(3), P. 213 - 223

Published: Dec. 1, 2023

seeds, a member of the Apiaceae family, have historically been consumed as part Iranian diet.

Language: Английский

Citations

5
Froriepia subpinnata Leaf Extract-Induced Apoptosis in the MCF-7 Breast Cancer Cell Line by Increasing Intracellular Oxidative Stress DOI Creative Commons

Hanieh Rostamabadi,

Mohammas Rasoul Samandari Bahraseman,

Keyvan Esmaeilzadeh‐Salestani

et al.

Deleted Journal, Journal Year: 2023, Volume and Issue: In Press(In Press)

Published: Oct. 14, 2023

Background: Froriepia subpinnata (F. subpinnata) is one of the plants used in diet Iranian people. Previous studies have investigated antioxidant and antibacterial effects this plant extract, but no study has been conducted on its anticancer properties. Objectives: In study, we effect F. extract MCF-7 breast cancer cells. Methods: The inhibitory leaf was determined growth cells by MTT test. ROS (reactive oxygen species) test to investigate impact intracellular oxidative stress. Flow cytometry real-time PCR tests were apoptosis-related molecular processes. GC-MS analysis performed determine most abundant components. Results: showed that phytol, mono-ethylhexyl phthalate (MEHP), cinnamaldehyde, neophytadiene constituted 60% extracted content. assay demonstrated caused 50% lethality at a 400 μg/mL dose MCF7 low doses decreased level for 24 hours MCF-7, increasing concentration, levels increased. At IC50 (inhibitory concentration (IC) associated with impact), increased 3.5 times compared control group. Examining N-acetyl cysteine (NAC) agent could prevent lethal eliminate increase results specifically induced apoptosis through internal pathway cell line. Conclusions: can be considered further studies.

Language: Английский

Citations

4