Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma

Zhang, Kai; Yuan, Enwu

doi:10.3389/fimmu.2023.1142126

Cited by 4 publications

(2 citation statements)

References 53 publications

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“…Quality control and cell screening were carried out on the GSE149614 dataset using the Seurat package [ 15 ] as reported by the previous study [ 16 ], yielding a total of 31,396 cells and 17 distinct subgroups for additional analysis. These distinct groupings were identified based on several marker genes (Figure S1).…”

Section: Methodsmentioning

confidence: 99%

Increased PAFAH1B3 was associated with poor prognosis and T-cell exhaustion microenvironment in hepatocellular carcinoma

Zhang

2023

Discov Onc

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The link between T-cell exhaustion (TEX) and PAFAH1B3 in hepatocellular carcinoma (HCC) remains unknown, even though both of them are related to overall survival. PAFAH1B3 expression was investigated in TCGA and ICGC data, and 50 paired clinical tissue section samples were used for qRT-PCR and immunohistochemistry (IHC) confirmation. The Immunocell Abundance Identifier (ImmuCellAI) was used to precisely calculate the abundance of TEX, and its accuracy was verified by single-cell RNA-seq and labeling of CD8 + T cells in clinical tissue sections. The IMVigor 210 cohort was used to demonstrate the predictive value of PAFAH1B3 for immunotherapy efficacy. Increased PAFAH1B3 is a standalone effector of poor prognosis in HCC patients. Patients who had greater PAFAH1B3 levels had more TEX infiltration. PAFAH1B3 expression was increased in TEX in the single-cell RNA-seq data. Patients with high PAFAH1B3 expression were more likely to respond favorably to PD1/PD-L1 treatment. In conclusion, PAFAH1B3 is closely related to TEX in the tumor microenvironment (TME) and can be a useful indicator for PD1/PD-L1 therapy.

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Section: Methodsmentioning

confidence: 99%

Increased PAFAH1B3 was associated with poor prognosis and T-cell exhaustion microenvironment in hepatocellular carcinoma

Zhang

2023

Discov Onc

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“…Lymphocytes constitute most immune cells in HCC, and studies indicate that abundant lymphocyte infiltration in HCC is associated with a better prognosis (12). Previous studies of lymphocyte infiltration primarily relied on the technique of genomics and transcriptomics, which required complicated examination and additional cost.…”

Section: Introductionmentioning

confidence: 99%

Novel immune classification based on machine learning of pathological images predicts early recurrence of hepatocellular carcinoma

Tan,

Hu,

Zhang

et al. 2024

Front. Oncol.

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IntroductionImmune infiltration within the tumor microenvironment (TME) plays a significant role in the onset and progression of hepatocellular carcinoma (HCC). Machine learning applied to pathological images offers a practical means to explore the TME at the cellular level. Our former research employed a transfer learning procedure to adapt a convolutional neural network (CNN) model for cell recognition, which could recognize tumor cells, lymphocytes, and stromal cells autonomously and accurately within the images. This study introduces a novel immune classification system based on the modified CNN model.MethodPatients with HCC from both Beijing Hospital and The Cancer Genome Atlas (TCGA) database were included in this study. Additionally, least absolute shrinkage and selection operator (LASSO) analyses, along with logistic regression, were utilized to develop a prognostic model. We proposed an immune classification based on the percentage of lymphocytes, with a threshold set at the median lymphocyte percentage.ResultPatients were categorized into high or low infiltration subtypes based on whether their lymphocyte percentages were above or below the median, respectively. Patients with different immune infiltration subtypes exhibited varying clinical features and distinct TME characteristics. The low-infiltration subtype showed a higher incidence of hypertension and fatty liver, more advanced tumor stages, downregulated immune-related genes, and higher infiltration of immunosuppressive cells. A reliable prognostic model for predicting early recurrence of HCC based on clinical features and immune classification was established. The area under the curve (AUC) of the receiver operating characteristic (ROC) curves was 0.918 and 0.814 for the training and test sets, respectively.DiscussionIn conclusion, we proposed a novel immune classification system based on cell information extracted from pathological slices, provides a novel tool for prognostic evaluation in HCC.

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Serum IL‐24 combined with CA125 as screening and prognostic biomarkers for NSCLC

Zhang,

Qu,

Deng

et al. 2024

Cell Biology International

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Noninvasive and effective methods for early screening of non‐small cell lung cancer (NSCLC) still need to be developed. At present, a reasonable conclusion is that a combination of tumor markers is a superior predictor of screening. Cytokines, as important regulators of cancer development, have great potential for the screening and prognosis of NSCLC. This study screened novel biomarkers related to the early screening and prognosis of NSCLC. In the present study, the biological significance and immunoregulation of interleukin‐24 (IL‐24) were analyzed based on The Cancer Genome Atlas data. Next, 150 serum samples from initially treated patients with NSCLC and 70 controls were collected, and we obtained pathological sections from 60 patients with NSCLC. The ELISA and immunohistochemistry results showed the differential expression of IL‐24 and carbohydrate antigen 125 (CA125). The results show that IL‐24 is an important tumor suppressor in NSCLC that helps to improve the poor prognosis of these patients. A significantly negative correlation between IL‐24 and CA125 levels was also found. Notably, serum IL‐24 levels were significantly negatively correlated with the TNM stage of patients with NSCLC, consistent with an important role for tumor suppressors in NSCLC. The receiver operating characteristic curve analysis showed that a combination of IL‐24 and CA125 was an effective panel for discriminating patients with NSCLC from HD, and individuals with other lung diseases. Serum IL‐24 and CA125 levels were identified as independent prognostic markers for NSCLC. The IL‐24 and CA125 panel exhibited good performance in the screening of NSCLC.

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Combined analysis of bulk and single-cell RNA sequencing reveals novel natural killer cell-related prognostic biomarkers for predicting immunotherapeutic response in hepatocellular carcinoma

Cited by 4 publications

References 53 publications

Increased PAFAH1B3 was associated with poor prognosis and T-cell exhaustion microenvironment in hepatocellular carcinoma

Increased PAFAH1B3 was associated with poor prognosis and T-cell exhaustion microenvironment in hepatocellular carcinoma

Novel immune classification based on machine learning of pathological images predicts early recurrence of hepatocellular carcinoma

Serum IL‐24 combined with CA125 as screening and prognostic biomarkers for NSCLC

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