Long Non-Coding RNA Profile Study Identifies an Immune-Related lncRNA Prognostic Signature for Kidney Renal Clear Cell Carcinoma DOI Creative Commons

Zhuolun Sun,

Changying Jing, Chutian Xiao

et al.

Frontiers in Oncology, Journal Year: 2020, Volume and Issue: 10

Published: Aug. 20, 2020

Kidney renal clear cell carcinoma (KIRC) is the predominant pathological subtype of (RCC) in adults. Long non-coding RNAs (lncRNAs) are an important class gene expression regulators and serve fundamental roles immune regulation. The intent this study to develop a novel immune-related lncRNA signature accurately predict prognosis for KIRC patients. Here, we performed genome-wide comparative analysis profiles 537 patients from Cancer Genome Atlas (TCGA) database. Cox regression model-identified lncRNAs were extracted constructing five (AC008105.3, LINC02084, AC243960.1, AC093278.2, AC108449.2) with ability Univariate multivariate analyses demonstrated that could act as independent prognostic predictor overall survival (OS). With further investigation on different clinicopathological parameters, found divide samples into high-risk groups shorter OS low-risk longer subgroups. Principal component suggested drew distinction between high- based lncRNAs. status two was observed set enrichment ESTIMATE algorithm. Except expressions other four significantly upregulated tumor tissues. In summary, identified immune-lncRNA had clinical implications prediction be exploited underlying therapeutic targets

Language: Английский

LncRNA‐mediated posttranslational modifications and reprogramming of energy metabolism in cancer DOI Creative Commons

Yue‐Tao Tan,

Jin‐Fei Lin,

Ting Li

et al.

Cancer Communications, Journal Year: 2020, Volume and Issue: 41(2), P. 109 - 120

Published: Oct. 29, 2020

Abstract Altered metabolism is a hallmark of cancer, and the reprogramming energy has historically been considered general phenomenon tumors. It well recognized that long noncoding RNAs (lncRNAs) regulate in cancer. However, lncRNA‐mediated posttranslational modifications metabolic are unclear at present. In this review, we summarized current understanding interactions between alterations cancer‐associated enzymes, transcription factors, other proteins involved pathways. addition, discuss mechanisms through which these contribute to tumor initiation progression, key roles clinical significance functional lncRNAs. We believe an in‐depth cancer can help identify cellular vulnerabilities be exploited for diagnosis therapy.

Language: Английский

Citations

496
Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer DOI Creative Commons
Zaoqu Liu, Long Liu, Siyuan Weng

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 10, 2022

Long noncoding RNAs (lncRNAs) are recently implicated in modifying immunology colorectal cancer (CRC). Nevertheless, the clinical significance of immune-related lncRNAs remains largely unexplored. In this study, we develope a machine learning-based integrative procedure for constructing consensus lncRNA signature (IRLS). IRLS is an independent risk factor overall survival and displays stable powerful performance, but only demonstrates limited predictive value relapse-free survival. Additionally, possesses distinctly superior accuracy than traditional variables, molecular features, 109 published signatures. Besides, high-risk group sensitive to fluorouracil-based adjuvant chemotherapy, while low-risk benefits more from bevacizumab. Notably, abundant lymphocyte infiltration, high expression CD8A PD-L1, response pembrolizumab. Taken together, could serve as robust promising tool improve outcomes individual CRC patients.

Language: Английский

Citations

438
Tumor immune microenvironment lncRNAs DOI Creative Commons

Eun-Gyeong Park,

Sung-Jin Pyo,

Youxi Cui

et al.

Briefings in Bioinformatics, Journal Year: 2021, Volume and Issue: 23(1)

Published: Nov. 5, 2021

Abstract Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression other functional evidence support the idea that lncRNAs have distinct cellular functions tumor microenvironment (TIME). To date, majority lncRNA studies heavily relied on bulk RNA-sequencing data which various types contribute to an averaged signal, limiting discovery functions. Single-cell (scRNA-seq) is a potential solution for tackling this limitation despite lack annotations low abundance yet lncRNAs. Hence, updated further understanding will be necessary characterizing genes TIME. In review, we discuss specifically expressed cells, summarize regulatory at type level highlight how scRNA-seq approach can help study TIME

Language: Английский

Citations

156
Integrative analysis from multi-center studies identities a consensus machine learning-derived lncRNA signature for stage II/III colorectal cancer DOI
Zaoqu Liu, Chunguang Guo, Qin Dang

et al.

EBioMedicine, Journal Year: 2021, Volume and Issue: 75, P. 103750 - 103750

Published: Dec. 15, 2021

Language: Английский

Citations

122
BABEL enables cross-modality translation between multiomic profiles at single-cell resolution DOI Creative Commons
Kevin Wu, Kathryn E. Yost, Howard Y. Chang

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(15)

Published: April 7, 2021

Simultaneous profiling of multiomic modalities within a single cell is grand challenge for single-cell biology. While there have been impressive technical innovations demonstrating feasibility-for example, generating paired measurements transcriptome (single-cell RNA sequencing [scRNA-seq]) and chromatin accessibility assay transposase-accessible using [scATAC-seq])-widespread application joint challenging due to its experimental complexity, noise, cost. Here, we introduce BABEL, deep learning method that translates between the profiles cell. Leveraging an interoperable neural network model, BABEL can predict expression directly from cell's scATAC-seq vice versa after training on relevant data. This makes it possible computationally synthesize when only one modality experimentally available. Across several ATAC gene datasets in human mouse, validate accurately these individual cells. also generalizes well types new biological contexts not seen during training. Starting patient-derived basal carcinoma (BCC), generated enabled fine-grained classification complex states, despite having never BCC These predictions are comparable analyses scRNA-seq data diverse related BABEL's We further show incorporate additional modalities, such as protein epitope profiling, thus enabling translation across chromatin, RNA, protein. offers powerful approach exploration hypothesis generation.

Language: Английский

Citations

105
The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer DOI Creative Commons
Vincenza Ylenia Cusenza, Annalisa Tameni, Antonino Neri

et al.

Frontiers in Oncology, Journal Year: 2023, Volume and Issue: 13

Published: March 9, 2023

Most of our transcribed RNAs are represented by non-coding sequences. Long (lncRNAs) transcripts with no or very limited protein coding ability and a length >200nt. They can be epigenetically modified. N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G) 2’-O-methylation (Nm) some the lncRNAs epigenetic modifications. The modifications RNA controlled three classes enzymes, each playing role in specific phase modification. These enzymes defined as “writers”, “readers” “erasers”. m6A m5C most studied RNA. alter structure properties, thus modulating functions interactions lncRNAs. aberrant expression several is linked to development variety cancers signatures m6A- m5C-related increasingly recognized potential biomarkers prognosis, predictors disease stage overall survival. In present manuscript, up date literature reviewed focus on their significance cancer.

Language: Английский

Citations

42
The function of LncRNAs and their role in the prediction, diagnosis, and prognosis of lung cancer DOI Creative Commons
Yu Chen, Emory Zitello,

Rui Guo

et al.

Clinical and Translational Medicine, Journal Year: 2021, Volume and Issue: 11(4)

Published: April 1, 2021

Abstract Lung cancer remains a major threat to human health. Low dose CT scan (LDCT) has become the main method of early screening for lung due low sensitivity chest X‐ray. However, LDCT not only high false positive rate, but also entails risks overdiagnosis and cumulative radiation exposure. In addition, by subsequent follow‐up can increase risk cancer. Many studies have shown that long noncoding RNAs (lncRNAs) remain stable in blood, profiling blood advantages being noninvasive, readily accessible inexpensive. Serum or plasma assay lncRNAs be used as novel detection assist while improving accuracy screening. LncRNAs participate regulation various biological processes. A large number researches reported are key regulators involved progression cancers through multiple action models. Especially, some affect hallmarks addition their diagnostic value, possess promising potential other clinical applications toward predictive markers chemosensitivity, radiosensitivity, epidermal growth factor receptor (EGFR)‐targeted therapy, well prognosis. Different been implicated regulate EGFR‐targeted therapy diverse mechanisms. Although many challenges need addressed future, bright prospects an adjunct radiographic methods management

Language: Английский

Citations

85
Identification of immune-related LncRNA for predicting prognosis and immunotherapeutic response in bladder cancer DOI Creative Commons
Yucai Wu, Lei Zhang, Shiming He

et al.

Aging, Journal Year: 2020, Volume and Issue: unknown

Published: Nov. 18, 2020

Long noncoding RNAs (lncRNAs) have multiple functions in the cancer immunity response and tumor microenvironment.To investigate immune-related lncRNA (IRlncRNA) signature for predicting prognosis immunotherapeutic bladder (BLCA), we extracted BLCA data from The Cancer Genome Atlas (TCGA) database.Finally, a total of 405 cases were enrolled 8 prognostic IRlncRNAs (MIR181A2HG, AC114730.3,LINC00892, PTPRD-AS1, LINC01013, MRPL23-AS1, LINC01395, AC002454.1)were identified training set.Risk scores calculated to divide patients into high-risk low-risk groups, tended poor overall survival (OS).Multivariate Cox regression analysis confirmed that IRlncRNA could be an independent factor.The results subsequently validating set.Additionally, this 8-IRlncRNA classifier was related recurrence free (RFS) BLCA.Functional characterization revealed mediated phenotype.This also associated with immune cell infiltration (i.e., macrophages M0, M2, Tregs, CD8 T cells, neutrophils) checkpoint inhibitors (ICIs) immunotherapy-related biomarkers [mismatch repair (MMR) genes, mutation burden (TMB) genes].The present study highlighted value as predictor BLCA.

Language: Английский

Citations

82
miRNAs and lncRNAs as Novel Therapeutic Targets to Improve Cancer Immunotherapy DOI Open Access
Maria Teresa Di Martino, Caterina Riillo, Francesca Scionti

et al.

Cancers, Journal Year: 2021, Volume and Issue: 13(7), P. 1587 - 1587

Published: March 30, 2021

Immunotherapy is presently one of the most promising areas investigation and development for treatment cancer. While immune checkpoint-blocking monoclonal antibodies chimeric antigen receptor (CAR) T-cell-based therapy have recently provided in some cases valuable therapeutic options, goal cure has not yet been achieved malignancies more efforts are urgently needed. Noncoding RNAs (ncRNA), including microRNAs (miRNAs) long noncoding (lncRNAs), regulate several biological processes via selective targeting crucial molecular signaling pathways. Recently, key roles miRNA lncRNAs as regulators immune-response cancer progressively emerged, since they may act (i) by shaping intrinsic tumor cell microenvironment (TME) properties; (ii) regulating angiogenesis, immune-escape, epithelial-to-mesenchymal transition, invasion, drug resistance; (iii) acting potential biomarkers prognostic assessment prediction response to immunotherapy. In this review, we provide an overview on role ncRNAs modulating TME. We discuss use or targets clinical translation new therapeutics. Finally, combinatory approaches based ncRNA agents immune-checkpoint inhibitor CAR-T experimental human

Language: Английский

Citations

71
Increased TIGIT expressing NK cells with dysfunctional phenotype in AML patients correlated with poor prognosis DOI

Guanfang Liu,

Qi Zhang, Jingying Yang

et al.

Cancer Immunology Immunotherapy, Journal Year: 2021, Volume and Issue: 71(2), P. 277 - 287

Published: June 15, 2021

Language: Английский

Citations

59