Multi-omics characterization of a scoring system to quantify hypoxia patterns in patients with head and neck squamous cell carcinoma DOI Creative Commons
Cong Peng, Huiping Ye, Zhengyang Li

et al.

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 3, 2022

Abstract The 5-year survival rate of patients with head and neck squamous cell carcinoma (HNSCC) remains <50% due to risk the recurrence metastasis. Hypoxia patterns are a hallmark HNSCC that associated its occurrence progression. However, precise role hypoxia during HNSCC, such as relationship between hypoxia, tumor immune landscape communication orchestration largely unknown. current study integrated data from bulk single-cell RNA sequencing analyses define HNSCC. First, scoring system named score (HS) was constructed based on hypoxia-related genes (HRGs) expression. outcomes, stromal/immune/Estimate scores, responses targeted inhibitors, chemotherapeutic, immunotherapy were distinct high HS group low group. Single-cell datasets showed different distributions in populations. Furthermore, HLA-DPA1/CD4 axis identified unique interaction CD4+ T Conv pDC cells. These findings may enhance understanding characteristics

Language: Английский

Predictive biomarkers of colon cancer immunotherapy: Present and future DOI Creative Commons

Wanting Hou,

Yi Cheng, Hong Zhu

et al.

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

Published: Nov. 22, 2022

Immunotherapy has revolutionized colon cancer treatment. Immune checkpoint inhibitors (ICIs) have shown clinical benefits for patients, especially those with high microsatellite instability (MSI-H). In 2020, the US Food and Drug Administration (FDA)-approved ICI pembrolizumab as first-line treatment metastatic MSI-H patients. Additionally, neoadjuvant immunotherapy presented efficacy in treating early-stage Although MSI been thought of an effective predictive biomarker immunotherapy, only a small proportion patients were MSI-H, certain intrinsic or acquired resistance to immunotherapy. Thus, further search biomarkers stratify is meaningful Except MSI, other biomarkers, such PD-L1 expression level, tumor mutation burden (TMB), tumor-infiltrating lymphocytes (TILs), gut microbiota, ctDNA, circulating immune cells also proposed be correlated patient survival some studies. Moreover, developing new diagnostic techniques helps identify accurate this review, we outline reported discuss prospects technological changes development

Language: Английский

Citations

94
Proteomics: An In‐Depth Review on Recent Technical Advances and Their Applications in Biomedicine DOI Open Access
Jing Liang, Jun Tian,

Huadong Zhang

et al.

Medicinal Research Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

ABSTRACT Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of structure, abundance, and function biological samples, enabling the holistic characterization overall organisms. Nowadays, breadth emerging methodologies proteomics is unprecedentedly vast, with constant optimization technologies sample processing, data collection, analysis, its scope application steadily transitioning from bench to clinic. Here, we offer an insightful review technical developments applications biomedicine over past 5 years. We focus on profound contributions profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations conformation, unearthing protein–protein interactions. Moreover, summarize cutting‐edge potential breakthroughs pipeline principal challenges proteomics. Based these, aspire broaden applicability inspire researchers enhance our understanding complex systems by utilizing such techniques.

Language: Английский

Citations

2
Ferroptosis in gastrointestinal cancer: from mechanisms to implications DOI Creative Commons
Ruoxi Zhang, Rui Kang, Daolin Tang

et al.

Cancer Letters, Journal Year: 2023, Volume and Issue: 561, P. 216147 - 216147

Published: March 24, 2023

Language: Английский

Citations

26
New insights into immune cells in cancer immunotherapy: from epigenetic modification, metabolic modulation to cell communication DOI Creative Commons
Sha Qin,

Bin Xie,

Qingyi Wang

et al.

MedComm, Journal Year: 2024, Volume and Issue: 5(6)

Published: May 23, 2024

Abstract Cancer is one of the leading causes death worldwide, and more effective ways attacking cancer are being sought. immunotherapy a new therapeutic method after surgery, radiotherapy, chemotherapy, targeted therapy. aims to kill tumor cells by stimulating or rebuilding body's immune system, with specific efficiency high safety. However, only few patients respond due complex variable characters escape, behavior regulatory mechanisms need be deeply explored from dimensions. Epigenetic modifications, metabolic modulation, cell‐to‐cell communication key factors in cell adaptation response microenvironment. They collectively determine state function through modulating gene expression, changing energy nutrient demands. In addition, engage networks other components, which mediated exosomes, cytokines, chemokines, pivotal shaping progression response. Understanding interactions combined effects such multidimensions modulation important for revealing failure developing targets strategies.

Language: Английский

Citations

13
An empirical review on the resistance mechanisms of epidermal growth factor receptor inhibitors and predictive molecular biomarkers in colorectal cancer DOI
Sankha Bhattacharya

Critical Reviews in Oncology/Hematology, Journal Year: 2023, Volume and Issue: 183, P. 103916 - 103916

Published: Jan. 28, 2023

Language: Английский

Citations

10
p52-ZER6/DAZAP1 axis promotes ferroptosis resistance and colorectal cancer progression via regulating SLC7A11 mRNA stabilization DOI Creative Commons

Qiu Li,

Wenfang Li, Lei Zhang

et al.

Acta Pharmaceutica Sinica B, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

0
The role of hypoxia-senescence co-related molecular subtypes and prognostic characteristics in hepatocellular carcinoma DOI Creative Commons

Fuqing Chen,

Yifan Cai, Xiangmei Chen

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 11, 2025

Hepatocellular carcinoma (HCC) is known for its high invasiveness, fatality rate. Both hypoxia and senescence play crucial roles in the initiation progression of cancer, yet their prognostic implications HCC are to be fully understood. The hypoxia-senescence co-related genes (HSCRGs) were screened from public databases. Transcriptome data clinical information obtained patients with using Cancer Genome Atlas, GSE76427, International Consortium (ICGC). random forest tree algorithm was used identify characteristic disease, verified by related experiments. SVM classify based on HSCRGs. prediction model HSCRGs established LASSO, univariate multivariate COX regression analysis. We ICGC outside validation. risk score analyzed subgroup analysis, immune infiltration, functional strength. expression patterns key tumor microenvironment decoded single cell A total 184 identified. pattern characteristics MLH1 gene verified. Two subtypes identified Then, a established, as an independent indicator HCC. new nomogram constructed shows good ability. further determined that level infiltration cells checkpoints significantly affected score. different between two groups. high-risk group dominated immunosuppressed cells, prognosis poor. Single-cell analysis revealed seven microenvironment. Finally, qPCR results levels genes. great significance prediction, stratification targeted therapy

Language: Английский

Citations

0
A novel ferroptosis-related gene prognostic index for prognosis and response to immunotherapy in patients with prostate cancer DOI Creative Commons
Yuliang Wang, Jiaqi Fan, Tao Chen

et al.

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

Published: Aug. 10, 2022

Background Prostate cancer (PCa) is among the leading causes of death worldwide. Ferroptosis refers to an iron-dependent form regulated cell and involved in prostate tumorigenesis. A few ferroptosis-related gene signatures have been developed predict prognosis for PCa patients. However, previous were typically established based on biochemical recurrence-free survival, which has proven not be a good surrogate overall survival (OS). This study aimed construct novel prognostic index (FRGPI) disease-free (DFS) response immunotherapy patients after radical prostatectomy. Methods Gene expression clinicopathological data obtained from TCGA database. Ferroptosis-related hub genes associated with DFS identified by in-depth bioinformatics analysis using comprehensive algorithm functional enrichment, consensus clustering, weighted co-expression network (WGCNA), protein-protein interaction (PPI) construction. The FRGPI was basis selected multivariate cox regression further validated two additional cohorts. Next, clinicopathological, molecular, immune profiles characterized compared between FRGPI-high FRGPI-low subgroups. Finally, predictive role estimated metastatic urothelial cohort treated anti-PD-L1 agent. Results constructed four (E2F1, CDC20, TYMS, NUP85), had worse than Multivariate revealed that could act as independent factor nomogram comprising other parameters quantitatively. In addition, results demonstrated high scores showed significantly positive correlation features, higher mutation counts, increased frequency copy number variations (CNVs), homologous recombination deficiency (HRD) scores, mRNAsi, more importantly, enhanced sensitivity immunotherapy. Conclusions only promising robust biomarker, but also potential indicator immunotherapeutic outcomes

Language: Английский

Citations

16
Identification of a novel 5-methylcytosine-related signature for prognostic prediction of kidney renal papillary cell carcinoma and a Putative target for drug repurposing DOI Creative Commons
Zhen Zhang,

Chuanhua Cao,

Chunli Zhou

et al.

Translational Oncology, Journal Year: 2023, Volume and Issue: 36, P. 101741 - 101741

Published: July 29, 2023

Many studies have demonstrated the crucial roles of 5-methylcytosine (m5C) RNA methylation in cancer pathogenesis.Two datasets, including TCGA-KIRP and ICGC, related clinical information were downloaded, where expression 13 m5C regulators was examined. We applied LASSO regression to construct a multi-m5C-regulator-based signature TCGA cohort, which further validated using ICGC cohort. Univariate multivariate Cox regressions evaluate independent prognostic value our model. The differences biological functions immune characterizations between high low-risk groups divided based on risk scores also investigated via multiple approaches, such as enrichment analyses, mutation mining, scoring. Finally, sensitivities commonly used targeted drugs tested, connectivity MAP (cMAP) utilized screen potentially effective molecules for patients high-risk group. Experimental validation done following qPCR tests Caki-2 HK-2 cell lines.3 regulators, ALYREF, DNMT3B YBX1, involved Survival analysis revealed worse prognosis results indicated model's superior predictive performance compared single-factor evaluation. Functional analyses higher frequency poorer tumor microenvironment qPCR-based that DNMT3B, YBX1 significantly up-regulated lines with lines. Molecules like BRD-K72451865, Levosimendan, BRD-K03515135 advised by cMAP group.Our study presented novel model KIRP prognosis. Furthermore, provide new insights investigating events pathogenesis.

Language: Английский

Citations

8
Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma DOI
Haikun Zhang,

Peiling Dong,

Hailang Fan

et al.

Functional & Integrative Genomics, Journal Year: 2023, Volume and Issue: 23(2)

Published: June 1, 2023

Language: Английский

Citations

7