1
|
Bai Y, Li Y, Qin Y, Yang X, Tseng GC, Kim S, Park HJ. The microRNA target site profile is a novel biomarker in the immunotherapy response. Front Oncol 2023; 13:1225221. [PMID: 38188295 PMCID: PMC10771317 DOI: 10.3389/fonc.2023.1225221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
MicroRNAs (miRNAs) bind on the 3' untranslated region (3'UTR) of messenger RNAs (mRNAs) and regulate mRNA expression in physiological and pathological conditions, including cancer. Thus, studies have identified miRNAs as potential biomarkers by correlating the miRNA expression with the expression of important mRNAs and/or clinical outcomes in cancers. However, tumors undergo pervasive 3'UTR shortening/lengthening events through alternative polyadenylation (APA), which varies the number of miRNA target sites in mRNA, raising the number of miRNA target sites (numTS) as another important regulatory axis of the miRNA binding effects. In this study, we developed the first statistical method, BIOMATA-APA, to identify predictive miRNAs based on numTS features. Running BIOMATA-APA on The Cancer Genome Atlas (TCGA) and independent cohort data both with immunotherapy and no immunotherapy, we demonstrated for the first time that the numTS feature 1) distinguishes different cancer types, 2) predicts tumor proliferation and immune infiltration status, 3) explains more variation in the proportion of tumor-infiltrating immune cells, 4) predicts response to immune checkpoint blockade (ICB) therapy, and 5) adds prognostic power beyond clinical and miRNA expression. To the best of our knowledge, this is the first pan-cancer study to systematically demonstrate numTS as a novel type of biomarker representing the miRNA binding effects underlying tumorigenesis and pave the way to incorporate miRNA target sites for miRNA biomarker identification. Another advantage of examining the miRNA binding effect using numTS is that it requires only RNA-Seq data, not miRNAs, thus resulting in high power in the miRNA biomarker identification.
Collapse
Affiliation(s)
- Yulong Bai
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yujia Li
- Statistics-Oncology, Eli Lilly and Company, Indianapolis, IN, United States
| | - Yidi Qin
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xinshuo Yang
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ, United States
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Soyeon Kim
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
2
|
Song Q, Ruiz J, Xing F, Lo HW, Craddock L, Pullikuth AK, Miller LD, Soike MH, O'Neill SS, Watabe K, Chan MD, Su J. Single-cell sequencing reveals the landscape of the human brain metastatic microenvironment. Commun Biol 2023; 6:760. [PMID: 37479733 PMCID: PMC10362065 DOI: 10.1038/s42003-023-05124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Brain metastases is the most common intracranial tumor and account for approximately 20% of all systematic cancer cases. It is a leading cause of death in advanced-stage cancer, resulting in a five-year overall survival rate below 10%. Therefore, there is a critical need to identify effective biomarkers that can support frequent surveillance and promote efficient drug guidance in brain metastasis. Recently, the remarkable breakthroughs in single-cell RNA-sequencing (scRNA-seq) technology have advanced our insights into the tumor microenvironment (TME) at single-cell resolution, which offers the potential to unravel the metastasis-related cellular crosstalk and provides the potential for improving therapeutic effects mediated by multifaceted cellular interactions within TME. In this study, we have applied scRNA-seq and profiled 10,896 cells collected from five brain tumor tissue samples originating from breast and lung cancers. Our analysis reveals the presence of various intratumoral components, including tumor cells, fibroblasts, myeloid cells, stromal cells expressing neural stem cell markers, as well as minor populations of oligodendrocytes and T cells. Interestingly, distinct cellular compositions are observed across different samples, indicating the influence of diverse cellular interactions on the infiltration patterns within the TME. Importantly, we identify tumor-associated fibroblasts in both our in-house dataset and external scRNA-seq datasets. These fibroblasts exhibit high expression of type I collagen genes, dominate cell-cell interactions within the TME via the type I collagen signaling axis, and facilitate the remodeling of the TME to a collagen-I-rich extracellular matrix similar to the original TME at primary sites. Additionally, we observe M1 activation in native microglial cells and infiltrated macrophages, which may contribute to a proinflammatory TME and the upregulation of collagen type I expression in fibroblasts. Furthermore, tumor cell-specific receptors exhibit a significant association with patient survival in both brain metastasis and native glioblastoma cases. Taken together, our comprehensive analyses identify type I collagen-secreting tumor-associated fibroblasts as key mediators in metastatic brain tumors and uncover tumor receptors that are potentially associated with patient survival. These discoveries provide potential biomarkers for effective therapeutic targets and intervention strategies.
Collapse
Affiliation(s)
- Qianqian Song
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jimmy Ruiz
- Hematology & Oncology, Department of Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
- W.G. (Bill) Hefner Department of Veteran Affairs Medical Center, Salisbury, NC, USA.
| | - Fei Xing
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Hui-Wen Lo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lou Craddock
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Ashok K Pullikuth
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michael H Soike
- Hazlerig-Salter Department of Radiation Oncology, University of Alabama-Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Stacey S O'Neill
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michael D Chan
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
| |
Collapse
|
3
|
Su R, Zhang H, Zhang L, Khan AR, Zhang X, Wang R, Shao C, Wei X, Xu X. Systemic analysis identifying
PVT1
/
DUSP13
axis for microvascular invasion in hepatocellular carcinoma. Cancer Med 2022; 12:8937-8955. [PMID: 36524545 PMCID: PMC10134337 DOI: 10.1002/cam4.5546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Microvascular invasion (MVI) is an independent detrimental risk factor for tumor recurrence and poor survival in hepatocellular carcinoma (HCC). Competitive endogenous RNA (ceRNA) networks play a pivotal role in the modulation of carcinogenesis and progression among diverse tumor types. However, whether the ceRNA mechanisms are engaged in promoting the MVI process in patients with HCC remains unknown. METHODS A ceRNA regulatory network was constructed based on RNA-seq data of patients with HCC from The Cancer Genome Atlas (TCGA) database. In total, 10 hub genes of the ceRNA network were identified using four algorithms: "MCC," "Degree," "Betweenness," and "Stress." Transcriptional expressions were verified by in situ hybridization using clinical samples. Interactions between ceRNA modules were validated by luciferase reporting assay. Logistic regression analysis, correlation analysis, enrichment analysis, promoter region analysis, methylation analysis, and immune infiltration analysis were performed to further investigate the molecular mechanisms and clinical transformation value. RESULTS The ceRNA regulatory network featuring a tumor invasion phenotype consisting of 3 long noncoding RNAs, 3 microRNAs, and 93 mRNAs was constructed using transcriptional data from the TCGA database. Systemic analysis and experimentally validation identified a ceRNA network (PVT1/miR-1258/DUSP13 axis) characterized by lipid regulatory potential, immune properties, and abnormal methylation states in patients with HCC and MVI. Meanwhile, 28 transcriptional factors were identified as potential promotors of PVT1 with 3 transcriptional factors MXD3, ZNF580, and KDM1A promising as therapeutic targets in patients with HCC and MVI. Furthermore, miR-1258 was an independent predictor for MVI in patients with HCC. CONCLUSION The PVT1/DUSP13 axis is significantly associated with MVI progression in HCC patients. This study provides new insight into mechanisms related to lipids, immune phenotypes, and abnormal epigenetics in oncology research.
Collapse
Affiliation(s)
- Renyi Su
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
| | - Huizhong Zhang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
| | - Lincheng Zhang
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
| | - Abdul Rehman Khan
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
| | - Xuanyu Zhang
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital Zhejiang University School of Medicine Hangzhou China
| | - Rui Wang
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
| | - Chuxiao Shao
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Lishui Hospital Zhejiang University School of Medicine Lishui China
| | - Xuyong Wei
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
| | - Xiao Xu
- Institute of Organ Transplantation, Zhejiang University Hangzhou China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine Hangzhou China
- Westlake Laboratory of Life Sciences and Biomedicine Hangzhou China
| |
Collapse
|
4
|
Song Q, Wang J, Bar-Joseph Z. scSTEM: clustering pseudotime ordered single-cell data. Genome Biol 2022; 23:150. [PMID: 35799304 PMCID: PMC9264648 DOI: 10.1186/s13059-022-02716-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
We develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metrics to summarize the expression of genes and assigns a p-value to clusters enabling the identification of significant profiles and comparison of profiles across different paths. Application of scSTEM to several scRNA-seq datasets demonstrates its usefulness and ability to improve downstream analysis of biological processes. scSTEM is available at https://github.com/alexQiSong/scSTEM.
Collapse
Affiliation(s)
- Qi Song
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Jingtao Wang
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA. .,Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
5
|
Xu S, Gao R, Zhou Y, Yang Y, Zhang Y, Li Q, Luo C, Liu SM. Clinical Diagnostic and Prognostic Potential of NDRG1 and NDRG2 in Hepatocellular Carcinoma Patients. Front Oncol 2022; 12:862216. [PMID: 35795037 PMCID: PMC9252526 DOI: 10.3389/fonc.2022.862216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
Background Primary liver cancer is still the most common lethal malignancy. The N-myc downstream-regulated gene family (NDRG1–4) is a group of multifunctional proteins associated with carcinogenesis. However, systematic evaluation of the diagnostic and prognostic values of NDRG1 or NDRG2 expression in liver cancer is poorly investigated. Method The gene expression matrix of liver hepatocellular carcinoma (LIHC) was comprehensively analyzed by the “limma” and “Dseq2” R packages. The Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) were used to identify the biological functional differences. A single-sample GSEA (ssGSEA) was conducted to quantify the extent of immune cell infiltration. Finally, the clinical and prognostic information of LIHC patients was systematically investigated using Kaplan–Meier analysis and logistic and Cox regression analysis. Results Compared with normal tissues, NDRG1 expression was higher, whereas NDRG2 expression was lower in tumor tissues (P <0.001). The area under the receiver operator characteristic curve (AUROC) of NDRG1 and NDRG2 for LIHC was 0.715 and 0.799, respectively. Kaplan–Meier analysis revealed that NDRG1 and NDRG2 were independent clinical prognostic biomarkers for the overall survival (OS, P = 0.001 and 2.9e−06), progression-free interval (PFI, P = 0.028 and 0.005) and disease-specific survival (DSS, P = 0.027 and P <0.001). The C-indexes and calibration plots of the nomogram suggest that NDRG1 and NDRG2 have an effective predictive performance for OS (C-index: 0.676), DSS (C-index: 0.741) and PFI (C-index: 0.630) of liver cancer patients. The mutation rate of NDRG1 in liver cancer reached up to 14%, and DNA methylation levels of NDRG1 and NDRG2 promoters correlated significantly with clinical prognosis. Conclusions The mRNA expression and DNA methylation of NDRG superfamily members have the potential for LIHC diagnosis and prognosis via integrative analysis from multiple cohorts.
Collapse
Affiliation(s)
- Shaohua Xu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ruihuan Gao
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yidan Zhou
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qianyuan Li
- The First College of Clinical Medical Science, Three Gorges University, Hubei, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, Three Gorges University, Hubei, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Song-Mei Liu,
| |
Collapse
|
6
|
Wei X, Su R, Yang M, Pan B, Lu J, Lin H, Shu W, Wang R, Xu X. Quantitative proteomic profiling of hepatocellular carcinoma at different serum alpha-fetoprotein level. Transl Oncol 2022; 20:101422. [PMID: 35430532 PMCID: PMC9034393 DOI: 10.1016/j.tranon.2022.101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
Serum AFP equal to 400 ng/mL is a pivotal turning point not only in prognosis but also metabolic and invasion associated pathways. Adjacent noncancerous tissues are not biological normal components at protein level. Four druggable targets (C1QBP, HSPE1, CHDH, ITGAL) are identified as potential prognostic biomarkers in hepatocellular carcinoma.
Purpose Hepatocellular carcinoma (HCC) is characterized by a poor long-term prognosis and high mortality rate. Serum alpha-fetoprotein (AFP) levels show great prognostic value in patients undergoing hepatectomy. This study aims to explore proteomic profiling in HCC samples based on AFP subgroups and identify potential key targets involved in HCC progression. Methods Twelve paired tumor and adjacent noncancerous tissue samples were collected from patients with HCC who underwent primary curative resection from January 2012 to December 2013. Clinical information was curated from four tissue microarrays to conduct survival analysis based on serum AFP levels. TMT-based quantitative proteomic analyses and bioinformatics analyses were performed to comprehensively profile molecular features. Immunohistochemistry was carried out to validate protein expression of identified targets. Kaplan-Meier survival analysis was performed to assess the overall survival and recurrence-free survival based on protein expressions. Results AFP (400 ng/mL) was a turning point in prognosis, metabolic- and invasion-associated pathways. The mass spectrometry analysis yielded a total of 5573 identified proteins. Annotations of 151 differentially expressed proteins in tumors and 95 proteins in paracancerous tissues (1.2-fold) showed similarities in biological processes, cellular components, molecular functions. Furthermore, differentially expressed hub proteins with five innovatively nominated druggable targets (C1QBP, HSPE1, GLUD2 for tumors and CHDH, ITGAL for paracancerous tissues), of which four (C1QBP, HSPE1, CHDH, ITGAL) targets were associated with poor overall survival (all Log-rank P < 0.05). Conclusions Our quantitative proteomics analyses identified four key prognostic biomarkers in HCC and provide opportunities for translational medicine and new treatment.
Collapse
|
7
|
Wang L, Luo J, Li Y, Lu Y, Zhang Y, Tian B, Zhao Z, Hu QY. Mitochondrial-Associated Protein LRPPRC is Related With Poor Prognosis Potentially and Exerts as an Oncogene Via Maintaining Mitochondrial Function in Pancreatic Cancer. Front Genet 2022; 12:817672. [PMID: 35237297 PMCID: PMC8885106 DOI: 10.3389/fgene.2021.817672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background: The mitochondrial-associated protein leucine-rich pentatricopeptide repeat-containing (LRPPRC) exerts multiple functions involved in physiological processes, including mitochondrial gene translation, cell cycle progression, and tumorigenesis. Previously, LRPPRC was reported to regulate mitophagy by interacting with Bcl-2 and Beclin-1 and thus modifying the activation of PI3KCIII and autophagy. Considering that LRPPRC was found to be negatively associated with survival rate, we hypothesize that LRPPRC may be involved in pancreatic cancer progression via its regulation of autophagy. Methods: Real-time quantitative polymerase chain reaction was performed to detect the expression of LRPPRC in 90 paired pancreatic cancer and adjacent tissues and five pancreatic cancer cell lines. Mitochondrial reactive oxidative species level and function were measured. Mitophagy was measured by performing to detect LC3 levels. Results: By performing a real-time quantitative polymerase chain reaction, the association of LRPPRC with the prognosis of pancreatic cancer was established, and pancreatic cancer tissues had significantly higher LRPPRC expression than adjacent tissues. LRPPRC was negatively associated with the overall survival rate. LRPPRC was also upregulated in pancreatic cancer cell lines. Knockdown of LRPPRC promoted reactive oxidative species accumulation, decreased mitochondrial membrane potential, promoted autophagy/mitophagy, and induced mitochondrial dysfunction. Subsequently, knockdown of LRPPRC inhibited malignant behaviors in PANC-1 cells, including proliferation, migration, invasion, tumor formation, and chemoresistance to gemcitabine. Finally, by inhibiting autophagy/mitophagy using 3-MA, the inhibitory effect of LRPPRC knockdown on proliferation was reversed. Conclusion: Taken together, our results indicate that LRPPRC may act as an oncogene via maintaining mitochondrial homeostasis and could be used as a predictive marker for patient prognosis in pancreatic cancer.
Collapse
Affiliation(s)
- Li Wang
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Jun Luo
- School of Medicine, Chengdu Women’s and Children’s Central Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuchen Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yanrong Lu
- Key Laboratory of Transplant Engineering and Immunology, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Zhang
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Ziyi Zhao
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiong-ying Hu
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
8
|
Zhou Y, Tang W, Zhuo H, Zhu D, Rong D, Sun J, Song J. Cancer-associated fibroblast exosomes promote chemoresistance to cisplatin in hepatocellular carcinoma through circZFR targeting signal transducers and activators of transcription (STAT3)/ nuclear factor -kappa B (NF-κB) pathway. Bioengineered 2022; 13:4786-4797. [PMID: 35139763 PMCID: PMC8973934 DOI: 10.1080/21655979.2022.2032972] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chemoresistance in hepatocellular carcinoma (HCC) has been found to be influenced by exosomal transport of circRNAs. However, the role of circZFR in HCC chemoresistance still remains unclear. In the present study, circZFR was highly expressed in cisplatin (DDP)-resistant HCC cell lines and could regulate DDP resistance of the HCC cells. Also, circZFR was highly expressed in cancer-associated fibroblast (CAFs) and the exosome of CAFs. In addition, supplementation of CAFs in culture medium could promote DDP resistance of HCC cells. In vivo tumor xenograft experiments showed that knockdown of circZFR inhibited tumor growth and weakened DDP resistance, while CAFs-derived exosomes incubation increased the expression of circZFR, inhibited the STAT3/NF-κB pathway, promoted tumor growth, and enhanced DDP resistance. In general, CAFs-derived exosomes deliver circZFR to HCC cells, inhibit the STAT3/NF-κB pathway, and promote HCC development and chemoresistance. The results provided a new sight for the prevention and treatment of chemoresistance in HCC.
Collapse
Affiliation(s)
- Yun Zhou
- Department of Ultrasonography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Weiwei Tang
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; Nhc Key Laboratory of Living Donor Liver Transplantation, Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Han Zhuo
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; Nhc Key Laboratory of Living Donor Liver Transplantation, Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Deming Zhu
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; Nhc Key Laboratory of Living Donor Liver Transplantation, Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dawei Rong
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; Nhc Key Laboratory of Living Donor Liver Transplantation, Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin Sun
- Department of Nuclear Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhua Song
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; Nhc Key Laboratory of Living Donor Liver Transplantation, Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
9
|
Cai Y, Jia Y. Circular RNA SOX5 promotes the proliferation and inhibits the apoptosis of the hepatocellular carcinoma cells by targeting miR-502-5p/synoviolin 1 axis. Bioengineered 2022; 13:3362-3370. [PMID: 35048790 PMCID: PMC8973662 DOI: 10.1080/21655979.2022.2029110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We aimed to explore the role of circ-SOX5 in the pathogenesis of hepatocellular carcinoma (HCC). The circRNAs in HCC were screened using the GEO database. RT-qPCR was used to detect mRNA expression. Targeting relationships were confirmed by dual luciferase reporter assay and RNA pull-down assay. CCK-8 and EDU staining were used to measure cell viability and proliferation, respectively. Cell apoptosis was determined using flow cytometry. Protein expression was determined by Western blotting. Circ-SOX5 expression was increased in HCC tissues. Inhibition of circ-SOX5 expression reduced the viability, proliferation, and colony formation, and increased the apoptosis of HCC cells. However, miR-502-5p inhibition or overexpression of synoviolin 1 (SYVN1) can reverse the effects of circ-SOX5 knockdown on proliferation and apoptosis. This study demonstrated that the circ-SOX5/miR-502-5p/SYVN1 axis promotes the development of HCC by regulating cell apoptosis. Therefore, circ-SOX5 may be a potential biomarker of HCC.
Collapse
Affiliation(s)
- Yu Cai
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, China
| | - Yuanyuan Jia
- Department of Faculty Development and Teaching Evaluation Office, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, China
| |
Collapse
|
10
|
Shi X, Zhang J, Jiang Y, Zhang C, Luo X, Wu J, Li J. Comprehensive Analyses of the Expression, Genetic Alteration, Prognosis Significance, and Interaction Networks of m 6A Regulators Across Human Cancers. Front Genet 2022; 12:771853. [PMID: 35003212 PMCID: PMC8733627 DOI: 10.3389/fgene.2021.771853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/23/2021] [Indexed: 02/03/2023] Open
Abstract
Accumulating lines of evidence indicate that the deregulation of m6A is involved in various cancer types. The m6A RNA methylation is modulated by m6A methyltransferases, demethylases, and reader proteins. Although the aberrant expression of m6A RNA methylation contributes to the development and progression of multiple cancer types, the roles of m6A regulators across numerous types of cancers remain largely unknown. Here, we comprehensively investigated the expression, genetic alteration, and prognosis significance of 20 commonly studied m6A regulators across diverse cancer types using TCGA datasets via bioinformatic analyses. The results revealed that the m6A regulators exhibited widespread dysregulation, genetic alteration, and the modulation of oncogenic pathways across TCGA cancer types. In addition, most of the m6A regulators were closely relevant with significant prognosis in many cancer types. Furthermore, we also constructed the protein–protein interacting network of the 20 m6A regulators, and a more complex interacting regulatory network including m6A regulators and their corresponding interacting factors. Besides, the networks between m6A regulators and their upstream regulators such as miRNAs or transcriptional factors were further constructed in this study. Finally, the possible chemicals targeting each m6A regulator were obtained by bioinformatics analysis and the m6A regulators–potential drugs network was further constructed. Taken together, the comprehensive analyses of m6A regulators might provide novel insights into the m6A regulators’ roles across cancer types and shed light on their potential molecular mechanisms as well as help develop new therapy approaches for cancers.
Collapse
Affiliation(s)
- Xiujuan Shi
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Jieping Zhang
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Yuxiong Jiang
- School of Medicine, Tongji University, Shanghai, China
| | - Chen Zhang
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaoli Luo
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Jiawen Wu
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Jue Li
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China.,Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
11
|
Chen K, Xing J, Yu W, Xia Y, Zhang Y, Cheng F, Rao T. Identification and Validation of Hub Genes Associated with Bladder Cancer by Integrated Bioinformatics and Experimental Assays. Front Oncol 2022; 11:782981. [PMID: 34988018 PMCID: PMC8721040 DOI: 10.3389/fonc.2021.782981] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer (BC) is the most common malignant tumor of the urinary system and is associated with high morbidity and mortality; however, the molecular mechanism underlying its occurrence is not clear. In this study, the gene expression profile and related clinical information of GSE13507 were downloaded from the Gene Expression Omnibus (GEO) database. RNA sequencing (RNA-seq) expression data and related clinical information were retrieved from The Cancer Genome Atlas (TCGA) database. Overlapping genes were identified by differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). Then, we carried out functional enrichment analysis to understand the potential biological functions of these co-expressed genes. Finally, we performed a protein-protein interaction (PPI) analysis combined with survival analysis. Using the CytoHubba plug-in of Cytoscape, TROAP, CENPF, PRC1, AURKB, CCNB2, CDC20, TTK, CEP55, ASPM, and CDCA8 were identified as candidate central genes. According to the survival analysis, the high expression of TTK was related to the poor overall survival (OS) of patients with BC. TTK may also affect the bladder tumor microenvironment (TME) by affecting the number of immune cells. The expression level of TTK was verified by immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR), and the tumor-promoting effect of TTK in BC cells was confirmed in vitro. Our results also identified the MSC-AS1/hsa-miR-664b-3p/TTK regulatory axis, which may also play an important role in the progression of BC, but further research is needed to verify this result. In summary, our results provide a new idea for accurate early diagnosis, clinical treatment, and prognosis of BC.
Collapse
Affiliation(s)
- Kang Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ji Xing
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuqi Xia
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yunlong Zhang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ting Rao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
12
|
Yang Y, Meng WJ, Wang ZQ. Cancer Stem Cells and the Tumor Microenvironment in Gastric Cancer. Front Oncol 2022; 11:803974. [PMID: 35047411 PMCID: PMC8761735 DOI: 10.3389/fonc.2021.803974] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/08/2021] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) remains one of the leading causes of cancer-related death worldwide. Cancer stem cells (CSCs) might be responsible for tumor initiation, relapse, metastasis and treatment resistance of GC. The tumor microenvironment (TME) comprises tumor cells, immune cells, stromal cells and other extracellular components, which plays a pivotal role in tumor progression and therapy resistance. The properties of CSCs are regulated by cells and extracellular matrix components of the TME in some unique manners. This review will summarize current literature regarding the effects of CSCs and TME on the progression and therapy resistance of GC, while emphasizing the potential for developing successful anti-tumor therapy based on targeting the TME and CSCs.
Collapse
Affiliation(s)
| | - Wen-Jian Meng
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | | |
Collapse
|
13
|
Zhao Z, Zeng J, Guo Q, Pu K, Yang Y, Chen N, Zhang G, Zhao M, Zheng Q, Tang J, Hu Q. Berberine Suppresses Stemness and Tumorigenicity of Colorectal Cancer Stem-Like Cells by Inhibiting m 6A Methylation. Front Oncol 2021; 11:775418. [PMID: 34869024 PMCID: PMC8634032 DOI: 10.3389/fonc.2021.775418] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background Cancer stem cells (CSCs) are able to survive after cancer therapies, resulting in tumor progression and recurrence, as is seen in colorectal cancer. Therapies targeting CSCs are regarded as novel and promising strategies for efficiently eradicating tumors. Berberine, an isoquinoline alkaloid extracted from the Chinese herbal medicine Coptis chinensis, was found to have antitumor activities against colorectal cancer, without knowing whether it exerts inhibitory effects on colorectal CSCs and the potential mechanisms. Methods In this study, we examined the inhibitory roles of Berberine on CSCs derived from HCT116 and HT29 by culturing in serum-free medium. We also examined the effects of Berberine on m6A methylation via regulating fat mass and obesity-associated protein (FTO), by downregulating β-catenin. Results We examined the effects of Berberine on the tumorigenicity, growth, and stemness of colorectal cancer stem-like cells. The regulatory effect of Berberine on N6-methyladenosine (m6A), an abundant mRNA modification, was also examined. Berberine treatment decreased cell proliferation by decreasing cyclin D1 and increasing p27 and p21 and subsequently induced cell cycle arrest at the G1/G0 phase. Berberine treatment also decreased colony formation and induced apoptosis. Berberine treatment transcriptionally increased FTO and thus decreased m6A methylation, which was reversed by both FTO knockdown and the addition of the FTO inhibitor FB23-2. Berberine induced FTO-related decreases in stemness in HCT116 and HT29 CSCs. Berberine treatment also increased chemosensitivity in CSCs and promoted chemotherapy agent-induced apoptosis. Moreover, we also found that Berberine treatment increased FTO by decreasing β-catenin, which is a negative regulator of FTO. Conclusions Our observation that Berberine effectively decreased m6A methylation by decreasing β-catenin and subsequently increased FTO suggests a role of Berberine in modulating stemness and malignant behaviors in colorectal CSCs.
Collapse
Affiliation(s)
- Ziyi Zhao
- Traditional Chinese Medicine (TCM) Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Chengdu, China.,Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jinhao Zeng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Geriatric Department, Traditional Chinese Medicine (TCM) Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Chengdu, China
| | - Qiang Guo
- Department of Geriatrics, Chengdu First People's Hospital, Chengdu, China
| | - Kunming Pu
- Department of Ultrasound, the Second People's Hospital of Chengdu, Chengdu, China
| | - Yi Yang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Nianzhi Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Gang Zhang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Maoyuan Zhao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiao Zheng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jianyuan Tang
- Traditional Chinese Medicine (TCM) Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Chengdu, China.,Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiongying Hu
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
14
|
Deng M, Peng L, Li J, Liu X, Xia X, Li G. PPP1R14B Is a Prognostic and Immunological Biomarker in Pan-Cancer. Front Genet 2021; 12:763561. [PMID: 34858479 PMCID: PMC8631915 DOI: 10.3389/fgene.2021.763561] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/18/2021] [Indexed: 12/24/2022] Open
Abstract
Recent studies have shown that PPP1R14B was highly expressed in tumor tissues and patients with high expression of PPP1R14B had poor survival rates. However, the function and mechanisms of PPP1R14B in tumor progression remain ill defined. There was also lack of pan-cancer evidence for the relationship between PPP1R14B and various tumor types based on abundant clinical data. We used the TCGA project and GEO databases to perform pan-cancer analysis of PPP1R14B, including expression differences, correlations between expression levels and survival, genetic alteration, immune infiltration, and relevant cellular pathways, to investigate the functions and potential mechanisms of PPP1R14B in the pathogenesis or clinical prognosis of different cancers. Herein, we found that PPP1R14B was involved in the prognosis of pan-cancer and closely related to immune infiltration. Increased PPP1R14B expression correlated with poor prognosis and increased immune infiltration levels in myeloid-derived suppressor cells (MDSCs). Our studies suggest that PPP1R14B can be used as a prognostic biomarker for pan-cancer. Our findings may provide an antitumor strategy targeting PPP1R14B, including manipulation of tumor cell growth or the tumor microenvironment, especially myeloid-derived suppressor cell infiltration.
Collapse
Affiliation(s)
- Mingxia Deng
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Long Peng
- Department of Cardiovascular Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiamin Li
- Department of General Surgery, Dongguan Tungwah Hospital, Dongguan, China
| | - Xiong Liu
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xichun Xia
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Guangqiang Li
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, Guangzhou, China
| |
Collapse
|
15
|
Wu G, Yang Y, Zhu Y, Li Y, Zhai Z, An L, Liu M, Zheng Y, Wang Y, Zhou Y, Guo Q. Comprehensive Analysis to Identify the Epithelial-Mesenchymal Transition-Related Immune Signatures as a Prognostic and Therapeutic Biomarkers in Hepatocellular Carcinoma. Front Surg 2021; 8:742443. [PMID: 34722623 PMCID: PMC8554059 DOI: 10.3389/fsurg.2021.742443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease with the high rates of the morbidity and mortality due to the lack of the effective prognostic model for prediction. Aim: To construct a risk model composed of the epithelial–mesenchymal transition (EMT)-related immune genes for the assessment of the prognosis, immune infiltration status, and chemosensitivity. Methods: We obtained the transcriptome and clinical data of the HCC samples from The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC) databases. The Pearson correlation analysis was applied to identify the differentially expressed EMT-related immune genes (DE-EMTri-genes). Subsequently, the univariate Cox regression was introduced to screen out the prognostic gene sets and a risk model was constructed based on the least absolute shrinkage and selection operator-penalized Cox regression. Additionally, the receiver operating characteristic (ROC) curves were plotted to compare the prognostic value of the newly established model compared with the previous model. Furthermore, the correlation between the risk model and survival probability, immune characteristic, and efficacy of the chemotherapeutics were analyzed by the bioinformatics methods. Results: Six DE-EMTri-genes were ultimately selected to construct the prognostic model. The area under the curve (AUC) values for 1-, 2-, and 3- year were 0.773, 0.721, and 0.673, respectively. Stratified survival analysis suggested that the prognosis of the low-score group was superior to the high-score group. Moreover, the univariate and multivariate analysis indicated that risk score [hazard ratio (HR) 5.071, 95% CI 3.050, 8.432; HR 4.396, 95% CI 2.624, 7.366; p < 0.001] and stage (HR 2.500, 95% CI 1.721, 3.632; HR 2.111, 95% CI 1.443, 3.089; p < 0.001) served as an independent predictive factors in HCC. In addition, the macrophages, natural killer (NK) cells, and regulatory T (Treg) cells were significantly enriched in the high-risk group. Finally, the patients with the high-risk score might be more sensitive to cisplatin, doxorubicin, etoposide, gemcitabine, and mitomycin C. Conclusion: We established a reliable EMTri-genes-based prognostic signature, which may hold promise for the clinical prediction.
Collapse
Affiliation(s)
- Guozhi Wu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yuan Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yu Zhu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Hematology, the First Hospital of Lanzhou University, Lanzhou, China
| | - Yemao Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Zipeng Zhai
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Lina An
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Min Liu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Qinghong Guo
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| |
Collapse
|
16
|
Si T, Huang Z, Jiang Y, Walker-Jacobs A, Gill S, Hegarty R, Hamza M, Khorsandi SE, Jassem W, Heaton N, Ma Y. Expression Levels of Three Key Genes CCNB1, CDC20, and CENPF in HCC Are Associated With Antitumor Immunity. Front Oncol 2021; 11:738841. [PMID: 34660300 PMCID: PMC8515852 DOI: 10.3389/fonc.2021.738841] [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: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is the most common primary liver cancer with a low 5-year survival rate. The heterogeneity of HCC makes monotherapy unlikely. The development of diagnostic programs and new treatments targeting common genetic events in the carcinogenic process are providing further insights into the management of HCC. The aim of this study was firstly to validate key genes that are involved in promoting HCC development and as biomarkers for early diagnosis and, secondly, to define their links with antitumor immunity including inhibitory checkpoints. Methods Multiple databases including Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, UALCAN, and Oncomine were used for target gene screening and establishment of a co-expression network. Clinical data and RNAseq of 367 HCC patients were downloaded from the Cancer Genome Atlas (TCGA) database. The diagnostic and prognostic value of screened genes were tested by receiver operating characteristic (ROC) curve and correlation analysis. The links with the key genes in HCC and antitumor immunity were defined using both blood and liver tissue collected prospectively from HCC patients in our center. Results Upregulation of CCNB1, CDC20, and CENPF was commonly observed in HCC and are involved in the p53 signal pathway. The hepatic mRNA expression levels of these three genes were strongly associated with patients' prognosis and expressed high value of area under the ROC curve (AUC). Further analysis revealed that these three genes were positively correlated with the gene expression levels of IFN-γ, TNF-α, and IL-17 in peripheral blood. In addition, the expression of CENPF showed positive correlation with the percentage of CD8pos T cells and negative correlation with the percentage of CD4pos T cells in the peripheral blood. In the HCC microenvironment, the transcript levels of these three genes and inhibitory checkpoint molecules including PD-1, CTLA-4, and TIM-3 were positively correlated. Conclusion The upregulation of CCNB1, CDC20, and CENPF genes was a common event in hepatocarcinogenesis. Expression levels of CCNB1, CDC20, and CENPF showed potential for early diagnosis and prediction of prognosis in HCC patients. There is a close association between three genes and Th1/Th17 cytokines as well as the count of CD4pos and CD8pos T cells. The positive correlation between the three genes and inhibitory checkpoint genes, PD-1, CTLA-4, and TIM-3, indicates that these genes are linked with weakened antitumor immunity in HCC. Our findings may provide further insights into developing novel therapies for HCC.
Collapse
Affiliation(s)
- Tengfei Si
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Zhenlin Huang
- The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanhang Jiang
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Abigail Walker-Jacobs
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Shaqira Gill
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Robert Hegarty
- Pediatric Liver, GI and Nutrition Centre, King's College Hospital, London, United Kingdom
| | - Mohammad Hamza
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Shirin Elizabeth Khorsandi
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom.,The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
| | - Wayel Jassem
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom
| | - Nigel Heaton
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom
| | - Yun Ma
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| |
Collapse
|
17
|
Liu L, Liu B, Yu J, Zhang D, Shi J, Liang P. Development of a Toll-Like Receptor-Based Gene Signature That Can Predict Prognosis, Tumor Microenvironment, and Chemotherapy Response for Hepatocellular Carcinoma. Front Mol Biosci 2021; 8:729789. [PMID: 34621787 PMCID: PMC8490642 DOI: 10.3389/fmolb.2021.729789] [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: 06/23/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
Objective: Emerging evidence highlights the implications of the toll-like receptor (TLR) signaling pathway in the pathogenesis and therapeutic regimens of hepatocellular carcinoma (HCC). Herein, a prognostic TLR-based gene signature was conducted for HCC. Methods: HCC-specific TLRs were screened in the TCGA cohort. A LASSO model was constructed based on prognosis-related HCC-specific TLRs. The predictive efficacy, sensitivity, and independency of this signature was then evaluated and externally verified in the ICGC, GSE14520, and GSE76427 cohorts. The associations between this signature and tumor microenvironment (stromal/immune score, immune checkpoint expression, and immune cell infiltrations) and chemotherapy response were assessed in HCC specimens. The expression of TLRs in this signature was verified in HCC and normal liver tissues by Western blot. Following si-MAP2K2 transfection, colony formation and apoptosis of Huh7 and HepG2 cells were examined. Results: Herein, we identified 60 HCC-specific TLRs. A TLR-based gene signature (MAP2K2, IRAK1, RAC1, TRAF3, MAP3K7, and SPP1) was conducted for HCC prognosis. High-risk patients exhibited undesirable outcomes. ROC curves confirmed the well prediction performance of this signature. Multivariate Cox regression analysis demonstrated that the signature was an independent prognostic indicator. Also, high-risk HCC was characterized by an increased immune score, immune checkpoint expression, and immune cell infiltration. Meanwhile, high-risk patients displayed higher sensitivity to gemcitabine and cisplatin. The dysregulation of TLRs in the signature was confirmed in HCC. MAP2K2 knockdown weakened colony formation and elevated apoptosis of Huh7 and HepG2 cells. Conclusion: Collectively, this TLR-based gene signature might assist clinicians to select personalized therapy programs for HCC patients.
Collapse
Affiliation(s)
- Lixia Liu
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Ultrasound, Affiliated Hospital of Hebei University, Baoding, China
| | - Bin Liu
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jie Yu
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Dongyun Zhang
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Jianhong Shi
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Ping Liang
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| |
Collapse
|
18
|
Song Q, Su J, Zhang W. scGCN is a graph convolutional networks algorithm for knowledge transfer in single cell omics. Nat Commun 2021; 12:3826. [PMID: 34158507 PMCID: PMC8219725 DOI: 10.1038/s41467-021-24172-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Single-cell omics is the fastest-growing type of genomics data in the literature and public genomics repositories. Leveraging the growing repository of labeled datasets and transferring labels from existing datasets to newly generated datasets will empower the exploration of single-cell omics data. However, the current label transfer methods have limited performance, largely due to the intrinsic heterogeneity among cell populations and extrinsic differences between datasets. Here, we present a robust graph artificial intelligence model, single-cell Graph Convolutional Network (scGCN), to achieve effective knowledge transfer across disparate datasets. Through benchmarking with other label transfer methods on a total of 30 single cell omics datasets, scGCN consistently demonstrates superior accuracy on leveraging cells from different tissues, platforms, and species, as well as cells profiled at different molecular layers. scGCN is implemented as an integrated workflow as a python software, which is available at https://github.com/QSong-github/scGCN .
Collapse
Affiliation(s)
- Qianqian Song
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
- Section on Gerontology and Geriatric Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, NC, USA.
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA.
| |
Collapse
|
19
|
Chen L, Fan R, Tang F. Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:343-345. [PMID: 34923125 PMCID: PMC8864189 DOI: 10.1016/j.gpb.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Affiliation(s)
- Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|