Identification and validation of a novel anoikis-related long non-coding RNA signature for pancreatic adenocarcinoma to predict the prognosis and immune response

Journal of Cancer Research and Clinical Oncology, Год журнала: 2023, Номер 149(16), С. 15069 - 15083

Опубликована: Авг. 24, 2023

Язык: Английский

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A novel PANoptosis-related long non-coding RNA index to predict prognosis, immune microenvironment and personalised treatment in hepatocellular carcinoma

Aging, Год журнала: 2024, Номер unknown

Опубликована: Янв. 26, 2024

Background: PANoptosis is involved in the interaction of apoptosis, necroptosis and pyroptosis, playing a role programmed cell death. Moreover, long non-coding RNAs (lncRNAs) regulate PCD. This work aims to explore PANoptosis-associated lncRNAs hepatocellular carcinoma (HCC). Methods: Co-expression analysis identified HCC. Cox Least Absolute Shrinkage Selection Operator (LASSO) algorithms were utilised filter establish PANoptosis-related lncRNA index (PANRI). Additionally, Cox, Kaplan–Meier receiver operating characteristic (ROC) curves systematically evaluate PANRI. Furthermore, Estimation STromal Immune cells MAlignant Tumor tissues using Expression data (ESTIMATE), single sample gene set enrichment (ssGSEA) immune checkpoints performed analyse potential PANRI differentiating different tumour microenvironment (TIME) populations. The consensus clustering algorithm was used distinguish individuals with HCC having TIME subtypes. Finally, lines HepG2 for further validation vitro experiments. Results: differentiates patients according risk. Notably, ESTIMATE ssGSEA revealed high infiltration status high-risk patients. divided into three clusters identify subtypes TIME. results showed that siRNA-mediated silencing AL049840.4 inhibited viability migration promoted apoptosis. Conclusions: first PANoptosis-related, lncRNA-based risk assess patient prognosis, response immunotherapy. study offers novel perspectives on

Язык: Английский

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Exploration of SUSD3 in pan-cancer: studying its role, predictive analysis, and biological significance in various malignant tumors in humans

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Март 21, 2025

Background The SUSD3 protein, marked by the Sushi domain, plays a key role in cancer progression, with its expression linked to tumor advancement and patient prognosis. Altered levels could serve as predictive biomarker for progression. Recognized novel susceptibility marker, presents promising target antibody-based therapies, offering potential approach prevention, diagnosis, treatment of breast cancer. Methods Using HPA GeneMANIA platforms, distribution protein across tissues was analyzed, while healthy were compared using Cancer Genome Atlas data. TISCH STOmics DB databases facilitated mapping different cell types spatial relationship markers. Univariate Cox regression assessed prognostic significance various cancers. Genomic alterations explored through cBioPortal database. predictor immunotherapy response investigated TIMER2.0, GSEA/GSVA identified related biological pathways. Drugs targeting CellMiner, CTRP, GDSC databases, complemented molecular docking studies. In vitro experiments demonstrated that knockdown lines significantly reduced proliferation migration. Results variations pan-cancer cohorts are closely prognosis malignancies. microenvironment (TME), is predominantly expressed monocytes/macrophages CD4+ T cells. Research indicates strong correlation between biomarkers, immune infiltration, immunomodulatory factors. To explore regulatory role, StromalScore, ImmuneScore, ESTIMATE, Immune Infiltration metrics employed. Molecular studies revealed selumetinib inhibits proliferation. Finally, Conclusion These findings provide valuable insights establish foundation further exploration SUSD3’s pan-carcinomas. Additionally, they offer perspectives targets development innovative therapeutic strategies treatment.

Язык: Английский

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GMIP: A Novel Prognostic Biomarker Influencing Immune Infiltration and Tumour Dynamics Across Cancer Types

Journal of Cellular and Molecular Medicine, Год журнала: 2025, Номер 29(8)

Опубликована: Апрель 1, 2025

ABSTRACT GMIP, a member of the RhoGAP family, plays critical role in cytoskeletal remodelling, cell migration and immune modulation. Its aberrant expression cancers suggests pivotal tumour progression. GMIP was assessed using transcriptomic datasets from GDC UCSC XENA, protein distribution across tissues via HPA GeneMANIA. The TISCH database identified primary GMIP‐expressing types microenvironment. Univariate Cox regression GMIP's prognostic potential, while cBioPortal GSCA explored genomic alterations. TIMER 2.0 used to investigate infiltration regulation. GSEA GSVA unveiled GMIP‐related biological pathways, molecular docking with CellMiner potential drug interactions. In vitro assays confirmed functional relevance breast cancer. exhibits differential multiple cancer types, demonstrating significant implications. is inversely correlated CNV methylation several cancers. closely linked immunotherapy biomarkers suppression, influencing therapeutic responses. Functional studies suggest that inhibition reduces proliferation migration. as promising oncological biomarker, particularly cancer, especially pronounced BRCA‐mutated tumours, underscoring its for novel anticancer interventions.

Язык: Английский

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

Biochemistry and Biophysics Reports, Год журнала: 2023, Номер 37, С. 101600 - 101600

Опубликована: Дек. 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.

Язык: Английский

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Predicting the immunity landscape and prognosis with an NCLs signature in liver hepatocellular carcinoma

PLoS ONE, Год журнала: 2024, Номер 19(4), С. e0298775 - e0298775

Опубликована: Апрель 25, 2024

Background Activated neutrophils release depolymerized chromatin and protein particles into the extracellular space, forming reticular Neutrophil Extracellular Traps (NETs). This process is accompanied by programmed inflammatory cell death of neutrophils, known as NETosis. Previous reports have demonstrated that NETosis plays a significant role in immune resistance microenvironmental regulation cancer. study sought to characterize function molecular mechanism NETosis-correlated long non-coding RNAs (NCLs) prognostic treatment liver hepatocellular carcinoma (LIHC). Methods We obtained transcriptomic clinical data from The Cancer Genome Atlas (TCGA) evaluated expression NCLs LIHC. A signature was constructed using Cox Last Absolute Shrinkage Selection Operator (Lasso) regression, while accuracy model validated ROC curves nomogram, etc. In addition, we analyzed associations between oncogenic mutation, infiltration evasion. Finally, LIHC patients were classified four subgroups based on consensus cluster analysis, drug sensitivity predicted. Results After screening, established risk combining 5 hub-NCLs its reliability. Independence checks suggest may serve an independent predictor prognosis. Enrichment analysis revealed concentration immune-related pathways high-risk group. Immune indicates immunotherapy could be more effective low-risk Upon consistent subgroup 4 presented better Sensitivity tests showed distinctions therapeutic effectiveness among various drugs different subgroups. Conclusion Overall, developed can discriminate through selected NCLs, with objective providing precise, personalized regimen.

Язык: Английский

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Cervical cancer‐specific long non‐coding RNA landscape reveals the favorable prognosis predictive performance of an ion‐channel‐related signature model

Cancer Medicine, Год журнала: 2024, Номер 13(11)

Опубликована: Июнь 1, 2024

Abstract Background Ion channels play an important role in tumorigenesis and progression of cervical cancer. Multiple long non‐coding RNA genes are widely involved ion channel‐related signaling regulation. However, the association potential clinical application lncRNAs prognosis cancer still poorly explored. Methods Thirteen patients with were enrolled current study. Whole transcriptome (involving both mRNAs lncRNAs) sequencing was performed on fresh tumor adjacent normal tissues that surgically resected from patients. A comprehensive cancer‐specific lncRNA landscape obtained by our custom pipeline. Then, a prognostic scoring model ion‐channel‐related established regression algorithms. The performance predictive as well its characteristics microenvironment (TME) status further evaluated. Results To comprehensively identify lncRNAs, we sequenced 26 samples integrated transcriptomic results. We built analysis pipeline to improve accuracy identification functional annotation 18,482 novel 159 channel‐ tumorigenesis‐related (ICTR‐) identified. Based nine ICTR‐lncRNAs, also validated robustness assessing Besides, TME characterized, found B cells, activated CD8+ T, tertiary lymphoid structures significantly associated ICTR‐lncRNAs signature scores. Conclusion provided thorough lncRNAs. Through integrative analyses, identified for Meanwhile, characterized status. This study improved knowledge prominent roles regulating channel

Язык: Английский

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Identification and validation of a cancer-associated fibroblasts-related scoring system to predict prognosis and immune landscape in hepatocellular carcinoma through integrated analysis of single-cell and bulk RNA-sequencing

Aging, Год журнала: 2023, Номер unknown

Опубликована: Окт. 18, 2023

Cancer-associated fibroblasts (CAFs) regulate the malignant biological behaviour of hepatocellular carcinoma (HCC) as a significant component tumour immune microenvironment (TIME). This study aimed to develop CAFs-based scoring system predict prognosis and TIME patients with HCC.Data for TCGA-LIHC GSE14520 cohorts were downloaded from The Cancer Genome Atlas Gene Expression Omnibus databases. Single-cell RNA-sequencing data HCC samples retrieved GSE166635 cohort. Least Absolute Shrinkage Selection Operator algorithm was employed CAFs-related (CAFRss). predictive value CAFRss determined using Kaplan-Meier, Cox regression Receiver Operating Characteristic curves. Additionally, TIMER platform, single sample Set Enrichment Analysis Estimation STromal Immune cells in MAlignant Tumour tissues algorithms performed determine landscape. Finally, pRRophic utilised drug sensitivity analysis.The evaluation demonstrated its superior ability clinical outcome HCC. effectively distinguished populations distinct landscapes. Furthermore, CAFRss-based risk stratification identified individuals 'hot tumours' predicted survival treated ICBs.The developed can serve tool determining differentiating diverse characteristics.

Язык: Английский

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Comprehensive analysis of cuproptosis-related long non-coding RNAs in prognosis, immune microenvironment infiltration and chemotherapy response of hepatocellular carcinoma

Medicine, Год журнала: 2023, Номер 102(50), С. e36611 - e36611

Опубликована: Дек. 15, 2023

The objective of this study is to explore the relationship between cuproptosis-related long noncoding RNAs (lncRNAs) in hepatocellular carcinoma (HCC). RNA-seq data, including lncRNAs and related clinical information HCC patients, were downloaded from Cancer Genome Atlas database. A signature composed 3 was constructed by LASSO analysis, patients classified into high- low-risk groups. Patients high-risk group had a poorer prognosis compared with group. Univariate Cox multivariate regression analyses confirmed that model an independent risk factor other biomarkers. Furthermore, gene set enrichment analysis indicated metabolism-related pathways enriched group, drug metabolism, fatty acid metabolism. Further research demonstrated there markedly differences response Immune showed most type immune cells immunological function different risk-group. Finally, TP53 mutation rate tumor mutational burden higher In conclusion, we prognostic based on expression predict patients' prognosis, microenvironment, further will be conducted uncover mechanisms.

Язык: Английский

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Comprehensive assessment of regulatory T-cells-related scoring system for predicting the prognosis, immune microenvironment and therapeutic response in hepatocellular carcinoma

Aging, Год журнала: 2024, Номер 16(6), С. 5288 - 5310

Опубликована: Март 8, 2024

Introduction: Regulatory T cells (Tregs) play important roles in tumor immunosuppression and immune escape. The aim of the present study was to construct a novel Tregs-associated biomarker for prediction tumour microenvironment (TIME), clinical outcomes, individualised treatment hepatocellular carcinoma (HCC). Methods: Single-cell sequencing data were obtained from three independent cohorts. Cox LASSO regression utilised develop Tregs Related Scoring System (TRSSys). GSE140520, ICGC-LIRI CHCC cohorts used validation TRSSys. Kaplan-Meier, ROC, evaluation ESTIMATE, TIMER 2.0, ssGSEA algorithm determine value TRSSys predicting TIME. GSVA, GO, KEGG, TMB analyses mechanistic exploration. Finally, drug sensitivity evaluated based on oncoPredict algorithm. pResults: Comprehensive showed that had good prognostic predictive efficacy applicability. Additionally, ssGSEA, ESTIMATE suggested could help distinguish different TIME subtypes beneficiary population immunotherapy. suggests provides basis treatment. Conclusions: constructed current is HCC with stability. risk stratification can identify landscape provide individualized options.

Язык: Английский

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