The Journal of Gene Medicine, Год журнала: 2023, Номер 26(1)
Опубликована: Дек. 7, 2023
Osteosarcoma is a very aggressive bone tumor mainly affecting teens and young adults. Disulfidptosis metabolic-related form of regulated cell death. However, the interconnection between disulfidptosis osteosarcoma has not been explored.
Язык: Английский
npj Digital Medicine, Год журнала: 2024, Номер 7(1)
Опубликована: Янв. 18, 2024
Abstract Small cell lung cancer (SCLC) is a highly aggressive subtype of characterized by rapid tumor growth and early metastasis. Accurate prediction prognosis therapeutic response crucial for optimizing treatment strategies improving patient outcomes. In this study, we conducted deep-learning analysis Hematoxylin Eosin (H&E) stained histopathological images using contrastive clustering identified 50 intricate histomorphological phenotype clusters (HPCs) as pathomic features. We two HPCs with significant prognostic value then integrated them into pathomics signature (PathoSig) the Cox regression model. PathoSig showed risk stratification overall survival disease-free successfully patients who may benefit from postoperative or preoperative chemoradiotherapy. The predictive power was validated in independent multicenter cohorts. Furthermore, can provide comprehensive information beyond current TNM staging system molecular subtyping. Overall, our study highlights potential utilizing histopathology images-based deep learning predictions evaluating SCLC. represents an effective tool that aids clinicians making informed decisions selecting personalized SCLC patients.
Язык: Английский
Процитировано
37
Molecular Cancer, Год журнала: 2024, Номер 23(1)
Опубликована: Июнь 20, 2024
Abstract Malignant tumors have increasing morbidity and high mortality, their occurrence development is a complicate process. The of sequencing technologies enabled us to gain better understanding the underlying genetic molecular mechanisms in tumors. In recent years, spatial transcriptomics been developed rapidly allow quantification illustration gene expression context tissues. Compared with traditional technologies, not only detect levels cells, but also inform location genes within tissues, cell composition biological interaction between cells. Here we summarize tools its application cancer research. We discuss limitations challenges current approaches, as well future prospects.
Язык: Английский
Процитировано
27
Journal of Cellular and Molecular Medicine, Год журнала: 2024, Номер 28(10)
Опубликована: Май 1, 2024
Abstract Smoking is a well‐known risk factor for non‐small‐cell lung cancer (NSCLC) and bladder urothelial carcinoma (BLCA). Despite this, there has been no investigation into prognostic marker based on smoking‐related genes that could universally predict prognosis in these cancers correlate with immune checkpoint therapy. This study aimed to identify differential NSCLC BLCA, analyse their roles patient therapy through subgroup analyses, shed light PRR11 as crucial gene both cancers. By examining co‐expressed genes, model was constructed its impact immunotherapy BLCA evaluated. Molecular docking tissue microarray analyses were conducted explore the correlation between reciprocal SPDL1. Additionally, miRNAs associated analysed. The confirmed strong link prognosis, BLCA. identified key smoking‐associated influences efficacy of by modulating stemness A established value validated NSCLC. Furthermore, it found regulates PDL1 via SPDL1, impacting immunotherapeutic involvement hsa‐miR‐200b‐3p regulation SPDL1 expression also highlighted. Overall, elucidates modulates influencing interaction potential upstream hsa‐miR‐200b‐3p.
Язык: Английский
Процитировано
13
Advanced Science, Год журнала: 2024, Номер 11(31)
Опубликована: Июнь 19, 2024
Abstract Small cell lung cancer (SCLC) is a highly aggressive malignancy characterized by rapid growth and early metastasis susceptible to treatment resistance recurrence. Understanding the intra‐tumoral spatial heterogeneity in SCLC crucial for improving patient outcomes clinically relevant subtyping. In this study, whole transcriptome‐wide analysis of 25 patients at sub‐histological resolution using GeoMx Digital Spatial Profiling technology performed. This deciphered multi‐regional heterogeneity, distinct molecular profiles, biological functions, immune features, subtypes within spatially localized histological regions. Connections between different transcript‐defined phenotypes their impact on survival therapeutic response are also established. Finally, gene signature, termed ITHtyper, based prevalence levels, which enables risk stratification from bulk RNA‐seq profiles identified. The prognostic value ITHtyper rigorously validated independent multicenter cohorts. study introduces preliminary tumor‐centric, regionally targeted transcriptome resource that sheds light previously unexplored SCLC. These findings hold promise improve tumor reclassification facilitate development personalized treatments patients.
Язык: Английский
Процитировано
10
Biomarkers, Год журнала: 2025, Номер unknown, С. 1 - 16
Опубликована: Янв. 31, 2025
Background Lung cancer is a primary global health concern, responsible for considerable portion of cancer-related fatalities worldwide. Understanding its molecular complexities crucial identifying potential targets treatment. The goal to slow disease progression and intervene early prevent the development advanced lung cases. Hence, there's an urgent need new biomarkers that can detect in stages. Methods: study conducted RNA-Seq analysis samples from publicly available SRA database (NCBI SRP009408), including both control tumour samples. genes with differential expression between healthy tissues were identified using R Bioconductor. Machine learning (ML) techniques, Random Forest, Lasso, XGBoost, Gradient Boosting, Elastic Net employed pinpoint significant followed by classifiers, Multilayer Perceptron (MLP), Support Vector Machines (SVM), k-Nearest Neighbors (k-NN). Gene ontology pathway analyses performed on differentially expressed (DEGs). top DEG machine combined protein-protein interaction (PPI) analysis, 10 hub essential progression. Results: integrated ML DEGs revealed significance specific samples, five upregulated (COL11A1, TOP2A, SULF1, DIO2, MIR196A2) downregulated (PDK4, FOSB, FLYWCH1, CYB5D2, MIR328), along their associated implicated pathways or co-expression networks identified. Among various algorithms employed, Forest XGBoost proved effective common genes, underscoring pathogenesis. MLP exhibited highest accuracy classifying all genes. Additionally, are pivotal pathogenesis: COL1A1, SOX2, SPP1, THBS2, POSTN, COL5A1, COL11A1, TIMP1, PKP1.
Язык: Английский
Процитировано
2
The Journal of Pathology Clinical Research, Год журнала: 2025, Номер 11(2)
Опубликована: Фев. 25, 2025
Abstract Papillary thyroid carcinoma (PTC) is one of the most common endocrine malignancies, with varying levels risk and clinical behavior. A better understanding molecular characteristics could improve diagnosis assessment. In this study, we performed whole transcriptomic sequencing on 113 PTC cases, including 70 high‐risk 43 low‐risk Chinese patients. Comparative transcriptional profiling analysis revealed two functionally distinct patterns gene dysregulation between subtypes. Low‐risk PTCs showed significant upregulation immune‐related genes increased immune cell infiltration, whereas presented extensive alterations in expression activation oncogenic signaling pathways. Additionally, developed a 31‐gene signature (PTCrisk) for differentiating from PTCs, which was validated across both in‐house external multicenter cohorts. PTCrisk scores were positively correlated key clinicopathological features, tumor size, lymph node metastasis, TNM stage, BRAF mutation status. Overall, our study provides further insights into stratification may contribute to development personalized therapeutic strategies
Язык: Английский
Процитировано
0
Research, Год журнала: 2025, Номер 8
Опубликована: Янв. 1, 2025
High-grade lung neuroendocrine carcinomas (Lu-NECs) are clinically refractory malignancies with poor prognosis and limited therapeutic advances. The biological molecular features underlying the histological heterogeneity of Lu-NECs not fully understood. In this study, we present a multi-omics integration whole-exome sequencing deep proteomic profiling in 93 Chinese to establish first comprehensive proteogenomic atlas disease spectrum. Our analyses revealed high degree mutational concordance among subtypes at genomic level; however, distinct profiles enabled clear differentiation subtypes, unveiling subtype-specific related tumor metabolism, immunity, proliferation. Furthermore, RB1 mutations confer divergent prognostic effects through cis- trans- regulation. addition, identified potential protein biomarkers for subtype classification risk stratification, which were validated by immunohistochemistry an independent cohort. This study provides valuable resource insight into Lu-NEC heterogeneity.
Язык: Английский
Процитировано
0
The Clinical Respiratory Journal, Год журнала: 2025, Номер 19(5)
Опубликована: Май 1, 2025
ABSTRACT Background G protein‐coupled receptors (GPCRs), the largest family of cell‐surface molecules involve in various signal transduction, have recently been recognized as important drivers cancer. However, few studies reported on potential GPCRs therapeutic targets or biomarkers lung adenocarcinoma (LUAD). Methods The expression profiles and clinical data LUAD GSE30219 GSE18842 datasets Cancer Genome Atlas were analyzed. LUAD‐associated module genes screened utilizing weighted gene co‐expression network analysis (WGCNA). Prognostic signature identified by univariate Cox survival analysis, LASSO regression, multivariate regression analyses. immune status was evaluated drug sensitivity determined, conducting vitro experiments for validation. Results Patients with exhibited lower GPCR score than controls, 38 dysregulated screening differential WGCNA genes. An optimal prognostic identified, including OR51E1, LGR4, ADRB1, ADGRD1, ADGRE3. model established based these five harbored moderate predictive performance patients LUAD. risk negatively correlated infiltrating levels multiple cells, M2 macrophages, myeloid dendritic neutrophils, but positively fewer such Th1/Th2 CD4 + T cell. ADGRE3 OR51E1 sensitivity, to cisplatin, ribociclib, pevonedistat. Silencing inhibited malignant cytological behaviors cells. Conclusion demonstrated LUAD,
Язык: Английский
Процитировано
0
Frontiers in Genetics, Год журнала: 2023, Номер 14
Опубликована: Ноя. 23, 2023
Objective: According to the 2020 data from World Health Organization (WHO), cancers stand as one of foremost contributors global mortality. Revealing novel cancer risk factors and protective is paramount importance in prevention disease occurrence. Studies on relationship between chemokines are ongoing; however, due coordination multiple potential mechanisms, specific causal association remains unclear. Methods: We performed a bidirectional Mendelian randomization analysis explore serum pan-carcinoma. All GWAS catalog IEU Open database. The inverse-variance weighted (IVW) method primarily employed for assessing statistical significance findings. In addition, threshold after hypothesis test (Bonferroni) was 0.0013, evidence considered if p -value < 0.05, but remained greater than Bonferroni’s threshold. Results: results indicate that CCL1 (odds ratio, OR = 1.18), CCL2 (OR 1.04), CCL8 1.36), CCL14 (Colorectal, 1.08, Small intestine, 0.77, Lung, 1.11), CCL15 0.85), CCL18 (Breast, 0.95, Prostate, 0.96), CCL19 (Lung, 0.66, 0.92), CCL20 0.53, Thyroid, 0.76), CCL21 0.62), CCL22 2.05), CCL23 1.31), CCL24 1.06), CCL27 1.49), CCL28 0.74), CXCL5 0.95), CXCL9 3.60), CXCL12 0.87, 0.58), CXCL13 0.93, 1.29), CXCL14 (Colon, 1.40) CXCL17 1.07) cancers. there reverse 0.94) breast cancer. Sensitivity were similar. other four MR Methods consistent with main results, leave-one-out showed not driven by Single nucleotide polymorphism (SNP). Moreover, no heterogeneity pleiotropy our analysis. Conclusion: Based two-sample Analysis method, we found might be upstream pathogenesis. These provide new insights into future use targets treatment. Our also important clues tumor prevention, changes chemokine concentration may recognized features precancerous lesions clinical trials.
Язык: Английский
Процитировано
6
British Journal of Cancer, Год журнала: 2024, Номер 131(6), С. 1068 - 1079
Опубликована: Авг. 2, 2024
Язык: Английский
Процитировано
2