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Zhang R, Dai J, Yao F, Zhou S, Huang W, Xu J, Yu K, Chen Y, Fan B, Zhang L, Xu J, Li Q. Hypomethylation-enhanced CRTC2 expression drives malignant phenotypes and primary resistance to immunotherapy in hepatocellular carcinoma. iScience 2024; 27:109821. [PMID: 38770131 PMCID: PMC11103543 DOI: 10.1016/j.isci.2024.109821] [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: 07/19/2023] [Revised: 11/22/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
The cyclic AMP-responsive element-binding protein (CREB)-regulated transcription coactivator 2 (CRTC2) is a crucial regulator of hepatic lipid metabolism and gluconeogenesis and correlates with tumorigenesis. However, the mechanism through which CRTC2 regulates hepatocellular carcinoma (HCC) progression is largely unknown. Here, we found that increased CRTC2 expression predicted advanced tumor grade and stage, as well as worse prognosis in patients with HCC. DNA promoter hypomethylation led to higher CRTC2 expression in HCC. Functionally, CRTC2 contributed to HCC malignant phenotypes through the activated Wnt/β-catenin pathway, which could be abrogated by the small-molecular inhibitor XAV-939. Moreover, Crtc2 facilitated tumor growth while concurrently downregulating the PD-L1/PD-1 axis, resulting in primary resistance to immunotherapy. In immunocompetent mice models of HCC, targeting Crtc2 in combination with anti-PD-1 therapy prominently suppressed tumor growth by synergistically enhancing responsiveness to immunotherapy. Collectively, targeting CRTC2 might be a promising therapeutic strategy to sensitize immunotherapy in HCC.
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Affiliation(s)
- Ruizhi Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
| | - Jingjing Dai
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210000, China
| | - Feifan Yao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
| | - Suiqing Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
| | - Wei Huang
- Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili 835000, China
| | - Jiali Xu
- Department of Anesthesiology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province 210000, China
| | - Kai Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
| | - Yining Chen
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210000, China
| | - Boqiang Fan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210000, China
| | - Liren Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
| | - Jing Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210000, China
| | - Qing Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Hepatobiliary Cancers, Nanjing, Jiangsu Province 210000, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province 210000, China
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2
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Fang M, Deibler SK, Nana AL, Vatsavayai SC, Banday S, Zhou Y, Almeida S, Weiss A, Brown RH, Seeley WW, Gao FB, Green MR. Loss of TDP-43 function contributes to genomic instability in amyotrophic lateral sclerosis. Front Neurosci 2023; 17:1251228. [PMID: 37849894 PMCID: PMC10577185 DOI: 10.3389/fnins.2023.1251228] [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: 07/01/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023] Open
Abstract
A common pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the cytoplasmic mislocalization and aggregation of the DNA/RNA-binding protein TDP-43, but how loss of nuclear TDP-43 function contributes to ALS and FTD pathogenesis remains largely unknown. Here, using large-scale RNAi screening, we identify TARDBP, which encodes TDP-43, as a gene whose loss-of-function results in elevated DNA mutation rate and genomic instability. Consistent with this finding, we observe increased DNA damage in induced pluripotent stem cells (iPSCs) and iPSC-derived post-mitotic neurons generated from ALS patients harboring TARDBP mutations. We find that the increase in DNA damage in ALS iPSC-derived neurons is due to defects in two major pathways for DNA double-strand break repair: non-homologous end joining and homologous recombination. Cells with defects in DNA repair are sensitive to DNA damaging agents and, accordingly, we find that ALS iPSC-derived neurons show a marked reduction in survival following treatment with a DNA damaging agent. Importantly, we find that increased DNA damage is also observed in neurons with nuclear TDP-43 depletion from ALS/FTD patient brain tissues. Collectively, our results demonstrate that ALS neurons with loss of nuclear TDP-43 function have elevated levels of DNA damage and contribute to the idea that genomic instability is a defining pathological feature of ALS/FTD patients with TDP-43 pathology.
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Affiliation(s)
- Minggang Fang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Sara K. Deibler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Alissa L. Nana
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Sarat C. Vatsavayai
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Shahid Banday
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - You Zhou
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - William W. Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Michael R. Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, United States
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3
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Huang K, Wu S, Yang X, Wang T, Liu X, Zhou X, Huang L. CAFuncAPA: a knowledgebase for systematic functional annotations of APA events in human cancers. NAR Cancer 2023; 5:zcad004. [PMID: 36694725 PMCID: PMC9869079 DOI: 10.1093/narcan/zcad004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Alternative polyadenylation (APA) is a widespread posttranscriptional regulation process. APA generates diverse mRNA isoforms with different 3' UTR lengths, affecting mRNA expression, miRNA binding regulation and alternative splicing events. Previous studies have demonstrated the important roles of APA in tumorigenesis and cancer progression through diverse aspects. Thus, a comprehensive functional landscape of diverse APA events would aid in a better understanding of the underlying mechanisms related to APA in human cancers. Here, we built CAFuncAPA (https://relab.xidian.edu.cn/CAFuncAPA/) to systematically annotate the functions of 15478 APA events in human pan-cancers. Specifically, we first identified APA events associated with cancer survival and tumor progression. We annotated the potential downstream effects of APA on genes/isoforms expression, regulation of miRNAs, RNA binding proteins (RBPs) and alternative splicing events. Moreover, we also identified up-regulators of APA events, including the effects of genetic variants on poly(A) sites and RBPs, as well as the effect of methylation phenotypes on APA events. These findings suggested that CAFuncAPA can be a helpful resource for a better understanding of APA regulators and potential functions in cancer biology.
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Affiliation(s)
- Kexin Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Sijia Wu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xiaotong Yang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
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A Pan-Cancer Analysis on the Systematic Correlation of MutS Homolog 2 (MSH2) to a Malignant Tumor. JOURNAL OF ONCOLOGY 2022; 2022:9175402. [PMID: 35368899 PMCID: PMC8970884 DOI: 10.1155/2022/9175402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/18/2022]
Abstract
MutS homolog 2 (MSH2) is a crucial participant in human DNA repair, and lots of the studies functionally associated with it were begun with hereditary nonpolyposis colorectal cancer (HNPCC). MSH2 has also been reported to take part in the progresses of various tumors' formation. With the help of GTEx, CCLE, and TCGA pan-cancer databases, the analysis of MSH2 gene distribution in both tumor tissues and normal control tissues was carried out. Kaplan-Meyer survival plots and COX regression analysis were conducted for the assessment into the MSH2's impact on tumor patients' clinical prognosis. In an investigation to the association of MSH2 expression with immune infiltration level of various tumors and a similar study on tumor immune neoantigens, microsatellite instability was subsequently taken. It was found that high expression of MSH2 is prevalent in most cancers. MSH2's efficacy on clinical prognosis as well as immune infiltration in tumor patients revealed a fact that expression of MSH2 in prostate adenocarcinoma (PRAD), brain lower-grade glioma (LGG), breast-invasive carcinoma (BRCA), and head and neck squamous cell carcinoma (HNSC) posed a significant correlation with the immune cell infiltration level of patients. Likewise as above, MSH2's expression comes in a similar trend with tumor immune neoantigens and microsatellite instability. MSH2's expression in the majority of tumors is a direct factor to the activation of tumor-associated pathways as well as immune-associated pathways. MSH2's early screening or even therapeutic target role for sarcoma (SARC) diagnosis is contributing to the efficiency of early screening and overall survival in SARC patients.
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5
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The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues. Int J Mol Sci 2022; 23:ijms23031103. [PMID: 35163027 PMCID: PMC8834906 DOI: 10.3390/ijms23031103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer cells accumulate epigenomic aberrations that contribute to cancer initiation and progression by altering both the genomic stability and the expression of genes. The awareness of such alterations could improve our understanding of cancer dynamics and the identification of new therapeutic strategies and biomarkers to refine tumor classification and treatment. Formalin fixation and paraffin embedding (FFPE) is the gold standard to preserve both tissue integrity and organization, and, in the last decades, a huge number of biological samples have been archived all over the world following this procedure. Recently, new chromatin immunoprecipitation (ChIP) techniques have been developed to allow the analysis of histone post-translational modifications (PTMs) and transcription factor (TF) distribution in FFPE tissues. The application of ChIP to genome-wide chromatin studies using real archival samples represents an unprecedented opportunity to conduct retrospective clinical studies thanks to the possibility of accessing large cohorts of samples and their associated diagnostic records. However, although recent attempts to standardize have been made, fixation and storage conditions of clinical specimens are still extremely variable and can affect the success of chromatin studies. The procedures introduced in the last few years dealt with this problem proponing successful strategies to obtain high-resolution ChIP profiles from FFPE archival samples. In this review, we compare the different FFPE-ChIP techniques, highlighting their strengths, limitations, common features, and peculiarities, as well as pitfalls and caveats related to ChIP studies in FFPE samples, in order to facilitate their application.
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6
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Zhou R, Chen X, Liang J, Chen Q, Tian H, Yang C, Liu C. A circadian rhythm-related gene signature associated with tumor immunity, cisplatin efficacy, and prognosis in bladder cancer. Aging (Albany NY) 2021; 13:25153-25179. [PMID: 34862329 PMCID: PMC8714136 DOI: 10.18632/aging.203733] [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] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022]
Abstract
Circadian dysregulation involves malignant tumor initiation and progression, but the understanding of circadian rhythm’s roles in bladder cancer (BCa) remains insufficient. The circadian rhythm-related genes were collected and clustered based on the Cancer Genome Atlas (TCGA), and the clustering was significantly associated with the prognosis and risk clinicopathological features. Through genomic difference analysis and gene pairing, a circadian rhythm-related signature was successfully established. Kaplan-Meier survival analysis and time-dependent receiver operating curves displayed that the prognosis model was a reliable prognosis biomarker both in the training cohort (n = 396, P = 2.687e-10) and external validation cohort (n = 224, P = 1.45e-02). The patients with high risk have high immune infiltration and high expression of immune checkpoint genes, which partly account for the poor prognosis. TIDE algorithm and the validation in IMvigor210 cohort indicated that the risk signature was a promising marker for the immunotherapeutic response. The risk model could also predict the therapeutic response of cisplatin, which was validated in the Genomics of Drug Sensitivity in Cancer database (P = 0.0049), TCGA (P = 0.038), and T24 BCa cells treated with cisplatin. The functional enrichment showed the risk model was significantly correlated with some malignant phenotypes, such as angiogenesis, epithelial-mesenchymal transition, and KRAS signaling pathway. Totally, we proposed a novel circadian rhythm-related signature for prognosis evaluation, which also helped to predict the immune infiltration and cisplatin sensitivity in BCa.
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Affiliation(s)
- Ranran Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xinyu Chen
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jingjing Liang
- Department of Cardiology, Shunde Hospital of Southern Medical University, Foshan, China
| | - Qi Chen
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Hu Tian
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Cheng Yang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Cundong Liu
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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7
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A Truncated NRIP1 Mutant Amplifies Microsatellite Instability of Colorectal Cancer by Regulating MSH2/MSH6 Expression, and Is a Prognostic Marker of Stage III Tumors. Cancers (Basel) 2021; 13:cancers13174449. [PMID: 34503257 PMCID: PMC8430632 DOI: 10.3390/cancers13174449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The alteration of mismatch repair (MMR) genes leads to microsatellite instability and plays a key role in colorectal cancer (CRC) pathogenesis and prognosis. The transcription factor NRIP1 is involved in intestinal tumorigenesis and is a good prognostic marker in CRC. In this study, we demonstrate that NRIP1 induces MSH2 and MSH6 MMR gene transcription and reduces microsatellite instability. A dominant-negative truncated NRIP1 mutant amplifies the MMR-deficient phenotype and appears as a key player in MSI-driven tumorigenesis since it significantly correlates with a short overall survival of patients with advanced CRC, especially MLH1-deficient ones. Abstract Microsatellite instability (MSI) is related to the alteration of mismatch repair (MMR) genes and plays a key role in colorectal cancer (CRC) pathogenesis. We previously reported that the transcription factor Nuclear Receptor Interacting Protein 1 (NRIP1) is involved in sporadic intestinal tumorigenesis. The aim of this study was to decipher its role in MSI CRC. By using different mouse models and engineered cell lines, we demonstrated that NRIP1 increased MSH2 and MSH6 MMR gene transcription and mRNA/protein levels. In human CRC cells, NRIP1 expression was associated with decreased MSI and the hypermutator phenotype, and with resistance to chemotherapy drugs. Using a cohort of 194 CRC patients, we detected in 22% of the cases a MSI-induced frameshift mutation in the NRIP1 coding sequence. This genetic alteration generates a truncated protein with a dominant negative activity that increased human CRC cell proliferation and impaired the regulation of MSH2 and MSH6 gene expression. Moreover, the NRIP1 mutant correlated with a decreased overall survival of patients with advanced CRC, especially when MLH1-deficient. By decreasing the expression of MSH2 and MSH6 gene expression, the NRIP1 variant may amplify MLH1-dependent CRC progression and behave as a new prognostic marker of advanced MSI CRC.
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8
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Wang Y, Liu Q, Zhang H. Phosphorylation of CREB-Specific Coactivator CRTC2 at Ser238 Promotes Proliferation, Migration, and Invasion of Colorectal Cancer Cells. Technol Cancer Res Treat 2020; 19:1533033820962111. [PMID: 33000695 PMCID: PMC7533939 DOI: 10.1177/1533033820962111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
cAMP response element binding protein (CREB)-regulated transcription coactivator 2 (CRTC2), a member of the novel CRTC family of transcriptional coactivators that activates basic leucine zipper transcription factors, including CREB, is overexpressed in many carcinomas, including colon cancer. Phosphorylation of CRTC2 protein at different residues is important for its subcellular localization and activity. However, the functions of some of the serine phosphorylation sites have not been elucidated. This study aimed to investigate the effects of phosphorylation of Ser127, Ser238, and Ser245 sites of CRTC2 in colorectal cancer (CRC) cells. Recombinant lentiviral particles with a CRTC2-targeting small hairpin RNA (shRNA) sequence were transfected into CRC cells to obtained shCRTC2 cell lines. Site-directed mutagenesis of Ser127, Ser238, and Ser245 cells were constructed by transfecting CRTC2 cDNA containing S127A, S238A, and S245A mutations into shCRTC2. Cell proliferation was measured by cell counting kit-8. Cell migration and invasion were examined by transwell assay. mRNA expression was assayed by qRT-PCR, and protein expression was determined by Western blot. Our results indicate that CRTC2 is overexpressed in CRC cells. Knockdown of CRTC2 inhibits the proliferation, migration, and invasion of CRC cells. When the phosphorylation of CRTC2 Ser238 decreases due to the lack of ERK2, the phosphorylation of Ser171 site increases. The proliferation, migration and invasion of CRC cells were inhibited, the nuclear aggregation of CRTC2 in the nucleus was reduced, and the interaction between CRTC2 and CREB was weaken. It is shown that the phosphorylation of CRTC2 Ser238 is important for CREB transcriptional activity. These findings may help in the identification of potentially new targets for CRC therapy.
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Affiliation(s)
- Yi Wang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hanshuo Zhang
- GeneX health Life Co., Ltd, Beijing, People's Republic of China
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9
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Abstract
Sequence analyses highlight a massive peptide sharing between immunoreactive Epstein-Barr virus (EBV) epitopes and human proteins that—when mutated, deficient or improperly functioning—associate with tumorigenesis, diabetes, lupus, multiple sclerosis, rheumatoid arthritis, and immunodeficiencies, among others. Peptide commonality appears to be the molecular platform capable of linking EBV infection to the vast EBV-associated diseasome via cross-reactivity and questions the hypothesis of the “negative selection” of self-reactive lymphocytes. Of utmost importance, this study warns that using entire antigens in anti-EBV immunotherapies can associate with autoimmune manifestations and further supports the concept of peptide uniqueness for designing safe and effective anti-EBV immunotherapies.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University School of Medicine, Tel-Hashomer, Israel.,I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Sechenov University, Moscow, Russia
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10
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Li X, Wu Y, Suo P, Liu G, Li L, Zhang X, Chen S, Xu M, Song L. Identification of a novel germline frameshift mutation p.D300fs of PMS1 in a patient with hepatocellular carcinoma: A case report and literature review. Medicine (Baltimore) 2020; 99:e19076. [PMID: 32000458 PMCID: PMC7004782 DOI: 10.1097/md.0000000000019076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RATIONALE PMS1 is one of the mismatch repair (MMR) genes with potential crucial roles in carcinogenesis. Very few reports have been identified on germline PMS1 mutations with definite disease phenotype. Here we report a case of hepatocellular carcinoma (HCC) with a novel potential pathogenic germline PMS1 mutation. PATIENT CONCERNS A 46-year-old Chinese male with Hepatitis B infection history presented a single cancerous nodule (10×12×10 mm) at the left lobe of liver. The nodule was considered malignant by type-B ultrasonic and computed tomography (CT) examinations. DIAGNOSIS AND INTERVENTION Liver lobectomy was performed to remove the liver cancerous nodule and postoperative TACE was performed for recurrence prevention. Pathological examination on resected tumor tissue confirmed the diagnosis of HCC. Whole-exome sequencing (WES) identified the c.900delT (p.D300fs) heterozygous germline mutation of PMS1, along with 253 nonsynonymous single nucleotide variations (SNVs), 14 Insertion or deletion mutations (INDELs) and 21 genes with copy number variations (CNVs). Three-dimensional prediction of protein tertiary structure suggested that the conformation of the enzyme active site and the ligand binding site might be changed due to the protein truncation. OUTCOMES The patient was still alive in good condition with no sign of recurrence in 12 months follow-up period. LESSONS The affected pathways in this case were unique from previously reported HCC patients with no PMS1 germline mutations. The novel PMS1 germline mutation may increase cancer risk. The roles of PMS1 germline mutations in carcinogenesis need further investigation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lele Song
- HaploX Biotechnology, Co., Ltd
- Department of Radiotherapy, the Eighth Medical Center of the Chinese PLA General Hospital, PR China
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11
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Yan L, You WQ, Sheng NQ, Gong JF, Hu LD, Tan GW, Chen HQ, Wang ZG. A CREB1/miR-433 reciprocal feedback loop modulates proliferation and metastasis in colorectal cancer. Aging (Albany NY) 2019; 10:3774-3793. [PMID: 30523220 PMCID: PMC6326693 DOI: 10.18632/aging.101671] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/15/2018] [Indexed: 12/28/2022]
Abstract
Increasing evidence has indicated the prognostic value of miR-433 across a series of malignancy types. However, the underlying mechanisms involved in cancer progression haven’t been sufficiently elucidated. In the present work, we found that miR-433 was downregulated in CRC tissues and cell lines. Ectopic expression of miR-433 obviously suppressed the proliferation, invasion and metastasis activity of CRC cells in vitro and in vivo. CREB1, CCAR1 and JNK1 were highly expressed and negatively correlated with miR-433 expression in CRC. CRC patients with higher expression of CREB1, CCAR1 or JNK1 presented a worse outcome relative to those with lower expression. CREB1 transactivated the expression of miR-433, and CREB1, CCAR1 and JNK1 simultaneously served as its targets, which in turn composed a feedback loop between CREB1 and miR-433. miR-433 blocked cell cycle progression and abolished EMT. Collectively, our study demonstrated the CREB1/miR-433 reciprocal feedback loop restrained the propagation, invasion and metastasis activities of CRC cells through abrogation of cell cycle progression and constraint of EMT.
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Affiliation(s)
- Li Yan
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wei-Qiang You
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Neng-Quan Sheng
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jian-Feng Gong
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lan-Dian Hu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ge-Wen Tan
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hong-Qi Chen
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhi-Gang Wang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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12
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Function and Transcriptional Regulation of Bovine TORC2 Gene in Adipocytes: Roles of C/EBP, XBP1, INSM1 and ZNF263. Int J Mol Sci 2019; 20:ijms20184338. [PMID: 31487963 PMCID: PMC6769628 DOI: 10.3390/ijms20184338] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 12/25/2022] Open
Abstract
The TORC2 gene is a member of the transducer of the regulated cyclic adenosine monophosphate (cAMP) response element binding protein gene family, which plays a key role in metabolism and adipogenesis. In the present study, we confirmed the role of TORC2 in bovine preadipocyte proliferation through cell cycle staining flow cytometry, cell counting assay, 5-ethynyl-2′-deoxyuridine staining (EdU), and mRNA and protein expression analysis of proliferation-related marker genes. In addition, Oil red O staining analysis, immunofluorescence of adiponectin, mRNA and protein level expression of lipid related marker genes confirmed the role of TORC2 in the regulation of bovine adipocyte differentiation. Furthermore, the transcription start site and sub-cellular localization of the TORC2 gene was identified in bovine adipocytes. To investigate the underlying regulatory mechanism of the bovine TORC2, we cloned a 1990 bp of the 5’ untranslated region (5′UTR) promoter region into a luciferase reporter vector and seven vector fragments were constructed through serial deletion of the 5′UTR flanking region. The core promoter region of the TORC2 gene was identified at location −314 to −69 bp upstream of the transcription start site. Based on the results of the transcriptional activities of the promoter vector fragments, luciferase activities of mutated fragments and siRNAs interference, four transcription factors (CCAAT/enhancer-binding protein C/BEPγ, X-box binding protein 1 XBP1, Insulinoma-associated 1 INSM1, and Zinc finger protein 263 ZNF263) were identified as the transcriptional regulators of TORC2 gene. These findings were further confirmed through Electrophoretic Mobility Shift Assay (EMSA) within nuclear extracts of bovine adipocytes. Furthermore, we also identified that C/EBPγ, XBP1, INSM1 and ZNF263 regulate TORC2 gene as activators in the promoter region. We can conclude that TORC2 gene is potentially a positive regulator of adipogenesis. These findings will not only provide an insight for the improvement of intramuscular fat in cattle, but will enhance our understanding regarding therapeutic intervention of metabolic syndrome and obesity in public health as well.
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Rodón L, Svensson RU, Wiater E, Chun MGH, Tsai WW, Eichner LJ, Shaw RJ, Montminy M. The CREB coactivator CRTC2 promotes oncogenesis in LKB1-mutant non-small cell lung cancer. SCIENCE ADVANCES 2019; 5:eaaw6455. [PMID: 31355336 PMCID: PMC6656544 DOI: 10.1126/sciadv.aaw6455] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/17/2019] [Indexed: 05/15/2023]
Abstract
The LKB1 tumor suppressor is often mutationally inactivated in non-small cell lung cancer (NSCLC). LKB1 phosphorylates and activates members of the AMPK family of Ser/Thr kinases. Within this family, the salt-inducible kinases (SIKs) modulate gene expression in part via the inhibitory phosphorylation of the CRTCs, coactivators for CREB (cAMP response element-binding protein). The loss of LKB1 causes SIK inactivation and the induction of the CRTCs, leading to the up-regulation of CREB target genes. We identified CRTC2 as a critical factor in LKB1-deficient NSCLC. CRTC2 is unphosphorylated and therefore constitutively activated in LKB1-mutant NSCLC, where it promotes tumor growth, in part via the induction of the inhibitor of DNA binding 1 (ID1), a bona fide CREB target gene. As ID1 expression is up-regulated and confers poor prognosis in LKB1-deficient NSCLC, our results suggest that small molecules that inhibit CRTC2 and ID1 activity may provide therapeutic benefit to individuals with NSCLC.
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Affiliation(s)
- Laura Rodón
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Robert U. Svensson
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037 USA
| | - Ezra Wiater
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Matthew G. H Chun
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037 USA
| | - Wen-Wei Tsai
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lillian J. Eichner
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037 USA
| | - Reuben J. Shaw
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037 USA
| | - Marc Montminy
- Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Corresponding author.
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Lee H, Lee M, Hong SK. CRTC2 as a novel prognostic biomarker for worse pathologic outcomes and biochemical recurrence after radical prostatectomy in patients with prostate cancer. Investig Clin Urol 2019; 60:84-90. [PMID: 30838340 PMCID: PMC6397930 DOI: 10.4111/icu.2019.60.2.84] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/21/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose To identify the association between tumor metabolism and prostate cancer (PCa), we investigated the relationship between expression of metabolism-related genes and clinicopathologic outcomes in patients with localized PCa. Materials and Methods We prospectively collected periprostatic adipose tissue from 40 PCa patients and extracted the RNA of each sample. After cDNA was synthesized from the extracted RNA, we analyzed the expression of 18 metabolism-related genes using real-time polymerase chain reaction. We divided the subjects according to the pathologic Gleason score (pGS) and compared the expression of each gene. Subsequently, the clinicopathologic outcomes were also compared according to the expression of each gene. Results When we compared the expression of 18 metabolism-related genes between the high (≥4+3) and low pGS groups (3+4), there were significant differences in the expression of six genes (SREBP, SCD, FASN, ACLY, ECHS, and CRTC2; p<0.05). Among them, the subjects with low expression for CRTC2 showed significantly worse pathologic outcomes in terms of high pGS (≥4+3) (p=0.020) and higher rates of seminal vesicle invasion (p=0.017). The low CRTC2 group also showed significantly inferior biochemical recurrence-free survival than the high CRTC2 group (p=0.048). Conclusions We found that high pGS patients showed significant differences in expression of several metabolism-related genes compared with low pGS patients. Among those genes, CRTC2 showed the strongest association with pathologic outcome, as well as postoperative survival.
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Affiliation(s)
- Hakmin Lee
- Department of Urology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Minseung Lee
- Department of Urology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Kyu Hong
- Department of Urology, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Urology, Seoul National University College of Medicine, Seoul, Korea
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Tasoulas J, Rodon L, Kaye FJ, Montminy M, Amelio AL. Adaptive Transcriptional Responses by CRTC Coactivators in Cancer. Trends Cancer 2019; 5:111-127. [PMID: 30755304 DOI: 10.1016/j.trecan.2018.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 01/09/2023]
Abstract
Adaptive stress signaling networks directly influence tumor development and progression. These pathways mediate responses that allow cancer cells to cope with both tumor cell-intrinsic and cell-extrinsic insults and develop acquired resistance to therapeutic interventions. This is mediated in part by constant oncogenic rewiring at the transcriptional level by integration of extracellular cues that promote cell survival and malignant transformation. The cAMP-regulated transcriptional coactivators (CRTCs) are a newly discovered family of intracellular signaling integrators that serve as the conduit to the basic transcriptional machinery to regulate a host of adaptive response genes. Thus, somatic alterations that lead to CRTC activation are emerging as key driver events in the development and progression of many tumor subtypes.
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Affiliation(s)
- Jason Tasoulas
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; These authors contributed equally
| | - Laura Rodon
- Peptide Biology Laboratories, Salk Institute, La Jolla, CA, USA; These authors contributed equally
| | - Frederic J Kaye
- Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Marc Montminy
- Peptide Biology Laboratories, Salk Institute, La Jolla, CA, USA
| | - Antonio L Amelio
- Department of Oral and Craniofacial Health Sciences, UNC School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, Cancer Cell Biology Program, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Amatori S, Persico G, Paolicelli C, Hillje R, Sahnane N, Corini F, Furlan D, Luzi L, Minucci S, Giorgio M, Pelicci PG, Fanelli M. Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology. Clin Epigenetics 2018; 10:143. [PMID: 30446010 PMCID: PMC6240272 DOI: 10.1186/s13148-018-0576-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The introduction of pathology tissue-chromatin immunoprecipitation (PAT-ChIP), a technique allowing chromatin immunoprecipitation (ChIP) from formalin-fixed paraffin-embedded (FFPE) tissues, has extended the application of chromatin studies to clinical patient samples. However, extensive crosslinking introduced during routine tissue fixation of clinical specimens may hamper the application of PAT-ChIP to genome-wide studies (PAT-ChIP-Seq) from archived tissue samples. The reduced efficiency in chromatin extraction from over-fixed formalin archival samples is the main hurdle to overcome, especially when low abundant epigenetic marks (e.g., H3K4me3) are investigated. RESULTS We evaluated different modifications of the original PAT-ChIP protocol to improve chromatin isolation from FFPE tissues. With this aim, we first made extensive usage of a normal human colon specimen fixed at controlled conditions (24 h, 48 h, and 72 h) to mimic the variability of tissue fixation that is most frequently found in archived samples. Different conditions of chromatin extraction were tested applying either diverse sonication protocols or heat-mediated limited reversal of crosslinking (LRC). We found that, if compared with canonical PAT-ChIP protocol, LRC strongly increases chromatin extraction efficiency, especially when 72-h fixed FFPE samples are used. The new procedure, that we named enhanced PAT-ChIP (EPAT-ChIP), was then applied at genome-wide level using an archival sample of invasive breast carcinoma to investigate H3K4me3, a lowly abundant histone modification, and H3K27me3 and H3K27ac, two additional well-known histone marks. CONCLUSIONS EPAT-ChIP procedure improves the efficiency of chromatin isolation from FFPE samples allowing the study of long time-fixed specimens (72 h), as well as the investigation of low distributed epigenetic marks (e.g., H3K4me3) and the analysis of multiple histone marks from low amounts of starting material. We believe that EPAT-ChIP will facilitate the application of chromatin studies to archived pathology samples, thus contributing to extend the current understanding of cancer epigenomes and enabling the identification of clinically useful tumor biomarkers.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino "Carlo Bo", Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giuseppe Persico
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino "Carlo Bo", Via Arco d'Augusto 2, 61032, Fano, PU, Italy
| | - Claudio Paolicelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino "Carlo Bo", Via Arco d'Augusto 2, 61032, Fano, PU, Italy
| | - Roman Hillje
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Nora Sahnane
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria, Via O. Rossi 9, 21100, Varese, Italy
| | - Francesco Corini
- U.O.C. Anatomia Patologica, "C. G. Mazzoni" Hospital, Via degli Iris 2, 63100, Ascoli Piceno, Italy
| | - Daniela Furlan
- Unit of Pathology, Department of Medicine and Surgery, University of Insubria, Via O. Rossi 9, 21100, Varese, Italy
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Marco Giorgio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino "Carlo Bo", Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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Steven A, Seliger B. Control of CREB expression in tumors: from molecular mechanisms and signal transduction pathways to therapeutic target. Oncotarget 2018; 7:35454-65. [PMID: 26934558 PMCID: PMC5085243 DOI: 10.18632/oncotarget.7721] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/26/2016] [Indexed: 12/11/2022] Open
Abstract
The cyclic AMP response element binding (CREB) protein has pleiotropic activities in physiologic processes. Due to its central position downstream of many growth signaling pathways CREB has the ability to influence cell survival, growth and differentiation of normal, but also of tumor cells suggesting an oncogenic potential of CREB. Indeed, increased CREB expression and activation is associated with tumor progression, chemotherapy resistance and reduced patients' survival. We summarize here the different cellular functions of CREB in tumors of distinct histology as well as its use as potential prognostic marker. In addition, the underlying molecular mechanisms to achieve constitutive activation of CREB including structural alterations, such as gene amplification and chromosomal translocation, and deregulation, which could occur at the transcriptional, post-transcriptional and post-translational level, will be described. Since downregulation of CREB by different strategies resulted in inhibition of cell proliferation, invasion and induction of apoptosis, the role of CREB as a promising target for cancer therapy will be also discussed.
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Affiliation(s)
- André Steven
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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18
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Shi S, Luo W, Zhang R, Wang C, Zheng Y, Song Y, Wang R, Zhang L, Zhang L, Li W, Luo Z. CRTC2 promotes non-small cell lung cancer A549 migration and invasion in vitro. Thorac Cancer 2018; 9:136-141. [PMID: 29105369 PMCID: PMC5754302 DOI: 10.1111/1759-7714.12550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND CRTC2 is highly expressed in lung cancer and contributes to lung cancer pathogenesis; however, whether CRTC2 promotes lung cancer metastasis remains unknown. In the present study, we investigated the role of CRTC2 in lung cancer metastasis in vitro. METHODS CRTC2 stable knockdown of lung cancer cell A549 was generated with small hairpin RNA and confirmed by quantitative reverse transcription-PCR and Western blot. Wound healing and invasion transwell assays were performed to explore migration and invasion activity, and Western blot was conducted to detect the expression of related proteins. RESULTS Suppression of CRTC2 significantly inhibited A549 cell migration and invasion in vitro. Mechanistic studies showed that knockdown of CRTC2 greatly downregulated MMP2 and MMP9 expression. CRTC2 silencing remarkably suppressed epithelial-mesenchymal transition by modulating the expression of E-cadherin and vimentin. Furthermore, suppression of CRTC2 expression significantly reduced MAPK/c-Jun N-terminal kinase activity. CONCLUSION CRTC2 may promote A549 migration and invasion by modulation of c-Jun N-terminal kinase-mediated epithelial-mesenchymal transition and matrix metalloproteinase expression.
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Affiliation(s)
- Shaoqing Shi
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Wei Luo
- Department of Respiratory MedicineThe People's Hospital of LeshanLeshanChina
| | - Rui Zhang
- Department of Thoracic SurgeryThe Seventh People's Hospital of ChengduChengduChina
| | - Chu Wang
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Yuanyuan Zheng
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Yunhua Song
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Rongchun Wang
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Liyan Zhang
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Lihua Zhang
- Department of Geriatric EndocrinologyThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
| | - Weimin Li
- Department of Respiratory MedicineWest China Hospital, Sichuan UniversityChengduChina
| | - Zhuang Luo
- Department of Respiratory MedicineThe First Affiliated Hospital of Kunming Medical UniversityKunmingChina
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Soler-Oliva ME, Guerrero-Martínez JA, Bachetti V, Reyes JC. Analysis of the relationship between coexpression domains and chromatin 3D organization. PLoS Comput Biol 2017; 13:e1005708. [PMID: 28902867 PMCID: PMC5612749 DOI: 10.1371/journal.pcbi.1005708] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/25/2017] [Accepted: 08/03/2017] [Indexed: 01/08/2023] Open
Abstract
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term “CODs”). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them. Prokaryotic operons normally comprise functionally related genes whose expression is coordinated. Even though operons do not exist in most eukaryotes, results from the last fifteen years indicate that gene order is nonetheless not random in eukaryotes, and that coexpressed genes tend to be grouped in the genome. We identify here about 500 coexpression domain (CODs) in normal breast tissue. Interestingly, we find that genes within CODs often are coexpressed with other genes that reside in other CODs placed very far away in the same chromosome, which is indicative of long-range inter-COD co-regulation. Furthermore, we find that coexpressed genes within CODs or within co-regulated CODs display similar three-dimensional chromatin contacts, suggesting a spatial coordination of CODs.
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Affiliation(s)
- María E. Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Sevilla, Spain
| | - José A. Guerrero-Martínez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Sevilla, Spain
| | - Valentina Bachetti
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Sevilla, Spain
| | - José C. Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Sevilla, Spain
- * E-mail:
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Escoubas CC, Silva-García CG, Mair WB. Deregulation of CRTCs in Aging and Age-Related Disease Risk. Trends Genet 2017; 33:303-321. [PMID: 28365140 DOI: 10.1016/j.tig.2017.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/15/2022]
Abstract
Advances in public health in the past century have seen a sharp increase in human life expectancy. With these changes have come an increased prevalence of age-related pathologies and health burdens in the elderly. Patient age is the biggest risk factor for multiple chronic conditions that often occur simultaneously within a single individual. An alternative to disease-centric therapeutic approaches is that of 'geroscience', which aims to define molecular mechanisms that link age to overall disease risk. One such mechanism is deregulation of CREB-regulated transcriptional coactivators (CRTCs). Initially identified for their role in modulating CREB transcription, the past 5 years has seen an expansion in knowledge of new cellular regulators and roles of CRTCs beyond CREB. CRTCs have been shown to modulate organismal aging in Caenorhabditis elegans and to impact on age-related diseases in humans. We discuss CRTC deregulation as a new driver of aging that integrates the link between age and disease risk.
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Affiliation(s)
- Caroline C Escoubas
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Carlos G Silva-García
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - William B Mair
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.
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Lu F, Zheng Y, Donkor PO, Zou P, Mu P. Downregulation of CREB Promotes Cell Proliferation by Mediating G1/S Phase Transition in Hodgkin Lymphoma. Oncol Res 2017; 24:171-9. [PMID: 27458098 PMCID: PMC7838744 DOI: 10.3727/096504016x14634208142987] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The cyclic-AMP response element-binding protein (CREB), a well-known nuclear transcription factor, has been shown to play an essential role in many cellular processes, including differentiation, cell survival, and cell proliferation, by regulating the expression of downstream genes. Recently, increased expression of CREB was frequently found in various tumors, indicating that CREB is implicated in the process of tumorigenesis. However, the effects of CREB on Hodgkin lymphoma (HL) remain unknown. To clarify the role of CREB in HL, we performed knockdown experiments in HL. We found that downregulation of CREB by short hairpin RNA (shRNA) resulted in enhancement of cell proliferation and promotion of G1/S phase transition, and these effects can be rescued by expression of shRNA-resistant CREB. Meanwhile, the expression level of cell cycle-related proteins, such as cyclin D1, cyclin E1, cyclin-dependent kinase 2 (CDK2), and CDK4, was elevated in response to depletion of CREB. Furthermore, we performed chromatin immunoprecipitation (ChIP) assay and confirmed that CREB directly bound to the promoter regions of these genes, which consequently contributed to the regulation of cell cycle. Consistent with our results, a clinical database showed that high expression of CREB correlates with favorable prognosis in B-cell lymphoma patients, which is totally different from the function of CREB in other cancers such as colorectal cancer, acute myeloid leukemia, and some endocrine cancers. Taken together, all of these features of CREB in HL strongly support its role as a tumor suppressor gene that can decelerate cell proliferation by inhibiting the expression of several cell cycle-related genes. Our results provide new evidence for prognosis prediction of HL and a promising therapeutic strategy for HL patients.
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Affiliation(s)
- Fangjin Lu
- Tianjin State Key Laboratory of Modern Chinese Medicine, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Chen L, Zhang YH, Lu G, Huang T, Cai YD. Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways. Artif Intell Med 2017; 76:27-36. [PMID: 28363286 DOI: 10.1016/j.artmed.2017.02.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/31/2017] [Accepted: 02/05/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cancer is a disease that involves abnormal cell growth and can invade or metastasize to other tissues. It is known that several factors are related to its initiation, proliferation, and invasiveness. Recently, it has been reported that long non-coding RNAs (lncRNAs) can participate in specific functional pathways and further regulate the biological function of cancer cells. Studies on lncRNAs are therefore helpful for uncovering the underlying mechanisms of cancer biological processes. METHODS We investigated cancer-related lncRNAs using gene ontology (GO) terms and KEGG pathway enrichment scores of neighboring genes that are co-expressed with the lncRNAs by extracting important GO terms and KEGG pathways that can help us identify cancer-related lncRNAs. The enrichment theory of GO terms and KEGG pathways was adopted to encode each lncRNA. Then, feature selection methods were employed to analyze these features and obtain the key GO terms and KEGG pathways. RESULTS The analysis indicated that the extracted GO terms and KEGG pathways are closely related to several cancer associated processes, such as hormone associated pathways, energy associated pathways, and ribosome associated pathways. And they can accurately predict cancer-related lncRNAs. CONCLUSIONS This study provided novel insight of how lncRNAs may affect tumorigenesis and which pathways may play important roles during it. These results could help understanding the biological mechanisms of lncRNAs and treating cancer.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China; College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Guohui Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China.
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.
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