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Long E, Patel H, Golden A, Antony M, Yin J, Funderburk K, Feng J, Song L, Hoskins JW, Amundadottir LT, Hung RJ, Amos CI, Shi J, Rothman N, Lan Q, Choi J. High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility. Am J Hum Genet 2024; 111:1405-1419. [PMID: 38906146 PMCID: PMC11267514 DOI: 10.1016/j.ajhg.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024] Open
Abstract
Genome-wide association studies (GWASs) have identified numerous lung cancer risk-associated loci. However, decoding molecular mechanisms of these associations is challenging since most of these genetic variants are non-protein-coding with unknown function. Here, we implemented massively parallel reporter assays (MPRAs) to simultaneously measure the allelic transcriptional activity of risk-associated variants. We tested 2,245 variants at 42 loci from 3 recent GWASs in East Asian and European populations in the context of two major lung cancer histological types and exposure to benzo(a)pyrene. This MPRA approach identified one or more variants (median 11 variants) with significant effects on transcriptional activity at 88% of GWAS loci. Multimodal integration of lung-specific epigenomic data demonstrated that 63% of the loci harbored multiple potentially functional variants in linkage disequilibrium. While 22% of the significant variants showed allelic effects in both A549 (adenocarcinoma) and H520 (squamous cell carcinoma) cell lines, a subset of the functional variants displayed a significant cell-type interaction. Transcription factor analyses nominated potential regulators of the functional variants, including those with cell-type-specific expression and those predicted to bind multiple potentially functional variants across the GWAS loci. Linking functional variants to target genes based on four complementary approaches identified candidate susceptibility genes, including those affecting lung cancer cell growth. CRISPR interference of the top functional variant at 20q13.33 validated variant-to-gene connections, including RTEL1, SOX18, and ARFRP1. Our data provide a comprehensive functional analysis of lung cancer GWAS loci and help elucidate the molecular basis of heterogeneity and polygenicity underlying lung cancer susceptibility.
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Affiliation(s)
- Erping Long
- State Key Laboratory of Respiratory Health and Multimorbidity, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyxandra Golden
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Michelle Antony
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karen Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jason W Hoskins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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Mei J, Wang Y, Song X, Xie XH, Wang G, Chen C, Chen G, Liu Z. The needle in the haystack: Identifying and validating common genes of depression, insomnia, and inflammation. J Affect Disord 2023; 342:45-53. [PMID: 37657625 DOI: 10.1016/j.jad.2023.08.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Insomnia, inflammation, and depression are often co-occurring conditions. The mechanisms underlying these conditions remain unclear. MATERIALS AND METHODS We collected microarray datasets of depression and insomnia from GEO and analyzed them for differentially expressed genes (DEGs). We then overlapped the DEGs with a list of inflammatory response-related genes to identify genes associated with all three conditions. We next performed analyses of enrichment analyses, KEGG mapping, and protein-protein interaction to identify hub genes. Furthermore, we established a depression rat model with inflammation and insomnia to validate the potential genes. At last, a two-sample Mendelian randomization (MR) study was conducted to confirm the association of identified target genes with depression outcomes. RESULTS We obtained 32 common DEGs associated with the depression, insomnia and inflammatory, and found that the PI3K-AKT signaling pathway might be involved in the inflammatory response in insomnia and depression. CREB1, CYBB, FYN, and CCR5 were identified as targets for the next validation. In model rats, the CCR5 and PI3K-AKT pathways were significantly up-regulated, while the model group exhibited significantly lower hippocampal p-CREB protein expression. The MR study suggested a potential causal relationship between CREB1 and the risk of depression (OR = 1.11, p = 0.013). LIMITATIONS The identified potential genes and pathways require further laboratory and clinical evidence verification. CONCLUSION We identified four potential inflammatory related-genes (CREB1, CYBB, FYN, and CCR5). CREB1 may be a potential inflammatory response-related biomarker and drug target for depression and insomnia, as validated by the followed rat model and MR study.
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Affiliation(s)
- Junhua Mei
- Department of Psychiatry, Renmin Hospital of Wuhan University, 238 Jiefang Rd, Wuhan 430060, China
| | - Ying Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, 238 Jiefang Rd, Wuhan 430060, China
| | - Xinhua Song
- Department of Psychiatry, Renmin Hospital of Wuhan University, 238 Jiefang Rd, Wuhan 430060, China
| | - Xin-Hui Xie
- Department of Psychiatry, Renmin Hospital of Wuhan University, 238 Jiefang Rd, Wuhan 430060, China
| | - Guang Wang
- Department of Neurology, Wuhan First Hospital, Hubei University of Chinese Medicine, Wuhan, China
| | - Chao Chen
- Department of Neurology, Wuhan First Hospital, Hubei University of Chinese Medicine, Wuhan, China
| | - Guohua Chen
- Department of Neurology, Wuhan First Hospital, No. 215 Zhongshan Road, Wuhan 430022, China.
| | - Zhongchun Liu
- Department of Psychiatry, Renmin Hospital of Wuhan University, 238 Jiefang Rd, Wuhan 430060, China; Taikang center for life and medical sciences, Wuhan University, Wuhan 430000, PR China.
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Ershov P, Yablokov E, Mezentsev Y, Ivanov A. Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers. Int J Mol Sci 2023; 24:10190. [PMID: 37373333 DOI: 10.3390/ijms241210190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Functions of about 10% of all the proteins and their associations with diseases are poorly annotated or not annotated at all. Among these proteins, there is a group of uncharacterized chromosome-specific open-reading frame genes (CxORFx) from the 'Tdark' category. The aim of the work was to reveal associations of CxORFx gene expression and ORF proteins' subinteractomes with cancer-driven cellular processes and molecular pathways. We performed systems biology and bioinformatic analysis of 219 differentially expressed CxORFx genes in cancers, an estimation of prognostic significance of novel transcriptomic signatures and analysis of subinteractome composition using several web servers (GEPIA2, KMplotter, ROC-plotter, TIMER, cBioPortal, DepMap, EnrichR, PepPSy, cProSite, WebGestalt, CancerGeneNet, PathwAX II and FunCoup). The subinteractome of each ORF protein was revealed using ten different data sources on physical protein-protein interactions (PPIs) to obtain representative datasets for the exploration of possible cellular functions of ORF proteins through a spectrum of neighboring annotated protein partners. A total of 42 out of 219 presumably cancer-associated ORF proteins and 30 cancer-dependent binary PPIs were found. Additionally, a bibliometric analysis of 204 publications allowed us to retrieve biomedical terms related to ORF genes. In spite of recent progress in functional studies of ORF genes, the current investigations aim at finding out the prognostic value of CxORFx expression patterns in cancers. The results obtained expand the understanding of the possible functions of the poorly annotated CxORFx in the cancer context.
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Affiliation(s)
- Pavel Ershov
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | | | - Yuri Mezentsev
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Weiskittel TM, Cao A, Meng-Lin K, Lehmann Z, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Yong Ung C, Li H. Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms. Pharmaceuticals (Basel) 2023; 16:752. [PMID: 37242535 PMCID: PMC10223789 DOI: 10.3390/ph16050752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Anticipating and understanding cancers' need for specific gene activities is key for novel therapeutic development. Here we utilized DepMap, a cancer gene dependency screen, to demonstrate that machine learning combined with network biology can produce robust algorithms that both predict what genes a cancer is dependent on and what network features coordinate such gene dependencies. Using network topology and biological annotations, we constructed four groups of novel engineered machine learning features that produced high accuracies when predicting binary gene dependencies. We found that in all examined cancer types, F1 scores were greater than 0.90, and model accuracy remained robust under multiple hyperparameter tests. We then deconstructed these models to identify tumor type-specific coordinators of gene dependency and identified that in certain cancers, such as thyroid and kidney, tumors' dependencies are highly predicted by gene connectivity. In contrast, other histologies relied on pathway-based features such as lung, where gene dependencies were highly predictive by associations with cell death pathway genes. In sum, we show that biologically informed network features can be a valuable and robust addition to predictive pharmacology models while simultaneously providing mechanistic insights.
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Affiliation(s)
- Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
- Mayo Clinic Alix School of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Andrew Cao
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Zachary Lehmann
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD 57006, USA
| | - Benjamin Feng
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Philip Wisniewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
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Liu JT, Sun ZX, Zhong R, Zhang YD, Wang T, Hou YD, Bao JH, Zhang L, Chen B. ZNRF2 as an oncogene is transcriptionally regulated by CREB1 in breast cancer models. Hum Cell 2023:10.1007/s13577-023-00913-7. [PMID: 37165255 DOI: 10.1007/s13577-023-00913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/29/2023] [Indexed: 05/12/2023]
Abstract
E3 ubiquitin ligase Zinc and Ring Finger 2 (ZNRF2) has been demonstrated to be engaged in the development of multiple cancers. Nevertheless, the function of ZNRF2 in breast cancer (BC) still unclear. In this work, we firstly analyzed the differentially expressed genes in BC by bioinformatics and found that ZNRF2 was highly expressed in BC. Consistently, we further confirmed that ZNRF2 was upregulated in BC tissues compared with adjacent normal tissues, and this was positively correlated with the poor prognosis and the higher pathological grades of patients with BC. Functional assays performed on HCC1937 and MCF-7 cells indicated that silencing of ZNRF2 suppressed cell proliferation, as evidenced by the decrease in the expression of cyclin A, PCNA and cyclin D1. Flow cytometry and Hoechst staining showed that knockdown of ZNRF2 induced cell apoptosis, which was verified by the upregulation of apoptosis genes such as Bax, cleaved PARP and Bim. ZNRF2 knockdown also inhibited in vivo tumor growth. But, instead, ZNRF2-overexpressed BC cells exhibited obvious malignant phenotypes. Additionally, we observed that cAMP response element binding protein 1 (CREB1) directly bound to the promoter sequence of ZNRF2 and thus activating its transcription, suggesting that ZNRF2 is transcriptionally regulated by CREB1. Additionally, ZNRF2 knockdown could reverse the proliferation-promoting action of CREB1 on BC cells, Hence, this study demonstrated that ZNRF2 might serve as a prospective therapeutic target for BC.
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Affiliation(s)
- Jin-Tao Liu
- Department of Thyroid Surgery, Dalian Municipal Central Hospital, Dalian, Liaoning, China
| | - Zhen-Xuan Sun
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Rui Zhong
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
| | - Yi-Dan Zhang
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
| | - Teng Wang
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
| | - Yu-Dong Hou
- Graduate School, China Medical University, Shenyang, Liaoning, China
| | - Jian-Heng Bao
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
| | - Lei Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, No. 155, Nanjing North Street, Shenyang, Liaoning, China.
| | - Bo Chen
- Department of Breast Surgery, The First Hospital of China Medical University, No. 155, Nanjing North Street, Shenyang, Liaoning, China.
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Lin J, Liu G, Chen L, Kwok HF, Lin Y. Targeting lactate-related cell cycle activities for cancer therapy. Semin Cancer Biol 2022; 86:1231-1243. [PMID: 36328311 DOI: 10.1016/j.semcancer.2022.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Lactate has long been considered as a metabolic by-product of aerobic glycolysis for cancer. However, more and more studies have shown that lactate can regulate cancer progression via multiple mechanisms such as cell cycle regulation, immune suppression, energy metabolism and so on. A recent discovery of lactylation attracted a lot of attention and is already a hot topic in the cancer field. In this review, we summarized the latest functions of lactate and its underlying mechanisms in cancer. We also included our analysis of protein lactylation in different rat organs and compared them with other published lactylation data. The unresolved challenges in this field were discussed, and the potential application of these new discoveries of lactate-related cell cycle activities for cancer target therapy was speculated.
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Affiliation(s)
- Jia Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Collaborative Innovation Center for Rehabilitation Technology, the Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, the Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, China
| | - Geng Liu
- Laboratory of Cancer Biology, Department of Oncology, University of Oxford, UK
| | - Lidian Chen
- Collaborative Innovation Center for Rehabilitation Technology, the Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, China.
| | - Hang Fai Kwok
- Cancer Centre, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR; MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida de Universidade, Taipa, Macau SAR; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Collaborative Innovation Center for Rehabilitation Technology, the Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, China; Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China.
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Tong L, Shan M, Zou W, Liu X, Felsher DW, Wang J. Cyclic adenosine monophosphate/phosphodiesterase 4 pathway associated with immune infiltration and PD-L1 expression in lung adenocarcinoma cells. Front Oncol 2022; 12:904969. [PMID: 35978822 PMCID: PMC9376450 DOI: 10.3389/fonc.2022.904969] [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: 03/26/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Background The cyclic adenosine monophosphate/phosphodiesterase 4 (cAMP/PDE4) pathway is involved in inflammation and immune regulation; however, the effect of cAMP/PDE4 on immune infiltration and immune evasion in lung adenocarcinoma (LUAD) remains unclear. Methods CBioPortal, which is the The Cancer Genome Atlas (TCGA) online database, and the Kaplan Meier plotter were used to analyze the association between genes and the prognosis of TCGA-LUAD. Tumor Immune Estimation Resource (TIMER) was used to analyze the association between gene expression and immune infiltration. The Genecards database was used to identify the transcription factors of related genes. The lung adenocarcinoma cell line H1299 and A549 were treated with cAMP pathway drugs. Flow cytometry and qRT-PCR were used to detect the PD-L1 protein and gene expression, respectively. A one-way analysis of variance with Tukey’s post-hoc test or a Student’s t-test were used. Results It was found that PDE4B and CREB1, which are downstream genes of the cAMP/PDE4 axis, were differentially expressed in LUAD and adjacent tissues and are correlated with the prognosis and immune infiltration of LUAD. In the CBioPortal database, cAMP pathway genes are closely related to programmed cell death-ligand 1 (PD-L1) expression in TCGA-LUAD. The protein-protein interaction revealed that there was a direct interaction between CREB1/CREBBP, which are the downstream molecules of the cAMP/PDE4 axis, and MYC; additionally, MYC was predicted to bind to the PD-L1 transcription site and regulate PD-L1 expression. CREB1 was also predicted to transcriptionally bind to both MYC and PD-L1. These results predicted the interaction network of cAMP/PDE4/CREB1/CREBP/MYC/PD-L1, and the core factor may be related to MYC. In the cell experiment, forskolin (an adenylate cyclase activator) and zardaverine (a PDE4 inhibitor) enhance the cAMP pathway and decrease PD-L1 expression, while SQ2253 (an adenylate cyclase inhibitor) inhibits the cAMP pathway and increases PD-L1 expression of the LUAD cell lines H1299 and A549, and MYC regulation by these drugs was positively correlated with PD-L1 regulation, which verified the regulation of the cAMP/PDE4 pathway on MYC and PD-L1. Conclusions This study showed that the cAMP/PDE4 pathway may play an important role in PD-L1 regulation and immune infiltration in LUAD.
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Affiliation(s)
- Ling Tong
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Minjie Shan
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wen Zou
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - XianLing Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Dean W. Felsher
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jingjing Wang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Jingjing Wang,
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Yao B, Zhang Q, Yang Z, An F, Nie H, Wang H, Yang C, Sun J, Chen K, Zhou J, Bai B, Gu S, Zhao W, Zhan Q. CircEZH2/miR-133b/IGF2BP2 aggravates colorectal cancer progression via enhancing the stability of m 6A-modified CREB1 mRNA. Mol Cancer 2022; 21:140. [PMID: 35773744 PMCID: PMC9245290 DOI: 10.1186/s12943-022-01608-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 06/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aberrant expression of circular RNAs (circRNAs) contributes to the initiation and progression of human malignancies, but the underlying mechanisms remain largely elusive. METHODS High-throughput sequencing was performed to screen aberrantly expressed circRNAs or miRNAs in colorectal cancer (CRC) and adjacent normal tissues. A series of gain- and loss-of-function studies were conducted to evaluate the biological behaviors of CRC cells. RNA pulldown, mass spectrometry, RIP, qRT-PCR, Western blot, luciferase reporter assays and MeRIP-seq analysis were further applied to dissect the detailed mechanisms. RESULTS Here, a novel circRNA named circEZH2 (hsa_circ_0006357) was screened out by RNA-seq in CRC tissues, whose expression is closely related to the clinicpathological characteristics and prognosis of CRC patients. Biologically, circEZH2 facilitates the proliferation and migration of CRC cells in vitro and in vivo. Mechanistically, circEZH2 interacts with m6A reader IGF2BP2 and blocks its ubiquitination-dependent degradation. Meanwhile, circEZH2 could serve as a sponge of miR-133b, resulting in the upregulation of IGF2BP2. Particularly, circEZH2/IGF2BP2 enhances the stability of CREB1 mRNA, thus aggravating CRC progression. CONCLUSIONS Our findings not only reveal the pivotal roles of circEZH2 in modulating CRC progression, but also advocate for attenuating circEZH2/miR-133b/IGF2BP2/ CREB1 regulatory axis to combat CRC.
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Affiliation(s)
- Bing Yao
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Qinglin Zhang
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhou Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Fangmei An
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - He Nie
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hui Wang
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Cheng Yang
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jing Sun
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Ke Chen
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jingwan Zhou
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Bing Bai
- Center for Precision Medicine, Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
| | - Shouyong Gu
- Institute of Geriatric Medicine, Jiangsu Province Geriatric Hospital, Nanjing, Jiangsu Province, China.
| | - Wei Zhao
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China. .,School of laboratory medicine, Chengdu medical college, Chengdu, China.
| | - Qiang Zhan
- Departments of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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Mehra S, Singh S, Nagathihalli N. Emerging Role of CREB in Epithelial to Mesenchymal Plasticity of Pancreatic Cancer. Front Oncol 2022; 12:925687. [PMID: 35800049 PMCID: PMC9253527 DOI: 10.3389/fonc.2022.925687] [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: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive solid malignancy with a high rate of metastasis and therapeutic resistance as its major hallmarks. Although a defining mutational event in pancreatic cancer initiation is the presence of oncogenic KRAS, more advanced PDAC lesions accumulate additional genomic alterations, including loss of tumor suppressor gene TP53. Co-occurrence of mutant KRAS and TP53 in PDAC promotes hyperactivation of cancer cell signaling pathways driving epithelial to mesenchymal plasticity (EMP). The cellular process of EMP influences the biological behavior of cancer cells by increasing their migratory and invasive properties, thus promoting metastasis. Our previous work has demonstrated that oncogenic KRAS-mediated activation of cyclic AMP response element-binding protein 1 (CREB) is one of the critical drivers of PDAC aggressiveness. The therapeutic approach of targeting this key transcription factor attenuates tumor burden in genetically engineered mouse models (GEMMs) of this disease. Herein, we discuss the significant role of CREB in perpetuating disease aggressiveness and therapeutic resistance through the EMP process. Furthermore, this review updates the therapeutic implications of targeting CREB, highlighting the challenges and emerging approaches in PDAC.
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Affiliation(s)
- Siddharth Mehra
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Samara Singh
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Nagaraj Nagathihalli
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
- *Correspondence: Nagaraj Nagathihalli,
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