1
|
Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
Collapse
Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
2
|
Zang Y, Ran X, Yuan J, Wu H, Wang Y, Li H, Teng H, Sun Z. Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer. Brief Bioinform 2024; 25:bbae023. [PMID: 38343327 PMCID: PMC10859687 DOI: 10.1093/bib/bbae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Hyperactive ribosome biogenesis (RiboSis) fuels unrestricted cell proliferation, whereas genomic hallmarks and therapeutic targets of RiboSis in cancers remain elusive, and efficient approaches to quantify RiboSis activity are still limited. Here, we have established an in silico approach to conveniently score RiboSis activity based on individual transcriptome data. By employing this novel approach and RNA-seq data of 14 645 samples from TCGA/GTEx dataset and 917 294 single-cell expression profiles across 13 cancer types, we observed the elevated activity of RiboSis in malignant cells of various human cancers, and high risk of severe outcomes in patients with high RiboSis activity. Our mining of pan-cancer multi-omics data characterized numerous molecular alterations of RiboSis, and unveiled the predominant somatic alteration in RiboSis genes was copy number variation. A total of 128 RiboSis genes, including EXOSC4, BOP1, RPLP0P6 and UTP23, were identified as potential therapeutic targets. Interestingly, we observed that the activity of RiboSis was associated with TP53 mutations, and hyperactive RiboSis was associated with poor outcomes in lung cancer patients without TP53 mutations, highlighting the importance of considering TP53 mutations during therapy by impairing RiboSis. Moreover, we predicted 23 compounds, including methotrexate and CX-5461, associated with the expression signature of RiboSis genes. The current study generates a comprehensive blueprint of molecular alterations in RiboSis genes across cancers, which provides a valuable resource for RiboSis-based anti-tumor therapy.
Collapse
Affiliation(s)
- Yue Zang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences and Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Xia Ran
- Liangzhu Laboratory, Zhejiang University Medical Center, China
| | - Jie Yuan
- BGI Education Center, University of Chinese Academy of Sciences, China
| | - Hao Wu
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Youya Wang
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - He Li
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhongsheng Sun
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Institute of Genomic Medicine, Wenzhou Medical University, and Beijing Institutes of Life Science, Chinese Academy of Sciences, Hangzhou, China
| |
Collapse
|
3
|
Liu XY, Tan Q, Li LX. A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker. Hereditas 2023; 160:38. [PMID: 38082360 PMCID: PMC10712082 DOI: 10.1186/s41065-023-00302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Dyskeratosis congenita 1 (DKC1), a critical component of telomerase complex, is highly expressed in a variety of human cancers. However, the association of DKC1 with cancer occurrence and development stages is not clear, making a pan-cancer analysis crucial. METHODS We conducted a study using various bioinformatic databases such as TIMER, GEPIA, UALCAN, and KM plotter Analysis to examine the different expressions of DKC1 in multiple tissues and its correlation with pathological stages. Through KEGG analysis, GO enrichment analysis and Venn analysis, we were able to reveal DKC1-associated genes and signaling pathways. In addition, we performed several tests including the CCK, wound healing assay, cell cycle arrest assay, transwell assay and Sa-β-gal staining on DKC1-deleted MDA-231 cells. RESULTS Our study demonstrates that DKC1 has relatively low expression specificity in different tissues. Furthermore, we found that in ACC, KICH, KIRP and LIHC, the expression level of DKC1 is positively correlated with pathological stages. Conversely, in NHSC, KIRP, LGG, LIHC, MESO and SARC, we observed a negative influence of DKC1 expression level on the overall survival rate. We also found a significant positive correlation between DKC1 expression and Tumor Mutational Burden in 14 tumors. Additionally, we observed a significantly negative impact of DKC1 DNA methylation on gene expression at the promoter region in BRCA. We also identified numerous phosphorylation sites concentrated at the C-terminus of the DKC1 protein. Our GO analysis revealed a correlation between DKC1 and ribosomal biosynthesis pathways, and the common element UTP14A was identified. We also observed decreased rates of cell proliferation, migration and invasion abilities in DKC1-knockout MDA-MB-231 cell lines. Furthermore, DKC1-knockout induced cell cycle arrest and caused cell senescence. CONCLUSIONS Our findings suggest that the precise expression of DKC1 is closely associated with the occurrence and developmental stages of cancer in multiple tissues. Depletion of DKC1 can inhibit the abilities of cancer cells to proliferate, migrate, and invade by arresting the cell cycle and inducing cell senescence. Therefore, DKC1 may be a valuable prognostic biomarker for the diagnosis and treatment of cancer in various tissues.
Collapse
Affiliation(s)
- Xin-Ying Liu
- School of Life and Health Sciences, Huzhou College, Huzhou, 313000, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Qing Tan
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Lin-Xiao Li
- School of Life and Health Sciences, Huzhou College, Huzhou, 313000, China.
| |
Collapse
|
4
|
Wu Z, Gong Z, Li C, Huang Z. RTEL1 is upregulated in colorectal cancer and promotes tumor progression. Pathol Res Pract 2023; 252:154958. [PMID: 37988793 DOI: 10.1016/j.prp.2023.154958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/23/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
As one of the most common cancers worldwide, the incidence of colorectal cancer (CRC) continues to increase. Metastasis is the leading cause of death for this malignant disease. Regulator of telomere elongation helicase 1 (RTEL1) is a key factor that maintains telomere stability and contributes to DNA repair. Recent advances have suggested that RTEL1 exerts other functions through various mechanisms. However, little is known about its role in human cancers, including CRC. In this study, we revealed that the copy number of RTEL1 was significantly higher in CRC tissues, especially in metastatic CRC tissues, than in paired normal tissues, which was associated with increased expression. Increased RTEL1 expression was significantly correlated with CRC progression and poor survival. Functionally, RTEL1 knockdown suppressed the proliferation and metastasis of CRC both in vitro and in vivo. In addition, multiple signalling pathways, including the mitotic cell cycle, DNA repair, and EMT, were potentially regulated by RTEL1. Notably, GPR17 appeared to be a candidate downstream target gene that partially mediated the tumor-promoting effects of RTEL1 in CRC. Altogether, our results indicate that RTEL1 plays a crucial role in CRC progression and appears to be a promising therapeutic target and prognosis for CRC.
Collapse
Affiliation(s)
- Zhuochao Wu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214062, Jiangsu, China
| | - Zhicheng Gong
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214062, Jiangsu, China
| | - Chaoqun Li
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214062, Jiangsu, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214062, Jiangsu, China.
| |
Collapse
|
5
|
Kong Y, Liu Y, Li X, Rao M, Li D, Ruan X, Li S, Jiang Z, Zhang Q. Palmitoylation landscapes across human cancers reveal a role of palmitoylation in tumorigenesis. J Transl Med 2023; 21:826. [PMID: 37978524 PMCID: PMC10655258 DOI: 10.1186/s12967-023-04611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Protein palmitoylation, which is catalyzed by palmitoyl-transferase and de-palmitoyl-transferase, plays a crucial role in various biological processes. However, the landscape and dynamics of protein palmitoylation in human cancers are not well understood. METHODS We utilized 23 palmitoyl-acyltransferases and seven de-palmitoyl-acyltransferases as palmitoylation-related genes for protein palmitoylation analysis. Multiple publicly available datasets were employed to conduct pan-cancer analysis, examining the transcriptome, genomic alterations, clinical outcomes, and correlation with c-Myc (Myc) for palmitoylation-related genes. Real-time quantitative PCR and immunoblotting were performed to assess the expression of palmitoylation-related genes and global protein palmitoylation levels in cancer cells treated with Myc depletion or small molecule inhibitors. Protein docking and drug sensitivity analyses were employed to predict small molecules that target palmitoylation-related genes. RESULTS We identified associations between palmitoylation and cancer subtype, stage, and patient survival. We discovered that abnormal DNA methylation and oncogenic Myc-driven transcriptional regulation synergistically contribute to the dysregulation of palmitoylation-related genes. This dysregulation of palmitoylation was closely correlated with immune infiltration in the tumor microenvironment and the response to immunotherapy. Importantly, dysregulated palmitoylation was found to modulate canonical cancer-related pathways, thus influencing tumorigenesis. To support our findings, we performed a proof-of-concept experiment showing that depletion of Myc led to reduced expression of most palmitoylation-related genes, resulting in decreased global protein palmitoylation levels. Through mass spectrometry and enrichment analyses, we also identified palmitoyl-acyltransferases ZDHHC7 and ZDHHC23 as significant contributors to mTOR signaling, DNA repair, and immune pathways, highlighting their potential roles in tumorigenesis. Additionally, our study explored the potential of three small molecular (BI-2531, etoposide, and piperlongumine) to modulate palmitoylation by targeting the expression or activity of palmitoylation-related genes or enzymes. CONCLUSIONS Overall, our findings underscore the critical role of dysregulated palmitoylation in tumorigenesis and the response to immunotherapy, mediated through classical cancer-related pathways and immune cell infiltration. Additionally, we propose that the aforementioned three small molecule hold promise as potential therapeutics for modulating palmitoylation, thereby offering novel avenues for cancer therapy.
Collapse
Affiliation(s)
- Yue Kong
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xianzhe Li
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Menglan Rao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Dawei Li
- Zhumadian Central Hospital, Huanghuai University, Zhumadian, 463000, China
| | - Xiaolan Ruan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Shanglin Li
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China.
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China.
| | - Qiang Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China.
| |
Collapse
|
6
|
Tian L, Gong L, Hao C, Feng Y, Yao S, Fei B, Wang X, Huang Z. ELOA promotes tumor growth and metastasis by activating RBP1 in gastric cancer. Cancer Med 2023; 12:18946-18959. [PMID: 37694492 PMCID: PMC10557880 DOI: 10.1002/cam4.6516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Elongin A (ELOA), our previous work revealed, serves as a novel tumor suppressor in colorectal cancer. However, the function and mechanism of ELOA in other cancer types, including gastric cancer (GC), remain to be elucidated. METHODS The expression of ELOA was measured by quantitative reverse transcription-polymerase chain reaction and western blot. The effects of ELOA on GC growth and metastasis were assessed through a series of in-vitro and in-vivo assays. Furthermore, the potential mechanism of ELOA was revealed by RNA sequencing, dual luciferase reporter assay, chromatin immunoprecipitation, and rescue experiments in GC. RESULTS We uncovered increased expression of ELOA in GC tissues compared with paired normal tissues via bioinformatic analyses and our sample detection. Enhanced ELOA expression in GC tissues was obviously correlated with poor tumor differentiation, lymph node metastasis, advanced tumor stage, and a poor prognosis. A series of functional experiments showed that ELOA promoted the proliferation and metastasis of GC. Mechanistically, we revealed that the decreased levels of miR-490-3p caused the upregulation of ELOA in GC. Both RNA-seq and ChIP assays revealed that ELOA transcriptionally activated retinol-binding protein 1 (RBP1) by binding to its promotor. Furthermore, specific knockdown of RBP1 reduced the tumor-promoting ability of ELOA in GC cells. CONCLUSIONS In summary, our findings demonstrate that ELOA exerts oncogenic properties by activating RBP1 expression, providing the basis for a promising therapeutic target in GC.
Collapse
Affiliation(s)
- Lu Tian
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Liang Gong
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of BiotechnologyJiangnan UniversityWuxiChina
| | - Chu Hao
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Yuyang Feng
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Surui Yao
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Bojian Fei
- Department of Gastrointestinal SurgeryAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Xue Wang
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| | - Zhaohui Huang
- Laboratory of Cancer Epigenetics, Wuxi School of MedicineJiangnan UniversityWuxiChina
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiChina
| |
Collapse
|
7
|
Zhang Y, Cui K, Yang Y, Liu B, Zhu M, Chen H, Zhao C, Zhou Y, Nie Y. Infiltration of a Unique CD8 +CD274 + Cell Subgroup in Hepatocellular Carcinoma is Associated with Poor Clinical Outcomes. J Hepatocell Carcinoma 2023; 10:1051-1067. [PMID: 37449280 PMCID: PMC10337689 DOI: 10.2147/jhc.s410756] [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: 03/23/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Immune checkpoint (IC) inhibitor-related immunotherapies have attracted considerable attention in hepatocellular carcinoma (HCC). High IC expression and high tumor infiltrating lymphocyte levels are the current indicators of sensitivity to IC inhibitors. Thus, it is imperative to apply precision medicine strategies for patient selection. Methods Six independent HCC cohorts were used for analysis at the single-cell and tissue levels. Multiplex immunofluorescence and immunochemistry staining assays were used to validate our results. A series of methodologies were used for immune-related evaluations. Results Herein, we uncovered a unique CD8+CD274+ cell subpopulation that is associated with tumor progression and poor survival in HCC at the single-cell level. We assessed this subset at the tissue level and found that the prognostic significance of CD274 is dependent on CD8A expression in HCC. Subsequently, we identified a unique high-risk subpopulation that showed high CD8A expression coupled with intense CD274 expression in multiple HCC cohorts. CD8AHighCD274High* subgroup was correlated with malignant indexes and remained an independent prognostic factor when considering the influence of these indexes. Molecular characteristic analyses showed that the CD8AHighCD274High* subgroup harbored more mutations, had higher immune response activity and presented enrichment of cancer-related biological processes. Moreover, this high-risk subpopulation in HCC was characterized by high immune cell infiltration, low tumor purity, and enrichment of cancer-related signatures. Finally, cases with this phenotype demonstrated higher immunomodulator and IC levels and greater sensitivity to IC inhibitors. Conclusion Our findings illustrate that some HCC patients may have a poor prognosis despite high CD8+ T-cell infiltration. These patients would probably benefit from IC inhibitor-based combination treatment.
Collapse
Affiliation(s)
- Yong Zhang
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, People’s Republic of China
| | - Yaoxiang Yang
- Department of Pathology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Bingxin Liu
- The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, People’s Republic of China
| | - Minzheng Zhu
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Hanqing Chen
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Chong Zhao
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Youlian Zhou
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Yuqiang Nie
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| |
Collapse
|
8
|
Fan X, Yang X, Guo N, Gao X, Zhao Y. Development of an endoplasmic reticulum stress-related signature with potential implications in prognosis and immunotherapy in head and neck squamous cell carcinoma. Diagn Pathol 2023; 18:51. [PMID: 37087456 PMCID: PMC10122290 DOI: 10.1186/s13000-023-01338-4] [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: 10/14/2022] [Accepted: 04/12/2023] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a multisite malignancy that responds well to immunotherapy. Despite the initial enthusiasm, the clinical benefits of immunotherapy in HNSCC patients are overall limited. Endoplasmic reticulum stress (ERS) has been indicated to play a key role in the process of anti-tumor immune response mediation. However, ERS-related biomarkers which can accurately predict prognosis and immunotherapy response in HNSCC are still lacking. METHODS AND RESULTS In this study, we identify and validate an ERS-related signature comprises of six genes (ASNS, EXOSC6, BAK1, TPP1, EXOSC8, and TATDN2) that can predict the prognosis of HNSCC patients. GSEA analysis indicates that the ERS-related signature is significantly correlated with tumor immunity in HNSCC. Moreover, the infiltration of naive B cells and CD8 + T cells are significantly diminished in patients with high-risk scores compared to those with low-risk scores, while macrophages and activated mast cells are remarkably enhanced. Furthermore, the ERS-related signature also displays a tremendous potential for predicting immunotherapy response in HNSCC. CONCLUSIONS Our study identifies an ERS-related signature that can predict the prognosis of HNSCC patients and highlights its potential value as a predictive biomarker of immunotherapy response, potentially enabling more precise and personalized immunotherapy response and paving the way for further investigation of the prognostic and therapeutic potentials of ERS.
Collapse
Affiliation(s)
- Xinlong Fan
- Second Ward of Head & Neck Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, 110042, Shenyang, Liaoning Province, P R China
| | - Xiao Yang
- Second Ward of Head & Neck Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, 110042, Shenyang, Liaoning Province, P R China
| | - Nan Guo
- Second Ward of Head & Neck Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, 110042, Shenyang, Liaoning Province, P R China
| | - Xin Gao
- Second Ward of Head & Neck Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, 110042, Shenyang, Liaoning Province, P R China
| | - Yuejiao Zhao
- Second Ward of Head & Neck Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, 110042, Shenyang, Liaoning Province, P R China.
| |
Collapse
|
9
|
Li X, Meng X, Chen H, Fu X, Wang P, Chen X, Gu C, Zhou J. Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer. NPJ Syst Biol Appl 2023; 9:4. [PMID: 36765073 PMCID: PMC9918494 DOI: 10.1038/s41540-023-00267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
A deep understanding of the complex interaction mechanism between the various cellular components in tumor microenvironment (TME) of lung adenocarcinoma (LUAD) is a prerequisite for understanding its drug resistance, recurrence, and metastasis. In this study, we proposed two complementary computational frameworks for integrating multi-source and multi-omics data, namely ImmuCycReg framework (single sample level) and L0Reg framework (population or subtype level), to carry out difference analysis between the normal population and different LUAD subtypes. Then, we aimed to identify the possible immune escape pathways adopted by patients with different LUAD subtypes, resulting in immune deficiency which may occur at different stages of the immune cycle. More importantly, combining the research results of the single sample level and population level can improve the credibility of the regulatory network analysis results. In addition, we also established a prognostic scoring model based on the risk factors identified by Lasso-Cox method to predict survival of LUAD patients. The experimental results showed that our frameworks could reliably identify transcription factor (TF) regulating immune-related genes and could analyze the dominant immune escape pathways adopted by each LUAD subtype or even a single sample. Note that the proposed computational framework may be also applicable to the immune escape mechanism analysis of pan-cancer.
Collapse
Affiliation(s)
- Xiong Li
- School of Software, East China Jiaotong University, Nanchang, 330013, China.
| | - Xu Meng
- grid.440711.7School of Software, East China Jiaotong University, Nanchang, 330013 China
| | - Haowen Chen
- grid.67293.39College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xiangzheng Fu
- grid.67293.39College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Peng Wang
- grid.67293.39College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xia Chen
- grid.67293.39College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Changlong Gu
- grid.67293.39College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Juan Zhou
- grid.440711.7School of Software, East China Jiaotong University, Nanchang, 330013 China
| |
Collapse
|
10
|
Eid RA, Eldeen MA, Soltan MA, Al-Shraim M, Aldehri M, Alqahtani LS, Alsharif G, Albogami S, Jafri I, Fayad E, Park MN, Bibi S, Behairy MY, Kim B, Zaki MSA. Integrative analysis of WDR12 as a potential prognostic and immunological biomarker in multiple human tumors. Front Genet 2023; 13:1008502. [PMID: 36726716 PMCID: PMC9885372 DOI: 10.3389/fgene.2022.1008502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Mammalian WD-repeat protein 12 (WDR12), a family member of proteins containing repeats of tryptophan-aspartic acid (WD), is a potential homolog of yeast Ytm1p and consists of seven repeats of WD. Aim of the study: This study aims to investigate the potential oncogenic effects of WDR12 in various human malignancies throughout a pan-cancer analysis that has been carried out to examine the various patterns in which this gene is expressed and behaves in tumor tissues. Methods: Herein, we used The Cancer Genome Atlas (TCGA) and various computational tools to explore expression profiles, prognostic relevance, genetic mutations, immune cell infiltration, as well as the functional characteristics of WDR12 in multiple human cancers. Results: We found that WDR12 was inconsistently expressed in various cancers and that variations in WDR12 expression predicted survival consequences for cancer patients. Furthermore, we observed a significant correlation between WDR12 gene mutation levels and the prognosis of some tumors. Furthermore, significant correlations were found between WDR12 expression patterns and cancer-associated fibroblast (CAF) infiltration, myeloid-derived suppressor cells (MDSCs), tumor mutation burden, microsatellite instability and immunoregulators. Ultimately, pathway enrichment analysis revealed that WDR12-related pathways are involved in carcinogenesis. Conclusions: The findings of our study are stisfactory, demonstrating that WDR12 could serve as a promising reliable prognostic biomarker, as well as a therapeutic target for novel cancer therapeutic approaches.
Collapse
Affiliation(s)
- Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig, Egypt,*Correspondence: Muhammad Alaa Eldeen, ; Bonglee Kim,
| | - Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
| | - Mubarak Al-Shraim
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Majed Aldehri
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Leena S. Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ghadi Alsharif
- College of Clinical Laboratory Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Moon Nyeo Park
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, China
| | - Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea,*Correspondence: Muhammad Alaa Eldeen, ; Bonglee Kim,
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia,Department of Histology and Cell Biology, College of Medicine, Zagazig University, Zagazig, Egypt
| |
Collapse
|
11
|
Zhang Q, Cui K, Yang X, He Q, Yu J, Yang L, Yao G, Guo W, Luo Z, Liu Y, Chen Y, He Z, Lan P. c-Myc-IMPDH1/2 axis promotes tumourigenesis by regulating GTP metabolic reprogramming. Clin Transl Med 2023; 13:e1164. [PMID: 36629054 PMCID: PMC9832425 DOI: 10.1002/ctm2.1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Metabolic reprogramming is a hallmark of cancer. Metabolic rate-limiting enzymes and oncogenic c-Myc (Myc) play critical roles in metabolic reprogramming to affect tumourigenesis. However, a systematic assessment of metabolic rate-limiting enzymes and their relationship with Myc in human cancers is lacking. METHODS Multiple Pan-cancer datasets were used to develop the transcriptome, genomic alterations, clinical outcomes and Myc correlation landscapes of 168 metabolic rate-limiting enzymes across 20 cancers. Real-time quantitative PCR and immunoblotting were, respectively, used to examine the mRNA and protein of inosine monophosphate dehydrogenase 1 (IMPDH1) in human colorectal cancer (CRC), azoxymethane/dextran sulphate sodium-induced mouse CRC and spontaneous intestinal tumours from APCMin/+ mice. Clone formation, CCK-8 and subcutaneous xenograft model were applied to investigate the possible mechanisms connecting IMPDH1 to CRC growth. Co-immunoprecipitation and protein half-life assay were used to explore the mechanisms underlying the regulation of IMPDH1. RESULTS We explored the global expression patterns, dysregulation profiles, genomic alterations and clinical relevance of 168 metabolic rate-limiting enzymes across human cancers. Importantly, a series of enzymes were associated with Myc, especially top three upregulated enzymes (TK1, RRM2 and IMPDH1) were positively correlated with Myc in multiple cancers. As a proof-of-concept exemplification, we demonstrated that IMPDH1, a rate-limiting enzyme in GTP biosynthesis, is highly upregulated in CRC and promotes CRC growth in vitro and in vivo. Mechanistically, IMPDH2 stabilizes IMPDH1 by decreasing the polyubiquitination levels of IMPDH1, and Myc promotes the de novo GTP biosynthesis by the transcriptional activation of IMPDH1/2. Finally, we confirmed that the Myc-IMPDH1/2 axis is dysregulated across human cancers. CONCLUSIONS Our study highlights the essential roles of metabolic rate-limiting enzymes in tumourigenesis and their crosstalk with Myc, and the Myc-IMPDH1/2 axis promotes tumourigenesis by altering GTP metabolic reprogramming. Our results propose the inhibition of IMPDH1 as a viable option for cancer treatment.
Collapse
Affiliation(s)
- Qiang Zhang
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Kaisa Cui
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
| | - Xiaoya Yang
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Qilang He
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jing Yu
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Li Yang
- Zhumadian Central HospitalHuanghuai UniversityZhumadianHenanChina
| | - Gang Yao
- The People's Hospital of Zhengyang CountyZhumadianHenanChina
| | - Weiwei Guo
- The People's Hospital of Zhengyang CountyZhumadianHenanChina
| | - Zhanhao Luo
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Yugeng Liu
- Center for Synthetic MicrobiomeInstitute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
| | - Yuan Chen
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhen He
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| | - Ping Lan
- The Sixth Affiliated HospitalSchool of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of GastroenterologyGuangzhouGuangdongChina
| |
Collapse
|
12
|
Cui K, Gong L, Zhang H, Chen Y, Liu B, Gong Z, Li J, Wang Y, Sun S, Li Y, Zhang Q, Cao Y, Li Q, Fei B, Huang Z. EXOSC8 promotes colorectal cancer tumorigenesis via regulating ribosome biogenesis-related processes. Oncogene 2022; 41:5397-5410. [PMID: 36348012 DOI: 10.1038/s41388-022-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Extensive protein synthesis is necessary for uncontrolled cancer cell proliferation, requiring hyperactive ribosome biogenesis. Our previous Pan-cancer study has identified EXOSC8 as a potential copy number variation (CNV)-driven rRNA metabolism-related oncogene in colorectal cancer (CRC). Herein, we further investigated proliferation-prompting functions and mechanisms of EXOSC8 in CRC by performing in silico analyses and wet-lab experiments. We uncovered that increased EXOSC8 expression and CNV levels are strongly associated with ribosome biogenesis-related factor levels in CRC, including ribosome proteins (RPs), eukaryotic translation initiation factors and RNA polymerase I/III. EXOSC8 silence decreases nucleolar protein and proliferation marker levels, as well as rRNA/DNA and global protein syntheses. Clinically, EXOSC8 is upregulated across human cancers, particularly CNV-driven upregulation in CRC was markedly associated with poor clinical outcomes. Mechanistically, EXOSC8 knockdown increased p53 levels in CRC, and the oncogenic proliferation phenotypes of EXOSC8 depended on p53 in vitro and in vivo. We discovered that EXOSC8 knockdown in CRC cells triggers ribosomal stress, nucleolar RPL5/11 being released into the nucleoplasm and "hijacking" Mdm2 to block its E3 ubiquitin ligase function, thus releasing and activating p53. Furthermore, our therapeutic experiments provided initial evidence that EXOSC8 might serve as a potential therapeutic target in CRC. Our findings revealed, for the first time, that the RNA exosome gene (EXOSC8) promotes CRC tumorigenesis by regulating cancer-related ribosome biogenesis in CRC. This study further extends our previous Pan-cancer study of the rRNA metabolism-related genes. The inhibition of EXOSC8 is a novel therapeutic strategy for the RPs-Mdm2-p53 ribosome biogenesis surveillance pathway in CRC.
Collapse
Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China.
| | - Liang Gong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Han Zhang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Ying Chen
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Bingxin Liu
- The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Zhicheng Gong
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Jiuming Li
- Key Laboratory of Environment Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yuanben Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Shengbai Sun
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Yajun Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Outstanding Overseas Scientists Center for Pulmonary Fibrosis of Henan Province, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan, 453000, China
| | - Qiang Zhang
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China
| | - Qilin Li
- Computer Vision Lab, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bojian Fei
- Department of Surgical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, China.
| |
Collapse
|
13
|
Cui K, Yao S, Liu B, Sun S, Gong L, Li Q, Fei B, Huang Z. A novel high-risk subpopulation identified by CTSL and ZBTB7B in gastric cancer. Br J Cancer 2022; 127:1450-1460. [PMID: 35941174 PMCID: PMC9553888 DOI: 10.1038/s41416-022-01936-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is characterised by a heterogeneous tumour microenvironment (TME) that is closely associated with the response to treatment, especially immunotherapies. However, most previous GC molecular subtyping systems need complex gene signatures and examination methods, restricting their clinical applications. Thus, we developed a new TME-based molecular subtype using only two genes. METHODS Nine independent GC cohorts at the tissue- or single-cell level with more than 2000 patients were used in this study, including data we examined by single-cell sequencing, quantitative RT-PCR and immunochemistry/immunofluorescence staining. Nine different methods, five existing molecular subtypes and a series of signatures were used to evaluate the TME and molecular characteristics of GC. RESULTS We established a CTSL/ZBTB7B subtyping system and uncovered the novel CTSLHighZBTB7BLow high-risk subgroup, but characterised by relative higher immune cell infiltration and lower tumour purity. This subgroup demonstrate higher levels of immune checkpoints and more enrichment of cancer-related pathways compared with other cases. CONCLUSIONS We identified a high-risk subpopulation with unique TME features based on expressions of CTSL and ZBTB7B, suggesting a counterbalancing phenotype between immunostimulatory and immunosuppressive mechanisms. This subtyping system could be used to select treatment and management strategies for GC.
Collapse
Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, 214122, Wuxi, Jiangsu, China
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, China
| | - Bingxin Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, 214122, Wuxi, Jiangsu, China
| | - Shengbai Sun
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, China
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, 214122, Wuxi, Jiangsu, China
| | - Liang Gong
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, 214122, Wuxi, Jiangsu, China
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 214122, Wuxi, Jiangsu, China
| | - Qilin Li
- Computer Vision Lab, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bojian Fei
- Department of Surgical Oncology, Affiliated Hospital of Jiangnan University, 214122, Wuxi, Jiangsu, China.
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062, Wuxi, Jiangsu, China.
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, 214122, Wuxi, Jiangsu, China.
| |
Collapse
|
14
|
Liu S, Liu W, Ding Z, Yang X, Jiang Y, Wu Y, Liu Y, Wu J. Identification and validation of a novel tumor driver gene signature for diagnosis and prognosis of head and neck squamous cell carcinoma. Front Mol Biosci 2022; 9:912620. [PMID: 36339718 PMCID: PMC9631213 DOI: 10.3389/fmolb.2022.912620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2023] Open
Abstract
Objective: Head and neck squamous cell carcinoma (HNSCC) is a common heterogeneous cancer with complex carcinogenic factors. However, the current TNM staging criteria to judge its severity to formulate treatment plans and evaluate the prognosis are particularly weak. Therefore, a robust diagnostic model capable of accurately diagnosing and predicting HNSCC should be established. Methods: Gene expression and clinical data were retrieved from The Cancer Genome Atlas and Gene Expression Omnibus databases. Key prognostic genes associated with HNSCC were screened with the weighted gene co-expression network analysis and least absolute shrinkage and selection operator (LASSO) Cox regression model analysis. We used the timeROC and survival R packages to conduct time-dependent receiver operating characteristic curve analyses and calculated the area under the curve at different time points of model prediction. Patients in the training and validation groups were divided into high- and low-risk subgroups, and Kaplan-Meier (K-M) survival curves were plotted for all subgroups. Subsequently, LASSO and support vector machine algorithms were used to screen genes to construct diagnostic model. Furthermore, we used the Wilcoxon signed-rank test to compare the half-maximal inhibitory concentrations of common chemotherapy drugs among patients in different risk groups. Finally, the expression levels of eight genes were measured using quantitative real-time polymerase chain reaction and immunohistochemistry. Results: Ten genes (SSB, PFKP, NAT10, PCDH9, SHANK2, PAX8, CELSR3, DCLRE1C, MAP2K7, and ODF4) with prognostic potential were identified, and a risk score was derived accordingly. Patients were divided into high- and low-risk groups based on the median risk score. The K-M survival curves confirmed that patients with high scores had significantly worse overall survival. Receiver operating characteristic curves proved that the prognostic signature had good sensitivity and specificity for predicting the prognosis of patients with HNSCC. Univariate and multivariate Cox regression analyses confirmed that the gene signature was an independent prognostic risk factor for HNSCC. Diagnostic model was built by identifying eight genes (SSB, PFKP, NAT10, PCDH9, CELSR3, DCLRE1C, MAP2K7, and ODF4). The high-risk group showed higher sensitivity to various common chemotherapeutic drugs. DCLRE1C expression was higher in normal tissues than in HNSCC tissues. Conclusion: Our study identified the important role of tumor-driver genes in HNSCC and their potential clinical diagnostic and prognostic values to facilitate individualized management of patients with HNSCC.
Collapse
Affiliation(s)
- Shixian Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Weiwei Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Zhao Ding
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Xue Yang
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yuan Jiang
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yu Wu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yehai Liu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jing Wu
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
15
|
Wang T, Ba X, Zhang X, Zhang N, Wang G, Bai B, Li T, Zhao J, Zhao Y, Yu Y, Wang B. Pan-cancer analyses of classical protein tyrosine phosphatases and phosphatase-targeted therapy in cancer. Front Immunol 2022; 13:976996. [PMID: 36341348 PMCID: PMC9630847 DOI: 10.3389/fimmu.2022.976996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/04/2022] [Indexed: 09/23/2023] Open
Abstract
Protein tyrosine phosphatases function in dephosphorylating target proteins to regulate signaling pathways that control a broad spectrum of fundamental physiological and pathological processes. Detailed knowledge concerning the roles of classical PTPs in human cancer merits in-depth investigation. We comprehensively analyzed the regulatory mechanisms and clinical relevance of classical PTPs in more than 9000 tumor patients across 33 types of cancer. The independent datasets and functional experiments were employed to validate our findings. We exhibited the extensive dysregulation of classical PTPs and constructed the gene regulatory network in human cancer. Moreover, we characterized the correlation of classical PTPs with both drug-resistant and drug-sensitive responses to anti-cancer drugs. To evaluate the PTP activity in cancer prognosis, we generated a PTPscore based on the expression and hazard ratio of classical PTPs. Our study highlights the notable role of classical PTPs in cancer biology and provides novel intelligence to improve potential therapeutic strategies based on pTyr regulation.
Collapse
Affiliation(s)
- Tao Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xinlei Ba
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xiaonan Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
| | - Na Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Guowen Wang
- Department of Thoracic surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Bin Bai
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Tong Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jiahui Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yanjiao Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yang Yu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Bing Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| |
Collapse
|
16
|
Zhang Y, Yang X, Hu Y, Huang X. Integrated Bioinformatic Investigation of EXOSCs in Hepatocellular Carcinoma Followed by the Preliminary Validation of EXOSC5 in Cell Proliferation. Int J Mol Sci 2022; 23:ijms232012161. [PMID: 36293016 PMCID: PMC9603681 DOI: 10.3390/ijms232012161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/01/2022] [Accepted: 10/09/2022] [Indexed: 11/29/2022] Open
Abstract
The Exosome complex (EXOSC) is a multiprotein complex that was originally discovered as the machinery of RNA degradation. Interestingly, recent studies have reported that EXOSC family members (EXOSCs) are associated with various human diseases, including cancers. It will be interesting to investigate whether EXOSCs are related to the processes of hepatocellular carcinoma (HCC). In this study, multiple public databases and experimental validation were utilized to systemically investigate the role of EXOSCs, especially EXOSC5, in HCC. It is worth considering that the mRNA and protein levels of many EXOSCs were elevated in HCC, although there were some differences in the results from different database analyses. The over-expression of EXOSCs could predict HCC to some extent, as evidenced by the positive correlation between the elevated EXOSCs and alpha fetoprotein (AFP) levels, as well as with a high accuracy, as shown by the receiver operating characteristic curve analysis. Additionally, higher mRNA expressions of specific EXOSCs were significantly related to clinical cancer stage, shorter overall survival and disease-free survival in HCC patients. A moderate mutation rate of EXOSCs was also observed in HCC. Furthermore, a gene functional enrichment analysis indicated that EXOSCs were mainly involved in the metabolism of RNA. Moreover, we revealed that the expression of EXOSCs is remarkably related to immune cell infiltration. Finally, EXOSC5 was upregulated in HCC tissues and cell lines, promoting cell growth and proliferation via activated signal transducer and activator of transcription 3 (STAT3). The bioinformatic analyses, following verification in situ and in vitro, provided a direction for further functions and underlying mechanism of EXOSCs in HCC.
Collapse
Affiliation(s)
| | | | | | - Xin Huang
- Correspondence: ; Tel./Fax: +86-731-88912463
| |
Collapse
|
17
|
Cao Y, Duan H, Su A, Xu L, Lai B. A pan-cancer analysis confirms PTPN11's potential as a prognostic and immunological biomarker. Aging (Albany NY) 2022; 14:5590-5610. [PMID: 35802774 PMCID: PMC9320542 DOI: 10.18632/aging.204171] [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: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022]
Abstract
Protein tyrosine phosphatase, non-receptor type 11 (PTPN11) is a multifunctional tyrosine phosphatase and has a significant part in many types of tumors. As of yet, neither the expression profile of PTPN11 nor its significance in pan-cancer diagnosis has been clarified. With the assistance of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we have comprehensively mapped the expression profiles, prognostic significance, genetic alteration, phosphorylation status, infiltration of immune cells, and functional properties of PTPN11 in 33 human tumors. There was an inconsistent expression of PTPN11 in different tumors, and the alteration of PTPN11 expression predicted the survival outcomes of cancer patients. A significant association was found between the genetic alteration levels of PTPN11 and some tumor predictions. Besides, the reduced PTPN11 phosphorylation levels were observed in breast cancer, clear cell RCC, head and neck carcinoma, and lung adenocarcinoma (LUAD). Furthermore, there was a significant association between PTPN11 expression and infiltration of cancer-associated fibroblasts and endothelial cells, along with tumor mutation burden, microsatellite instability, mismatch repair genes, and immunoregulators. Finally, pathway enrichment analysis demonstrated that PTPN11-associated terms and pathways were involved in malignancy. Taken together, PTPN11 may become a new biomarker and target for cancer therapy.
Collapse
Affiliation(s)
- Yapeng Cao
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Haixia Duan
- Department of Reproduction Gynecology, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710061, China
| | - Ailing Su
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Liran Xu
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Baochang Lai
- Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| |
Collapse
|
18
|
Azzarito G, Visentin M, Leeners B, Dubey RK. Transcriptomic and Functional Evidence for Differential Effects of MCF-7 Breast Cancer Cell-Secretome on Vascular and Lymphatic Endothelial Cell Growth. Int J Mol Sci 2022; 23:ijms23137192. [PMID: 35806196 PMCID: PMC9266834 DOI: 10.3390/ijms23137192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 01/14/2023] Open
Abstract
Vascular and lymphatic vessels drive breast cancer (BC) growth and metastasis. We assessed the cell growth (proliferation, migration, and capillary formation), gene-, and protein-expression profiles of Vascular Endothelial Cells (VECs) and Lymphatic Endothelial Cells (LECs) exposed to a conditioned medium (CM) from estrogen receptor-positive BC cells (MCF-7) in the presence or absence of Estradiol. We demonstrated that MCF-7-CM stimulated growth and capillary formation in VECs but inhibited LEC growth. Consistently, MCF-7-CM induced ERK1/2 and Akt phosphorylation in VECs and inhibited them in LECs. Gene expression analysis revealed that the LECs were overall (≈10-fold) more sensitive to MCF-7-CM exposure than VECs. Growth/angiogenesis and cell cycle pathways were upregulated in VECs but downregulated in LECs. An angiogenesis proteome array confirmed the upregulation of 23 pro-angiogenesis proteins in VECs. In LECs, the expression of genes related to ATP synthesis and the ATP content were reduced by MCF-7-CM, whereas MTHFD2 gene, involved in folate metabolism and immune evasion, was upregulated. The contrasting effect of MCF-7-CM on the growth of VECs and LECs was reversed by inhibiting the TGF-β signaling pathway. The effect of MCF-7-CM on VEC growth was also reversed by inhibiting the VEGF signaling pathway. In conclusion, BC secretome may facilitate cancer cell survival and tumor growth by simultaneously promoting vascular angiogenesis and inhibiting lymphatic growth. The differential effects of BC secretome on LECs and VECs may be of pathophysiological relevance in BC.
Collapse
Affiliation(s)
- Giovanna Azzarito
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
| | - Michele Visentin
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Brigitte Leeners
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
| | - Raghvendra K. Dubey
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Correspondence:
| |
Collapse
|
19
|
Cui K, Gong L, Wang K, Wang Y, Huang L, Liu B, Li Q, Zhang Q, Fei B, Huang Z. Ferroptosis-Associated Molecular Features to Aid Patient Clinical Prognosis and Therapy Across Human Cancers. Front Immunol 2022; 13:888757. [PMID: 35812384 PMCID: PMC9266629 DOI: 10.3389/fimmu.2022.888757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Ferroptosis is a new non-apoptotic form that regulates cell death and is mainly dependent on iron-mediated oxidative damage and subsequent cell membrane damage. Ferroptosis may be a potential therapeutic strategy for immunotherapy, chemotherapy, and radiotherapy in human cancers. Numerous studies have analyzed ferroptosis-correlated signatures or genes, but a systematic landscape of associations among tumor ferroptosis, clinical outcomes, tumor microenvironment, and therapies in human cancers is lacking. Here, we developed a relative ferroptosis level (RFL) combined with drive/suppress regulators and validated it in the Gene Expression Omnibus datasets of ferroptotic drug treatment. Based on this effective evaluation method, we classified about 7,000 tumor samples into high and low RFL groups in each cancer type and observed that high RFL cases demonstrate favorable survival outcomes in nine cancer types from The Cancer Genome Atlas. Then, several RFL-correlated candidate genes that have not been reported to be ferroptosis-related were selected and experimentally validated in five cancer cell lines using Erastin treatment. We further showed that both immunostimulatory and immunosuppressive phenotypes were observed in high RFL tumors, suggesting that the consideration of ferroptosis could be a potential strategy in cancer immunotherapy. Moreover, we found that high RFL cases/cells showed responder or sensitivity to chemotherapy and radiotherapy. Our study provides a comprehensive molecular-level understanding of ferroptosis and may have practical implications for clinical cancer therapies, including immunotherapy, chemotherapy, and radiotherapy.
Collapse
Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Liang Gong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Kang Wang
- Department of Radiology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yuanben Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Liuying Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Bingxin Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Qilin Li
- Computer Vision Lab, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Qiang Zhang
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Bojian Fei
- Department of Surgical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
- *Correspondence: Zhaohui Huang,
| |
Collapse
|
20
|
Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
Collapse
Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| |
Collapse
|
21
|
Liang W, Mo C, Wei J, Chen W, Gong W, Shi J, Hou X, Li C, Deng Y, Ou M. FAM65A as a novel prognostic biomarker in human tumors reveal by a pan-cancer analysis. Discov Oncol 2021; 12:60. [PMID: 35201499 PMCID: PMC8777545 DOI: 10.1007/s12672-021-00456-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Family with sequence similarity 65 member A (FAM65A), also known as RIPOR1, is differentially expressed between human tumor and non-tumor tissues in kinds of cancers. In addition, it was reported that the product of FAM65A may be a biomarker for cholangiocarcinoma patients. However, there is still no evidence on the relationship between the FAM65A and different types of tumors. Our study is mainly for exploring the prognostic values of FAM65A in pan-cancer and for further discovering a potential therapeutics target. METHODS We analyzed FAM65A expression, prognostic values, genetic alteration, protein phosphorylation, immune infiltration and enrichment analysis across different types of human malignant tumors based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Additionally, Real-Time PCR (RT-qPCR) was performed to further confirm the roles of FAM65A in the pathogenesis of colorectal cancer. RESULTS We found that FAM65A expression was associated with the prognosis of multiple human tumors, especially colorectal cancer. Moreover, we also observed that FAM65A was highly expressed in colorectal cancer through RT-qPCR. We observed that decreasing phosphorylation level of the S351 locus in colon adenocarcinoma, uterine corpus endometrial carcinoma and lung adenocarcinoma. And the expression of FAM65A was positively related to cancer-associated fibroblasts (CAFs) infiltration in many tumors, such as colon adenocarcinoma. Therefore, FAM65A may be a potential prognostic biomarker of human tumors.
Collapse
Affiliation(s)
- Wenken Liang
- College of Life Science, Guangxi Normal University, No. 1, Yanshan Middle Road, Guilin, 541000, China
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Jianfen Wei
- College of Life Science, Guangxi Normal University, No. 1, Yanshan Middle Road, Guilin, 541000, China
| | - Wei Chen
- Gastrointestinal Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541000, China
| | - Weiwei Gong
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Jianling Shi
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Chunhong Li
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China
| | - Yecheng Deng
- College of Life Science, Guangxi Normal University, No. 1, Yanshan Middle Road, Guilin, 541000, China.
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Guilin, 541000, China.
| |
Collapse
|
22
|
Lin H, Feng L, Cui KS, Zeng LW, Gao D, Zhang LX, Xu WH, Sun YH, Shu HB, Li S. The membrane-associated E3 ubiquitin ligase MARCH3 downregulates the IL-6 receptor and suppresses colitis-associated carcinogenesis. Cell Mol Immunol 2021; 18:2648-2659. [PMID: 34785732 DOI: 10.1038/s41423-021-00799-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 02/07/2023] Open
Abstract
The IL-6-STAT3 axis is critically involved in inflammation-associated carcinogenesis (IAC). How this axis is regulated to modulate IAC remains unknown. Here, we show that the plasma membrane-associated E3 ubiquitin ligase MARCH3 negatively regulates STAT3 activation triggered by IL-6, as well as another IL-6 subfamily member, Oncostatin M (OSM). MARCH3 is associated with the IL-6 receptor α-chain (IL-6Rα) and its coreceptor gp130. Biochemical experiments indicated that MARCH3 mediates the polyubiquitination of IL-6Rα at K401 and gp130 at K849 following IL-6 stimulation, leading to their translocation to and degradation in lysosomes. MARCH3 deficiency increases IL-6- and OSM-triggered activation of STAT3 and induction of downstream effector genes in various cell types. MARCH3 deficiency enhances dextran sulfate sodium (DSS)-induced STAT3 activation, increases the expression of inflammatory cytokines, and exacerbates colitis, as well as azoxymethane (AOM)/DSS-induced colitis-associated cancer in mice. In addition, MARCH3 is downregulated in human colorectal cancer tissues and associated with poor survival across different cancer types. Our findings suggest that MARCH3 is a pivotal negative regulator of IL-6-induced STAT3 activation, inflammation, and inflammation-associated carcinogenesis.
Collapse
Affiliation(s)
- Heng Lin
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Lu Feng
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Kai-Sa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, 214062, Jiangsu, China
| | - Lin-Wen Zeng
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Deng Gao
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Long-Xiang Zhang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Wen-Hua Xu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Yu-Hao Sun
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China
| | - Hong-Bing Shu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China.
| | - Shu Li
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University; Medical Research Institute; Frontier Science Center for Immunology and Metabolism; Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences; Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
23
|
Khan R, Palo A, Dixit M. Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model. Sci Rep 2021; 11:22505. [PMID: 34795329 PMCID: PMC8602605 DOI: 10.1038/s41598-021-01665-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/02/2021] [Indexed: 12/20/2022] Open
Abstract
FRG1 has a role in tumorigenesis and angiogenesis. Our preliminary analysis showed that FRG1 mRNA expression is associated with overall survival (OS) in certain cancers, but the effect varies. In cervix and gastric cancers, we found a clear difference in the OS between the low and high FRG1 mRNA expression groups, but the difference was not prominent in breast, lung, and liver cancers. We hypothesized that FRG1 expression level could affect the functionality of the correlated genes or vice versa, which might mask the effect of a single gene on the OS analysis in cancer patients. We used the multivariate Cox regression, risk score, and Kaplan Meier analyses to determine OS in a multigene model. STRING, Cytoscape, HIPPIE, Gene Ontology, and DAVID (KEGG) were used to deduce FRG1 associated pathways. In breast, lung, and liver cancers, we found a distinct difference in the OS between the low and high FRG1 mRNA expression groups in the multigene model, suggesting an independent role of FRG1 in survival. Risk scores were calculated based upon regression coefficients in the multigene model. Low and high-risk score groups showed a significant difference in the FRG1 mRNA expression level and OS. HPF1, RPL34, and EXOSC9 were the most common genes present in FRG1 associated pathways across the cancer types. Validation of the effect of FRG1 mRNA expression level on these genes by qRT-PCR supports that FRG1 might be an upstream regulator of their expression. These genes may have multiple regulators, which also affect their expression, leading to the masking effect in the survival analysis. In conclusion, our study highlights the role of FRG1 in the survivability of cancer patients in tissue-specific manner and the use of multigene models in prognosis.
Collapse
Affiliation(s)
- Rehan Khan
- grid.419643.d0000 0004 1764 227XSchool of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050 Odisha India
| | - Ananya Palo
- grid.419643.d0000 0004 1764 227XSchool of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050 Odisha India
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050, Odisha, India. .,School of Biological Sciences, NISER, Room No.- 203, P.O. Jatni, Khurda, Odisha, 752050, India.
| |
Collapse
|
24
|
Gong L, Li Y, Cui K, Chen Y, Hong H, Li J, Li D, Yin Y, Wu Z, Huang Z. Nanobody-Engineered Natural Killer Cell Conjugates for Solid Tumor Adoptive Immunotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2103463. [PMID: 34761524 DOI: 10.1002/smll.202103463] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Cancer immunotherapy based on natural killer (NK) cells is demonstrated to be a promising strategy. However, NK cells are deficient in ligands that target specific tumors, resulting in limited antitumor efficacy. Here, a glycoengineering approach to imitate the chimeric antigen receptor strategy and decorate NK cells with nanobodies to promote NK-based immunotherapy in solid tumors is proposed. Nanobody 7D12, which specifically recognizes the human epidermal growth factor receptor (EGFR) that is overexpressed on many solid tumors, is coupled to the chemically synthesized DBCO-PEG4 -GGG-NH2 by sortase A-mediated ligation to generate DBCO-7D12. The NK92MI cells bearing azide groups are then equipped with DBCO-7D12 via bioorthogonal click chemistry. The resultant 7D12-NK92MI cells exhibit high specificity and affinity for EGFR-overexpressing tumor cells in vitro and in vivo by the 7D12-EGFR interaction, causing increased cytokine secretion to more effectively kill EGFR-positive tumor cells, but not EGFR-negative cancer cells. Importantly, the 7D12-NK92MI cells also show a wide anticancer spectrum and extensive tumor penetration. Furthermore, mouse experiments reveal that 7D12-NK92MI treatment achieves excellent therapeutic efficacy and outstanding safety. The authors' works provide a cell modification strategy using specific protein ligands without genetic manipulation and present a potential novel method for cancer-targeted immunotherapy by NK cells.
Collapse
Affiliation(s)
- Liang Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Yanchun Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Laboratory of Cancer Epigenetics, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Ying Chen
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Laboratory of Cancer Epigenetics, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Haofei Hong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Jiuming Li
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Laboratory of Cancer Epigenetics, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Dan Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Laboratory of Cancer Epigenetics, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Zhimeng Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, P. R. China
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- Laboratory of Cancer Epigenetics, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| |
Collapse
|
25
|
Song Y, Nie L, Zhang YT. LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response. PeerJ 2021; 9:e12116. [PMID: 34616607 PMCID: PMC8462375 DOI: 10.7717/peerj.12116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/15/2021] [Indexed: 12/20/2022] Open
Abstract
Background Cervical cancer is the fourth most common gynecological tumor in terms of both the incidence and mortality of females worldwide. Cervical squamous cell carcinoma (CSCC) accounts for 70–80% of cervical cancers, and endocervical adenocarcinoma (EAC) accounts for 20–25%. Unlike CSCC, EAC has worse clinical outcomes and prognosis. In this study, we explored the relationship between various types of long noncoding RNAs (lncRNAs) and pathological types of cervical cancer. Methods RNA sequencing (RNA-Seq) and clinical data from The Cancer Genome Atlas (TCGA) were used in this study. A single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE package were used to assess lncRNA activity and immune responses, respectively. RT-qPCR was performed to verify our findings. Results We explored the relationship between various types of lncRNAs and pathological types of cervical cancer. A series of long intergenic noncoding RNAs (lincRNAs) and antisense RNAs, which are the major types of lncRNAs, were identified to be specifically expressed in EAC and associated with a poor recurrence prognosis in patients with cervical cancer, suggesting that they might serve as independent prognostic markers of recurrence in patients with cervical cancer. RT-qPCR was performed to verify the 10 EAC-specific lncRNAs in cervical cancer samples we collected. Furthermore, the overexpression of these lncRNAs was positively correlated with EAC pathology levels but negatively correlated with immune responses in the microenvironment of cervical cancer. Conclusions These lncRNAs potentially represent new biomarkers for the prediction of the recurrence prognosis and help obtain deeper insights into potential immunotherapeutic approaches for treating cervical cancer.
Collapse
Affiliation(s)
- Yong Song
- Department of Public Health, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,School of Health Sciences, Wuhan University, Wuhan, Hubei, China
| | - Long Nie
- Department of Oncology, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, China
| | - Yu-Ting Zhang
- School of Nursing, Health Science Center, Shenzhen University, Shenzhen, Guangdong, China
| |
Collapse
|
26
|
Xu J, Huang QY, Ge CJ. Identification of prognostic long intergenic non-coding RNAs as competing endogenous RNAs with KRAS mutations in colorectal cancer. Oncol Lett 2021; 22:717. [PMID: 34429757 PMCID: PMC8371979 DOI: 10.3892/ol.2021.12978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/28/2021] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer (CRC) is recognized as a common type of human cancer, and KRAS mutations are correlated with poor CRC survival outcomes. The evaluation and prediction of CRC results remain challenging. In the present study, RNA sequencing and clinical data from The Cancer Genome Atlas were used to identify KRAS mutation-related prognostic long intergenic non-coding RNAs (lincRNAs) in CRC. Significantly dysregulated lincRNAs and independent prognostic lincRNAs with KRAS mutations in CRC were identified. Two lincRNAs with KRAS mutations, LINC00265 and AL390719.2, were selected as key prognostic lincRNAs for both 10- and 5-year survival rates. In addition, competing endogenous (ce)RNA models were constructed to comprehensively assess the oncogenic performance of the two key lincRNAs. The ceRNA models suggested that LINC00265 and AL390719.2 are critical for the cell cycle and cancer pathways. Finally, reverse transcription-quantitative PCR was used to validate the ceRNA models in 12 pairs of CRC tissue samples. These prognostic lincRNAs may provide novel biomarkers for the prognostic prediction of CRC. The ceRNA model may also demonstrate the underlying mechanism of these lincRNAs in CRC.
Collapse
Affiliation(s)
- Jun Xu
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Qiu-Yun Huang
- Department of General Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Cun-Jin Ge
- Department of Gastroenterology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| |
Collapse
|
27
|
Wu Y, Liang X, Ni J, Zhao R, Shao S, Lu S, Han W, Yu L. Effect of ISM1 on the Immune Microenvironment and Epithelial-Mesenchymal Transition in Colorectal Cancer. Front Cell Dev Biol 2021; 9:681240. [PMID: 34350177 PMCID: PMC8326811 DOI: 10.3389/fcell.2021.681240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Background: An increasing number of studies have shown that Isthmin 1 (ISM1), a secreted protein, is important in tumorigenesis and invasion, including in colorectal cancer (CRC). However, the mechanisms are still unclear. This study aims to explore the function and prognosis capacity of ISM1 in CRC. Methods: We investigated the expression of ISM1 in 18 CRC tissues vs. adjacent normal tissues from GSE50760, 473 CRC tissues vs. 41 normal tissues from The Cancer Genome Atlas (TCGA), and across gastrointestinal cancer types. Differences were further confirmed in CRC tissues via quantitative real-time polymerase chain reaction (qRT-PCR). Then, we analyzed correlations between clinicopathologic features and ISM1 expression, including prognostic prediction value, using the Kaplan–Meier method and multivariate Cox regression. Gene set enrichment analysis (GSEA) was performed to identify ISM1-related pathways. In vitro experiments were performed to verify the role of ISM1 in epithelial-mesenchymal transition (EMT) and CRC progression. Results: Multiple datasets showed that ISM1 is upregulated in CRC tissues, which was validated. Patients with higher ISM1 expression had shorter overall survival (OS), and ISM1 expression served as an independent prognostic factor. Enrichment analysis showed that ISM1 upregulation was positively correlated with cancer-related pathways, such as EMT, hypoxia, and the Notch and KRAS signaling pathways. We were exclusively interested in the connection between ISM1 and EMT because 71% of genes in this pathway were significantly positively co-expressed with ISM1, which may account for why patients with higher ISM1 expression are prone to regional lymph node involvement and progression to advanced stages. In addition, we found that ISM1 was positively correlated with multiple immunosuppressive pathways such as IL2/STAT5, TNF-α/NF-κB, and TGF-β, and immune checkpoints, including PD-L1, PD-1, CTLA-4, and LAG3, which may account for upregulation of ISM1 in immunotherapy-resistant patients. Notably, through in vitro experiments, we found that ISM1 promoted EMT and colon cancer cell migration and proliferation. Conclusion: ISM1 is critical for CRC development and progression, which enhances our understanding of the low response rate of CRC to immunotherapy via immunosuppressive signaling pathways.
Collapse
Affiliation(s)
- Yuhui Wu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojing Liang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junjie Ni
- Department of Breast and Thyroid Surgery, Jinhua Municipal Central Hospital, Jinhua, China
| | - Rongjie Zhao
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shengpeng Shao
- Department of Urinary Surgery, The First People's Hospital of Fuyang, Hangzhou, China
| | - Si Lu
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Liangliang Yu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
28
|
FBXL6 degrades phosphorylated p53 to promote tumor growth. Cell Death Differ 2021; 28:2112-2125. [PMID: 33568778 PMCID: PMC8257708 DOI: 10.1038/s41418-021-00739-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/10/2021] [Accepted: 01/20/2021] [Indexed: 01/31/2023] Open
Abstract
The ubiquitin-proteasome system regulates many distinct biological processes. Its dysregulation causes various diseases, including but not limited to cancer. In this study, based on the analysis of gene expression in several colorectal cancer (CRC) datasets, we show that FBXL6, a poorly-characterized F-box protein, is amplified, over-expressed, and highly correlated with poor prognosis in human CRC patients. Mechanistically, FBXL6 targets phospho-p53 (S315) to mediate its polyubiquitination and proteasomal degradation, thereby inhibiting p53 signaling. FBXL6 depletion inhibits proliferation of p53 wild-type (WT) CRC cells by inducing cell cycle arrest and apoptosis. Furthermore, p53 transcriptionally suppresses FBXL6 expression by binding its core promoter region. Taken together, these results identify the feed-forward loop of FBXL6-p53 as a potential therapeutic target for CRC treatments.
Collapse
|
29
|
Chen Y, Zhao H, Xiao Y, Shen P, Tan L, Zhang S, Liu Q, Gao Z, Zhao J, Zhao Y, Guo Y, Feng Y. Pan-cancer analysis reveals an immunological role and prognostic potential of PXN in human cancer. Aging (Albany NY) 2021; 13:16248-16266. [PMID: 34135128 PMCID: PMC8266322 DOI: 10.18632/aging.203154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Paxillin (PXN) is a protein involved in numerous physiological processes, and its presence is closely related to the occurrence and development of many types of tumors. However, no studies have analyzed PXN from a pan-cancer perspective. We analyzed PXN expression, immune cell infiltration, prognosis, and biological function across different types of tumors included in The Cancer Genome Atlas and Gene Expression Omnibus datasets. The results showed that expression of PXN varies in different tumors. Expression of PXN strongly correlated with prognosis in patients with tumors; higher PXN expression usually was linked to poor overall and disease-free survival. Expression of PXN in breast invasive carcinoma and lymphoid neoplasm diffuse large B-cell lymphoma was related to the degree of CD8+ T-cell infiltration, and infiltration of cancer-associated fibroblasts, such as kidney renal papillary cell carcinoma and brain lower-grade glioma, was also observed in other tumors. The results of pan-cancer analysis showed that abnormal PXN expression was related to poor prognosis, immune infiltration, and protein phosphorylation in different tumor types. Therefore, the PXN gene may become a potential biomarker of clinical tumor prognosis.
Collapse
Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, China.,Laboratory of Myopia, NHC Key Laboratory of Myopia, Fudan University, Chinese Academy of Medical Sciences, Shanghai 200000, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, China
| | - Yan Xiao
- Nursing Department, Ganzhou Municipal Hospital, Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Peijun Shen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Central South University, Changsha, Hunan 410011, China
| | - Li Tan
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Shaohui Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qiong Liu
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhengrong Gao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yunzhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| |
Collapse
|
30
|
Cui K, Wu X, Gong L, Yao S, Sun S, Liu B, Zhou M, Yin Y, Huang Z. Comprehensive Characterization of Integrin Subunit Genes in Human Cancers. Front Oncol 2021; 11:704067. [PMID: 34222028 PMCID: PMC8242346 DOI: 10.3389/fonc.2021.704067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Although integrin subunit genes (ITGs) have been reported to be associated with some human cancer types, a systematic assessment of ITGs across human cancers is lacking. Hence, we performed comprehensive analyses to investigate mRNA expression, copy number variation (CNV), DNA methylation, mutation, and clinical landscapes of ITGs in more than 8000 cancer patients from The Cancer Genome Atlas (TCGA) dataset. Landscapes of ITGs were established across 20 human cancer types. We observed that ITGs are extensively dysregulated with heterogeneity in different system cancer types, part of which are driven by CNV, DNA hypomethylation or mutation. Furthermore, dysregulated prognosis-related ITGs were systematically identified in each cancer type, including ITGA11 in stomach adenocarcinoma (STAD). The models based on dysregulated ITGs with clinical relevance and TNM staging indexes are good indicators in STAD and head and neck squamous cell carcinoma. Finally, ITGA11 is overexpressed and associated with poor survival in STAD cases from the TCGA and additionally Gene Expression Omnibus cohorts. Functionally, ITGA11 knockdown inhibits malignant phenotypes in STAD cell lines AGS and MKN45, demonstrating the oncogenic role of ITGA11 in STAD. Together, this study highlights the important roles of ITGs in tumorigenesis as potential prognostic biomarkers, and provide an effective resource that identifies cancer-related genes of ITGs in human cancers.
Collapse
Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xiaohan Wu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Liang Gong
- Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Shengbai Sun
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Bingxin Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Mingyue Zhou
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| |
Collapse
|
31
|
Zhang H, Cui K, Yao S, Yin Y, Liu D, Huang Z. Comprehensive molecular and clinical characterization of SLC1A5 in human cancers. Pathol Res Pract 2021; 224:153525. [PMID: 34171602 DOI: 10.1016/j.prp.2021.153525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
Although SLC1A5 has been reported to be closely associated with some cancer types, a comprehensive and systematic assessment of SLC1A5 across human cancers is lacking. Thus, Pan-cancer analysis of SLC1A5 was performed across 30 types of human cancers in this study. We examined mRNA expression, protein expression, copy number variation (CNV), DNA methylation, clinical relevance, cell functions, drug response and total immune infiltrates of SLC1A5 in more than 9000 patients across 30 human cancer types from The Cancer Genome Atlas (TCGA) dataset. Additionally, nine independent Gene Expression Omnibus datasets, more than 800 cancer cell lines from the Cancer Cell Line Encyclopedia dataset and the Project Achilles dataset were used to validate our findings in the TCGA dataset. Landscapes of SLC1A5 were established across multiple cancers. We showed that SLC1A5 is upregulated in multiple cancers, particularly in digestive and respiratory system cancers. SLC1A5 upregulation may be driven by CNV gain and DNA hypomethylation in human cancers. Furthermore, SLC1A5 overexpression is associated with tumor progression and poor survival in multiple cancers. Moreover, we systematically explored the potential effects of SLC1A5 expression on cell functions and drug response in human cancers. SLC1A5 knockdown showed significant proliferation-inhibiting effects in most human cancer types, especially in the digestive system and KRAS-mutant cancers. SLC1A5 expression is associated with proliferation activities of KRAS-mutant cancer cell lines and drug response of many anti-cancer drugs. Finally, we demonstrated that SLC1A5-realted tumor immune microenvironment characteristics showed strong heterogeneity in human cancers. Taken together, our findings highlight the important roles of SLC1A5 in tumorigenesis, progression, prognosis and therapy.
Collapse
Affiliation(s)
- Han Zhang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Dengyang Liu
- Department of Digestive Center, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China.
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi 214062, Jiangsu, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, China.
| |
Collapse
|
32
|
Wang W, Xu SW, Zhu XY, Guo QY, Zhu M, Mao XL, Chen YH, Li SW, Luo WD. Identification and Validation of a Novel RNA-Binding Protein-Related Gene-Based Prognostic Model for Multiple Myeloma. Front Genet 2021; 12:665173. [PMID: 33981333 PMCID: PMC8107400 DOI: 10.3389/fgene.2021.665173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background Multiple myeloma (MM) is a malignant hematopoietic disease that is usually incurable. RNA-binding proteins (RBPs) are involved in the development of many tumors, but their prognostic significance has not been systematically described in MM. Here, we developed a prognostic signature based on eight RBP-related genes to distinguish MM cohorts with different prognoses. Method After screening the differentially expressed RBPs, univariate Cox regression was performed to evaluate the prognostic relevance of each gene using The Cancer Genome Atlas (TCGA)-Multiple Myeloma Research Foundation (MMRF) dataset. Lasso and stepwise Cox regressions were used to establish a risk prediction model through the training set, and they were validated in three Gene Expression Omnibus (GEO) datasets. We developed a signature based on eight RBP-related genes, which could classify MM patients into high- and low-score groups. The predictive ability was evaluated using bioinformatics methods. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and gene set enrichment analyses were performed to identify potentially significant biological processes (BPs) in MM. Result The prognostic signature performed well in the TCGA-MMRF dataset. The signature includes eight hub genes: HNRNPC, RPLP2, SNRPB, EXOSC8, RARS2, MRPS31, ZC3H6, and DROSHA. Kaplan-Meier survival curves showed that the prognosis of the risk status showed significant differences. A nomogram was constructed with age; B2M, LDH, and ALB levels; and risk status as prognostic parameters. Receiver operating characteristic (ROC) curve, C-index, calibration analysis, and decision curve analysis (DCA) showed that the risk module and nomogram performed well in 1, 3, 5, and 7-year overall survival (OS). Functional analysis suggested that the spliceosome pathway may be a major pathway by which RBPs are involved in myeloma development. Moreover, our signature can improve on the R-International Staging System (ISS)/ISS scoring system (especially for stage II), which may have guiding significance for the future. Conclusion We constructed and verified the 8-RBP signature, which can effectively predict the prognosis of myeloma patients, and suggested that RBPs are promising biomarkers for MM.
Collapse
Affiliation(s)
- Wei Wang
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Shi-Wen Xu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xia-Yin Zhu
- Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China.,Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, China
| | - Qun-Yi Guo
- Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China.,Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, China
| | - Min Zhu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xin-Li Mao
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, China.,Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Ya-Hong Chen
- Health Management Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Shao-Wei Li
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, China.,Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Wen-da Luo
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China.,Department of Hematology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China.,Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou, China
| |
Collapse
|
33
|
Bi G, Liang J, Zheng Y, Li R, Zhao M, Huang Y, Zhan C, Xu S, Fan H. Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer types. J Transl Med 2021; 19:124. [PMID: 33766047 PMCID: PMC7995758 DOI: 10.1186/s12967-021-02773-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Tumor invasiveness reflects many biological changes associated with tumorigenesis, progression, metastasis, and drug resistance. Therefore, we performed a systematic assessment of invasiveness-related molecular features across multiple human cancers. Materials and methods Multi-omics data, including gene expression, miRNA, DNA methylation, and somatic mutation, in approximately 10,000 patients across 30 cancer types from The Cancer Genome Atlas, Gene Expression Omnibus, PRECOG, and our institution were enrolled in this study. Results Based on a robust gene signature, we established an invasiveness score and found that the score was significantly associated with worse prognosis in almost all cancers. Then, we identified common invasiveness-associated dysregulated molecular features between high- and low-invasiveness score group across multiple cancers, as well as investigated their mutual interfering relationships thus determining whether the dysregulation of invasiveness-related genes was caused by abnormal promoter methylation or miRNA expression. We also analyzed the correlations between the drug sensitivity data from cancer cell lines and the expression level of 685 invasiveness-related genes differentially expressed in at least ten cancer types. An integrated analysis of the correlations among invasiveness-related genetic features and drug response were conducted in esophageal carcinoma patients to outline the complicated regulatory mechanism of tumor invasiveness status in multiple dimensions. Moreover, functional enrichment suggests the invasiveness score might serve as a predictive biomarker for cancer patients receiving immunotherapy. Conclusion Our pan-cancer study provides a comprehensive atlas of tumor invasiveness and may guide more precise therapeutic strategies for tumor patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02773-x
Collapse
Affiliation(s)
- Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yuansheng Zheng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Runmei Li
- Department of Biostatistics, Public Health, Fudan University, Shanghai, 200000, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Songtao Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Hong Fan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| |
Collapse
|
34
|
Cui K, Yao S, Zhang H, Zhou M, Liu B, Cao Y, Fei B, Huang S, Huang Z. Identification of an immune overdrive high-risk subpopulation with aberrant expression of FOXP3 and CTLA4 in colorectal cancer. Oncogene 2021; 40:2130-2145. [PMID: 33627780 DOI: 10.1038/s41388-021-01677-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/17/2021] [Accepted: 01/22/2021] [Indexed: 01/30/2023]
Abstract
Colorectal cancer (CRC) is characterized by a heterogeneous tumor microenvironment (TME) that regulates cancer progression and therapeutic response. Overexpression of FOXP3 and CTLA4 is associated with immunosuppressive TME and poor prognosis in many cancer types. However, opposite results were reported in CRC. Thus, we performed comprehensive analyses to evaluate the exact prognostic value of FOXP3 and CTLA4 in CRC. Here, the expression levels of FOXP3 and CTLA4 were used to construct a subtyping system based on >1200 CRC patients from multiple independent public datasets. We revealed that, in CRC patients with relatively high expression of FOXP3, there exist two different subpopulations with opposite survival patterns according to CLTA4 expression. We further established a method for evaluating all cohorts and identified a novel FOXP3HighCTLA4High* CRC risk subpopulation that accounts for 5-10% of CRC patients. Moreover, different methods of functional enrichment and immune evaluation were used to analyze the TME characteristics of different FOXP3/CTLA4 subtypes. The FOXP3HighCTLA4High* CRC risk subpopulation was characterized by an immune overdrive TME phenotype, including high immune cell infiltration, low tumor purity, high immune checkpoint levels, and TGF-β activation. Finally, the constructed FOXP3/CTLA4 subtyping system was further validated by quantitative RT-PCR, immunochemistry staining, and multicolor immunofluorescence in an independent CRC cohort we collected. This high-risk subpopulation was also observed in kidney cancers and low-grade glioma patients by a Pan-cancer analysis. Together, our study revealed that the established FOXP3/CTLA4 molecular subtyping system could be used to select treatment and management strategies for CRC and other cancers.
Collapse
Affiliation(s)
- Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Han Zhang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Mingyue Zhou
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Bingxin Liu
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Bojian Fei
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China. .,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
| |
Collapse
|
35
|
Guo F, Zhang B, Yang H, Fu Y, Wang Y, Huang J, Cheng M, Li X, Shen Z, Li L, He P, Xiang AP, Wang S, Zhang H. Systemic transcriptome comparison between early- And late-onset pre-eclampsia shows distinct pathology and novel biomarkers. Cell Prolif 2020; 54:e12968. [PMID: 33332660 PMCID: PMC7848957 DOI: 10.1111/cpr.12968] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Objectives Pre‐eclampsia is a leading cause of morbidity and mortality during pregnancy. Although the two forms of this disorder, early‐ (EOPE) and late‐onset of pre‐eclampsia (LOPE) are different, the underlying pathology remains elusive. We aim to unravel the difference and to identify novel biomarkers for EOPE and LOPE. Materials and Methods A complete comparison of both placental and peripheral blood transcriptomes was performed to investigate the pathology of pre‐eclampsia. Single‐cell transcriptomics of the maternal‐fetal interface were integrated to identify novel biomarkers for EOPE and LOPE which were further verified at protein or mRNA level in patients. Results We found that the transcriptomes of placentae from EOPE, but not LOPE, were significantly different from their respective controls. Conversely, the transcriptomes of peripheral blood from LOPE were more different from their controls than EOPE. Importantly, we identified that several classical biomarkers of pre‐eclampsia were expressed specifically in extravillous trophoblast and syncytiotrophoblast and only upregulated in EOPE, suggesting they should not be applied to all pre‐eclampsia patients in general. We further identified novel biomarkers for EOPE and LOPE from differentially expressed genes (DEGs) of placental and peripheral blood, respectively. The new biomarkers EBI3, IGF2, ORMDL3, GATA2 and KIR2DL4 were experimentally verified with patient blood samples. Conclusion Our data demonstrate distinct pathology of EOPE and LOPE, and uncover new biomarkers that can be applied in diagnosis for pre‐eclampsia.
Collapse
Affiliation(s)
- Fang Guo
- Department of Obstetrics, First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Bao Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hao Yang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yixi Fu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jianming Huang
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Mi Cheng
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Shuaiyu Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
36
|
Development and validation of a novel metabolic signature for predicting prognosis in patients with laryngeal cancer. Eur Arch Otorhinolaryngol 2020; 278:1129-1138. [PMID: 33108563 DOI: 10.1007/s00405-020-06444-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Despite advances in the development of treatments for laryngeal cancer (LC), including surgical treatments and radio-chemotherapy, the survival rate of LC remains low. Therefore, novel metabolic signatures are urgently needed to evaluate the prognosis of LC patients. METHODS Differentially expressed metabolic genes were extracted via bioinformatics analysis from the raw data of The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases. Univariate Cox regression and LASSO analyses were performed to identify metabolic genes that were significantly correlated with overall survival (OS). Using the Kaplan-Meier analysis and receiver operating characteristics, the prognostic power of candidate signatures was evaluated in the two databases. Gene Set Enrichment Analysis (GSEA) was performed to explore significant signaling pathways and underlying mechanisms in the high- and low-risk groups. RESULTS Thirteen metabolism genes showed superior ability to predict OS for LC when compared to clinical variables, and patients in the high-risk group showed significantly poorer OS than those in the low-risk group. The area under the curve of receiver operating curves for 5- and 3-year OS was 0.929 and 0.899, respectively, which were better than the OS obtained with clinicopathological variables. Similar results obtained in the GEO cohort indicated that this gene signature could differentiate between LC patients with and without recurrence. CONCLUSION To our knowledge, this study is the first to report that the 13 metabolic genes could serve as an independent biomarker for LC, which could provide vital prognostic information and prediction for personalized treatment of LC.
Collapse
|
37
|
Sun Y, Wang Q, Zhang Y, Geng M, Wei Y, Liu Y, Liu S, Petersen RB, Yue J, Huang K, Zheng L. Multigenerational maternal obesity increases the incidence of HCC in offspring via miR-27a-3p. J Hepatol 2020; 73:603-615. [PMID: 32593682 DOI: 10.1016/j.jhep.2020.03.050] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Obesity is an independent risk factor for malignancies, including hepatocellular carcinoma (HCC). However, it remains unknown whether maternal obesity affects the incidence of HCC in offspring. Thus, we aimed to investigate this association and its underlying mechanisms. METHODS Diethylnitrosamine (DEN) was used to induce HCC in a high-fat diet (HFD)-induced multigenerational obesity model. RNA-sequencing was performed to identify the genes and microRNAs (miRNAs) that were altered over generations. The role of the miR-27a-3p-Acsl1/Aldh2 axis in HCC was evaluated in cell lines and HCC-bearing nude mice, and its intergenerational impact was studied in pregnant mice and their offspring. RESULTS Under HFD stress, maternal obesity caused susceptibility of offspring to DEN-induced HCC, and such susceptibility was cumulative over generations. We identified that Acsl1 and Aldh2, direct targets of miR-27a-3p, were gradually changed over generations. Under hyperlipidemic conditions, downregulation of Acsl1 and Aldh2 increased cell proliferation (in vitro) or tumor growth (in vivo) in synergy. Intratumor injection of an miR-27a-3p agomir exacerbated tumor growth by downregulating Acsl1 and Aldh2; while intratumor injection of an miR-27a-3p antagomir had the opposite effect. Moreover, serum miR-27a-3p levels gradually increased in the HFD-fed maternal lineage over generations. Injecting pregnant mice with an miR-27a-3p agomir not only upregulated hepatic miR-27a-3p and downregulated Acsl1/Aldh2 in offspring (fetus, young and adult stages), but also exacerbated HCC development in DEN-treated offspring. In human HCC, upregulated miR-27a-3p and downregulated Acsl1/Aldh2 were negatively correlated with survival on TCGA analysis; while, hepatic miR-27a-3p was negatively correlated with Acsl1/Aldh2 expression in tumor/non-tumor tissues from fatty/non-fatty livers. CONCLUSIONS Maternal obesity plays a role in regulating cumulative susceptibility to HCC development in offspring over multiple generations through the miR-27a-3p-Acsl1/Aldh2 axis. LAY SUMMARY It is not currently known how maternal obesity affects the incidence of liver cancer in offspring. In this study, we identified a microRNA (miR-27a-3p) that was upregulated in obese mothers and could be passed on to their offspring. This microRNA enhanced the risk of liver cancer in offspring by regulating 2 genes (Acsl1 and Aldh2). This mechanism could be a future therapeutic target.
Collapse
Affiliation(s)
- Yu Sun
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Qing Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Yu Zhang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030
| | - Mengyuan Geng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Yujuan Wei
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030
| | - Yanrui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Shanshan Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mt. Pleasant, MI, USA, 48858
| | - Junqiu Yue
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430030.
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China, 430072; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China, 430072.
| |
Collapse
|
38
|
Effect of bovine leukemia virus (BLV) infection on bovine mammary epithelial cells RNA-seq transcriptome profile. PLoS One 2020; 15:e0234939. [PMID: 32579585 PMCID: PMC7313955 DOI: 10.1371/journal.pone.0234939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/04/2020] [Indexed: 01/25/2023] Open
Abstract
Bovine leukemia virus (BLV) is a δ-retrovirus responsible for Enzootic Bovine Leukosis (EBL), a lymphoproliferative disease that affects cattle. The virus causes immune system deregulation, favoring the development of secondary infections. In that context, mastitis incidence is believed to be increased in BLV infected cattle. The aim of this study was to analyze the transcriptome profile of a BLV infected mammary epithelial cell line (MAC-T). Our results show that BLV infected MAC-T cells have an altered expression of IFN I signal pathway and genes involved in defense response to virus, as well as a collagen catabolic process and some protooncogenes and tumor suppressor genes. Our results provide evidence to better understand the effect of BLV on bovine mammary epithelial cell's immune response.
Collapse
|
39
|
GLIS2 promotes colorectal cancer through repressing enhancer activation. Oncogenesis 2020; 9:57. [PMID: 32483180 PMCID: PMC7264249 DOI: 10.1038/s41389-020-0240-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/03/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
Gene transcription is coordinately regulated by multiple transcription factors. However, a systematic approach is still lacking to identify co-regulators for transcription factors. Here, we performed ChIP-Seq analysis and predicted the regulators for p53-mediated transcription process, from which we confirmed the roles of GLIS2, MAZ and MEF2A in regulating p53 target genes. We revealed that GLIS2 selectively regulates the transcription of PUMA but not p21. GLIS2 deficiency caused the elevation of H3K27ac and p53 binding on the PUMA enhancer, and promoted PUMA expression. It increased the rate of apoptosis, but not cell cycle. Moreover, GLIS2 represses H3K27ac level on enhancers, regulates the gene expression related with focal adhesion and promotes cell migration, through inhibiting p300. Big data analysis supports GLIS2 as an oncogene in colon cancer, and perhaps other cancers. Taken together, we have predicted candidates for p53 transcriptional regulators, and provided evidence for GLIS2 as an oncogene through repressing enhancer activation.
Collapse
|