Transcriptomic Gene Network Profiling and Weak Signal Detection for Prediction of Ovarian Cancer Occurrence, Survival, and Severity by Integrating Bulk and Single-cell RNAseq Data DOI Open Access
Yanming Li, Mihaela E. Sardiu, Devin C. Koestler

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 24, 2023

Abstract Background Ovarian cancer (OC) is a significant gynecological malignancy characterized by its high mortality rate, poor long-term survival and late-stage diagnosis. OC the 5th leading cause of death among woman counts 2.1% all death. rates are much lower than other cancers that affect woman. Its 5-year rate less 50%. Only ∼17% patients diagnosed within early stage. The majority at an advanced stage, making detection effective treatment critical challenges. Currently, identified predictive genes still very sparse, resulting in pool prognostic performance. There exists unmet needs to identify novel gene biomarkers for occurrence, survival, clinical stages promote likelihood perform optimal treatments or therapeutic strategies earliest stage possible. Methods Previous RNAseq analysis on focused detecting differentially expressed (DE) only. Many genes, although having weak marginal differential effects, may exude strong effects disease outcomes though regulating DE genes. In this work, we employed new machine learning method, netLDA, detect such coregulating with predicting netLDA detects networks (PGN) containing as hub PGNs. network structures detected PGNs along therein then used outcome prediction test datasets. Results We different sets signature Previously EPCAM, UBE2C, CHD1L, TP53 , CD24 WFDC2 FANCI, were confirmed. also including GIGYF2, GNPAT, RAD54L ELL. overlapped OC-related biological pathways KEGG tight junction, ribosome cell cycle pathways. incorporation significantly improved Cellular mapping selected feature using single-cell data further revealed heterogeneous expression distributions types. Conclusions established transcriptomic profile prediction. provide targets diagnostics drug development OC.

Language: Английский

MicroRNAs in disease States DOI
Mehdi Alizadeh, Hassan Ghasemi,

Donya Bazhan

et al.

Clinica Chimica Acta, Journal Year: 2025, Volume and Issue: 569, P. 120187 - 120187

Published: Feb. 10, 2025

Language: Английский

Citations

1
Integrative machine learning frameworks to uncover specific protein signature in neuroendocrine cervical carcinoma DOI Creative Commons
Tao Shen, Tingting Dong,

Haiyang Wang

et al.

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

Published: Jan. 10, 2025

Neuroendocrine cervical carcinoma (NECC) is a rare but highly aggressive tumor. The clinical management of NECC follows neuroendocrine neoplasms and cancer in general. However, the diagnosis prognosis remain dismal. aim this study was to identify specific protein signature for NECC. Protein gene expression data other cancers were retrieved or downloaded from self-collected samples public resources. Eleven machine-learning algorithms packaged into 66 combinations, which we selected optimal algorithm, including randomForest, SVM-RFE, LASSO, select key dysregulated proteins (kNsDEPs). diagnostic effect kNsDEPs validated by set predictive models immunohistochemical staining method. dysregulation patterns further investigated carcinomas. Our results showed that displays distinctive biological characteristics, such as HPV18 infection, exhibits unique molecular features, particularly an enrichment cytoskeleton-related functions. Furthermore, secretagogin (SCGN), adenylyl cyclase-associated 2 (CAP2), calcyclin-binding (CACYBP) identified kNsDEPs. These play central role cytoskeleton binding showcase robust ability specificity Moreover, concurrent upregulation SCGN CACYBP, along with downregulation CAP2, represents feature NECC, distinguishing it This uncovers significance elucidates their regulated networks context It highlights pivotal diagnosis, thus offering promising prospects development biomarkers

Language: Английский

Citations

0
miR-1264 Exacerbates Proliferation, Migration and Invasion of Endometrial Cancer Cells by Targeting MSH2 DOI
Wen Han, Yong Xiang,

Ji‐Yu Wang

et al.

Reproductive Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Language: Английский

Citations

0
Blood Plasma Small Non-Coding RNAs as Diagnostic Molecules for the Progesterone-Receptor-Negative Phenotype of Serous Ovarian Tumors DOI Open Access
Angelika V. Timofeeva, Ivan S. Fedorov, A.V. Asaturova

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(15), P. 12214 - 12214

Published: July 30, 2023

The expression level of the progesterone receptor (PGR) plays a crucial role in determining biological characteristics serous ovarian carcinoma. Low PGR is associated with chemoresistance and poorer outcome. In this study, our objective was to explore relationship between tumor levels RNA profiles (miRNAs, piwiRNAs, mRNAs) understand their behavior. To achieve this, we employed next-generation sequencing small non-coding RNAs, quantitative RT-PCR, immunohistochemistry analyze both FFPE frozen samples, as well blood plasma from patients benign cystadenoma (BSC), borderline (SBT), low-grade carcinoma (LGSOC), high-grade (HGSOC). Our findings revealed significant upregulation MMP7 MUC16, along downregulation PGR, LGSOC HGSOC compared BSC. We observed correlations tissue contents miR-199a-5p, miR-214-3p, miR-424-3p, miR-424-5p, miR-125b-5p, which potentially target MMP7, MMP9, content miR-16-5p, miR-17-5p, miR-20a-5p, miR-93-5p, are epithelial–mesenchymal transition (EMT) cells. EMT-associated miRNAs were significantly correlated hsa_piR_022437, hsa_piR_009295, hsa_piR_020813, hsa_piR_004307, hsa_piR_019914 tissues. developed two optimal logistic regression models using quantitation hsa_piR_022437 or hsa_piR_019914, miR-93-5p tissue, exhibited ability diagnose PGR-negative phenotype 93% sensitivity. Of particular interest, miR-16-5p could be used 86% sensitivity even before surgery chemotherapy. This knowledge can help choosing most effective treatment strategy for aggressive type cancer, such neoadjuvant chemotherapy followed by cytoreduction combination hyperthermic intraperitoneal targeted therapy, thus enhancing treatment’s effectiveness patient’s longevity.

Language: Английский

Citations

7
The role of microRNA-9 in Ovarian and Cervical Cancers: an Updated Overview DOI
Riccardo Di Fiore,

Rosa Drago‐Ferrante,

Sherif Suleiman

et al.

European Journal of Surgical Oncology, Journal Year: 2024, Volume and Issue: unknown, P. 108546 - 108546

Published: July 1, 2024

Language: Английский

Citations

2
Blood Plasma Small Non-Coding RNAs as Diagnostic Molecules of Progesterone Receptor-Negative Phenotype of Serous Ovarian Tumors DOI Open Access
Angelika V. Timofeeva, Ivan S. Fedorov, A.V. Asaturova

et al.

Published: July 18, 2023

Progesterone receptor (PGR) expression level determines biological characteristics of the serous ovarian carcinoma, and low PGR appears to be associated with chemoresistance worse outcome. In this study, we aimed find relationships between tumor progesterone RNA-profile (miRNAs, piwiRNAs, mRNAs), determining its behavior. For purpose, applied next generation sequencing small noncoding RNAs, quantitative RT-PCR, immunohistochemistry analyze FFPE frozen samples as well blood plasma from patients benign cystadenoma (BSC), borderline tumour (SBT), low-grade high-grade carcinoma (LGSOC HGSOC, respectively). We found significant upregulation MMP7 MUC16 downregulation in LGSOC HGSOC comparison BSC. The tissue content miR-199a-5p, miR-214-3p, miR-424-3p, miR-424-5p, miR-125b-5p significantly inversely correlated serum CA125 concentration, directly tissue. On contrary, miR-16-5p, miR-17-5p, miR-20a-5p, miR-93-5p, responsible for epithelial-mesenchymal transition (EMT) cell, concentration Levels EMT-associated miRNAs hsa_piR_022437, hsa_piR_009295, hsa_piR_020813, hsa_piR_004307, hsa_piR_019914 tissues. Among them, hsa_piR_004307 inversly tumor. Two optimal logistic regression models were developed based on quantitation hsa_piR_022437 or hsa_piR_019914, miR-93-5p tissue, both which diagnose PGR-negative phenotype 93% sensitivity. According FunRich3.1.3 functional enrichment analysis tool, 72 gene-targets miRNA piRNA identified here markers proven mutated different cancers such ovarian, breast, colorectal, liver, stomach, lung, endometrial, thyroid cancer. levels miR-16-5p can used 86% sensitivity before surgery chemotherapy choose treatment strategy most aggressive type cancer (for instance, neoadjuvant followed by cytoreduction combination hyperthermic intraperitoneal chemotherapy) increase effectiveness longevity patient.

Language: Английский

Citations

4
MiR-449a: A Potential Biomarker for Vocal Function Preservation in Combination Therapy for Laryngeal Cancer DOI Open Access
Amal F. Gharib, Abdulraheem Ali Almalki, Amani A. Alrehaili

et al.

Published: April 15, 2024

Background/Objectives: Laryngeal squamous cell carcinoma (LSCC) is the most prevalent form, accounting for nearly 95% of laryngeal cancer. This study evaluates effectiveness chemotherapy and radiation therapy combined treating LSCC, along with exploring miR-449a as a potential biomarker predicting treatment response prognosis in LSCC patients. Patients Methods: The had 81 patients advanced cancer 50 healthy controls. Chemotherapy was given two cycles, followed by an evaluation response. Disease progression cases surgical resection therapy. Positive responders after third cycle. also assessed expression levels tumor tissue, normal serum samples from control subjects. Results: 31% achieved complete response, 49% showed partial participants maintained integrity vocal function. After therapy, 74% 65 responded completely preserved functions. Lower MiR-449a found tissues were correlated aggressive behavior, poor prognostic markers, decreased survival. Conversely, elevated seen responders. Conclusions: Combined chemo radiotherapy preserve function improve outcomes LSCC. promising indicator diagnosis efficacy

Language: Английский

Citations

1
A New Approach to Melanoma Treatment: microRNAs DOI
Süleyman İlhan, Ferdi Oğuz, Harika Atmaca

et al.

Current Topics in Medicinal Chemistry, Journal Year: 2024, Volume and Issue: 24(16), P. 1362 - 1376

Published: April 27, 2024

Abstract:: Although immunotherapy and targeted therapy have radically changed melanoma treatment, the development of resistance reduction patient responses are still significant problems. Small molecule inhibitors needed to overcome this situation, biomarkers that can estimate whether patients will reply existing treatments need be developed. miRNAs involved in diverse processes such as tumor development, progression, metastasis, invasion. While some act suppressors, others may oncogenic. also contribute drug resistance. There is increasing evidence demonstrating possible effect on diagnosis treatment markers melanoma. The manuscript focuses current challenges highlighting issues reduced despite revolutionary advancements immunotherapy. It underscores for small creation predicting treatments. role invasion has been highlighted. certain function exhibit oncogenic properties. Furthermore, presented potential significance symptom identification These findings indicate a promising avenue future research clinical applications. In summary, article effectively communicates key insights, making it valuable resource those interested treatment.

Language: Английский

Citations

1
Global research states and trends of micro RNA in irritable bowel syndrome: a bibliometric analysis DOI Creative Commons
Hongxiu Chen, Zhifang Xu,

Honggang Zhao

et al.

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

Published: July 5, 2024

Irritable bowel syndrome (IBS) is a common chronic gastrointestinal disorder, but its diagnosis and treatment remain obscure. Non-coding RNAs (ncRNAs), as potential biomarkers, have attracted increasing attention in digestive diseases. Here, we present comprehensive research status, development trends, valuable insights this subject area. The literature search was performed using Web of Science Core Collection. VOSviewer 1.6.20, Citespace 6.2.R4, Microsoft Excel 2021 were used for bibliometric analysis. A total 124 articles included the Overall, publication patterns fluctuated. Globally, People's Republic China, USA, Germany top three contributors publications. Guangzhou University Chinese Medicine, California, Mayo Clinic, Los Angeles contributed highest number pathways specific mechanisms by which ncRNAs regulate transcription translation thus pathophysiological processes IBS are main hotspots field. We found that microRNA (miRNAs) intricately involved regulation key pathologies such viscera sensitivity, intestinal permeability, mucosal barrier, immunoinflammatory response, brain-gut axis IBS, these topics garnered significant community. Notably, microecological disorders also associated with pathogenesis, ncRNA may play an important role interactions between host flora. This first study to comprehensively summarize trends related (especially miRNAs). Our findings will help understand provide guidance future studies.

Language: Английский

Citations

1
An NIR-driven biosensor based on the metal-enhanced fluorescence effect and a signal amplification strategy for miRNA detection DOI Creative Commons
Dabin Liu, Wen‐Zhang Zhu, Bin Qiu

et al.

RSC Advances, Journal Year: 2024, Volume and Issue: 14(54), P. 39908 - 39920

Published: Jan. 1, 2024

Herein, a fluorescent biosensor was used for the detection of miRNA-155 based on UCNP@PDA/AuNP (UP/Au) composite and two TMSD steps. The proposed exhibited sensitive with low limit 19.76 fM.

Language: Английский

Citations

1