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Hu X, Cao P, Wang F, Wang T, Duan J, Chen X, Ma X, Zhang Y, Chen J, Liu H, Zhang H, Wu X. Alternative polyadenylation quantitative trait loci contribute to acute myeloid leukemia risk genes regulation. Leuk Res 2024; 141:107499. [PMID: 38640632 DOI: 10.1016/j.leukres.2024.107499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with a high relapse rate and progressive drug resistance. Alternative polyadenylation (APA) contributes to post-transcriptional dysregulation, but little is known about the association between APA and AML. The APA quantitative trait locus (apaQTL) is a powerful method to investigate the relationship between APA and single nucleotide polymorphisms (SNPs). We quantified APA usage in 195 Chinese AML patients and identified 4922 cis-apaQTLs related to 1875 genes, most of which were newly reported. Cis-apaQTLs may modulate the APA selection of 115 genes through poly(A) signals. Colocalization analysis revealed that cis-apaQTLs colocalized with cis-eQTLs may regulate gene expression by affecting miRNA binding sites or RNA secondary structures. We discovered 207 cis-apaQTLs related to AML risk by comparing genotype frequency with the East Asian healthy controls from the 1000 Genomes Project. Genes with cis-apaQTLs were associated with hematological phenotypes and tumor incidence according to the PHARMGKB and MGI databases. Collectively, we profiled an atlas of cis-apaQTLs in Asian AML patients and found their association with APA selection, gene expression, AML risk, and complex traits. Cis-apaQTLs may provide insights into the regulatory mechanisms related to APA in AML occurrence, progression, and prognosis.
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Affiliation(s)
- Xi Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Panxiang Cao
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Fang Wang
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Tong Wang
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Junbo Duan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xue Chen
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Xiaoli Ma
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Yang Zhang
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Jiaqi Chen
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China
| | - Hongxing Liu
- Division of Pathology and Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang 065201, China.
| | - Huqin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Xiaoming Wu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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Yang R, Zhou D, Tan X, Zhao Z, Lv Y, Tian X, Ren L, Wang Y, Li J, Zhao Y, Zhang J. Genome-Wide Association Study of Body Conformation Traits in Tashi Goats ( Capra hircus). Animals (Basel) 2024; 14:1145. [PMID: 38672293 PMCID: PMC11047570 DOI: 10.3390/ani14081145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was "olfactory transduction", and the most significantly enriched gene ontology (GO) terms were "cellular process", "cellular anatomical entity", and "molecular transducer activity". Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.
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Affiliation(s)
- Rong Yang
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Di Zhou
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Xiaoshan Tan
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Zhonghai Zhao
- Zunyi Animal Husbandry and Fishery Station, Zunyi 563000, China
| | - Yanli Lv
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Xingzhou Tian
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Liqun Ren
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Yan Wang
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Jun Li
- Guizhou Provincial Breeding Livestock and Poultry Germplasm Determination Center, Guiyang 550018, China; (R.Y.); (Y.L.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
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Ma X, Zang X, Yang L, Zhou W, Li Y, Wei J, Guo J, Han J, Liang J, Jin T. Genetic polymorphisms in CYP2B6 may be associated with lung cancer risk in the Chinese Han population. Expert Rev Respir Med 2023; 17:1297-1305. [PMID: 38166557 DOI: 10.1080/17476348.2024.2302199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/02/2024] [Indexed: 01/04/2024]
Abstract
BACKGROUND Our study aimed to elucidate the association between single nucleotide polymorphisms (SNPs) in CYP2B6 gene and susceptibility to lung cancer (LC). METHODS Five SNPs in CYP2B6 were genotyped in Chinese Han population (507 cases and 505 controls) utilizing Agena MassARRAY. The relationship between these SNPs and LC susceptibility was assessed using odds ratios, 95% confidence intervals, and χ2 tests. Additionally, multifactor dimensionality reduction was employed to analyze SNP-SNP interactions. Bioinformatics methods were applied to investigate the function of these SNPs. RESULTS We found that rs2099361 was associated with an increased susceptibility to LC in the codominant model (OR = 1.31, p = 0.045). Stratification analysis revealed the allele G at rs4803418 and the allele T at rs4803420 of CYP2B6 (BMI >24 kg/m2) were significantly linked to decreased susceptibility of LC. Conversely, the allele C at rs12979270 (BMI >24 kg/m2) showed increased susceptibility to LC. Moreover, a robust redundant relationship between rs12979270 and rs4803420 was identified in the study. According to the VannoPortal database, we found that rs4803420, rs12979270 and rs2099361 may modulate the binding affinity of LMNB1, SP1 and HDAC2, respectively. CONCLUSIONS Our results suggest that SNPs in the CYP2B6 gene play crucial roles in LC susceptibility.
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Affiliation(s)
- Xiaoya Ma
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Xufeng Zang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Leteng Yang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Wenqian Zhou
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Yujie Li
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Jie Wei
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Jinping Guo
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Junhui Han
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Jing Liang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
| | - Tianbo Jin
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, China
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Li ZH, Li JY, Zhu YJ, Dai L, Wu ZT, Nong JS, Zhuo T, Li FL, He LY, Liang HH, Zang FL, Wang YY, Chen MW, Huang WJ, Cao JB. Analysis of Nucleoporin 107 Overexpression and Its Association with Prognosis and Immune Infiltration in Lung Adenocarcinoma by Bioinformatics Methods. Int J Gen Med 2023; 16:5449-5465. [PMID: 38021066 PMCID: PMC10676695 DOI: 10.2147/ijgm.s441185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) has high morbidity and mortality. Current studies indicate nucleoporin 107 (NUP107) is involved in the construction of nuclear pore complex, and NUP107 overexpression contributes to the growth and development in most types of cancers, but its effect in LUAD has not been elucidated. Methods Differences in NUP107 expression were investigated using the Cancer Genome Atlas (TCGA) and multiple Gene Expression Omnibus (GEO) data sets. Enrichment analysis were implemented to probe the NUP107 function. The association of NUP107 with the degree of immune cell infiltration was investigated by the TIMER database, single-sample gene set enrichment analysis (ssGSEA), and ESTIMATE. The association of NUP107 expression with tumor mutation burden (TMB), TP53, and immune checkpoint was analyzed. Single-cell RNA sequencing data were used to detect NUP107 expression in different cell clusters. Finally, we performed real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) to prove the difference of NUP107 expression. Results NUP107 was overexpressed in LUAD and mainly expressed in cancer stem cell (CSC). Overexpression of NUP107 in LUAD suggested a poorer prognosis. Functional enrichment analysis pointed out that NUP107 was mainly linked to the regulation of cell cycle. Both immune cell infiltration and TMB were found to be in connection with NUP107. Cases in the group with high NUP107 expression had poorer immune infiltration, but had higher expression of immune checkpoints, TMB, and proportion of TP53 mutations. Conclusion NUP107 is a sensitive diagnostic and prognostic factor for LUAD and may be involved in tumor progression through its effects on cell cycle and immune infiltration.
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Affiliation(s)
- Zi-Hao Li
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Jia-Yi Li
- Department of Nephrology, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Yong-Jie Zhu
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Lei Dai
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zuo-Tao Wu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Ju-Sen Nong
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Ting Zhuo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Fu-Li Li
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Ling-Yun He
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Hong-Hua Liang
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Feng-Ling Zang
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Yong-Yong Wang
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Ming-Wu Chen
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Wei-Jia Huang
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
| | - Jian-Bin Cao
- Department of Thoracic Surgery, Liuzhou People’s Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, People’s Republic of China
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Zhang W, Hu Y, Qian M, Mao L, Yuan Y, Xu H, Liu Y, Qiu A, Zhou Y, Dong Y, Wu Y, Chen Q, Tao X, Tian T, Zhang L, Cui J, Chu M. A novel APA-based prognostic signature may predict the prognosis of lung adenocarcinoma in an East Asian population. iScience 2023; 26:108068. [PMID: 37860689 PMCID: PMC10583048 DOI: 10.1016/j.isci.2023.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/23/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The role of alternative polyadenylation (APA) in tumor development is becoming increasingly evident, but the impact of APA events on the prognosis of LUAD patients is unclear. Therefore, in the present study, we aimed to analyze specific APA events in LUAD to identify novel prognostic biomarkers for LUAD. We first identified prognostic candidate genes for LUAD associated with APA events and validated them in both the East Asian and the USA cohorts, finding that five genes (DCUN1D5, PSMC4, TFAM, THRA, and TMEM100) were of prognostic significance in both populations. Based on this, an APA-based prognostic signature was constructed for the East Asian population. The predictive accuracy of the prognostic signature was further evaluated by the time-dependent ROC, with 1-, 2-, and 3-year AUCs of 0.86, 0.81, and 0.71, respectively. This study may provide new markers for individualized diagnosis and prognostic assessment of LUAD and potential targets for precision treatment.
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Affiliation(s)
- Wendi Zhang
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yang Hu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Min Qian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Liping Mao
- Department of Oncology, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong, Jiangsu, China
| | - Yanqiong Yuan
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Huiwen Xu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Anni Qiu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yan Zhou
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yang Dong
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
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Mi K, Zeng L, Chen Y, Yang S. Integrative Analysis of Single-Cell and Bulk RNA Sequencing Reveals Prognostic Characteristics of Macrophage Polarization-Related Genes in Lung Adenocarcinoma. Int J Gen Med 2023; 16:5031-5050. [PMID: 37942473 PMCID: PMC10629586 DOI: 10.2147/ijgm.s430408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a group of cancers with poor prognosis. The combination of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) can identify important genes involved in cancer development and progression from a broader perspective. Methods The scRNA-seq data and bulk RNA-seq data of LUAD were downloaded from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. Analyzing scRNA-seq for core cells in the GSE131907 dataset, and the uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Macrophage polarization-associated subtypes were acquired from the TCGA-LUAD dataset after analysis, followed by further identification of differentially expressed genes (DEGs) in the TCGA-LUAD dataset (normal/LUAD tissue samples, two subtypes). Venn diagrams were utilized to visualize differentially expressed and highly variable macrophage polarization-related genes. Subsequently, a prognostic risk model for LUAD patients was constructed by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO), and the model was investigated for stability in the external data GSE72094. After analyzing the correlation between the trait genes and significantly mutated genes, the immune infiltration between the high/low-risk groups was then examined. The Monocle package was applied to analyze the pseudo-temporal trajectory analysis of different cell clusters in macrophage clusters. Subsequently, cell clusters of data macrophages were selected as key cell clusters to explore the role of characteristic genes in different cell populations and to identify transcription factors (TFs) that affect signature genes. Finally, qPCR were employed to validate the expression levels of prognosis signature genes in LUAD. Results 424 macrophage highly variable genes, 3920 DEGs, and 9561 DEGs were obtained from macrophage clusters, the macrophage polarization-related subtypes, and normal/LUAD tissue samples, respectively. Twenty-eight differentially expressed and highly mutated MPRGs were obtained. A prognostic risk model with 7 DE-MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) was constructed. This prognostic model still has a good prediction effect in the GSE72094 dataset. ZNF536 and DNAH9 were mutated in the low-risk group, while COL11A1 was mutated in the high-risk group, and they were highly correlated with the characteristic genes. A total of 11 immune cells were significantly different in the high/low-risk groups. Five cell types were again identified in the macrophage cluster, and then NK cells: CD56hiCD62L+ differentiated earlier and were present mainly on 2 branches. While macrophages were present on 2 branches and differentiated later. It was found that the expression levels of BCLAF1 and MAX were higher in cluster 1, which might be the TFs affecting the expression of the characteristic genes. Moreover, qPCR confirmed that the expression of the prognosis genes was generally consistent with the results of the bioinformatic analysis. Conclusion Seven MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) were identified as prognostic genes for LUAD and revealed the mechanisms of MPRGs at the single-cell level.
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Affiliation(s)
- Ke Mi
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Lizhong Zeng
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
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Liu H, Yu Z, Liu Y, Li M, Chen C, Zhu Z, Liu F, Tan L. Investigation of Diagnostic and Prognostic Value of CLEC4M of Non-Small Cell Lung Carcinoma Associated with Immune Microenvironment. Int J Gen Med 2023; 16:1317-1332. [PMID: 37089135 PMCID: PMC10115202 DOI: 10.2147/ijgm.s397695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
Purpose C-type lectin domain family 4 member M (CLEC4M) has been found to be involved in the occurrence and development of cancer, but its role in NSCLC remains to be fully explored. Our work aims to evaluate the diagnostic and prognostic value of CLEC4M in NSCLC and to investigate the underlying mechanisms of CLEC4M in the immune microenvironment of NSCLC. Methods Integrating publicly accessible data and clinical tissue samples to verify the expression of CLEC4M in NSCLC. The diagnostic value of CLEC4M was determined by receiver operating characteristic (ROC) curve. Kaplan-Meier survival analysis, nomogram plot, univariate and multivariate Cox regression models were performed to evaluate the prognostic impact of CLEC4M on NSCLC patients. The correlation between CLEC4M and tumor immune infiltration was estimated using TIMER and UALCAN databases. Functional assessments including GO, KEGG pathway and GSEA analyses were implemented to illustrate the potential mechanisms of CLEC4M in NSCLC. Results CLEC4M was significantly downregulated in NSCLC tissue, as confirmed by immunohistochemistry of clinical tissues. The high AUC value of ROC curves demonstrated the diagnostic accuracy of CLEC4M in NSCLC. Additionally, low CLEC4M expression was associated with poor survival in NSCLC patients. Furthermore, CLEC4M was found to be significantly associated with tumor immune infiltration, and CLEC4M may be involved in immune activation and proliferation inhibition through the functional assessment, suggesting that CLEC4M may be a therapeutic target for NSCLC patients. Conclusion Our findings reveal CLEC4M is significantly downregulated in NSCLC tissues, and illustrate the diagnostic and prognostic value of CLEC4M in NSCLC, as well as its potential serve as an immune-related therapeutic target.
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Affiliation(s)
- Huan Liu
- Department of Precision Medicine Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
- Key Laboratory of Cancer Prevention and Treatment of Huaihua, Huaihua, People’s Republic of China
| | - Zhiping Yu
- School of Pharmacy, Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Yueguang Liu
- Department of Clinicopathology Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
| | - Mingzhen Li
- Department of Precision Medicine Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
- Key Laboratory of Cancer Prevention and Treatment of Huaihua, Huaihua, People’s Republic of China
| | - Cheng Chen
- Department of Precision Medicine Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
- Key Laboratory of Cancer Prevention and Treatment of Huaihua, Huaihua, People’s Republic of China
| | - Zhiyu Zhu
- Department of Clinicopathology Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
| | - Fang Liu
- Department of Clinicopathology Center, The Second People’s Hospital of Huaihua, Huaihua, People’s Republic of China
| | - Liming Tan
- Key Laboratory of Cancer Prevention and Treatment of Huaihua, Huaihua, People’s Republic of China
- School of Pharmacy, Xuzhou Medical University, Xuzhou, People’s Republic of China
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