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Fei Y, Wu Y, Chen L, Yu H, Pan L. Comprehensive pan-carcinoma analysis of ITGB1 distortion and its potential clinical significance for cancer immunity. Discov Oncol 2024; 15:47. [PMID: 38402311 PMCID: PMC10894187 DOI: 10.1007/s12672-024-00901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
The human protein-coding gene ITGB1 (Integrin 1), also known as CD29, has a length of 58048 base pairs. The Integrin family's most prevalent subunit, it participates in the transmission of numerous intracellular signaling pathways. A thorough examination of ITGB1's functions in human malignancies, however, is inadequate and many of their relationships to the onset and development of human cancers remain unknown. In this work, we examined ITGB1's role in 33 human cancers. Finally, a multi-platform analysis revealed that three of the 33 malignancies had significantly altered ITGB1 expression in tumor tissues in comparison to normal tissues. In addition, it was discovered through survival analysis that ITGB1 was a stand-alone prognostic factor in a number of cancers. ITGB1 expression was linked to immune cell infiltration in colon cancer, according to an investigation of immune infiltration in pan-cancer. In the gene co-expression research, ITGB1 showed a positive connection with the majority of the cell proliferation and EMT indicators, indicating that ITGB1 may have an essential function in controlling cancer metastasis and proliferation. Our pan-cancer analysis of ITGB1 gives evidence in favor of a further investigation into its oncogenic function in various cancer types.
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Affiliation(s)
- Yuchang Fei
- Department of Integrated Chinese and Western Medicine, The First People's Hospital of Jiashan, Jiashan Hospital Affiliated of Jiaxing University, Jiashan, Zhejiang, China.
| | - Yulun Wu
- Center for Rehabilitation Medicine, Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Department of Rehabilitation Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Luting Chen
- Department of Integrated Chinese and Western Medicine, The First People's Hospital of Wenling, Wenling, Zhejiang, China
| | - Huan Yu
- The Department of Traditional Chinese Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Lei Pan
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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Lv T, Liu H, Mao L, Song Y, Liao L, Zhong K, Shuai B, Luo Y, Guo T, Huang W, Zhang S. Cancer-associated fibroblast-derived extracellular vesicles promote lymph node metastases in oral cavity squamous cell carcinoma by encapsulating ITGB1 and BMI1. BMC Cancer 2024; 24:113. [PMID: 38254031 PMCID: PMC10804601 DOI: 10.1186/s12885-024-11855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) have been revealed to facilitate the development of oral squamous cavity cell carcinoma (OCSCC), while its supporting role in lymph node metastases is under continuous investigation. This study aimed to examine the function of cancer-associated fibroblasts (CAF)-derived EVs (CAF-EVs) during lymph node metastasis in OCSCC and the mechanisms. METHODS CAF were isolated from OCSCC tissues of patients, and CAF-EVs were extracted and identified. EdU, colony formation, wound healing, and Transwell assays were performed. The OCSCC cells before and after CAF-EVs treatment were injected into mice to probe the effects of CAF-EVs on tumor growth and lymph node metastasis, respectively. The effect of CAF-EVs treatment on transcriptome changes in OCSCC cells was analyzed. Clinical data of patients with OCSCC were analyzed to determine the prognostic significance of the selected genes. Finally, loss-of-function assays were conducted to corroborate the involvement of polycomb complex protein BMI-1 (BMI1) and integrin beta1 (ITGB1). RESULTS CAF-EVs promoted the malignant behavior of OCSCC cells and accelerated tumor growth and lymph node metastasis in mice. CAF-EVs significantly increased the expression of BMI1 and ITGB1, and the expression of BMI1 and ITGB1 was negatively correlated with the overall survival and relapse-free survival of OCSCC patients. Knockdown of BMI1 or ITGB1 in OCSCC cells abated the promoting effects of CAF-EVs in vitro and in vivo. CONCLUSION CAF-EVs elicited the metastasis-promoting properties in OCSCC by elevating BMI1 and ITGB1, suggesting that BMI1 and ITGB1 could be potential biomarkers and therapeutic targets for OCSCC.
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Affiliation(s)
- Tianzhu Lv
- Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Hongjing Liu
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Ling Mao
- Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Yanrong Song
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Lili Liao
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Kun Zhong
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Binbin Shuai
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Yingkun Luo
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Tingting Guo
- Comprehensive Emergency Department of Stomatology, Stomatological Hospital of Guizhou Medical University, 550004, Guiyang, Guizhou, P.R. China
| | - Wentao Huang
- School of Savaid Stomatology, Hangzhou Medical College, 311399, Hangzhou, Zhejiang, P.R. China.
| | - Shenyingjie Zhang
- Medical Department, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), 310006, Hangzhou, Zhejiang, P.R. China
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Wang Y, Song W, Li Y, Liu Z, Zhao K, Jia L, Wang X, Jiang R, Tian Y, He X. Integrated analysis of tumor microenvironment features to establish a diagnostic model for papillary thyroid cancer using bulk and single-cell RNA sequencing technology. J Cancer Res Clin Oncol 2023; 149:16837-16850. [PMID: 37733241 PMCID: PMC10645658 DOI: 10.1007/s00432-023-05420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Characterizing tumor microenvironment using single-cell RNA sequencing has been a promising strategy for cancer diagnosis and treatment. However, a few studies have focused on diagnosing papillary thyroid cancer (PTC) through this technology. Therefore, our study explored tumor microenvironment (TME) features and identified potential biomarkers to establish a diagnostic model for papillary thyroid cancer. METHODS The cell types were identified using the markers from the CellMarker database and published research. The CellChat package was conducted to analyze the cell-cell interaction. The SCEVAN package was used to identify malignant thyroid cells. The SCP package was used to perform multiple single-cell downstream analyses, such as GSEA analysis, enrichment analysis, pseudotime trajectory analysis, and differential expression analysis. The diagnostic model of PTC was estimated using the calibration curves, receiver operating characteristic curves, and decision curve analysis. RT-qPCR was performed to validate the expression of candidate genes in human papillary thyroid samples. RESULTS Eight cell types were identified in the scRNA-seq dataset by published cell markers. Extensive cell-cell interactions like FN1/ITGB1 existed in PTC tissues. We identified 26 critical genes related to PTC progression. Further, eight subgroups of PTC tumor cells were identified and exhibited high heterogeneity. The MDK/LRP1, MDK/ALK, GAS6/MERTK, and GAS6/AXL were identified as potential ligand-receptor pairs involved in the interactions between fibroblasts/endothelial cells and tumor cells. Eventually, the diagnostic model constructed by TRPC5, TENM1, NELL2, DMD, SLC35F3, and AUTS2 showed a good efficiency for distinguishing the PTC and normal tissues. CONCLUSIONS Our study comprehensively characterized the tumor microenvironment in papillary thyroid cancer. Through combined analysis with bulk RNA-seq, six potential diagnostic biomarkers were identified and validated. The diagnostic model we constructed was a promising tool for PTC diagnosis. Our findings provide new insights into the heterogeneity of thyroid cancer and the theoretical basis for diagnosing thyroid cancer.
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Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Wenbin Song
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yingxi Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Zhaoyi Liu
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Lanning Jia
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yao Tian
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
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Song C, Li T, Zhang C, Li S, Lu S, Zou Y. RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis. Life Sci Alliance 2023; 6:e202302013. [PMID: 37541848 PMCID: PMC10403638 DOI: 10.26508/lsa.202302013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Proper retinoic acid (RA) signaling is essential for normal craniofacial development. Both excessive RA and RA deficiency in early embryonic stage may lead to a variety of craniofacial malformations, for example, cleft palate, which have been investigated extensively. Dysregulated Wnt and Shh signaling were shown to underlie the pathogenesis of RA-induced craniofacial defects. In our present study, we showed a spatiotemporal-specific effect of RA signaling in regulating early development of facial prominences. Although inhibited Wnt activities was observed in E12.5/E13.5 mouse palatal shelves, early exposure of excessive RA induced Wnt signaling and Wnt-related gene expression in E11.5/E12.5 mouse embryonic frontonasal/maxillary processes. A conserved regulatory network of miR-484-Fzd5 was identified to play critical roles in RA-regulated craniofacial development using RNA-seq. In addition, subsequent osteogenic/chondrogenic differentiation were differentially regulated in discrete mouse embryonic facial prominences in response to early RA induction, demonstrated using both in vitro and in vivo analyses.
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Affiliation(s)
- Chao Song
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Ting Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Chunlei Zhang
- First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Shufang Li
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
| | - Songhui Lu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yi Zou
- The Key Laboratory of Virology of Guangzhou, Jinan University, Guangzhou, China
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Xu C, Xie XL, Kang N, Jiang HQ. Evaluation of ITGB1 expression as a predictor of the therapeutic effects of immune checkpoint inhibitors in gastric cancer. BMC Gastroenterol 2023; 23:298. [PMID: 37667169 PMCID: PMC10478479 DOI: 10.1186/s12876-023-02930-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Gastric cancer (CC) is a disease with high incidence and mortality rate. Immunotherapy is an important method for gastric cancer while lack of effective predictor. Integrins play an important role in the development. We aimed to explore the predictive value of β1 integrin (ITGB1) as a predictor of immunnotherapy in gastric cancer. METHODS Differential expression analysis was conducted using the Gene Expression Profiling Interactive Analysis (GEPIA) 2.0 and GEO databases. GEPIA data were used to evaluate the prognostic value of ITGB1 in gastric cancer (GC). Transcriptomic and clinical data of GC and normal tissues were downloaded from The Cancer Genome Atlas database, and the TIMER database was used to evaluate the association between ITGB1 and immune infiltration. Time-dependent receiver operating characteristic (ROC) curve analysis was used to determine the prognostic value of ITGB1. To verify ITGB1 expression at the protein level, immunohistochemical staining was conducted. In addition, to analyze the correlation of ITGB1 with PD-1 and PD-L1, we examined levels of PD-1 and PD-L1 by IHC and determined the predictive value of ITGB1 for anti-PD-1 therapy in GC by ROC curve analysis. RESULTS Compared with normal tissues, analysis of GEPIA and data at protein levels showed significantly higher expression of ITGB1 in GC. In addition, higher expression of ITGB1 was associated with worse pathological G-staging and tumor T-staging, which suggested that ITGB1 is a risk factor for poor prognosis in GC. The level of ITGB1 expression was positively correlated with CD8 + T cells, neutrophils, macrophages, and dendritic cells. ITGB1 expression was also correlated with PD-L1 expression, and this was further verified at the protein level by immunohistochemical analysis. The area under the ROC curve was 0.808. CONCLUSION ITGB1 may be a promising prognostic biomarker and effective predictor for anti-PD-1 therapy in GC. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
- Chao Xu
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
- Handan Central Hospital, No.15, Zhonghua Road, Handan, 056001, Hebei Province, China
| | - Xiao-Li Xie
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Ning Kang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Hui-Qing Jiang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
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Xie H, Qin C, Zhou X, Liu J, Yang K, Nong J, Luo J, Peng T. Prognostic value and potential molecular mechanism of ITGB superfamily members in hepatocellular carcinoma. Medicine (Baltimore) 2023; 102:e34765. [PMID: 37603520 PMCID: PMC10443747 DOI: 10.1097/md.0000000000034765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
We analyzed the prognostic value and potential molecular mechanisms of the members of integrin β (ITGB)superfamily in hepatocellular carcinoma (HCC) using data from The Cancer Genome Atlas (TCGA), cBioPortal, Gene Expression Profiling Interactive Analysis (GEPIA), Human Protein Atlas (HPA) HPA, Search Tool for the Retrieval of Interacting Genes/Proteins, GeneMANIA, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), TIMER and Gene set enrichment analysis (GSEA) databases. ITGB4/5 mRNA was upregulated in HCC tissues in contrast to the normal liver tissues, whereas ITGB2/3/8 levels were lower in the former. ITGB4 was the most frequently mutated ITGB gene in HCC. Receiver operating characteristic curve (ROC) analysis showed that the expression levels of ITGB2/3/4/5/7/8 had significant diagnostic value in distinguishing HCC tissues from healthy liver tissues, ITGB8 had the highest diagnostic efficacy. The ITGB1/3/6/8 were also upregulated in the HCC tissues in contrast to healthy liver tissues. The expression of ITGB8 was verified by immunohistochemistry (IHC). Furthermore, ITGB6 and ITGB7 expression levels were strongly associated with the overall survival (OS) of HCC patients. The ITGB superfamily members exhibited homology and interactions in protein structure. In addition, ITGB6 together with ITGB7 were negatively related to the infiltration of multiple immune cell populations. GSEA results showed that ITGB6 was enriched in HCC migration and recurrence, whereas ITGB7 was significantly enriched in HIPPO, TOLL and JAK-STAT signaling pathways. In conclusion, ITGB6 and ITGB7 genes are possible to be prognostic biomarkers for HCC.
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Affiliation(s)
- Haixiang Xie
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Chongjiu Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Junqi Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Kejian Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Jusen Nong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Jianzhu Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People’s Republic of China
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Jing W, Zhang R, Chen X, Zhang X, Qiu J. Association of Glycosylation-Related Genes with Different Patterns of Immune Profiles and Prognosis in Cervical Cancer. J Pers Med 2023; 13:jpm13030529. [PMID: 36983711 PMCID: PMC10054345 DOI: 10.3390/jpm13030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
(1) Background: Although the application of modern diagnostic tests and vaccination against human papillomavirus has markedly reduced the incidence and mortality of early cervical cancer, advanced cervical cancer still has a high death rate worldwide. Glycosylation is closely associated with tumor invasion, metabolism, and the immune response. This study explored the relationship among glycosylation-related genes, the immune microenvironment, and the prognosis of cervical cancer. (2) Methods and results: Clinical information and glycosylation-related genes of cervical cancer patients were downloaded from the TCGA database and the Molecular Signatures Database. Patients in the training cohort were split into two subgroups using consensus clustering. A better prognosis was observed to be associated with a high immune score, level, and status using ESTIMATE, CIBERSORT, and ssGSEA analyses. The differentially expressed genes were revealed to be enriched in proteoglycans in cancer and the cytokine–cytokine receptor interaction, as well as in the PI3K/AKT and the Hippo signaling pathways according to functional analyses, including GO, KEGG, and PPI. The prognostic risk model generated using the univariate Cox regression analysis, LASSO algorithm and multivariate Cox regression analyses, and prognostic nomogram successfully predicted the survival and prognosis of cervical cancer patients. (3) Conclusions: Glycosylation-related genes are correlated with the immune microenvironment of cervical cancer and show promising clinical prediction value.
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Affiliation(s)
- Wanling Jing
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 200433, China (R.Z.)
| | - Runjie Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 200433, China (R.Z.)
- Obstetrics and Gynecology Department, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai 200336, China
| | - Xinyi Chen
- Obstetrics and Gynecology Department, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai 200336, China
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 200433, China (R.Z.)
- Correspondence: (X.Z.); (J.Q.)
| | - Jin Qiu
- Obstetrics and Gynecology Department, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai 200336, China
- Correspondence: (X.Z.); (J.Q.)
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Xu C, Shi J, Huang R, Wu Z, Wu S, Bao W. Transcriptome-Wide lncRNA and mRNA Profiling of Spleens from Meishan Pigs at Different Development Stages. Animals (Basel) 2022; 12:2676. [PMID: 36230417 DOI: 10.3390/ani12192676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
Simple Summary Meishan pig is a local pig breed in China, which has higher immunity than commercial pig breeds for some diseases. The spleen has hematopoietic and immune response functions, making it a good organ model for studying immunity. We depicted the expression profiles of lncRNA-mRNA in the spleen of Meishan pigs at different developmental time points (7 d, 21 d, 35 d, 120 d and 180 d). In addition, we found that AKT3, CBL and PTK2B may be involved in immune regulation in Meishan pigs through a competing endogenous RNA network. This result provides valuable genomic resources for studying immune regulation in animals and finds potential molecular markers for pig disease resistance breeding. Abstract Meishan is a well-established local Chinese breed known for its high fecundity, strong immune response and high meat quality. However, the molecular mechanism of immune regulation during the development of Meishan pigs still remains unclear. Here, we performed the transcriptional sequencing of spleen tissues from Meishan pigs at different development stages. In total, 10,268 lncRNAs were identified, including 1254 novel lncRNAs and 9014 known lncRNAs. Time series analysis revealed that genes of the up-regulated module were enriched in pathways associated with transport, immunity, and histone acetylation modifications, while genes of the down-regulated module were enriched in DNA metabolic process and cell cycle. Weighted gene co-expression network analysis (WGCNA) showed the functional linkage between mRNAs and lncRNAs, indicating that lncRNAs are important regulatory elements of mRNAs. Notably, a lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network that contained 3 mRNAs (AKT3, CBL and PTK2B), 17 lncRNAs and 67 miRNAs were screened out, which probably plays a critical role in immune regulation of Meishan pigs. Our findings not only revealed the transcriptome profile of spleen development, but also provide novel insights into the mechanism of lncRNA-miRNA-mRNA axis in the immune response in Meishan pigs.
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