Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma DOI Creative Commons
Rongjie Zhang, Qian Li, Xiaoxiao Yu

et al.

Heliyon, Journal Year: 2023, Volume and Issue: 9(11), P. e22083 - e22083

Published: Nov. 1, 2023

The increasing evidence suggests that necroptosis mediates many behaviors of tumors, as well the regulation tumor microenvironment. Long non-coding RNAs (lncRNAs) are involved in a variety regulatory processes during development and significantly associated with patient prognosis. It necroptosis-related lncRNAs (NRlncRNAs) may serve biomarkers for prognosis hepatocellular carcinoma (HCC).lncRNA expression profiles HCC were obtained from TCGA database. LncRNAs extracted using correlation analysis. Prognostic models constructed based on least absolute shrinkage selection operator algorithm (LASSO) multivariate Cox regression differences microenvironment between high-risk low-risk groups further analyzed. Single-cell RNA sequencing data was performed to assess enrichment genes immune cell subsets. Finally, real-time RT-PCR used detect prognosis-related different lines.We prognostic signature 8 NRlncRNAs, which also showed good predictive accuracy. model patients score worse than (P < 0.05). Combined clinical characteristics risk HCC, Nomogram drawn reference practice. In addition, infiltration analysis single low level observed at high there significant NRlncRNAs macrophages. results RT-qPCR highly expressed lines human liver cancer tissues.This provide meaningful insights immunotherapy responses HCC.

Language: Английский

An integrative analysis revealing cuproptosis-related lncRNAs signature as a novel prognostic biomarker in hepatocellular carcinoma DOI Creative Commons

Xilang Chen,

Mengyu Sun,

Weibo Feng

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 10, 2023

Background: Cuproptosis is a newly defined form of cell death, whether cuproptosis involved in hepatocellular carcinoma (HCC) remains elusive. Method: We obtained patients’ RNA expression data and follow-up information from University California Santa Cruz (UCSC) The Cancer Genome Atlas (TCGA). analyzed the mRNA level Cuproptosis-related genes (CRGs) performed univariate Cox analysis. Liver (LIHC) was chosen for further investigation. Real-Time quantitative PCR (RT-qPCR), Western blotting (WB), Immunohistochemical (IHC), Transwell assays were used to determine patterns functions CRGs LIHC. Next, we identified CRGs-related lncRNAs (CRLs) differentially expressed CRLs between HCC normal cases. Univariate analysis, least absolute shrinkage selection operator (LASSO) analysis regression construct prognostic model. multivariate assess risk model can act as an independent factor overall survival duration. Different groups immune correlation tumor mutation burden (TMB), Gene Set Enrichment Analysis (GSEA) different groups. Finally, assessed performance predictive drug sensitivity. Results: levels have significant differences tissues. High Dihydrolipoamide S-Acetyltransferase ( DLAT ) correlated metastasis cells indicated poor prognosis patients. Our consisted four cuproptosis-related lncRNA (AC011476.3, AC026412.3, NRAV, MKLN1-AS). well predicting rates. results suggested that score serve element durations. Survival revealed low patients extended periods compared with those high risk. has positive B CD4 + T Th2, while negative relationship endothelial hematopoietic cells. Besides, checkpoint higher folds high-risk set than low-risk set. group had rates genetic having shorter time. GSEA signaling pathways enriched mostly immune-related, metabolic-related group. Drugs sensitivity our ability predict efficacy clinical treatment. Conclusion: formula novel predictor

Language: Английский

Citations

8
A novel signature of cuproptosis-related lncRNAs predicts prognosis in glioma: Evidence from bioinformatic analysis and experiments DOI Creative Commons
Di Chen, Yuan Xu, Xueping Gao

et al.

Frontiers in Pharmacology, Journal Year: 2023, Volume and Issue: 14

Published: April 10, 2023

Background: Glioma patients often experience unfavorable outcomes and elevated mortality rates. Our study established a prognostic signature utilizing cuproptosis-associated long non-coding RNAs (CRLs) identified novel biomarkers therapeutic targets for glioma. Methods: The expression profiles related data of glioma were obtained from Cancer Genome Atlas, an accessible online database. We then constructed using CRLs evaluated the prognosis by means Kaplan-Meier survival curves receiver operating characteristic curves. A nomogram based on clinical features was employed to predict individual probability patients. Functional enrichment analysis conducted identify crucial CRL-related enriched biological pathways. role LEF1-AS1 in validated two cell lines (T98 U251). Results: developed model with 9 CRLs. Patients low-risk had considerably longer overall (OS). CRL may serve independently as indicator In addition, functional revealed significant multiple immunological Notable differences observed between risk groups terms immune infiltration, function, checkpoints. further four drugs their different IC50 values groups. Subsequently, we discovered molecular subtypes (cluster one cluster two), subtype exhibiting remarkably OS compared subtype. Finally, that inhibition curbed proliferation, migration, invasion cells. Conclusion: signatures confirmed reliable therapy response Inhibition effectively suppressed growth, gliomas; therefore, presents itself promising biomarker potential target

Language: Английский

Citations

8
PANoptosis-related long non-coding RNA signature to predict the prognosis and immune landscapes of pancreatic adenocarcinoma DOI Creative Commons

Qinying Zhao,

Yingquan Ye, Quan Zhang

et al.

Biochemistry and Biophysics Reports, Journal Year: 2023, Volume and Issue: 37, P. 101600 - 101600

Published: Dec. 7, 2023

Cancer growth is significantly influenced by processes such as pyroptosis, apoptosis, and necroptosis that underlie PANoptosis, a proinflammatory programmed cell death. Several studies have examined the long non-coding RNAs (lncRNAs) associated with pancreatic adenocarcinoma (PAAD). However, predictive value of lncRNAs related to PANoptosis for PAAD has not been established.

Language: Английский

Citations

8
Cuproptosis-related lncRNAs predict the prognosis and immune response in hepatocellular carcinoma DOI
Qiongyue Zhang, Yan Huang, Yu Xia

et al.

Clinical and Experimental Medicine, Journal Year: 2022, Volume and Issue: 23(6), P. 2051 - 2064

Published: Sept. 24, 2022

Language: Английский

Citations

12
Single-cell and bulk RNA sequencing identifies T cell marker genes score to predict the prognosis of pancreatic ductal adenocarcinoma DOI Creative Commons
Haoran Zheng, Yimeng Li, Yujia Zhao

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: March 6, 2023

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the lethal malignancies, with limited biomarkers identified to predict its prognosis and treatment response immune checkpoint blockade (ICB). This study aimed explore predictive ability T cell marker genes score (TMGS) their overall survival (OS) ICB by integrating single-cell RNA sequencing (scRNA- seq ) bulk RNA- data. Multi-omics data PDAC were applied in this study. The uniform manifold approximation projection (UMAP) was utilized for dimensionality reduction cluster identification. non-negative matrix factorization (NMF) algorithm molecular subtypes clustering. Least Absolute Shrinkage Selection Operator (LASSO)-Cox regression adopted TMGS construction. prognosis, biological characteristics, mutation profile, function status between different groups compared. Two via NMF: proliferative (C1) (C2). Distinct prognoses characteristics observed them. developed based on 10 (TMGs) through LASSO-Cox regression. an independent prognostic factor OS PDAC. Enrichment analysis indicated that cycle proliferation-related pathways are significantly enriched high-TMGS group. Besides, related more frequent KRAS , TP53 CDKN2A germline mutations than low-TMGS Furthermore, associated attenuated antitumor immunity reduced infiltration compared However, high correlated higher tumor burden (TMB), a low expression level inhibitory molecules, dysfunction score, thus having rate. On contrary, favorable rate chemotherapeutic agents targeted therapy. By combining scRNA- data, we novel biomarker, TMGS, which has remarkable performance predicting guiding pattern patients

Language: Английский

Citations

7
Emerging roles and potential clinical applications of long non-coding RNAs in hepatocellular carcinoma DOI

Jiaqi Sheng,

Enjun Lv,

Limin Xia

et al.

Biomedicine & Pharmacotherapy, Journal Year: 2022, Volume and Issue: 153, P. 113327 - 113327

Published: June 29, 2022

Language: Английский

Citations

11
Comprehensive analysis of nine m7G-related lncRNAs as prognosis factors in tumor immune microenvironment of hepatocellular carcinoma and experimental validation DOI Creative Commons

Tao Wang,

Zhijia Zhou,

Xuan Wang

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 23, 2022

Background: Hepatocellular carcinoma (HCC) remains the most prevalent gastrointestinal malignancy worldwide, with robust drug resistance to therapy. N7-methylguanosine (m7G) mRNA modification has been significantly related massive human diseases. Considering effect of m7G-modified long non-coding RNAs (lncRNAs) in HCC progression is unknown, study aims at investigating a prognostic signature improve clinical outcomes for patients HCC. Methods: Two independent databases (TCGA and ICGC) were used analyze RNAseq data patients. First, co-expression analysis was applied obtain m7G-related lncRNAs. Moreover, consensus clustering employed divide into clusters. Then, using least absolute shrinkage selection operator-Cox regression analysis, lncRNA (m7G-LPS) first tested training set then confirmed both testing ICGC sets. The expression levels nine lncRNAs further via real-time PCR cell lines, principal component receiver operating characteristic curve. m7G-LPS could two different risk groups optimal score. Kaplan-Meier curves, tumor mutation burden (TMB), therapeutic effects chemotherapy agents, expressions immune checkpoints performed enhance availability immunotherapeutic treatments Results: A total 1465 associated m7G genes finally selected from TCGA database, through univariate Cox regression, 22 concerning patients' overall survival (OS). whole grouped subgroups, OS Cluster 1 longer than that 2. Furthermore, identified conduct m7G-LPS, which verified. nomogram combined age, gender, grade, stage, showed strong reliability accuracy predicting Finally, checkpoint expression, TMB, several agents remarkably scores. More importantly, TMB-high worst among four groups. Conclusion: model we established validated by abundant algorithms, provided new perspective on tumorigenesis thus improved individualized

Language: Английский

Citations

10
Prediction of Prognosis and Molecular Mechanism of Ferroptosis in Hepatocellular Carcinoma Based on Bioinformatics Methods DOI Creative Commons

Yuanpeng Xiong,

Yonghao Ouyang,

Kang Fang

et al.

Computational and Mathematical Methods in Medicine, Journal Year: 2022, Volume and Issue: 2022, P. 1 - 26

Published: June 21, 2022

As an iron-dependent type of programmed cell death, ferroptosis plays important role in the pathogenesis and progression hepatocellular carcinoma (HCC). Long noncoding RNAs (lncRNAs) have been linked to prognosis patients with HCC a number studies. Nevertheless, predictive value lncRNAs (FRLs) associated has not fully elucidated. Download RNA sequencing data clinical profiles from The Cancer Genome Atlas (TCGA) database. FRLs were determined by Pearson's correlation analysis. After that, prognostic signature for was established using Cox LASSO regression analyses. Meanwhile, survival analysis, analysis clinicopathological features, regression, receiver operating characteristic (ROC) curve, nomogram used analyze FRL signature's capacity. relationship between risk score, immune infiltration, chemotherapy drug sensitivity is further studied. In total, 93 found be HCC. A five-FRL comprising AC015908.3, LINC01138, AC009283.1, Z83851.1, LUCAT1 created order enhance prediction patients. demonstrated good potency, according Kaplan-Meier ROC curves. factor independent various factors stratified high-risk group shown enriched tumorigenesis immune-related pathways GSEA Additionally, checkpoint molecules, half-inhibitory concentrations differed considerably groups, implying that this could evaluate efficacy immunotherapy. helpful assessing improving therapy options, so it can applied clinically.

Language: Английский

Citations

9
Prognostic prediction of head and neck squamous cell carcinoma: Construction of cuproptosis‐related long non‐codingRNAsignature DOI Creative Commons
Qi Huang,

Quanjie You,

Ning Zhu

et al.

Journal of Clinical Laboratory Analysis, Journal Year: 2022, Volume and Issue: 36(11)

Published: Oct. 3, 2022

Recently, a new type of programmed cell death, cuproptosis, has been identified to play important role in the progression tumors. We constructed cuproptosis-related long non-coding RNA (lncRNA) signature predict prognostic significance for head and neck squamous carcinoma (HNSCC).The risk model was developed based on differentially expressed lncRNAs associated with cuproptosis. Principal component analysis used assess validity. The Kaplan-Meier curves were analyzed compare overall survival (OS), disease-specific (DSS), progression-free (PFS) values. multivariate univariate Cox regression analyses evaluate efficiency. Furthermore, functional enrichment, immune infiltration, tumor mutation burden (TMB), sensitivity toward chemotherapy also explored.Six (AL109936.2, CDKN2A-DT, AC090587.1, KLF3-AS1, AL133395.1, LINC01063) construct independent predictor HNSCC. area under curve C-index values obtained using higher than corresponding clinical factors. Analysis indicated that OS, PFS, DSS time recorded patients low-risk group belonging high-risk group. By enrichment analysis, we observed genes enriched response tumor-associated pathways. characterized by score exhibited better infiltration other individuals chemotherapeutic agents (cisplatin, docetaxel, paclitaxel) those group.A lncRNA-based functioned as an prognosis HNSCC constructed. chemosensitivity individual can be potentially predicted this signature.

Language: Английский

Citations

8
Anoikis-related lncRNA signature predicts prognosis and is associated with immune infiltration in hepatocellular carcinoma DOI Creative Commons

Jiahong Zhu,

Wenjing Zhao,

Junkai Yang

et al.

Anti-Cancer Drugs, Journal Year: 2024, Volume and Issue: unknown

Published: March 11, 2024

Anoikis is a programmed cell death process triggered when cells are dislodged from the extracellular matrix. Numerous long noncoding RNAs (lncRNAs) have been identified as significant factors associated with anoikis resistance in various tumor types, including glioma, breast cancer, and bladder cancer. However, relationship between lncRNAs prognosis of hepatocellular carcinoma (HCC) has received limited research attention. Further needed to investigate this potential link understand role progression HCC. We developed prognostic signature based on differential expression implicated A co-expression network anoikis-related mRNAs was established using data obtained The Cancer Genome Atlas (TCGA) for Cox regression analyses were conducted formulate an lncRNA (ARlncSig) training cohort, which subsequently validated both testing cohort combined dataset comprising two cohorts. Receiver operating characteristic curves, nomograms, decision curve ARlncSig score clinical characteristics demonstrated robust predictive ability. Moreover, gene set enrichment analysis revealed several immune processes high-risk group compared low-risk group. Furthermore, differences observed subpopulations, checkpoint genes, response chemotherapy immunotherapy high- groups. Lastly, we levels five included quantitative real-time PCR. In conclusion, our model holds substantial value regarding HCC patients provide guidance individualized immunotherapy. study, 36 genes Gene Ontology Set Enrichment Analysis databases. also 22 differentially expressed that correlated these TCGA. Using analyses, then Additionally, collected eight pairs liver cancer tissues adjacent Affiliated Tumor Hospital Nantong University further analysis. aim study biomarker prognosis. risk stratification system called ARlncSig, uses categorize into low- Patients exhibited significantly lower overall survival rates those model’s performance supported by receiver curve, nomogram calibration, correlation analysis, curve. function, checkpoint, chemotherapy, subpopulations Finally, PCR lncRNAs. demonstrates critical may personalized

Language: Английский

Citations

1