NEK2 is a potential pan-cancer biomarker and immunotherapy target DOI Creative Commons
Lanyue Zhang, Yang Li,

Juexiao Deng

et al.

Discover Oncology, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 7, 2024

NEK2 is a member of the NEKs family and plays an important role in cell mitosis. Increasing evidence suggests that associated with development multiple tumors, but systematic studies cancer are still lacking. Therefore, we evaluated prognostic value 33 cancers to elucidate potential function pan-cancers. We investigated pan-cancers utilizing The Cancer Genome Atlas (TCGA) Genotype-Tissue Expression (GTEx) database. Additionally, analyzed association between gene expression across various cancers, protein expression, tumor microenvironment (TME), drug sensitivity using several software web platforms.The oncogenic was initially explored bioinformatics methods. Furthermore, conducted vitro experiments preliminarily validate cervical cancer. overexpressed almost all mutation poorer prognosis. In addition, correlation immune features such as infiltration, checkpoint genes, mutational burden (TMB), Microsatellite instability(MSI) etc. suggest could potentially be applied immunotherapy tumors. may pan-cancer biomarker immunotherapeutic target for improving efficacy therapy.

Language: Английский

Potential anti-liver cancer targets and mechanisms of kaempferitrin based on network pharmacology, molecular docking and experimental verification DOI
Siyu Zhou, Huidong Zhang, Jiao Li

et al.

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 178, P. 108693 - 108693

Published: June 3, 2024

Language: Английский

Citations

5
SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation DOI Creative Commons
Yanlin Li, Fengcheng Li,

Zixin Duan

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D595 - D603

Published: Oct. 16, 2024

Abstract Synthetic binding proteins (SBPs) represent a pivotal class of artificially engineered proteins, meticulously crafted to exhibit targeted properties and specific functions. Here, the SYNBIP database, comprehensive resource for SBPs, has been significantly updated. These enhancements include (i) featuring 3D structures 899 SBP–target complexes illustrate epitopes (ii) using SBPs in monomer or complex forms with target their sequence space expanded five times 12 025 by integrating structure-based protein generation framework property prediction tool, (iii) offering detailed information on 78 473 newly identified SBP-like scaffolds from RCSB Protein Data Bank, an additional 16 401 555 ones AlphaFold Structure Database, (iv) database is regularly updated, incorporating 153 new SBPs. Furthermore, structural models all have enhanced through application AlphaFold2, clinical statuses concurrently refreshed. Additionally, design methods employed each SBP are now prominently featured database. In sum, 2.0 designed provide researchers essential data, facilitating innovation research, diagnosis therapy. freely accessible at https://idrblab.org/synbip/.

Language: Английский

Citations

4
Uncovering the role of TREM-1 in celiac disease: In silico insights into the recognition of gluten-derived peptides and inflammatory mechanisms DOI
Amanda de Oliveira Matos, Pedro Henrique dos Santos Dantas, José Rodrigues do Carmo Neto

et al.

Computers in Biology and Medicine, Journal Year: 2025, Volume and Issue: 189, P. 109981 - 109981

Published: March 7, 2025

Language: Английский

Citations

0
Lung Cancer Biomarker Database (LCBD): a comprehensive and curated repository of lung cancer biomarkers DOI Creative Commons
Yinghong Li, Zhuohao Tong,

Yinqi Yang

et al.

BMC Cancer, Journal Year: 2025, Volume and Issue: 25(1)

Published: March 15, 2025

Lung cancer remains a leading cause of cancer-related mortality, primarily because the lack effective diagnostic and therapeutic biomarkers. To address issue fragmented biomarker data across numerous publications, we have developed Cancer Biomarker Database (LCBD, http://lcbd.biomarkerdb.com ). We comprehensively reviewed biomarker-related studies up to June 30, 2023, extracted relevant information. The identified biomarkers were systematically annotated, including genes, proteins, GO terms, KEGG pathways, types, molecular developmental stages, discovery methods, sources, populations, sample sizes. LCBD online platform was integrate lung data, provide search, browsing, download functions for researchers. validate in LCBD, conducted three case comparing models with without data. After deduplication summarization, collected 1,447 unique that annotated. then specifically use diagnosis. validity confirmed using prognostic models, immune infiltration models. provides centralized biomarkers, facilitating early screening personalized treatment. This database is poised become valuable resource research strategies.

Language: Английский

Citations

0
Rapid detection of procalcitonin using dual-color carbon quantum dots as fluorescent probes in FRET assay DOI
Yuxin Tian, Yuwei Du, Chen Zhang

et al.

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, Journal Year: 2025, Volume and Issue: unknown, P. 126207 - 126207

Published: April 1, 2025

Language: Английский

Citations

0
Identification of key mitochondria-related genes and their relevance to the immune system linking Parkinson's disease and primary Sjögren's syndrome through integrated bioinformatics analyses DOI Creative Commons
Yuan Zong, Yi Yang, Jiawen Zhao

et al.

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 175, P. 108511 - 108511

Published: April 23, 2024

Mitochondria are the metabolic hubs of cells, regulating energy production and antigen presentation, which essential for activation, proliferation, function immune cells. Recent evidence indicates that mitochondrial presentation may have an impact on diseases such as Parkinson's disease (PD) autoimmune diseases. However, there is limited knowledge about mechanisms regulate antigens in these In current study, RNA sequencing was performed labial minor salivary gland (LSG) from 25 patients with primary Sjögren's syndrome (pSS) 14 non-pSS aged controls. Additionally, we obtained gene expression omnibus datasets associated PD NCBI Gene Expression Omnibus (GEO) databases. Single-sample Set Enrichment Analysis (ssGSEA), ESTIMATE Spearman correlations were conducted to explore association between related genes system. Furthermore, applied weighted Co-expression Network (WGCNA) identify hub mitochondria-related investigate correlated networks both Single cell transcriptome analysis, immunohistochemical (IHC) staining quantitative real-time PCR (qRT–PCR) used verify activation pathway. Pearson CIBERSORT algorithms employed further reveal correlation pathways infiltration. The analysis revealed presence overlapping DNA damage pSS PD. Reactive oxygen species (ROS), senescence marker p53, inflammatory markers CD45 Bcl-2 found be regionally distributed LSGs patients. WGCNA identified STING pathway central closely IHC staining, qRT-PCR confirmed Subsequent, bioinformatic proportion infiltrating cells STING-high STING-low groups study demonstrated innate adaptive well functional microenvironment pSS. Our uncovered a connects dysfunction pSS, potentially offering valuable insights into therapeutic targets conditions.

Language: Английский

Citations

3
Crosstalk of different cell-death patterns predicts prognosis and drug sensitivity in glioma DOI

Meini Yu,

Diwei Huo,

Kexin Yu

et al.

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 175, P. 108532 - 108532

Published: April 29, 2024

Language: Английский

Citations

3
Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways DOI Creative Commons
Salvatore D’Antona, Danilo Porro, Francesca Gallivanone

et al.

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 174, P. 108346 - 108346

Published: March 26, 2024

Language: Английский

Citations

2
OncoSexome: the landscape of sex-based differences in oncologic diseases DOI Creative Commons
Xinyi Shen, Yintao Zhang, Jiamin Li

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1443 - D1459

Published: Nov. 13, 2024

The NIH policy on sex as biological variable (SABV) emphasized the importance of sex-based differences in precision oncology. Over 50% clinically actionable oncology genes are sex-biased, indicating drug efficacy. Research has identified non-reproductive cancers, highlighting need for comprehensive cancer data. We therefore developed OncoSexome, a multidimensional knowledge base describing (https://idrblab.org/OncoSexome/) across four key topics: antineoplastic drugs and responses (SDR), oncology-related biomarkers (SBM), risk factors (SRF) microbial landscape (SML). SDR covers 2051 anticancer drugs; SBM describes 12 551 sex-differential biomarkers; SRF illustrates 350 sex-dependent factors; SML demonstrates 1386 microbes with abundances associated development. OncoSexome is unique illuminating multifaceted influences cancer, providing both external endogenous contributors to development broadest oncological classes. Given increasing global research interest differences, expected impact future practices significantly.

Language: Английский

Citations

2
FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response DOI Creative Commons
Yuan Zhou, Zhen Chen,

Mengjie Yang

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(3)

Published: March 27, 2024

Ferroptosis is a non-apoptotic, iron-dependent regulatory form of cell death characterized by the accumulation intracellular reactive oxygen species. In recent years, large and growing body literature has investigated ferroptosis. Since ferroptosis associated with various physiological activities regulated variety cellular metabolism mitochondrial activity, been closely related to occurrence development many diseases, including cancer, aging, neurodegenerative ischemia-reperfusion injury other pathological death. The regulation mainly focuses on three pathways: system Xc-/GPX4 axis, lipid peroxidation iron metabolism. genes involved in these processes were divided into driver, suppressor marker. Importantly, small molecules or drugs that mediate expression are often good treatments clinic. Herein, newly developed database, named 'FERREG', documented (i) providing data ferroptosis-related diseases occurrence, progression drug response; (ii) explicitly describing molecular mechanisms underlying each regulation; (iii) fully referencing collected cross-linking them available databases. Collectively, FERREG contains 51 targets, 718 regulators, 445 158 disease responses. can be accessed at https://idrblab.org/ferreg/.

Language: Английский

Citations

2