Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences DOI Creative Commons
Sushmita Basu, Jing Yu, Daisuke Kihara

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Computational prediction of nucleic acid-binding residues in protein sequences is an active field research, with over 80 methods that were released the past 2 decades. We identify and discuss 87 sequence-based predictors include dozens recently published are surveyed for first time. overview historical progress examine multiple practical issues availability impact predictors, key features their predictive models, important aspects related to training assessment. observe decade has brought increased use deep neural networks language which contributed substantial gains performance. also highlight advancements vital challenging cross-predictions between deoxyribonucleic acid (DNA)-binding ribonucleic (RNA)-binding targeting two distinct sources binding annotations, structure-based versus intrinsic disorder-based. The trained on structure-annotated interactions tend perform poorly disorder-annotated vice versa, only a few target well across both annotation types. significant problem, some DNA-binding or RNA-binding indiscriminately predicting Moreover, we show web servers cited substantially more than tools without implementation no longer working implementations, motivating development long-term maintenance servers. close by discussing future research directions aim drive further this area.

Language: Английский

The Regulation of Trace Metal Elements in Cancer Ferroptosis DOI Creative Commons

Xiaoyan Wang,

Yuanyuan Xue, Lei Chang

et al.

Advanced Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Abstract Ferroptosis, as novel type of regulated cell death that has garnered widespread attention over the past decade, witnessed continuous discovery an increasing number regulatory mechanisms. Trace metal elements play a multifaceted and crucial role in oncology. Interestingly, it been increasingly evident these elements, such copper, are involved regulation iron accumulation, lipid peroxidation antiferroptotic systems, suggesting existence “nonferrous” mechanisms ferroptosis. In this review, comprehensive overview composition mechanism ferroptosis is provided. The interaction between copper metabolism (including cuproptosis) cancer, well roles other trace (such zinc, manganese, cobalt, molybdenum) specifically focused. Furthermore, applications nanomaterials based on metals cancer therapy also reviewed potential strategies for co‐targeting cuproptosis explored. Nevertheless, light intricate ambiguous nature interactions, ongoing research essential to further elucidate ferroptosis, thereby facilitating development therapeutic targets approaches treatment.

Language: Английский

Citations

1
Role of long non-coding RNAs in the regulation of ferroptosis in tumors DOI Creative Commons

Ying Ju,

Yuanhao Lv,

Xu Liu

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: March 21, 2025

Normal cells begin to grow indefinitely and immortalize form tumor after an external stimulus resulting in a genetic mutation. Effective killing of is the basis various cancer therapies. Ferroptosis class cell death types dependent on iron cellular lipid peroxidation. Tumors themselves are iron-dependent, conventional radiotherapy also sensitizes ferroptosis. Increasing sensitivity ferroptosis may be potential therapeutic strategy overcome resistance mechanisms therapy. Long noncoding RNAs (LncRNAs) transcripts more than 200 nucleotides length that regulate gene expression at multiple levels involved biological processes such as differentiation, cycle arrest, maintenance stemness. Recent studies have found lncRNAs through influence or ameliorate chemotherapeutic agents. With continuous maturation nanomaterials technology, it provide new means for treatment by regulating ferroptosis-related inside tumors well increasing Fe 2+ ROS tumors. In this paper, we systematically introduce regulatory mechanism ferroptosis, role immunotherapy application combined with nanomaterials, which provides perspectives

Language: Английский

Citations

0
SOX12 promotes serine synthesis and tumor progression in endometrial cancer DOI
Zi‐Hui Zhang, Hui Yan, Qiong Wan

et al.

Cellular Signalling, Journal Year: 2025, Volume and Issue: unknown, P. 111870 - 111870

Published: May 1, 2025

Language: Английский

Citations

0
The recent advancements of ferroptosis of gynecological cancer DOI Creative Commons

Shenglan Tang,

Li Chen

Cancer Cell International, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 26, 2024

Ovarian, endometrial, and cervical cancer are the most common types of gynecologic tumor in women. Surgery, combined with radiotherapy chemotherapy, is commonly used to treat these tumors. Unfortunately, difficulties early diagnosis acquired drug resistance have resulted poor outcomes for patients. Ferroptosis a form regulated cell death that depends on iron characterized by accumulation, reactive oxygen species production, lipid peroxidation. The strong association between ferroptosis many diseases, especially has been confirmed numerous studies. Many studies demonstrated involved initiating, progressing metastasizing This review summarizes pathogenesis its development, treatment, prognosis tumors, further explore potential utility treating

Language: Английский

Citations

3
The Promotive and Inhibitory Role of Long Non-Coding RNAs in Endometrial Cancer Course—A Review DOI Open Access
Patryk Jasielski, Izabela Zawlik, Anna Bogaczyk

et al.

Cancers, Journal Year: 2024, Volume and Issue: 16(11), P. 2125 - 2125

Published: June 3, 2024

Endometrial cancer is one of the most common malignant tumours in women. The development this tumour associated with several genetic disorders, many which are still unknown. One type RNA molecules currently being intensively studied types long non-coding RNAs (lncRNAs). LncRNA-coding genes occupy a large fraction human genome. LncRNAs regulate aspects cell development, metabolism, and other physiological processes. Diverse lncRNA can function as suppressor or an oncogene that alter migration, invasion, proliferation, apoptosis, immune system response. Recent studies suggest selected lncRNAs important endometrial course. Our article describes over 70 involved cancer, were via vivo vitro research. It was proved could both promote inhibit cancer. In future, may become therapeutic target. aim study to review role carcinoma uterine body.

Language: Английский

Citations

2
The multifaceted perspectives on the regulation of lncRNAs in hepatocellular carcinoma ferroptosis: from bench-to-bedside DOI Creative Commons
Xin Jin,

C. Huang,

Yue Tian

et al.

Clinical and Experimental Medicine, Journal Year: 2024, Volume and Issue: 24(1)

Published: July 3, 2024

Despite being characterized by high malignancy, morbidity, and low survival rates, the underlying mechanism of hepatocellular carcinoma (HCC) has not been fully elucidated. Ferroptosis, a non-apoptotic form regulated cell death, possesses distinct morphological, biochemical, genetic characteristics compared to other types death. Dysregulated actions within molecular network that regulates ferroptosis have identified as significant contributors progression HCC. Long non-coding RNAs (lncRNAs) emerged influential diverse cellular processes, regulating gene function expression through multiple mechanistic pathways. An increasing body evidence indicates deregulated lncRNAs are implicated in malignant events such proliferation, growth, invasion, metabolism influencing Therefore, elucidating inherent role modulatory functions on HCC might promote development novel therapeutic interventions for this disease. This review provides succinct overview roles ferroptosis-related treatment, aiming drive promising targets biomarkers patients.

Language: Английский

Citations

2
Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next generation sequencing data analysis DOI Open Access
Basavaraj Vastrad, Chanabasayya Vastrad

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

Published: May 8, 2024

Abstract Endometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain intercourse and infertility. However, early diagnosis endometriosis still restricted. The purpose this investigation to identify validate key biomarkers endometriosis. Next generation sequencing (NGS) dataset GSE243039 was obtained from Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) between normal control samples were identified. After screening DEGs, gene ontology (GO) REACTOME pathway enrichment analyses performed. Furthermore, protein-protein interaction (PPI) network constructed modules analysed using Human Integrated Protein-Protein Interaction rEference (HIPIE) database Cytoscape software, hub Subsequantely, miRNAs genes, TFss miRNet NetworkAnalyst tool, possible TFs predicted. Finally, receiver operating characteristic curve (ROC) analysis used genes. A total 958 including 479 up regulated down screened samples. GO DEGs showed that they mainly involved in multicellular organismal process, developmental signaling by GPCR muscle contraction. Further PPI identified 10 VCAM1, SNCA, PRKCB, ADRB2, FOXQ1, MDFI, ACTBL2, PRKD1, DAPK1 ACTC1. Possible target miRNAs, hsa-mir-3143 hsa-mir-2110, TFs, TCF3 CLOCK, predicted constructing miRNA-hub regulatory TF-hub network. This bioinformatics techniques explore potential novel biomarkers. These might provide new ideas methods for diagnosis, treatment, monitoring

Language: Английский

Citations

1
Implications of ITCH-mediated ubiquitination of SIX1 on CDC27-cyclinB1 signaling in nasopharyngeal carcinoma DOI Creative Commons
Zehua Lin,

Weisong Cai,

Ying Sun

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Oct. 15, 2024

Nasopharyngeal carcinoma (NPC) presents a significant medical challenge due to its high incidence rate and poor prognosis, which are attributed primarily tumor metastasis drug resistance. Sine oculis homeobox homolog 1 (SIX1) has been identified as crucial target for cancer treatment. However, role in NPC remains incompletely understood. This study investigated the mechanisms by degradation of SIX1 protein, is mediated ubiquitin, affects malignant characteristics throughout cell cycle. Our findings reveal that reduced expression itchy E3 ubiquitin ligase (ITCH) impedes leading enhance oncogenic properties. Knockdown experiments was inhibited demonstrated decrease proliferation, migration, invasion lines, whereas overexpression yielded opposite effects. Further experimental validation revealed promotes progression via division cycle 27 (CDC27)/cyclin B1 axis. These provide valuable insights into potential therapeutic targets prognostic indicators treatment, emphasizing ITCH/SIX1/CDC27/cyclin axis promising novel therapies.

Language: Английский

Citations

1
Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next-generation sequencing data analysis DOI Creative Commons
Basavaraj Vastrad, Chanabasayya Vastrad

Egyptian Journal of Medical Human Genetics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 12, 2024

Abstract Background Endometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain intercourse and infertility. However, early diagnosis endometriosis still restricted. The purpose this investigation to identify validate key biomarkers endometriosis. Methods Next-generation sequencing dataset GSE243039 was obtained from Gene Expression Omnibus database, differentially expressed genes (DEGs) between normal control samples were identified. After screening DEGs, gene ontology (GO) REACTOME pathway enrichment analyses performed. Furthermore, protein–protein interaction (PPI) network constructed modules analyzed using Human Integrated Protein–Protein Interaction rEference database Cytoscape software, hub Subsequently, miRNAs genes, TFs miRNet NetworkAnalyst tool, possible predicted. Finally, receiver operating characteristic curve analysis used genes. Results A total 958 including 479 upregulated downregulated screened samples. GO DEGs showed that they mainly involved in multicellular organismal process, developmental signaling by GPCR muscle contraction. Further PPI identified 10 vcam1, snca, prkcb, adrb2, foxq1, mdfi, actbl2, prkd1, dapk1 actc1. Possible target miRNAs, hsa-mir-3143 hsa-mir-2110, TFs, tcf3 (transcription factor 3) clock (clock circadian regulator), predicted constructing miRNA-hub regulatory TF-hub network. Conclusions This bioinformatics techniques explore potential novel biomarkers. These might provide new ideas methods for diagnosis, treatment monitoring

Language: Английский

Citations

0
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences DOI Creative Commons
Sushmita Basu, Jing Yu, Daisuke Kihara

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Computational prediction of nucleic acid-binding residues in protein sequences is an active field research, with over 80 methods that were released the past 2 decades. We identify and discuss 87 sequence-based predictors include dozens recently published are surveyed for first time. overview historical progress examine multiple practical issues availability impact predictors, key features their predictive models, important aspects related to training assessment. observe decade has brought increased use deep neural networks language which contributed substantial gains performance. also highlight advancements vital challenging cross-predictions between deoxyribonucleic acid (DNA)-binding ribonucleic (RNA)-binding targeting two distinct sources binding annotations, structure-based versus intrinsic disorder-based. The trained on structure-annotated interactions tend perform poorly disorder-annotated vice versa, only a few target well across both annotation types. significant problem, some DNA-binding or RNA-binding indiscriminately predicting Moreover, we show web servers cited substantially more than tools without implementation no longer working implementations, motivating development long-term maintenance servers. close by discussing future research directions aim drive further this area.

Language: Английский

Citations

0