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Wan L, Su S, Liu J, Zou B, Jiang Y, Jiao B, Tang S, Zhang Y, Deng C, Xiao W. The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles. Evol Bioinform Online 2024; 20:11769343241261814. [PMID: 38883803 PMCID: PMC11179516 DOI: 10.1177/11769343241261814] [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: 03/04/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Background Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.
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Affiliation(s)
- Linrong Wan
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Siyuan Su
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Jinyun Liu
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Bangxing Zou
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yaming Jiang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Beibei Jiao
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Shaokuan Tang
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Youhong Zhang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Cao Deng
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Wenfu Xiao
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
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Williams I, DeHart H, O'Malley M, Walker B, Ulhaskumar V, Ray H, Delaney JR, Nephew KP, Carpenter RL. MYC and HSF1 Cooperate to Drive PLK1 inhibitor Sensitivity in High Grade Serous Ovarian Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598486. [PMID: 38915574 PMCID: PMC11195273 DOI: 10.1101/2024.06.11.598486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Ovarian cancer is a deadly female cancer with high rates of recurrence. The primary treatment strategy for patients is platinum-based therapy regimens that almost universally develop resistance. Consequently, new therapeutic avenues are needed to overcome the plateau that current therapies have on patient outcomes. We describe a gene amplification involving both HSF1 and MYC, wherein these two genes on chromosome 8q are co-amplified in over 7% of human tumors that is enriched to over 30% of patients with ovarian cancer. We further found that HSF1 and MYC transcriptional activity is correlated in human tumors and ovarian cancer cell lines, suggesting they may cooperate in ovarian cancer cells. CUT&RUN for HSF1 and MYC in co-amplified ovarian cancer cells revealed that HSF1 and MYC have overlapping binding at a substantial number of locations throughout the genome where their binding peaks are near identical. Consistent with these data, a protein-protein interaction between HSF1 and MYC was detected in ovarian cancer cells, implying these two transcription factors have a molecular cooperation. Further supporting their cooperation, growth of HSF1-MYC co-amplified ovarian cancer cells were found to be dependent on both HSF1 and MYC. In an attempt to identify a therapeutic target that could take advantage of this dependency on both HSF1 and MYC, PLK1 was identified as being correlated with HSF1 and MYC in primary human tumor specimens, consistent with a previously established effect of PLK1 on HSF1 and MYC protein levels. Targeting PLK1 with the compound volasertib (BI-6727) revealed a greater than 200-fold increased potency of volasertib in HSF1-MYC co-amplified ovarian cancer cells compared to ovarian cancer cells wild-type HSF1 and MYC copy number, which extended to several growth assays, including spheroid growth. Volasertib, and other PLK1 inhibitors, have not shown great success in clinical trials and this study suggests that targeting PLK1 may be viable in a precision medicine approach using HSF1-MYC co-amplification as a biomarker for response.
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Wang J, Gu S, Qin B. Eosinophil and mast cell-derived exosomes promote integrity of intestinal mucosa via the NEAT1/miR-211-5p/glial cell line-derived neurotrophic factor axis in duodenum. ENVIRONMENTAL TOXICOLOGY 2023; 38:2595-2607. [PMID: 37466184 DOI: 10.1002/tox.23895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/31/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Exosomes are applied as biomarkers in several diseases according to their disease-specific profiles. However, the exosomes effects in functional dyspepsia (FD) are still fragmentary. Here we examined the role of Eosinophil and mast cell derived-exosomes in FD progression. METHODS Fifty FD subjects and age- and sex-matched healthy controls were included in this retrospective cohort study. Duodenal mucosa and gastric juice were collected to analyze molecular difference. Eosinophil and mast cell were evaluated by immunofluorescence and microarray was subjected to examine the expression levels of NEAT1, miR-211-5p, and glial cell line-derived neurotrophic factor (GDNF), which were subsequently were tested by quantitative reverse transcription PCR (RT-qPCR) validation cohorts. CCK-8 assays, and wound healing assays were used to evaluate integrity of intestinal mucosal barrier in vitro. Rats' weights and gastric emptying rates were used as evaluation of FD severity in vivo. RESULTS Eosinophil and mast cell were enriched and secreted more exosomes in duodenal mucosa of FD patients. We identified differential lncRNAs that were consistently and significantly up regulated in FD cases. Of these, NEAT1 was further validated by RT-qPCR and had closely relationship with GDNF. MiR-211-5p level was found to be reduced in FD and negatively related with NEAT1 and GDNF. Furthermore, NEAT1and GDNF relived FD while miR-211-5p made symptoms worse. The NEAT1/miR-211-5p/GDNF axis had a good predictive ability for FD. CONCLUSIONS The NEAT1/miR-211-5p/GDNF could be a potential FD biomarker.
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Affiliation(s)
- Jue Wang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sai Gu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Qin
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Roshani M, Molavizadeh D, Sadeghi S, Jafari A, Dashti F, Mirazimi SMA, Ahmadi Asouri S, Rajabi A, Hamblin MR, Anoushirvani AA, Mirzaei H. Emerging roles of miR-145 in gastrointestinal cancers: A new paradigm. Biomed Pharmacother 2023; 166:115264. [PMID: 37619484 DOI: 10.1016/j.biopha.2023.115264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Gastrointestinal (GI) carcinomas are a group of cancers affecting the GI tract and digestive organs, such as the gastric, liver, bile ducts, pancreas, small intestine, esophagus, colon, and rectum. MicroRNAs (miRNAs) are small functional non-coding RNAs (ncRNAs) which are involved in regulating the expression of multiple target genes; mainly at the post-transcriptional level, via complementary binding to their 3'-untranslated region (3'-UTR). Increasing evidence has shown that miRNAs have critical roles in modulating of various physiological and pathological cellular processes and regulating the occurrence and development of human malignancies. Among them, miR-145 is recognized for its anti-oncogenic properties in various cancers, including GI cancers. MiR-145 has been implicated in diverse biological processes of cancers through the regulation of target genes or signaling, including, proliferation, differentiation, tumorigenesis, angiogenesis, apoptosis, metastasis, and therapy resistance. In this review, we have summarized the role of miR-145 in selected GI cancers and also its downstream molecules and cellular processes targets, which could lead to a better understanding of the miR-145 in these cancers. In conclusion, we reveal the potential diagnostic, prognostic, and therapeutic value of miR-145 in GI cancer, and hope to provide new ideas for its application as a biomarker as well as a therapeutic target for the treatment of these cancer.
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Affiliation(s)
- Mohammad Roshani
- Internal Medicine and Gastroenterology, Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Danial Molavizadeh
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Sara Sadeghi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Ameneh Jafari
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for BasicSciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Ali Rajabi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Ali Arash Anoushirvani
- Department of Internal Medicine, Firoozgar Hospital, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Internal Medicine, Firoozgar Hospital, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Yang J, Ren B, Ren J, Yang G, Fang Y, Wang X, Zhou F, You L, Zhao Y. Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications. J Exp Clin Cancer Res 2023; 42:155. [PMID: 37370109 DOI: 10.1186/s13046-023-02698-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/03/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) tends to undergo distant metastasis, especially liver metastasis, leading to a poor prognosis. Metabolic remodelling and epigenetic reprogramming are two important hallmarks of malignant tumours and participate in regulating PDAC tumorigenesis and metastasis. However, the interaction between these two processes during PDAC metastasis has not been fully elucidated. METHODS We performed metabolomics analysis to identify the critical metabolites associated with PDAC liver metastasis and focused on guanidinoacetic acid (GAA). Intracellular GAA content was significantly increased in liver metastatic PDAC cells compared to primary cancer cells in mouse xenograft tumour models. The effects of GAA supplementation and glycine amidinotransferase (GATM) knockdown on PDAC metastasis were assessed by analysing cell migration, filopodia formation, epithelial-mesenchymal transition (EMT), and in vivo metastasis in different cell and animal models. Next, ChIP‒qPCR, 3C‒qPCR, and CRISPRi/dCas9-KRAB experiments were used to validate the "epigenome-metabolome" mechanism. Finally, the results of in vitro approaches, including RNA-seq, CUT&RUN, RT‒qPCR, and western blot analyses, as well as luciferase reporter gene assay and transwell assay, revealed the GAA-c-Myc-HMGA axis and transcription-activating histone modifications reprogramming. RESULTS A high level of intracellular GAA was associated with PDAC liver metastasis. GAA could promote the migration, EMT, and liver metastasis of pancreatic cancer cells in vitro and in vivo. Next, we explored the role of GATM-mediated de novo GAA synthesis in pancreatic cancer metastasis. High expression of GATM was positively correlated with advanced N stage in PDAC. Knockdown of GATM significantly reduced the intracellular level of GAA, suppressed EMT, and inhibited PDAC liver metastasis, and these effects were attenuated by GAA supplementation. Mechanistically, we identified the active enhancers looped to the Gatm gene locus that promoted GATM expression and PDAC liver metastasis. Furthermore, we found that GAA promoted cell migration and EMT by regulating c-Myc-mediated high mobility group AT-hook protein expression. Moreover, GAA increased the H3K4me3 modification level by upregulating histone methyltransferases, which induced the transcription of metastasis-related genes, including Myc. CONCLUSIONS These findings revealed the critical role of the epigenome-metabolome interaction in regulating PDAC liver metastasis and suggested potential therapeutic strategies targeting GAA metabolism and epigenetic regulatory mechanisms.
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Affiliation(s)
- Jinshou Yang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Bo Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Jie Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Gang Yang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Yuan Fang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Xing Wang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Feihan Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China.
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, People's Republic of China.
- National Science and Technology Key Infrastructure On Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, People's Republic of China.
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Li N, Zhou Y, Cai J, Wang Y, Zhou X, Hu M, Li Y, Zhang H, Li J, Cai B, Yuan X. A novel trans-acting lncRNA of ACTG1 that induces the remodeling of ovarian follicles. Int J Biol Macromol 2023:125170. [PMID: 37276900 DOI: 10.1016/j.ijbiomac.2023.125170] [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: 01/17/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Previous studies have implicated the attractive role of long noncoding RNAs (lncRNAs) in the remodeling of mammalian tissues. The migration of granulosa cells (GCs), which are the main supporting cells in ovarian follicles, stimulates the follicular remodeling. Here, with the cultured GCs as the follicular model, the actin gamma 1 (ACTG1) was observed to significantly promote the migration and proliferation while inhibit the apoptosis of GCs, suggesting that ACTG1 was required for ovarian remodeling. Moreover, we identified the trans-regulatory lncRNA of ACTG1 (TRLA), which was epigenetically targeted by histone H3 lysine 4 acetylation (H3K4ac). Mechanistically, the 2-375 nt of TRLA bound to ACTG1's mRNA to increase the expression of ACTG1. Furthermore, TRLA facilitated the migration and proliferation while inhibited the apoptosis of GCs, thereby accelerating follicular remodeling. Besides, TRLA acted as a ceRNA for miR-26a to increase the expression of high-mobility group AT-hook 1 (HMGA1). Collectively, TRLA induces the remodeling of ovarian follicles via complementary to ACTG1's mRNA and regulating miR-26a/HMGA1 axis in GCs. These observations revealed a novel and promising trans-acting lncRNA mechanism mediated by H3K4ac, and TRLA might be a new target to restore follicular remodeling and development.
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Affiliation(s)
- Nian Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yinqi Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yifei Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiaofeng Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Mengting Hu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yubin Li
- Reproductive Medical Center, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong 510080, China
| | - Hao Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bing Cai
- Reproductive Medical Center, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong 510080, China.
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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Ren S, Zhu Y, Wang S, Zhang Q, Zhang N, Zou X, Wei C, Wang Z. The pseudogene DUXAP10 contributes to gefitinib resistance in NSCLC by repressing OAS2 expression. Acta Biochim Biophys Sin (Shanghai) 2023; 55:81-90. [PMID: 36471952 PMCID: PMC10157544 DOI: 10.3724/abbs.2022176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Gefitinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI),is the currently recommended first-line therapy for advanced EGFR-mutant lung cancer, and understanding the mechanism of resistance is the key to formulating therapeutic strategies for EGFR-TKIs. In this study, we evaluate the expression patterns and potential biological functions of the pseudogene DUXAP10 in gefitinib resistance. We find that pseudogene DUXAP10 expression is significantly upregulated in NSCLC gefitinib-resistant cells and tissues. Gain and loss of function assays reveal that knockdown of DUXAP10 by siRNA reverses gefitinib resistance both in vitro and in vivo. Furthermore, DUXAP10 interacts with the histone methyltransferase enhancer of zeste homolog 2 (EZH2) to repress the expression of 2',5'-oligoadenylate synthetase (OAS2). Overall, our study highlights the pivotal role of DUXAP10 in gefitinib resistance, and the DUXAP10/EZH2/OAS2 axis might be a promising therapeutic target to overcome acquired gefitinib resistance in NSCLC.
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Affiliation(s)
- Shengnan Ren
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Department of OncologySir Run Run HospitalNanjing Medical UniversityNanjing210011China
| | - Ya Zhu
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Siying Wang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Qinqiu Zhang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Niu Zhang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Xiaoteng Zou
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Chenchen Wei
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Zhaoxia Wang
- Cancer Medical Centerthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
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Li S, Shen S, Ge W, Cen Y, Zhang S, Cheng X, Wang X, Xie X, Lu W. Long non-coding RNA SLC25A21-AS1 inhibits the development of epithelial ovarian cancer by specifically inducing PTBP3 degradation. Biomark Res 2023; 11:12. [PMID: 36717926 PMCID: PMC9885650 DOI: 10.1186/s40364-022-00432-x] [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: 08/25/2022] [Accepted: 11/03/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Epithelial ovarian cancer (EOC) is a highly prevalent disease that rapidly metastasizes and has poor prognosis. Most women are in the middle or late stages when diagnosed and have low survival rates. Recently, long non-coding RNAs (lncRNAs) were recognized to play pivotal roles in the development of EOC. METHODS The expression of SLC25A21 antisense RNA 1 (SLC25A21-AS1) and Polypyrimidine Tract Binding Protein 3 (PTBP3) in EOC cells was assessed via qPCR. The proliferation activity of these cells was detected by EdU and Cell counting kit-8 (CCK8) assays, while the death rate of apoptotic cells and the cell cycle were detected by flow cytometry. Detection of cell transfer rate by transwell assay. Protein expression was measured through western blotting. Interactions between SLC25A21-AS1 and PTBP3 were detected through RNA immunoprecipitation (RIP), IF-FISH co-localization experiments and electrophoretic mobility shift assay (EMSA). The in vivo importance of SLC25A21-AS1 as a tumor suppressor modulator was assessed using murine xenograft models. RESULTS The lncRNA SLC25A21-AS1 has negligible expression in ovarian cancer tissues compared with that in normal ovarian tissues. A series of functional experiments revealed that the upregulation of SLC25A21-AS1 markedly blocked the proliferation and metastasis of EOC cells in vitro, while its downregulation had the opposite effect. Overexpression of SLC25A21-AS1 in a nude mouse model of EOC in vivo resulted in slower tumor growth and weakened metastatic potential. Moreover, SLC25A21-AS1 reduced the protein stability of PTBP3 and promoted its degradation. A series of subsequent experiments found that SLC25A21-AS1 inhibits EOC cell proliferation and metastasis by modulating PTBP3 through the ubiquitin-proteasome pathway and that the combination of SLC25A21-AS1 and PTBP3 provides the necessary conditions for the for the function to be realized. CONCLUSIONS Our research reveals the effect of SLC25A21-AS1 in EOC development and suggests SLC25A21-AS1 can serve as a prognostic target by promoting the degradation of PTBP3 to improve patient survival.
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Affiliation(s)
- Sihui Li
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Shizhen Shen
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Wanzhong Ge
- grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, 310058 China ,grid.13402.340000 0004 1759 700XDivision of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XInstitute of Genetics, Zhejiang University, Hangzhou, 310058 China
| | - Yixuan Cen
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Songfa Zhang
- grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology; Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Xiaodong Cheng
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology; Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Xinyu Wang
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology; Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Xing Xie
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology; Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006 China
| | - Weiguo Lu
- grid.13402.340000 0004 1759 700XWomen’s Reproductive Health Laboratory of Zhejiang Province; Women’s Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XDepartment of Gynecologic Oncology; Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, 310058 China
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9
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Qu Q, Liu L, Cui Y, Chen Y, Wang Y, Wang Y. Exosomes from Human Omental Adipose-Derived Mesenchymal Stem Cells Secreted into Ascites Promote Peritoneal Metastasis of Epithelial Ovarian Cancer. Cells 2022; 11:3392. [PMID: 36359787 PMCID: PMC9655202 DOI: 10.3390/cells11213392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 03/26/2024] Open
Abstract
Epithelial ovarian cancer (EOC) patients frequently develop peritoneal metastasis, especially in the human omentum. However, the mechanism underlying this propensity remains unknown. A previous study found that human omental adipose-derived mesenchymal stem cells are potentially involved in ovarian cancer growth and metastasis, but the results were inconsistent and even contradictory. In addition, the underlying mechanisms of visceral adipose metastasis remain poorly understood. Here, our goal is to clarify the role and mechanism of human omental adipose-derived mesenchymal stem cells (HO-ADSCs) in EOC cancer growth and metastasis. We first found that human omental tissue conditioned medium (HO-CM) enhances EOC cell function. Subsequent coculture studies indicated that HO-ADSCs increase the growth, migratory and invasive capabilities of ovarian cancer cells. Then, we demonstrated that exosomes secreted by HO-ADSCs (HO-ADSC exosomes) enhanced ovarian cancer cell function, and further mechanistic studies showed that the FOXM1, Cyclin F, KIF20A, and MAPK signaling pathways were involved in this process. In addition, subcutaneous tumorigenesis and peritoneal metastatic xenograft experiments provided evidence that HO-ADSC exosomes promote ovarian cancer growth and metastasis in vivo. Finally, our clinical studies provided evidence that ascites from ovarian cancer patients enhance EOC cell line proliferation, migration, and invasion in vitro. The present study indicated that HO-ADSC exosomes are secreted into ascites and exert a tumor-promoting effect on EOC growth and metastasis, providing a new perspective and method to develop future novel therapeutic strategies for the treatment of ovarian cancer.
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Affiliation(s)
- Qingxi Qu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Linghong Liu
- Research Center of Stem Cell and Regenerative Medicine, Shandong University, Jinan 250012, China
- Laboratory of Cryomedicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yuqian Cui
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yu Chen
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yaodu Wang
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, China
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10
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Wang L, Zhang J, Xia M, Liu C, Zu X, Zhong J. High Mobility Group A1 (HMGA1): Structure, Biological Function, and Therapeutic Potential. Int J Biol Sci 2022; 18:4414-4431. [PMID: 35864955 PMCID: PMC9295051 DOI: 10.7150/ijbs.72952] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
High mobility group A1 (HMGA1) is a nonhistone chromatin structural protein characterized by no transcriptional activity. It mainly plays a regulatory role by modifying the structure of DNA. A large number of studies have confirmed that HMGA1 regulates genes related to tumours in the reproductive system, digestive system, urinary system and haematopoietic system. HMGA1 is rare in adult cells and increases in highly proliferative cells such as embryos. After being stimulated by external factors, it will produce effects through the Wnt/β-catenin, PI3K/Akt, Hippo and MEK/ERK pathways. In addition, HMGA1 also affects the ageing, apoptosis, autophagy and chemotherapy resistance of cancer cells, which are linked to tumorigenesis. In this review, we summarize the mechanisms of HMGA1 in cancer progression and discuss the potential clinical application of targeted HMGA1 therapy, indicating that targeted HMGA1 is of great significance in the diagnosis and treatment of malignancy.
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Affiliation(s)
- Lu Wang
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Ji Zhang
- Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518033, Guangdong, China
| | - Min Xia
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Chang Liu
- Department of Endocrinology and Metabolism, The First People's Hospital of Chenzhou, First School of Clinical Medicine, University of Southern Medical, Guangzhou 510515, Guangdong, China
| | - Xuyu Zu
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Jing Zhong
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.,Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
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11
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Nsengimana B, Khan FA, Awan UA, Wang D, Fang N, Wei W, Zhang W, Ji S. Pseudogenes and Liquid Phase Separation in Epigenetic Expression. Front Oncol 2022; 12:912282. [PMID: 35875144 PMCID: PMC9305658 DOI: 10.3389/fonc.2022.912282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Pseudogenes have been considered as non-functional genes. However, peptides and long non-coding RNAs produced by pseudogenes are expressed in different tumors. Moreover, the dysregulation of pseudogenes is associated with cancer, and their expressions are higher in tumors compared to normal tissues. Recent studies show that pseudogenes can influence the liquid phase condensates formation. Liquid phase separation involves regulating different epigenetic stages, including transcription, chromatin organization, 3D DNA structure, splicing, and post-transcription modifications like m6A. Several membrane-less organelles, formed through the liquid phase separate, are also involved in the epigenetic regulation, and their defects are associated with cancer development. However, the association between pseudogenes and liquid phase separation remains unrevealed. The current study sought to investigate the relationship between pseudogenes and liquid phase separation in cancer development, as well as their therapeutic implications.
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Affiliation(s)
- Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- School of Life Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Usman Ayub Awan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, Pakistan
| | - Dandan Wang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Na Fang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wenqiang Wei
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
| | - Weijuan Zhang
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- *Correspondence: Wenqiang Wei, ; Weijuan Zhang, ; Shaoping Ji,
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12
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HMGA1 Promotes Macrophage Recruitment via Activation of NF-κB-CCL2 Signaling in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:4727198. [PMID: 35785026 PMCID: PMC9242763 DOI: 10.1155/2022/4727198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Background Tumor-associated macrophages (TAMs) are known to generate an immune-suppressive tumor microenvironment (TME) and promote tumor progression. Hepatocellular carcinoma (HCC) is a devastating disease that evolves in the background of chronic inflammatory liver damage. In this study, we aimed to uncover the mechanism by which HCC cells recruit macrophages into the TME. Methods Bioinformatic analysis was performed to identify differentially expressed genes related to macrophage infiltration. An orthotopic HCC xenograft model was used to determine the role of macrophages in HCC tumor growth. Clodronate liposomes were used to delete macrophages. Western blotting analysis, quantitative real-time PCR, and enzyme-linked immunosorbent assay were performed to determine the underlying mechanisms. Results The high mobility group A1 (HMGA1) gene was identified as a putative modulator of macrophage infiltration in HCC. Deletion of macrophages with clodronate liposomes significantly abrogated the tumor-promoting effects of HMGA1 on HCC growth. Mechanistically, HMGA1 can regulate the expression of C-C Motif Chemokine Ligand 2 (CCL2), also referred to as monocyte chemoattractant protein 1 (MCP1), which is responsible for macrophage recruitment. Moreover, NF-κB was required for HMGA1-mediated CCL2 expression. Pharmacological or genetic inhibition of NF-κB largely blocked CCL2 levels in HMGA1-overexpressing HCC cells. Conclusions This study reveals HMGA1 as a crucial regulator of macrophage recruitment by activating NF-κB-CCL2 signaling, proves that HMGA1-induced HCC aggressiveness dependents on the macrophage, and provide an attractive target for therapeutic interventions in HCC.
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De Martino M, Pellecchia S, Esposito F, Tosti N, Quintavalle C, Eppenberger-Castori S, Carafa V, Righi A, Chieffi P, Fusco A, Terracciano LM, Pallante P. The role of HMGA1 protein in gastroenteropancreatic neuroendocrine tumors. Cell Cycle 2022; 21:1335-1346. [PMID: 35282770 PMCID: PMC9132388 DOI: 10.1080/15384101.2022.2050646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Neuroendocrine tumors (NETs) are neoplasms derived from neuroendocrine cells. One of their main features is to often remain asymptomatic and clinically undetectable. High Mobility Group A (HMGA) proteins belong to a family of non-histone chromatinic proteins able to modulate gene expression through the interaction with DNA and transcription factors. They are overexpressed in most of the human malignancies, playing a critical role in carcinogenesis. However, their expression levels and their role in neuroendocrine carcinogenesis has not been exhaustively evaluated until now. Therefore, in this study, we have addressed the validity of using the expression of HMGA1 as a diagnostic marker and have investigated its role in NET carcinogenesis. The expression of HMGA1 has been evaluated by qRT-PCR and immunohistochemistry, using NET tissue microarrays, in a cohort of gastroenteropancreatic (GEP)-NET samples. The expression levels of HMGA1 have been then correlated with the main clinical features of NET samples. Finally, the contribution of HMGA1 overexpression to NET development has been addressed as far as the modulation of proliferation and migration abilities of NET cells is concerned. Here, we report that HMGA1 is overexpressed in GEP-NET samples, at both mRNA and protein levels, and that the silencing of HMGA1 protein expression interferes with the ability of NET cells to proliferate and migrate through the downregulation of Cyclin E, Cyclin B1 and EZH2. These results propose the HMGA proteins as new diagnostic and prognostic markers.
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Affiliation(s)
- Marco De Martino
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy
| | - Simona Pellecchia
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy
| | - Francesco Esposito
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy
| | - Nadia Tosti
- Institute of Pathology, Molecular Pathology Division, University of Basel, Basel, Switzerland
| | - Cristina Quintavalle
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy.,Institute of Pathology, Molecular Pathology Division, University of Basel, Basel, Switzerland
| | | | - Vincenza Carafa
- Institute of Pathology, Molecular Pathology Division, University of Basel, Basel, Switzerland
| | - Alberto Righi
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Paolo Chieffi
- Department of Psychology, University of Campania "L. Vanvitelli", Caserta, Italy
| | - Alfredo Fusco
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Naples, Italy
| | - Luigi Maria Terracciano
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Department of Pathology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Pierlorenzo Pallante
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore", National Research Council (CNR), Naples, Italy
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14
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Mao S, Mo Z, Wu R, Lai B, Zhou Z, Song Y, Ouyang X, Zhu X. The double homeobox a pseudogene 8 accelerates cell proliferation, migration, and invasion in colon cancer. Bioengineered 2022; 13:8164-8173. [PMID: 35287542 PMCID: PMC9161926 DOI: 10.1080/21655979.2022.2053802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/11/2022] Open
Abstract
Double homeobox A pseudogene 8 (DUXAP8) is a known tumor promoter in several malignancies. Nonetheless, its function in colon cancer (CC) is indefinite. Herein, we explored the significance of DUXAP8 and its underlying mechanism in CC. Our data indicated that DUXAP8 was upregulated in CC, and it was related to advanced stages and lymph node metastases. Based on our Kaplan-Meier survival analysis, elevated DUXAP8 expression resulted in shorter patient overall survival (OS). Conversely, DUXAP8 silencing strongly suppressed cellular proliferation, migration and invasion in vitro. Based on our western blot analysis, DUXAP8 deficiency strongly inhibited the epithelial-mesenchymal transition (EMT) in vitro. Alternately, DUXAP8 overexpression accelerated cellular proliferation migration and invasion in CC. Finally, silencing DUXAP8 prevented tumorigenesis in a mouse xenograft model in vivo. Collectively, our results demonstrated that DUXAP8 regulates the occurrence and advancement of CC, and may serve as a regulatory hub for this disease.
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Affiliation(s)
- Shengxun Mao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaohong Mo
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Runxin Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Bin Lai
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhiyong Zhou
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Song
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xi Ouyang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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15
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Stasiak M, Kolenda T, Kozłowska-Masłoń J, Sobocińska J, Poter P, Guglas K, Paszkowska A, Bliźniak R, Teresiak A, Kazimierczak U, Lamperska K. The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules? Life (Basel) 2021; 11:life11121354. [PMID: 34947885 PMCID: PMC8705536 DOI: 10.3390/life11121354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.
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Affiliation(s)
- Maciej Stasiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
| | - Joanna Kozłowska-Masłoń
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Joanna Sobocińska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Paulina Poter
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Greater Poland Cancer Center, Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Kacper Guglas
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki and Wigury, 02-091 Warsaw, Poland
| | - Anna Paszkowska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Renata Bliźniak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland;
| | - Katarzyna Lamperska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
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16
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Song J, Cui D, Wang J, Qin J, Wang S, Wang Z, Zhai X, Ma H, Ma D, Liu Y, Jin B, Liu Z. Overexpression of HMGA1 confers radioresistance by transactivating RAD51 in cholangiocarcinoma. Cell Death Discov 2021; 7:322. [PMID: 34716319 PMCID: PMC8556338 DOI: 10.1038/s41420-021-00721-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/02/2021] [Accepted: 10/13/2021] [Indexed: 01/16/2023] Open
Abstract
Cholangiocarcinomas (CCAs) are rare but aggressive tumors of the bile ducts. CCAs are often diagnosed at an advanced stage and respond poorly to current conventional radiotherapy and chemotherapy. High mobility group A1 (HMGA1) is an architectural transcription factor that is overexpressed in multiple malignant tumors. In this study, we showed that the expression of HMGA1 is frequently elevated in CCAs and that the high expression of this gene is associated with a poor prognosis. Functionally, HMGA1 promotes CCA cell proliferation/invasion and xenograft tumor growth. Furthermore, HMGA1 transcriptionally activates RAD51 by binding to its promoter through two HMGA1 response elements. Notably, overexpression of HMGA1 promotes radioresistance whereas its knockdown causes radiosensitivity of CCA cells to X-ray irradiation. Moreover, rescue experiments reveal that inhibition of RAD51 reverses the effect of HMGA1 on radioresistance and proliferation/invasion. These findings suggest that HMGA1 functions as a novel regulator of RAD51 and confers radioresistance in cholangiocarcinoma.
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Affiliation(s)
- Jianping Song
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China.,Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Donghai Cui
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Jing Wang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Junchao Qin
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Shourong Wang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Zixiang Wang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Xiangyu Zhai
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Huan Ma
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Delin Ma
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China
| | - Yanfeng Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China.
| | - Bin Jin
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China. .,Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China.
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, 250012, Jinan, Shandong Province, China.
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Chen X, Chen Z, Wu H, Liu X, Nie F, Wang Z, Sun M. Comprehensive Genomic Characterization Analysis Identifies an Oncogenic Pseudogene RP11-3543B.1 in Human Gastric Cancer. Front Cell Dev Biol 2021; 9:743652. [PMID: 34660601 PMCID: PMC8511815 DOI: 10.3389/fcell.2021.743652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Gastrointestinal Cancer (GICs) is the most common group of malignancies, and many of its types are the leading causes of cancer related death worldwide. Pseudogenes have been revealed to have critical regulatory roles in human cancers. The objective of this study is to comprehensive characterize the pseudogenes expression profiling and identify key pseudogenes in the development of gastric cancer (GC). Methods: The pseudogenes expression profiling was analyzed in six types of GICs cancer from The Cancer Genome Atlas RNA-seq data to identify GICs cancer related pseudogenes. Meanwhile, the genomic characterization including somatic alterations of pseudogenes was analyzed. Then, CCK8 and colony formation assays were performed to evaluate the biological function of RP11-3543B.1 and miR-145 in gastric cancer cells. The mechanisms of pseudogene RP11-3543B.1 in GC cells were explored via using bioinformatics analysis, next generation sequencing and lucifarese reporter assay. Results: We identified a great number of pseudogenes with significantly altered expression in GICs, and some of these pseudogenes expressed differently among the six cancer types. The amplification or deletion in the pseudogenes-containing loci involved in the alterations of pseudogenes expression in GICs. Among these altered pseudogenes, RP11-3543B.1 is significantly upregulated in gastric cancer. Down-regulation of RP11-3543B.1 expression impaired GC cells proliferation both in vitro and in vivo. RP11-3543B.1 exerts oncogene function via targeting miR-145-5p to regulate MAPK4 expression in gastric cancer cells. Conclusion: Our study reveals the potential of pseudogenes expression as a new paradigm for investigating GI cancer tumorigenesis and discovering prognostic biomarkers for patients.
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Affiliation(s)
- Xin Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenyao Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xianghua Liu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Fengqi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhaoxia Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ming Sun
- Suzhou Cancer Center Core Laboratory, Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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18
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Ovarian Cancer Risk Scores Based on Immune-Related Pseudogenes to Predict Overall Survival and Guide Immunotherapy and Chemotherapy. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:1586312. [PMID: 34659427 PMCID: PMC8519701 DOI: 10.1155/2021/1586312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022]
Abstract
Background Ovarian cancer (OC) is the top of the aggressive malignancies in females with a poor survival rate. However, the roles of immune-related pseudogenes (irPseus) in the immune infiltration of OC and the impact on overall survival (OS) have not been adequately studied. Therefore, this study aims to identify a novel model constructed by irPseus to predict OS in OC and to determine its significance in immunotherapy and chemotherapy. Methods In this study, with the use of The Cancer Genome Atlas (TCGA) combined with Genotype-Tissue Expression (GTEx), 55 differentially expressed irPseus (DEirPseus) were identified. Then, we constructed 10 irPseus pairs with the help of univariate, Lasso, and multivariate Cox regression analysis. The prognostic performance of the model was determined and measured by the Kaplan-Meier curve, a time-dependent receiver operating characteristic (ROC) curve. Results After dividing OC subjects into high- and low-risk subgroups via the cut-off point, it was revealed that subjects in the high-risk group had a shorter OS. The multivariate Cox regression performed between the model and multiple clinicopathological variables revealed that the model could effectively and independently predict the prognosis of OC. The prognostic model characterized infiltration by various kinds of immune cells and demonstrated the immunotherapy response of subjects with cytotoxic lymphocyte antigen 4 (CTLA4), anti-programmed death-1 (PD-1), and anti-PD-ligand 1 (PD-L1) therapy. A high risk score was related to a higher inhibitory concentration (IC50) for etoposide (P=0.0099) and mitomycin C (P=0.0013). Conclusion It was the first study to identify a novel signature developed by DEirPseus pairs and verify the role in predicting OS, immune infiltrates, immunotherapy, and chemosensitivity. The irPseus are vital factors predicting the prognosis of OC and could act as a novel potential treatment target.
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Ye M, Lin Y, Pan S, Wang ZW, Zhu X. Applications of Multi-omics Approaches for Exploring the Molecular Mechanism of Ovarian Carcinogenesis. Front Oncol 2021; 11:745808. [PMID: 34631583 PMCID: PMC8497990 DOI: 10.3389/fonc.2021.745808] [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: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. The molecular mechanisms of ovarian carcinogenesis need to be explored in order to identify effective clinical therapies for ovarian cancer. Recently, multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (metabolites) levels. Multi-omics approaches can identify some diagnostic and prognostic biomarkers and therapeutic targets for ovarian cancer, and these molecular signatures are beneficial for clarifying the development and progression of ovarian cancer. Moreover, the discovery of molecular signatures and targeted therapy strategies could noticeably improve the prognosis of ovarian cancer patients.
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Affiliation(s)
| | | | | | - Zhi-wei Wang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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20
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Wang Y, Yu G, Liu Y, Xie L, Ge J, Zhao G, Lin J. Hypoxia-induced PTTG3P contributes to colorectal cancer glycolysis and M2 phenotype of macrophage. Biosci Rep 2021; 41:BSR20210764. [PMID: 34132347 PMCID: PMC8264182 DOI: 10.1042/bsr20210764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical factors in tumor progression and are ectopically expressed in malignant tumors. Until now, lncRNA pituitary tumor-transforming 3, pseudogene (PTTG3P) biological function in colorectal cancer (CRC) further needs to be clarified. qRT-PCR was used to measure the PTTG3P level and CCK-8, glucose uptake, lactate assay, adenosine triphosphate (ATP) assay, extracellular acidification rate (ECAR) assay, and xenograft mice model were adopted to evaluate the glycolysis and proliferation, and macrophage polarization were determined in CRC cells. Xenograft experiments were utilized to analyze tumor growth. Ectopic expression of PTTG3P was involved in CRC and related to dismal prognosis. Through gain- and loss-of-function approaches, PTTG3P enhanced cell proliferation and glycolysis through YAP1. Further, LDHA knockdown or glycolysis inhibitor (2-deoxyglucose (2-DG), 3-BG) recovered from PTTG3P-induced proliferation. And PTTG3P overexpression could facilitate M2 polarization of macrophages. Silenced PTTG3P decreased the level of inflammatory cytokines TNF-α, IL-1β and IL-6, and low PTTG3P expression related with CD8+ T, NK, and TFH cell infiltration. Besides, hypoxia-inducible factor-1α (HIF1A) could increase PTTG3P expression by binding to the PTTG3P promoter region. Hypoxia-induced PTTG3P contributes to glycolysis and M2 phenotype of macrophage, which proposes a novel approach for clinical treatment.
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Affiliation(s)
- Yue Wang
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Liaoning 110042, P.R. China
| | - Guilin Yu
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Liaoning 110042, P.R. China
| | - Yiyang Liu
- Department of Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, 533000, Guangxi Zhuang Autonomous Region, P.R. China
| | - Longfei Xie
- Department of Physics and Integrative Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Jinnian Ge
- Department of General Surgery, The Central Hospital of Shenyang Medical College, Liaoning 110031, P.R. China
| | - Guohua Zhao
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Liaoning 110042, P.R. China
| | - Jie Lin
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Liaoning 110042, P.R. China
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21
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Norcantharidin-blocked ANXA2P2 inhibits fibroblast proliferation by increasing UBAP2L mRNA stability through LIN28B. Life Sci 2021; 279:119645. [PMID: 34043991 DOI: 10.1016/j.lfs.2021.119645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/28/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022]
Abstract
AIMS Norcantharidin (NCTD) exhibits antitumor, anti-inflammatory, and anti-fibrosis properties, which makes NCTD an attractive candidate for the treatment of pathological scars. This study was designed to investigate the potential effects of NCTD on fibroblast proliferation and explore the underlying mechanisms. MATERIALS AND METHODS First, cell viability and cell apoptosis were evaluated to determine the effects of NCTD on human skin fibroblasts, at 10, 50, and 100 μM. To explore the mechanism, bioinformatics analyses, chromatin immunoprecipitation, RNA immunoprecipitation, and RNA pulldown assays, and luciferase reporter assays were performed to verify the relationships among NCTD, signal transducer and activator of transcription 3 (STAT3), annexin A2 pseudogene 2 (ANXA2P2), and ubiquitin-associated protein 2-like (UBAP2L) mRNA in fibroblasts. Loss-of-function experiments were performed to investigate the roles played by STAT3, ANXA2P2, and UBAP2L in the proliferation and apoptosis of fibroblasts. KEY FINDINGS We found that NCTD administration induced fibroblast apoptosis and inhibited fibroblast proliferation in a dose-dependent manner. Mechanistically, NCTD inhibited ANXA2P2 transcription through the inhibition of STAT3 phosphorylation. Subsequently, ANXA2P2 was found to enhance the physical interaction between UBAP2L mRNA and lin-28 homolog B (LIN28B), which increased the stability and levels of UBAP2L mRNA. Loss-of-function assays demonstrated that ANXA2P2 and UBAP2L knockdown induced fibroblast apoptosis and suppressed fibroblast proliferation. SIGNIFICANCE In conclusion, we confirmed that NCTD inhibits fibroblast proliferation by inhibiting the STAT3/ANXA2P2/UBAP2L axis, which suggested that NCTD could represent a new candidate for the treatment of pathological scars.
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Zhang X, Deng HW, Shen H, Ehrlich M. Prioritization of Osteoporosis-Associated Genome-wide Association Study (GWAS) Single-Nucleotide Polymorphisms (SNPs) Using Epigenomics and Transcriptomics. JBMR Plus 2021; 5:e10481. [PMID: 33977200 PMCID: PMC8101624 DOI: 10.1002/jbm4.10481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/10/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic risk factors for osteoporosis, a prevalent disease associated with aging, have been examined in many genome-wide association studies (GWASs). A major challenge is to prioritize transcription-regulatory GWAS-derived variants that are likely to be functional. Given the critical role of epigenetics in gene regulation, we have used an unusual epigenetics-based and transcription-based approach to identify some of the credible regulatory single-nucleotide polymorphisms (SNPs) relevant to osteoporosis from 38 reported bone mineral density (BMD) GWASs. Using Roadmap databases, we prioritized SNPs based upon their overlap with strong enhancer or promoter chromatin preferentially in osteoblasts relative to 12 heterologous cell culture types. We also required that these SNPs overlap open chromatin (Deoxyribonuclease I [DNaseI]-hypersensitive sites) and DNA sequences predicted to bind to osteoblast-relevant transcription factors in an allele-specific manner. From >50,000 GWAS-derived SNPs, we identified 14 novel and credible regulatory SNPs (Tier-1 SNPs) for osteoporosis risk. Their associated genes, BICC1, LGR4, DAAM2, NPR3, or HMGA2, are involved in osteoblastogenesis or bone homeostasis and regulate cell signaling or enhancer function. Four of these genes are preferentially expressed in osteoblasts. BICC1, LGR4, and DAAM2 play important roles in canonical Wnt signaling, a pathway critical for bone formation and repair. The transcription factors predicted to bind to the Tier-1 SNP-containing DNA sequences also have bone-related functions. We present evidence that some of the Tier-1 SNPs exert their effects on BMD risk indirectly through little-studied long noncoding RNA (lncRNA) genes, which may, in turn, control the nearby bone-related protein-encoding gene. Our study illustrates a method to identify novel BMD-related causal regulatory SNPs for future study and to prioritize candidate regulatory GWAS-derived SNPs, in general. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Xiao Zhang
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine Tulane University New Orleans LA USA.,Tulane Cancer Center and Hayward Genetics Center Tulane University New Orleans LA USA
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23
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De Martino M, Esposito F, Fusco A. The HMGA1-pseudogene7 shows oncogenic activity in vivo. Cell Cycle 2020; 19:2955-2959. [PMID: 33043837 DOI: 10.1080/15384101.2020.1829825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
We have recently reported that transgenic mice overexpressing the HMGA1-pseudogene7 develop hematological neoplasia marked by monoclonal B-cell populations, and diagnosed as Diffuse Large B-cell Lymphoma. These findings prove the HMGA1-pseudogene7 oncogenic role in vivo.
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Affiliation(s)
- Marco De Martino
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli "Federico II" , Naples, Italy
| | - Francesco Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli "Federico II" , Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale - CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli "Federico II" , Naples, Italy
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24
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Yang M, Guo Y, Liu X, Liu N. HMGA1 Promotes Hepatic Metastasis of Colorectal Cancer by Inducing Expression of Glucose Transporter 3 (GLUT3). Med Sci Monit 2020; 26:e924975. [PMID: 32989212 PMCID: PMC7532698 DOI: 10.12659/msm.924975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers worldwide, and more than half of CRC patients have CRC liver metastasis (CRCLM). Mounting evidence indicates that high mobility group protein A1(HMGA1) is overexpressed in many cancer types, but its role in CRCLM has been obscure. Material/Methods Using immunohistochemistry, we assessed the expression of HMGA1 in 73 patients with CRCLM, and compared HMGA1 mRNA in 17 pairs of CRCs, CRCLM tissues, and normal liver tissues. The clinical significance of HMGA1 was evaluated by analyzing its correlation with the clinicopathological factors and overall survival (OS) rates. The function of HMGA1 in CRC invasion was investigated and the underlying mechanism of HMGA1-induced invasion was explored with in vitro experiments. Results In CRCLMs, the high-HMGA1 and low-HMGA1 patients accounted for 53.42% and 46.58% of all patients, respectively. High HMGA1 expression in CRCLM was significantly associated with low OS rates. In vitro experiments demonstrated that HMGA1 promoted glucose transporter 3 (GLUT3) transcription and expression in CRC cells. GLUT3 was required in HMGA1-involved invasion, and GLUT3 expression was associated with poor prognosis of CRCLM. Conclusions High HMGA1 and GLUT3 expression in CRCLM was significantly correlated with poor prognosis of CRCLM. HMGA1 promoted CRC invasion by elevating GLUT3 transcription and expression.
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Affiliation(s)
- Meijing Yang
- Department of Geriatrics, YIDU Central Hospital, Weifang, Shandong, China (mainland)
| | - Yang Guo
- Department of Geriatrics, YIDU Central Hospital, Weifang, Shandong, China (mainland)
| | - Xiaoyun Liu
- Department of Cardiology, YIDU Central Hospital, Weifang, Shandong, China (mainland)
| | - Naiqing Liu
- Department of General Surgery, Linyi Central Hospital, Linyi, Shandong, China (mainland)
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25
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Lin W, Liu H, Tang Y, Wei Y, Wei W, Zhang L, Chen J. The development and controversy of competitive endogenous RNA hypothesis in non-coding genes. Mol Cell Biochem 2020; 476:109-123. [PMID: 32975695 DOI: 10.1007/s11010-020-03889-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
As a momentous post-transcriptional regulator, microRNAs (miRNAs) are attracting more and more attention. The classical miRNAs regulated mechanism shows it binds to the targets' 3'UTR thus play the role in post-transcription. Meanwhile, single miRNA can target multiple genes, so those should compete to bind that miRNA. Vice versa, single gene can sponge mass of miRNAs as well. Thus the competitive endogenous RNAs (ceRNAs) hypothesis was put forward in 2011. The ceRNA hypothesis has made huge achievements, in particular in non-coding genes, which including long non-coding RNAs (lncRNAs), circle RNAs (circRNAs) and pseudogenes, even viral transcripts. It also contributed greatly to epigenetics development. However, an increasing number of controversies have occurred with applause. Based on this situation, this review introduces something in detail about the ceRNAs hypothesis achieved in lncRNAs, circRNAs, pseudogenes and viral transcripts, respectively. Meanwhile, it also covers controversy of the ceRNAs hypothesis.
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Affiliation(s)
- Weimin Lin
- Nanjing Agricultural University, Nanjing, China
| | | | | | - Yuchen Wei
- Nanjing Agricultural University, Nanjing, China
| | - Wei Wei
- Nanjing Agricultural University, Nanjing, China
| | - Lifan Zhang
- Nanjing Agricultural University, Nanjing, China
| | - Jie Chen
- Nanjing Agricultural University, Nanjing, China.
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De Martino M, Palma G, Arra C, Chieffi P, Fusco A, Esposito F. Characterization of HMGA1P6 transgenic mouse embryonic fibroblasts. Cell Cycle 2020; 19:2281-2285. [PMID: 32787507 DOI: 10.1080/15384101.2020.1807080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Latest studies have shown that deregulated pseudogene transcripts contribute to cancer working as competing endogenous RNAs. Our research group has recently demonstrated that the overexpression of two HMGA1 pseudogenes, HMGA1P6 and HMGA1P7, has a critical role in cancer progression. These pseudogenes work sustaining the expression of HMGA1 and other cancer-related genes. We generated a mouse model overexpressing HMGA1P6 to better study the HMGA1-pseudogene function in a more physiological context. Here, we show the proliferation rate and the susceptibility to senescence of mouse embryonic fibroblasts obtained from HMGA1P6-overexpressing mice to better characterize the HMGA1-pseudogene function. Indeed, our study reports that mouse embryonic fibroblasts (MEFs) derived from HMGA1P6 mice express higher HMGA1 mRNA and protein levels. Moreover, these cells grow faster and senesce later than wild-type sustaining the oncogenic role of ceRNA crosstalk mediated by HMGA1Ps.
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Affiliation(s)
- Marco De Martino
- Istituto di Endocrinologia Ed Oncologia Sperimentale del CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi Di Napoli "Federico II" , Naples, Italy.,Department of Psychology, University of Campania "L. Vanvitelli" , Caserta, Italy
| | - Giuseppe Palma
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale dei Tumori, Fondazione Pascale, IRCCS , Naples, Italy
| | - Claudio Arra
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale dei Tumori, Fondazione Pascale, IRCCS , Naples, Italy
| | - Paolo Chieffi
- Department of Psychology, University of Campania "L. Vanvitelli" , Caserta, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia Ed Oncologia Sperimentale del CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi Di Napoli "Federico II" , Naples, Italy
| | - Francesco Esposito
- Istituto di Endocrinologia Ed Oncologia Sperimentale del CNR C/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi Di Napoli "Federico II" , Naples, Italy
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