Aggrephagy-related gene signature correlates with survival and tumor-associated macrophages in glioma: Insights from single-cell and bulk RNA sequencing DOI Creative Commons
Xiaowei Zhang,

Jiayu Tan,

Xinyu Zhang

et al.

Mathematical Biosciences & Engineering, Journal Year: 2024, Volume and Issue: 21(2), P. 2407 - 2431

Published: Jan. 1, 2024

<abstract> <p><italic>Background:</italic> Aggrephagy is a lysosome-dependent process that degrades misfolded protein condensates to maintain cancer cell homeostasis. Despite its importance in cellular quality control, the role of aggrephagy glioma remains poorly understood. <italic>Objective:</italic> To investigate expression aggrephagy-related genes (ARGs) and different types gliomas develop an ARGs-based prognostic signature predict prognosis, tumor microenvironment, immunotherapy response gliomas. <italic>Methods:</italic> ARGs were identified by searching Reactome database. We developed (ARPS) using data from Cancer Genome Atlas (TCGA, n = 669) Lasso-Cox regression. validated robustness clinical subgroups CGGA cohorts (n 970). Gene set enrichment analysis (GSEA) was used identify pathways enriched ARPS subgroups. The correlations between macrophages also investigated at single level. <italic>Results:</italic> A total 44 showed heterogeneous among Five (HSF1, DYNC1H1, DYNLL2, TUBB6, TUBA1C) ARPS, independent factor. GSEA gene sets patients with high-ARPS mostly cycle, DNA replication, immune-related pathways. High-ARPS subgroup had higher immune infiltration states, particularly macrophages, Treg cells, neutrophils. APRS positive association mutation burden (TMB) predictors. At level, we found correlated macrophage development ARGs-mediated subtypes distinct communication characteristics cells. VIM+ as pro-inflammatory interactions malignant <italic>Conclusion:</italic> novel based on for predicting response. highlight exhibit classical features. </p> </abstract>

Language: Английский

Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment DOI Creative Commons
Han Luo, Xuyang Xia, Li‐Bin Huang

et al.

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

Published: Nov. 4, 2022

Abstract Cancer-associated fibroblasts (CAFs) are the predominant components of tumor microenvironment (TME) and influence cancer hallmarks, but without systematic investigation on their ubiquitous characteristics across different types. Here, we perform pan-cancer analysis 226 samples 10 solid types to profile TME at single-cell resolution, illustrating commonalities/plasticity heterogenous CAFs. Activation trajectory major CAF is divided into three states, exhibiting distinct interactions with other cell components, relating prognosis immunotherapy. Moreover, minor represent alternative origin from (e.g., endothelia macrophages). Particularly, presentation endothelial-to-mesenchymal transition CAF, which may interact proximal SPP 1 + tumor-associated macrophages, implicated in survival stratifications. Our study comprehensively profiles shared dynamics CAFs, highlight heterogeneity plasticity Browser integrated information available https://gist-fgl.github.io/sc-caf-atlas/ .

Language: Английский

Citations

296
Advances in single-cell RNA sequencing and its applications in cancer research DOI Creative Commons
Dezhi Huang,

Naya Ma,

Xinlei Li

et al.

Journal of Hematology & Oncology, Journal Year: 2023, Volume and Issue: 16(1)

Published: Aug. 24, 2023

Abstract Cancers are a group of heterogeneous diseases characterized by the acquisition functional capabilities during transition from normal to neoplastic state. Powerful experimental and computational tools can be applied elucidate mechanisms occurrence, progression, metastasis, drug resistance; however, challenges remain. Bulk RNA sequencing techniques only reflect average gene expression in sample, making it difficult understand tumor heterogeneity microenvironment. The emergence development single-cell (scRNA-seq) technologies have provided opportunities subtle changes biology identifying distinct cell subpopulations, dissecting microenvironment, characterizing cellular genomic mutations. Recently, scRNA-seq technology has been increasingly used cancer studies explore which increased understanding tumorigenesis evolution. This review summarizes basic processes their increasing applications research clinical practice.

Language: Английский

Citations

85
Research Trends and Dynamics in Single-cell RNA Sequencing for Musculoskeletal Diseases: A Scientometric and Visualization Study DOI Creative Commons
Siyang Cao, Yihao Wei, Yaohang Yue

et al.

International Journal of Medical Sciences, Journal Year: 2025, Volume and Issue: 22(3), P. 528 - 550

Published: Jan. 1, 2025

Background: Worldwide, approximately 1.7 billion people are afflicted with musculoskeletal (MSK) diseases, posing significant health challenges. The introduction of single-cell RNA sequencing (scRNA-seq) technology provides novel insights and approaches to comprehend the onset, progression, treatment MSK diseases. Nevertheless, there is a remarkable lack analytical descriptive studies regarding trajectory, essential research directions, current situation, pivotal focuses, upcoming perspectives. Therefore, aim this present comprehensive overview advancements made in scRNA-seq for disorders over past 15 years. Methods: It utilizes robust dataset derived from Web Science Core Collection, encompassing January 1, 2009, through September 6, 2024. To achieve this, advanced methodologies were applied conduct thorough scientometric visual analyses. Results: findings underscore preeminent role China, which contributes 63.49% total publications, thereby exerting substantial impact within domain. Notable contributions came institutions such as Shanghai Jiao Tong University, Sun Yat-sen Harvard Medical School, Liu Yun being leading contributor. Frontiers Immunology published greatest number papers field. This study identified joint bone neoplasms, fractures, intervertebral disc degeneration main focuses. Conclusion: extensive analysis benefits both experienced novice researchers by facilitating immediate access critical data, fostering innovation

Language: Английский

Citations

3
Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research DOI Creative Commons
Han‐Eol Park,

Song Hyun Jo,

Rosalind H. Lee

et al.

Advanced Science, Journal Year: 2023, Volume and Issue: 10(16)

Published: April 7, 2023

Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization transcripts and related analyses in various applications for biological systems. By transitioning from conventional studies to "in situ" biology, can provide transcriptome-scale information. Currently, ability simultaneously characterize gene expression profiles cells relevant cellular environment paradigm shift studies. In this review, recent progress its neuroscience cancer are highlighted. Technical aspects existing technologies future directions new developments (as March 2023), computational analysis transcriptome data, application notes studies, discussions regarding multi-omics their expanding roles biomedical emphasized.

Language: Английский

Citations

40
From immunology to artificial intelligence: revolutionizing latent tuberculosis infection diagnosis with machine learning DOI Creative Commons
Linsheng Li,

Ling Yang,

Zhuang Li

et al.

Military Medical Research, Journal Year: 2023, Volume and Issue: 10(1)

Published: Nov. 28, 2023

Latent tuberculosis infection (LTBI) has become a major source of active (ATB). Although the tuberculin skin test and interferon-gamma release assay can be used to diagnose LTBI, these methods only differentiate infected individuals from healthy ones but cannot discriminate between LTBI ATB. Thus, diagnosis faces many challenges, such as lack effective biomarkers Mycobacterium (MTB) for distinguishing low diagnostic efficacy derived human host, absence gold standard Sputum culture, diagnosing tuberculosis, is time-consuming distinguish ATB LTBI. In this article, we review pathogenesis MTB immune mechanisms host in including innate adaptive responses, multiple evasion MTB, epigenetic regulation. Based on knowledge, summarize current status challenges present application machine learning (ML) diagnosis, well advantages limitations ML context. Finally, discuss future development directions applied diagnosis.

Language: Английский

Citations

32
Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity DOI Creative Commons

Yuhua Hu,

Feng Shen, Xi Yang

et al.

Clinical Epigenetics, Journal Year: 2023, Volume and Issue: 15(1)

Published: Oct. 11, 2023

Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as fundamental drivers carcinogenesis. However, recent research has shed light on crucial role epigenomic alterations in various cell types present within tumor microenvironment, suggesting their potential contribution formation and progression. Despite these significant findings, progress understanding epigenetic mechanisms regulating heterogeneity been impeded over past few years due lack appropriate technical tools methodologies.The emergence single-cell sequencing enhanced our governing by revealing distinct layers individual (chromatin accessibility, DNA/RNA methylation, histone modifications, nucleosome localization) diverse omics (transcriptomics, genomics, multi-omics) at level. These technologies provide us with new insights into molecular basis intratumoral help uncover key events driving development.This paper provides a comprehensive review emerging analytical experimental approaches omics, focusing specifically epigenomics. capture integrate multiple dimensions cells, thereby features. Additionally, this outlines future trends current limitations.

Language: Английский

Citations

28
Germinal center B-cell subgroups in the tumor microenvironment cannot be overlooked: their involvement in prognosis, immunotherapy response, and treatment resistance in head and neck squamous carcinoma DOI Creative Commons
Lin Li,

Jiani Zou,

Shengbin Pei

et al.

Heliyon, Journal Year: 2024, Volume and Issue: 10(19), P. e37726 - e37726

Published: Sept. 11, 2024

Language: Английский

Citations

14
Single‐cell RNA sequencing elucidated the landscape of breast cancer brain metastases and identified ILF2 as a potential therapeutic target DOI Creative Commons
Jindong Xie, Anli Yang, Qianwen Liu

et al.

Cell Proliferation, Journal Year: 2024, Volume and Issue: 57(11)

Published: June 29, 2024

Abstract Distant metastasis remains the primary cause of morbidity in patients with breast cancer. Hence, development more efficacious strategies and exploration potential targets for metastatic cancer are urgently needed. The data six brain metastases (BCBrM) from two centres were collected, a comprehensive landscape entire tumour ecosystem was generated through utilisation single‐cell RNA sequencing. We utilised Monocle2 CellChat algorithms to investigate interrelationships among each subcluster. In addition, multiple signatures collected evaluate key components subclusters multi‐omics methodologies. Finally, we elucidated common expression programs malignant cells, experiments conducted vitro vivo determine functions interleukin enhancer‐binding factor 2 ( ILF2 ), which is gene module, BCBrM progression. found that major cell type exhibited diverse characteristics. Besides, our study indicated specifically associated BCBrM, experimental validations further demonstrated deficiency hindered Our offers novel perspectives on heterogeneity suggests could serve as promising biomarker or therapeutic target BCBrM.

Language: Английский

Citations

13
Natural products and derivatives in renal, urothelial and testicular cancers: Targeting signaling pathways and therapeutic potential DOI
Dengxiong Li, Jie Wang,

Zhouting Tuo

et al.

Phytomedicine, Journal Year: 2024, Volume and Issue: 127, P. 155503 - 155503

Published: Feb. 28, 2024

Language: Английский

Citations

11
Efficiency of transurethral en‐bloc resection vs. conventional transurethral resection for non‐muscle‐invasive bladder cancer: An umbrella review DOI Creative Commons
Dengxiong Li, Qingxin Yu,

Ruicheng Wu

et al.

Cancer Medicine, Journal Year: 2024, Volume and Issue: 13(11)

Published: May 31, 2024

Abstract Background En‐Bloc transurethral resection of bladder tumor (ERBT) was clinically used to resect non‐muscle‐invasive cancer (NMIBC). However, discrepancies persist regarding the comparisons between ERBT and conventional (cTURBT). Methods We conducted a comprehensive search in PubMed, Embase, Web Science, Cochrane Database Systematic Reviews, performed manual searches reference lists collect extract data. Data evaluation carried out using Review Manager 5.4.0, Rx64 4.1.3, relevant packages. Results There were nine eligible meta‐analyses RCTs our study. NMIBC patients undergoing significant associated with lower rate perforation obturator nerve reflex compared those receiving cTURBT. Our pooled result indicated that cTURBT required similar operation time. Regarding postoperative outcomes, demonstrated superior performance terms detrusor muscle presence, catheterization time, residual tumor. exhibited higher three‐month recurrence‐free survival (RFS) ( p < 0.05; I 2 = 0%). In bipolar subgroup, had better 12‐month RFS than Simultaneously, exclusion Hybrid Knife data revealed improvement 50%). Conclusion Using combination umbrella review meta‐analysis, we or comparable perioperative outcome improved 3 12 month suggest maybe surgical method for

Language: Английский

Citations

11