Single-cell sequencing and bulk RNA data reveal the tumor microenvironment infiltration characteristics of disulfidptosis related genes in breast cancer

Chen, Yongxing; Jin, Can; Cui, Jiaxue; Diao, Yizhuo; Wang, Ruiqi; Xu, Rongxuan; Yao, Zhihan; Wu, Wei; Li, Xiaofeng

doi:10.1007/s00432-023-05109-y

Cited by 8 publications

(3 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This presents a novel therapeutic strategy for cancer treatment. While the exact molecular mechanisms of disulfidptosis in tumors require further investigation, a tumor prognosis model based on it has been outlined [ [37] , [38] , [39] ].…”

Section: Discussionmentioning

confidence: 99%

The development of prognostic gene markers associated with disulfidptosis in gastric cancer and their application in predicting drug response

Liu,

2024

Heliyon

View full text Add to dashboard Cite

Section: Discussionmentioning

confidence: 99%

The development of prognostic gene markers associated with disulfidptosis in gastric cancer and their application in predicting drug response

Liu,

2024

Heliyon

View full text Add to dashboard Cite

“…The hdWGCNA is an advanced computational framework designed to analyze and interpret high-dimensional transcriptomics data, such as single-cell RNA-seq or spatial transcriptomics (18). hdWGCNA was used in multiple cancer (including pancreatic cancer, breast cancer, and gastric cancer) (19)(20)(21). So far, hdWGCNA combining single-cell RNA sequencing has not been reported in sepsis.…”

Section: Discussionmentioning

confidence: 99%

Integrated multi-omics and artificial intelligence to explore new neutrophils clusters and potential biomarkers in sepsis with experimental validation

Xu,

Tao,

Zhang

2024

Front. Immunol.

View full text Add to dashboard Cite

BackgroundSepsis, causing serious organ and tissue damage and even death, has not been fully elucidated. Therefore, understanding the key mechanisms underlying sepsis-associated immune responses would lead to more potential therapeutic strategies.MethodsSingle-cell RNA data of 4 sepsis patients and 2 healthy controls in the GSE167363 data set were studied. The pseudotemporal trajectory analyzed neutrophil clusters under sepsis. Using the hdWGCNA method, key gene modules of neutrophils were explored. Multiple machine learning methods were used to screen and validate hub genes for neutrophils. SCENIC was then used to explore transcription factors regulating hub genes. Finally, quantitative reverse transcription-polymerase chain reaction was to validate mRNA expression of hub genes in peripheral blood neutrophils of two mice sepsis models.ResultsWe discovered two novel neutrophil subtypes with a significant increase under sepsis. These two neutrophil subtypes were enriched in the late state during neutrophils differentiation. The hdWGCNA analysis of neutrophils unveiled that 3 distinct modules (Turquoise, brown, and blue modules) were closely correlated with two neutrophil subtypes. 8 machine learning methods revealed 8 hub genes with high accuracy and robustness (ALPL, ACTB, CD177, GAPDH, SLC25A37, S100A8, S100A9, and STXBP2). The SCENIC analysis revealed that APLP, CD177, GAPDH, S100A9, and STXBP2 were significant associated with various transcriptional factors. Finally, ALPL, CD177, S100A8, S100A9, and STXBP2 significantly up regulated in peripheral blood neutrophils of CLP and LPS-induced sepsis mice models.ConclusionsOur research discovered new clusters of neutrophils in sepsis. These five hub genes provide novel biomarkers targeting neutrophils for the treatment of sepsis.

show abstract

“…Chen et al studied the tumor immune microenvironment infiltration characteristics of disulfidptosis-related genes in breast cancer and reported that TNFRSF14, among disulfidptosis-related genes, serves as a key regulatory gene. Targeting TNFRSF14 alongside immune checkpoint inhibition was observed to inhibit tumor proliferation and induce disulfidptosis in tumor cells (89). Alterations in characteristic tumor biomarkers are closely related to tumor occurrence and development (90).…”

Section: Discussionmentioning

confidence: 99%

Single-cell disulfidptosis regulator patterns guide intercellular communication of tumor microenvironment that contribute to kidney renal clear cell carcinoma progression and immunotherapy

Xu,

Li,

Qian

et al. 2024

Front. Immunol.

View full text Add to dashboard Cite

BackgroundDisulfidptosis, an emerging type of programmed cell death, plays a pivotal role in various cancer types, notably impacting the progression of kidney renal clear cell carcinoma (KIRC) through the tumor microenvironment (TME). However, the specific involvement of disulfidptosis within the TME remains elusive.MethodsAnalyzing 41,784 single cells obtained from seven samples of KIRC through single-cell RNA sequencing (scRNA-seq), this study employed nonnegative matrix factorization (NMF) to assess 24 disulfidptosis regulators. Pseudotime analysis, intercellular communication mapping, determination of transcription factor activities (TFs), and metabolic profiling of the TME subgroup in KIRC were conducted using Monocle, CellChat, SCENIC, and scMetabolism. Additionally, public cohorts were utilized to predict prognosis and immune responses within the TME subgroup of KIRC.ResultsThrough NMF clustering and differential expression marker genes, fibroblasts, macrophages, monocytes, T cells, and B cells were categorized into four to six distinct subgroups. Furthermore, this investigation revealed the correlation between disulfidptosis regulatory factors and the biological traits, as well as the pseudotime trajectories of TME subgroups. Notably, disulfidptosis-mediated TME subgroups (DSTN+CD4T-C1 and FLNA+CD4T-C2) demonstrated significant prognostic value and immune responses in patients with KIRC. Multiple immunohistochemistry (mIHC) assays identified marker expression within both cell clusters. Moreover, CellChat analysis unveiled diverse and extensive interactions between disulfidptosis-mediated TME subgroups and tumor epithelial cells, highlighting the TNFSF12-TNFRSF12A ligand-receptor pair as mediators between DSTN+CD4T-C1, FLNA+CD4T-C2, and epithelial cells.ConclusionOur study sheds light on the role of disulfidptosis-mediated intercellular communication in regulating the biological characteristics of the TME. These findings offer valuable insights for patients with KIRC, potentially guiding personalized immunotherapy approaches.

show abstract

Single-cell sequencing and bulk RNA data reveal the tumor microenvironment infiltration characteristics of disulfidptosis related genes in breast cancer

Cited by 8 publications

References 54 publications

The development of prognostic gene markers associated with disulfidptosis in gastric cancer and their application in predicting drug response

The development of prognostic gene markers associated with disulfidptosis in gastric cancer and their application in predicting drug response

Integrated multi-omics and artificial intelligence to explore new neutrophils clusters and potential biomarkers in sepsis with experimental validation

Single-cell disulfidptosis regulator patterns guide intercellular communication of tumor microenvironment that contribute to kidney renal clear cell carcinoma progression and immunotherapy

Contact Info

Product

Resources

About