Multi-omics analysis of Prolyl 3-hydroxylase 1 as a prognostic biomarker for immune infiltration in ccRCC DOI Creative Commons
Guixin Ding, Tianqi Wang, Fengze Sun

et al.

npj Precision Oncology, Journal Year: 2024, Volume and Issue: 8(1)

Published: Nov. 8, 2024

The formation of human collagen requires the presence Prolyl 3-hydroxylase 1 (P3H1), but regulatory mechanism P3H1 remained insufficiently understood. Our study aimed to identify role in clear cell renal carcinoma (ccRCC). expression ccRCC was validated using multiple databases and vitro experiments. We performed a correlation analysis with drug sensitivity, immune checkpoints, infiltration transcriptome single-cell sequencing. Drawing upon Encyclopedia RNA Interactomes database, we selected as focal point our investigation, meticulously uncovering intricate network microRNAs lncRNAs that potentially orchestrate ceRNA mechanisms. This employs multidimensional approach integrating assays multi-omics bioinformatics analyses investigate P3H1's impact on prognosis, modulation, network, therapeutic responses, aiming uncover new insights into its potential inform future clinical strategies.

Language: Английский

Unlocking biological insights from differentially expressed Genes: Concepts, methods, and future perspectives DOI Creative Commons
Huachun Yin, Hongrui Duo,

Li Song

et al.

Journal of Advanced Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Identifying differentially expressed genes (DEGs) is a core task of transcriptome analysis, as DEGs can reveal the molecular mechanisms underlying biological processes. However, interpreting significance large DEG lists challenging. Currently, gene ontology, pathway enrichment and protein-protein interaction analysis are common strategies employed by biologists. Additionally, emerging analytical strategies/approaches (such network module knowledge graphs, drug repurposing, cell marker discovery, trajectory communication analysis) have been proposed. Despite these advances, comprehensive guidelines for systematically thoroughly mining information within remain lacking.

Language: Английский

Citations

3
Building Up a Human Ovarian Antioxidant ceRNA Network, OvAnOx: A Bioinformatic Perspective for Research on Redox-Related Ovarian Functions and Dysfunctions DOI Open Access
Carla Tatone, Giovanna Di Emidio, Rosalia Battaglia

et al.

Published: Aug. 12, 2024

The ovary is the major determinant of female reproductive health. Ovarian functions are mainly related to primordial follicle pool, which gradually loss with aging. aging and dysfunctions share oxidative stress as common underlying mechanism. ROS signaling essential for normal ovarian processes yet can contribute various disorders when disrupted. Therefore, balance in redox system crucial proper functions. In present study, by focusing on mRNAs ncRNAs described taking into account only validated ncRNA interactions, we built up an antioxidant ceRNA network, namely OvAnOx ceRNA, composed 5 (SOD1, SOD2, CAT, PRDX3, GR), 10 miRNAs lncRNAs (XIST, FGD5-AS1, MALAT1, NEAT1, SNHG1). Our bioinformatic analysis indicated that components not defence, but also involved other Indeed, enzymes encoded mRNA operate within a regulatory network impacts reserve, dynamics, oocyte maturation pathological conditions. represents promising tool unravel complex dialogue between potential signalling pathways health, diseases.

Language: Английский

Citations

1
Podocyte Death in Diabetic Kidney Disease: Potential Molecular Mechanisms and Therapeutic Targets DOI Open Access

Suye Zhong,

Na Wang, Chun Zhang

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(16), P. 9035 - 9035

Published: Aug. 20, 2024

Cell deaths maintain the normal function of tissues and organs. In pathological conditions, abnormal activation or disruption cell death often leads to pathophysiological effects. Diabetic kidney disease (DKD), a significant microvascular complication diabetes, is linked high mortality morbidity rates, imposing substantial burden on global healthcare systems economies. Loss detachment podocytes are key changes in progression DKD. This review explores potential mechanisms apoptosis, necrosis, autophagy, pyroptosis, ferroptosis, cuproptosis, podoptosis podocytes, focusing how different modes contribute It recognizes limitations current research presents latest basic clinical studies targeting podocyte pathways Lastly, it focuses future treat DKD, with intention inspiring further development therapeutic strategies.

Language: Английский

Citations

1
Critical role of non-coding RNA-mediated ferroptosis in urologic malignancies DOI Creative Commons
Wei Li,

Liying Zheng,

Peiyue Luo

et al.

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

Published: Oct. 31, 2024

Urologic malignancies, characterized by their high aggressiveness and metastatic potential, pose a significant public health challenge globally. Ferroptosis, novel mode of cell death, typically arises from intracellular iron ion overload the accumulation lipid peroxides. This process has been shown to play crucial regulatory role in various pathological conditions, particularly cancer, including urologic cancers. However, comprehensive mechanisms underlying ferroptosis remain poorly understood, which somewhat limits its broader application cancer therapy. Non-coding RNAs (ncRNAs), encompass microRNAs (miRNAs), long non-coding (lncRNAs), circular (circRNAs), are transcripts that pivotal roles physiological processes, such as proliferation, differentiation, apoptosis, cycle regulation, modulating expression target genes. The biological functions potential ncRNAs context cancer-related have partially elucidated. Research indicates can influence progression cancers affecting migration, drug resistance through regulation ferroptosis. Consequently, this review aims clarify ncRNA-ferroptosis axis evaluate clinical significance ferroptosis-related ncRNAs, thereby providing new insights into biology therapeutic strategies may ultimately benefit diverse range patients.

Language: Английский

Citations

1
Resveratrol promotes mitophagy via the MALAT1/miR-143-3p/RRM2 axis and suppresses cancer progression in hepatocellular carcinoma DOI
Chunyan Feng, Chao Cai, Xinyi Shi

et al.

Journal of Integrative Medicine, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

Citations

1
MicroRNA networks in prolactinoma tumorigenesis: a scoping review DOI Creative Commons

Sevil Ghaffarzadeh Rad,

Fatemeh Nejadi Orang,

Mahdi Abdoli Shadbad

et al.

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

Published: Dec. 19, 2024

Language: Английский

Citations

1
Targeting mitochondrial damage: shining a new light on immunotherapy DOI Creative Commons
Wenjuan Zeng, Menghui Wang, Yuxin Zhang

et al.

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

Published: July 22, 2024

Mitochondrial damage has a particular impact on the immune system and tumor microenvironment, which can trigger cell stress, an inflammatory response, disrupt function, thus all of accelerate progression tumor. Therefore, it is essence to comprehend how function microenvironment interact with mitochondrial dysfunction for cancer treatment. Preserving integrity mitochondria or regulating cells, such as macrophages, may enhance efficacy therapy. Future research should concentrate interactions among mitochondria, system, identify new therapeutic strategies.

Language: Английский

Citations

0
Building a Human Ovarian Antioxidant ceRNA Network “OvAnOx”: A Bioinformatic Perspective for Research on Redox-Related Ovarian Functions and Dysfunctions DOI Creative Commons
Carla Tatone, Giovanna Di Emidio, Rosalia Battaglia

et al.

Antioxidants, Journal Year: 2024, Volume and Issue: 13(9), P. 1101 - 1101

Published: Sept. 12, 2024

The ovary is a major determinant of female reproductive health. Ovarian functions are mainly related to the primordial follicle pool, which gradually lost with aging. aging and dysfunctions share oxidative stress as common underlying mechanism. ROS signaling essential for normal ovarian processes, yet it can contribute various disorders when disrupted. Therefore, balance in redox system crucial proper functions. In present study, by focusing on mRNAs ncRNAs described taking into account only validated ncRNA interactions, we built an antioxidant ceRNA network, named OvAnOx ceRNA, composed 5 (SOD1, SOD2, CAT, PRDX3, GR), 10 miRNAs lncRNAs (XIST, FGD5-AS1, MALAT1, NEAT1, SNHG1). Our bioinformatic analysis indicated that components not defense but also involved other Indeed, enzymes encoded operate within regulatory network impacts reserve, follicular dynamics, oocyte maturation pathological conditions. represents promising tool unravel complex dialog between potential pathways health, aging, diseases.

Language: Английский

Citations

0
Identification of exosomal ceRNA networks as prognostic markers in clear cell renal cell carcinoma DOI Creative Commons
Tao Zhu, Haian Fu, Zhiqiang Wang

et al.

Medicine, Journal Year: 2024, Volume and Issue: 103(43), P. e40167 - e40167

Published: Oct. 25, 2024

Aggressive clear cell renal carcinoma (ccRCC) has a bad prognosis. We seek new ccRCC biomarkers for diagnosis and treatment. used exoRBase The Cancer Genome Atlas Database to compare DEmRNAs, DEmiRNAs, DElncRNAs, DEcircRNAs in normal tissues. CircRNAs circRNAs targeting microRNAs (miRNAs) were anticipated taken intersections, several databases assessed the targeted link between common miRNAs messenger RNAs (mRNAs). database was create predictive mRNA signature that validated E-MTAB-1980. Finally, we examined competing endogenous RNA network long noncoding using overall survival analysis. built first regulation of circRNA–lncRNA–miRNA–mRNA found it substantially correlates with unveiled ccRCC’s posttranscriptional mechanism greater detail. Our findings identified novel diagnosis, therapy,

Language: Английский

Citations

0
Multi-omics analysis of Prolyl 3-hydroxylase 1 as a prognostic biomarker for immune infiltration in ccRCC DOI Creative Commons
Guixin Ding, Tianqi Wang, Fengze Sun

et al.

npj Precision Oncology, Journal Year: 2024, Volume and Issue: 8(1)

Published: Nov. 8, 2024

The formation of human collagen requires the presence Prolyl 3-hydroxylase 1 (P3H1), but regulatory mechanism P3H1 remained insufficiently understood. Our study aimed to identify role in clear cell renal carcinoma (ccRCC). expression ccRCC was validated using multiple databases and vitro experiments. We performed a correlation analysis with drug sensitivity, immune checkpoints, infiltration transcriptome single-cell sequencing. Drawing upon Encyclopedia RNA Interactomes database, we selected as focal point our investigation, meticulously uncovering intricate network microRNAs lncRNAs that potentially orchestrate ceRNA mechanisms. This employs multidimensional approach integrating assays multi-omics bioinformatics analyses investigate P3H1's impact on prognosis, modulation, network, therapeutic responses, aiming uncover new insights into its potential inform future clinical strategies.

Language: Английский

Citations

0