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Yang X, Lei P, Huang L, Tang X, Wei B, Wei H. Prognostic value of LRRC4C in Colon and Gastric Cancers correlates with Tumour Microenvironment Immunity. Int J Biol Sci 2021; 17:1413-1427. [PMID: 33867855 PMCID: PMC8040466 DOI: 10.7150/ijbs.58876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
In this study, we aimed to use ESTIMATE and CIBERSORT computational methods to analyse transcriptional information on COAD and STAD in TCGA. We downloaded transcriptome RNA-seq data of 446 patients with colon cancer from TCGA and estimated the amount of immune and stromal components in the COAD samples using CIBERSORT algorithms. We analysed differentially expressed genes in 446 TCGA samples and 585 Series GSE39582 samples, in high- and low-scoring groups, using Cox regression. The expression of LRRC4C, correlated positively with clinicopathological characteristics and negatively with the survival of patients with COAD. Single-gene survival analysis using Gene Expression Profiling Interactive Analysis 2.0 and Kaplan-Meier plotter revealed an association between high levels of LRRC4C expression and poor prognosis in patients with colon and gastric cancers. Gene set enrichment analysis of COAD and STAD samples indicated that genes in groups expressing high and low LRRC4C levels were mainly enriched in immune-related activities and metabolic pathways, respectively. Difference and correlation analyses of the relationship between LRRC4C expression and tumour-infiltrating immune cells, determined using CIBERSORT algorithms, revealed that monocytes, resting mast cells, and M2 macrophages were positively correlated with LRRC4C expression.
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Affiliation(s)
- XiaoFeng Yang
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Purun Lei
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Lijun Huang
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Xiao Tang
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Bo Wei
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - HongBo Wei
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
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Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia. Genes (Basel) 2020; 11:genes11080868. [PMID: 32751923 PMCID: PMC7465400 DOI: 10.3390/genes11080868] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Acute myeloid leukemia (AML) is one of the most common malignant and aggressive hematologic tumors, and its pathogenesis is associated with abnormal post-transcriptional regulation. Unbalanced competitive endogenous RNA (ceRNA) promotes tumorigenesis and progression, and greatly contributes to tumor risk classification and prognosis. However, the comprehensive analysis of the circular RNA (circRNA)-long non-coding RNA (lncRNA)-miRNA-mRNA ceRNA network in the prognosis of AML is still rarely reported. Method: We obtained transcriptome data of AML and normal samples from The Cancer Genome Atlas (TCGA), Genotype-tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases, and identified differentially expressed (DE) mRNAs, lncRNAs, and circRNAs. Then, the targeting relationships among lncRNA-miRNA, circRNA-miRNA, and miRNA-mRNA were predicted, and the survival related hub mRNAs were further screened by univariate and multivariate Cox proportional hazard regression. Finally, the AML prognostic circRNA-lncRNA-miRNA-mRNA ceRNA regulatory network was established. Results: We identified prognostic 6 hub mRNAs (TM6SF1, ZMAT1, MANSC1, PYCARD, SLC38A1, and LRRC4) through Cox regression model, and divided the AML samples into high and low risk groups according to the risk score obtained by multivariate Cox regression. Survival analysis verified that the survival rate of the high-risk group was significantly reduced (p < 0.0001). The prognostic ceRNA network of 6 circRNAs, 32 lncRNAs, 8 miRNAs, and 6 mRNAs was established according to the targeting relationship between 6 hub mRNAs and other RNAs. Conclusion: In this study, ceRNA network jointly participated by circRNAs and lncRNAs was established for the first time. It comprehensively elucidated the post-transcriptional regulatory mechanism of AML, and identified novel AML prognostic biomarkers, which has important guiding significance for the clinical diagnosis, treatment, and further scientific research of AML.
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Zhao C, She X, Zhang Y, Liu C, Li P, Chen S, Sai B, Li Y, Feng J, Liu J, Sun Y, Xiao S, Li L, Wu M. LRRC4 Suppresses E-Cadherin-Dependent Collective Cell Invasion and Metastasis in Epithelial Ovarian Cancer. Front Oncol 2020; 10:144. [PMID: 32117780 PMCID: PMC7033568 DOI: 10.3389/fonc.2020.00144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/27/2020] [Indexed: 11/17/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the most malignant gynecological carcinoma and is of a high incidence of death due to detection at late stages when metastasis already occurs. However, the mechanism underlying metastasis of EOC remains unclear. Analysis of the open database and experiments with immunochemistry showed that LRRC4 is lowly expressed in high-grade serous ovarian cancer (HGSC) cells and during EOC metastasis. The 3D cell culture system and the orthotopic ovarian xenograft model infected with LRRC4-containing adeno-associated virus serotype 9 (AAV9) were used to confirm collective invasion and metastasis of cells in vitro and in vivo. Phos-tag SDS-PAGE was used to detect the phosphorylation of LRRC4 and PIK3R1. A number of experiments with methods such as co-immunoprecipitation and immunoblotting were performed to explore the mechanism for the actions of LRRC4 and PIK3R1 in EOC metastasis. An inverse correlation between LRRC4 and E-cadherin expression was detected in the regions of invasion in primary EOC tissues and metastatic ascites. LRRC4 binds to the cSH2 domain of PIK3R1 and inhibits the activity of PIK3R1, without disrupting the physical interactions between PIK3R1 and PIK3CA. LRRC4 inhibits EOC metastasis by targeting E-cadherin-dependent collective cell invasion and does so by inhibiting the PIK3R1-mediated AKT/GSK3β/β-catenin signaling pathway. LRRC4 functions as a tumor suppressor gene to inhibit EOC collective invasion and metastasis in vitro and in vivo and does so by directly binding to the cSH2 domain of PIK3R1 to exert its regulatory function. Our findings provide a potential novel approach for metastasis prognosis and a new strategy for the treatment of EOC.
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Affiliation(s)
- Chunhua Zhao
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Xiaoling She
- Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan Zhang
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
| | - Changhong Liu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
| | - Peiyao Li
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
| | - Shuai Chen
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Buqing Sai
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
| | - Yunchao Li
- Second Xiangya Hospital, Central South University, Changsha, China
| | - Jianbo Feng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
| | - Jia Liu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yingnan Sun
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Songshu Xiao
- Third Xiangya Hospital, Central South University, Changsha, China
| | - Liping Li
- The Affiliated Zhuzhou Hospital of XiangYa Medical School, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, China
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Peculis R, Balcere I, Rovite V, Megnis K, Valtere A, Stukens J, Arnicane L, Nikitina-Zake L, Lejnieks A, Pirags V, Klovins J. Polymorphisms in MEN1 and DRD2 genes are associated with the occurrence and characteristics of pituitary adenomas. Eur J Endocrinol 2016; 175:145-53. [PMID: 27185868 DOI: 10.1530/eje-15-0879] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 05/16/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Although pituitary adenomas (PAs) affect a significant proportion of the population, only a fraction have the potential to become clinically relevant during an individual's lifetime, causing hormonal imbalance or complications due to mass effect. The overwhelming majority of cases are sporadic and without a clear familial history, and the genotype-phenotype correlation in PA patients is poorly understood. Our aim was to investigate the involvement of genes known for their role in familial cases on drug response and tumor suppression in the development and pathology of PAs in a patient group from Latvia. DESIGN The study included 143 cases and 354 controls, we investigated the role of single-nucleotide polymorphisms (SNPs) in seven genes (SSTR2, SSTR5, DRD2, MEN1, AIP, GNAS, and PRKAR1A) associated with pituitary tumor occurrence, phenotype, and clinical symptoms. METHODS Genotyping of 96 tag and nonsynonymous SNPs was performed in the genomic regions of interest. RESULTS We discovered a significant association (OR=17.8, CI 0.95=2.18-145.5, P=0.0002) between a rare MEN1 mutation (rs2959656) and clinically active adenoma in our patients. Additionally, rs7131056 at DRD2 was associated with a higher occurrence of extrasellar growth in patients with prolactinoma and somatotropinoma (OR=2.79, CI 0.95=1.58-4.95, P=0.0004). CONCLUSIONS rs2959656, a nonsynonymous variant in MEN1, is associated with the development of clinically active PA. Furthermore, rs7131056 in DRD2 contributes to either faster growth of the adenoma or reduced symptomatic presentation, allowing PAs to become larger before detection.
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Affiliation(s)
- Raitis Peculis
- Latvian Biomedical Research and Study CentreRiga, Latvia
| | - Inga Balcere
- Pauls Stradiņš Clinical University HospitalRiga, Latvia Faculty of MedicineUniversity of Latvia, Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study CentreRiga, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study CentreRiga, Latvia
| | - Andra Valtere
- Riga Eastern Clinical University HospitalRiga, Latvia
| | - Janis Stukens
- Pauls Stradiņš Clinical University HospitalRiga, Latvia
| | | | | | | | - Valdis Pirags
- Latvian Biomedical Research and Study CentreRiga, Latvia Pauls Stradiņš Clinical University HospitalRiga, Latvia Faculty of MedicineUniversity of Latvia, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study CentreRiga, Latvia
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Common variants at 10p12.31, 10q21.1 and 13q12.13 are associated with sporadic pituitary adenoma. Nat Genet 2015; 47:793-7. [PMID: 26029870 DOI: 10.1038/ng.3322] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/07/2015] [Indexed: 01/02/2023]
Abstract
Pituitary adenoma is one of the most common intracranial neoplasms, and its genetic basis remains largely unknown. To identify genetic susceptibility loci for sporadic pituitary adenoma, we performed a three-stage genome-wide association study (GWAS) in the Han Chinese population. We first analyzed genome-wide SNP data in 771 pituitary adenoma cases and 2,788 controls and then carried forward the promising variants for replication in another 2 independent sets (2,542 cases and 3,620 controls in total). We identified three new susceptibility loci below the genome-wide significance threshold (P < 5 × 10(-8)) in the combined analyses: 10p12.31 (rs2359536, P(meta) = 2.25 × 10(-10) and rs10828088, P(meta) = 6.27 × 10(-10)), 10q21.1 (rs10763170, P(meta) = 6.88 × 10(-10)) and 13q12.13 (rs17083838, P(meta) = 1.89 × 10(-8)). This study is the first GWAS to our knowledge on sporadic pituitary adenoma, and our results provide insight into the genetic basis of this disease.
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Li P, Xu G, Li G, Wu M. Function and mechanism of tumor suppressor gene LRRC4/NGL-2. Mol Cancer 2014; 13:266. [PMID: 25526788 PMCID: PMC4349622 DOI: 10.1186/1476-4598-13-266] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/15/2014] [Indexed: 11/24/2022] Open
Abstract
LRRC4/NGL-2 (Leucine rich repeat containing 4/Netrin-G ligand-2), a relatively specific expressed gene in brain tissue, is a member of the LRRC4/ NGL (netrin-G ligand) family and belongs to the superfamily of LRR proteins. LRRC4/NGL-2 regulates neurite outgrowth and lamina-specific dendritic segmentation, suggesting that LRRC4/NGL-2 is important for the development of the nervous system. In addition, LRRC4/NGL-2 has been identified as a tumor suppressor gene. The overexpression of LRRC4/NGL-2 suppresses glioma cell growth, angiogenesis and invasion through complicated signaling regulation networks. LRRC4/NGL-2 also has the ability to form multiphase loops with miRNA, transcription factors and gene methylation modification; the loss of LRRC4/NGL-2 function may be an important event in multiple biological processes in gliomas. In summary, LRRC4/NGL-2 is a critical gene in the normal development and tumorigenesis of the nervous system.
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Affiliation(s)
| | | | | | - Minghua Wu
- Hunan Cancer Hospital and the Affiliated Tumor Hospital of Xiangya Medical School Central South University, Changsha, Hunan, China.
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