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Tang B, Yan R, Zhu J, Cheng S, Kong C, Chen W, Fang S, Wang Y, Yang Y, Qiu R, Lu C, Ji J. Integrative analysis of the molecular mechanisms, immunological features and immunotherapy response of ferroptosis regulators across 33 cancer types. Int J Biol Sci 2022; 18:180-198. [PMID: 34975326 PMCID: PMC8692154 DOI: 10.7150/ijbs.64654] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Ferroptosis is a recently described mode of cell death caused by the accumulation of intracellular iron and lipid reactive oxygen species (ROS), which play critical roles in tumorigenesis and cancer progression. However, the underlying molecular mechanisms and promising biomarkers of ferroptosis among cancers remain to be elucidated. In this study, 30 ferroptosis regulators in ferroptosis-related signaling pathways were identified and analyzed in 33 cancer types. We found transcriptomic aberrations and evaluated the prognostic value of ferroptosis regulators across 33 cancer types. Then, we predicted and validated potential transcription factors (including E2F7, KLF5 and FOXM1) and therapeutic drugs (such as cyclophosphamide, vinblastine, and gefitinib) that target ferroptosis regulators in cancer. Moreover, we explored the molecular mechanisms of ferroptosis and found that signaling pathways such as the IL-1 and IL-2 pathways are closely associated with ferroptosis. Additionally, we found that ferroptosis regulators have a close relationship with immunity-related parameters, including the immune score, immune cell infiltration level, and immune checkpoint protein level. Finally, we determined a ferroptosis score using GSVA method. We found that the ferroptosis score effectively predicted ferroptotic cell death in tumor samples. And ferroptosis score is served as an independent prognostic indicator for the incidence and recurrence of cancers. More importantly, patients with high ferroptosis scores received greater benefit from immunotherapy. We aslo created an online webserver based on the nomogram prognostic model to predict the survival in immunotherapy cohort. The reason for this outcome is partially the result of patients with a high ferroptosis rate also having high immune scores, HLA-related gene expression and immune checkpoint protein expression, such as PDL2 and TIM3. Moreover, patients with high ferroptosis scores exhibited CD8 T cell and TIL infiltration and immune-related signaling pathway enrichment. In summary, we systematically summarize the molecular characteristics, clinical relevance and immune features of ferroptosis across cancers and show that the ferroptosis score can be used as a prognostic factor and for the evaluation of immunotherapy effects.
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Affiliation(s)
- Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruochen Yan
- School of Medicine, Zhejiang University, Hangzhou 310012, China
| | - Jinyu Zhu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shimiao Cheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Chunli Kong
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Weiqian Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Shiji Fang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Yajie Wang
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Yang Yang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Rongfang Qiu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Chenying Lu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
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302
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Liang ZQ, Zhong LY, Li J, Shen JH, Tu XY, Zhong ZH, Zeng JJ, Chen JH, Wei ZX, Dang YW, Huang SN, Chen G. Clinicopathological significance and underlying molecular mechanism of downregulation of basonuclin 1 expression in ovarian carcinoma. Exp Biol Med (Maywood) 2022; 247:106-119. [PMID: 34644201 PMCID: PMC8777474 DOI: 10.1177/15353702211052036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, we aim to identify the clinical significance of basonuclin 1 (BNC1) expression in ovarian carcinoma (OV) and to explore its latent mechanisms. Via integrating in-house tissue microarrays, gene chips, and RNA-sequencing data, we explored the expression and clinical value of BNC1 in OV. Immunohistochemical staining was utilized to confirm the protein expression status of BNC1. A combined SMD of -2.339 (95% CI: -3.649 to -1.028, P < 0.001) identified that BNC1 was downregulated based on 1346 samples, and the sROC (AUC = 0.93) showed a favorable discriminatory ability of BNC1 in OV patients. We used univariate and multivariate Cox regulation to evaluate the prognostic role of BNC1 for OV patients, and a combined hazard ratio of 0.717 (95% CI: 0.445-0.989, P < 0.001) revealed that BNC1 was a protective factor for OV. Furthermore, the fraction of infiltrating naive B cells, memory B cells, and other immune cells showed statistical differences between the high- and low-BNC1 expression groups through cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Enrichment analysis showed that BNC1 may have a relationship with immune-related items in OV. By predicting the potential regulatory transcription factors (TFs) of BNC1, friend leukemia virus integration 1 (FLI1) may be a potential upstream TF of BNC1. Corporately, a decreasing trend of BNC1 may serve as a tumor suppressor and prognostic biomarker in OV patients. Moreover, BNC1 may take part in immune-related pathways and influence the fraction of tumor-infiltrating immune cells.
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Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Lu-Yang Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jie Li
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jin-Hai Shen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Xin-Yue Tu
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Zheng-Hong Zhong
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jing-Jing Zeng
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of
Guangxi Zhuang Autonomous Region, Nanning 530003, P. R. China
| | - Zhu-Xin Wei
- Department of Radiotherapy, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer
Hospital, Nanning 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of
Guangxi Medical University, Nanning 530021, P. R. China
- Gang Chen.
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303
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Johnson KS, Hussein S, Chakraborty P, Muruganantham A, Mikhail S, Gonzalez G, Song S, Jolly MK, Toneff MJ, Benton ML, Lin YC, Taube JH. CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression. Cancers (Basel) 2022; 14:cancers14010209. [PMID: 35008373 PMCID: PMC8750563 DOI: 10.3390/cancers14010209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.
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Affiliation(s)
- Kelsey S. Johnson
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shaimaa Hussein
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | - Arvind Muruganantham
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Sheridan Mikhail
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Giovanny Gonzalez
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shuxuan Song
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | | | | | - Yin C. Lin
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
- Dan L. Duncan Cancer Center, Houston, TX 76706, USA
- Correspondence:
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304
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Cai X, Zhou J, Deng J, Chen Z. Prognostic biomarker SMARCC1 and its association with immune infiltrates in hepatocellular carcinoma. Cancer Cell Int 2021; 21:701. [PMID: 34937564 PMCID: PMC8697473 DOI: 10.1186/s12935-021-02413-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
Background Epigenetic alterations contribute greatly to metastasis and dissemination in hepatocellular carcinoma (HCC). SMARCC1, as a SWI/SNF chromatin remodeling factor, has been reported to play important roles in many cancers. For the first time, with the bioinformatics analysis and wet-bench experiments, we explored the biological significance of SMARCC1 and its potential as putative therapeutic target in HCC. Methods The mRNA expression profiles and prognostic value of SMARCC1 were analyzed in the Oncomine, UALCAN and Kaplan–Meier Plotter databases. The expression of SMARCC1 and associated clinicopathological factors were further evaluated using a tissue microarray. Differentially expressed genes associated with SMARCC1 in HCC were obtained and analyzed via the LinkedOmics and GEPIA databases and Cytoscape software. To verify the important role of SMARCC1 in HCC, we knocked down and overexpressed SMARCC1 in different hepatic cell lines and conducted several functional experiments. Then, we evaluated the mutation profiles and transcriptional regulators of SMARCC1 using the cBioPortal, COSMIC, CistromeDB and TCGA databases. Finally, we addressed the relationship of SMARCC1 expression with immune cell infiltration via TIMER database analysis. Results Through data mining and tissue microarray verification, we found that the protein and mRNA levels of SMARCC1 are high in tumor tissues, which has remarkable diagnostic value in HCC patients. SMARCC1 and its hub genes showed prognostic value in HCC. Furthermore, we confirmed that SMARCC1 influenced the proliferation, migration, and invasion of HCC cells. Moreover, correlation analyses revealed that SMARCC1 expression was positively correlated with ZBTB40 transcription factors and negatively correlated with the DNA methylation level. Overall, we found that SMARCC1 affects immune infiltration and plays a tumor-promoting role in HCC. Conclusions SMARCC1 is overexpressed and is a putative prognostic predictor in HCC. Due to the tumor-promoting role of SMARCC1, treatments inhibiting DNA methyltransferases and transcription factors or weakening the role of SMARCC1 in immune infiltration might improve the survival of HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02413-w.
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305
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Zhang J, Zhang H, Wang Y, Wang Q. MCM2-7 in Clear Cell Renal Cell Carcinoma: MCM7 Promotes Tumor Cell Proliferation. Front Oncol 2021; 11:782755. [PMID: 34993142 PMCID: PMC8724441 DOI: 10.3389/fonc.2021.782755] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) accounts for 60-70% of renal cell carcinoma (RCC) cases. Finding more therapeutic targets for advanced ccRCC is an urgent mission. The minichromosome maintenance proteins 2-7 (MCM2-7) protein forms a stable heterohexamer and plays an important role in DNA replication in eukaryotic cells. In the study, we provide a comprehensive study of MCM2-7 genes expression and their potential roles in ccRCC. Methods The expression and prognosis of the MCM2-7 genes in ccRCC were analyzed using data from TCGA, GEO and ArrayExpress. MCM2-7 related genes were identified by weighted co-expression network analysis (WGCNA) and Metascape. CancerSEA and GSEA were used to analyze the function of MCM2–7 genes in ccRCC. The gene effect scores (CERES) of MCM2-7, which reflects carcinogenic or tumor suppressor, were obtained from DepMap. We used clinical and expression data of MCM2-7 from the TCGA dataset and the LASSO Cox regression analysis to develop a risk score to predict survival of patients with ccRCC. The correlations between risk score and other clinical indicators such as gender, age and stage were also analyzed. Further validation of this risk score was engaged in another cohort, E-MTAB-1980 from the ArrayExpress dataset. Results The mRNA and protein expression of MCM2-7 were increased in ccRCC compared with normal tissues. High MCM2, MCM4, MCM6 and MCM7 expression were associated with a poor prognosis of ccRCC patients. Functional enrichment analysis revealed that MCM2-7 might influence the progress of ccRCC by regulating the cell cycle. Knockdown of MCM7 can inhibit the proliferation of ccRCC cells. A two-gene risk score including MCM4 and MCM6 can predict overall survival (OS) of ccRCC patients. The risk score was successfully verified by further using Arrayexpress cohort. Conclusion We analyze MCM2-7 mRNA and protein levels in ccRCC. MCM7 is determined to promote tumor proliferation. Meanwhile, our study has determined a risk score model composed of MCM2-7 can predict the prognosis of ccRCC patients, which may help future treatment strategies.
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Affiliation(s)
- Junneng Zhang
- Laboratory Medicine Department, The Fifth Hospital of Xiamen, Xiamen, China
- *Correspondence: Junneng Zhang, ; Qingshui Wang,
| | - Huanzong Zhang
- Laboratory Medicine Department, The Fifth Hospital of Xiamen, Xiamen, China
| | - Yinghui Wang
- Laboratory Medicine Department, The Fifth Hospital of Xiamen, Xiamen, China
| | - Qingshui Wang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Junneng Zhang, ; Qingshui Wang,
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306
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Yi X, Zheng Z, Xu H, Zhou Y, Huang D, Wang J, Feng X, Zhao K, Fan X, Zhang S, Dong X, Wang Z, Shen Y, Cheng H, Shi L, Li MJ. Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience 2021; 24:103468. [PMID: 34888502 PMCID: PMC8634045 DOI: 10.1016/j.isci.2021.103468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/23/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022] Open
Abstract
Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and revealed many known and novel TRs manipulating context-specific pathways. To explore TR cooperation across broad tissue/cell types, we systematically leveraged large-scale open chromatin profiles, computational footprinting, and high-resolution chromatin interactions to investigate tissue/cell type-specific TR cooperation. We first delineated a landscape of TR cooperation across 40 human tissue/cell types. Network modularity analyses uncovered the commonality and specificity of TR cooperation in different conditions. We also demonstrated that TR cooperation information can better interpret the disease-causal variants identified by genome-wide association studies and recapitulate cell states during neural development. Our study characterizes shared and unique patterns of TR cooperation associated with the cell type specificity of gene regulation in 3D chromatin. Computational inference of transcriptional regulator (TR) cooperation in 3D chromatin A landscape of 3D TR cooperation across 40 human tissue/cell types TR cooperation can better interpret the disease-causal variants identified by GWAS Cooperation of certain TRs shapes context-specific gene regulation in cell development
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Affiliation(s)
- Xianfu Yi
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, China.,Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Zhanye Zheng
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hang Xu
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiangling Feng
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Ke Zhao
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shijie Zhang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiaobao Dong
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhao Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin 300070, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
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307
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Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun 2021; 12:7292. [PMID: 34911933 PMCID: PMC8674326 DOI: 10.1038/s41467-021-27615-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying precise molecular subtypes attributable to specific stages of localized prostate cancer has proven difficult due to high levels of heterogeneity. Bulk assays represent a population-average, which mask the heterogeneity that exists at the single-cell level. In this work, we sequence the accessible chromatin regions of 14,424 single-cells from 18 flash-frozen prostate tumours. We observe shared chromatin features among low-grade prostate cancer cells are lost in high-grade tumours. Despite this loss, high-grade tumours exhibit an enrichment for FOXA1, HOXB13 and CDX2 transcription factor binding sites, indicating a shared trans-regulatory programme. We identify two unique genes encoding neuronal adhesion molecules that are highly accessible in high-grade prostate tumours. We show NRXN1 and NLGN1 expression in epithelial, endothelial, immune and neuronal cells in prostate cancer using cyclic immunofluorescence. Our results provide a deeper understanding of the active gene regulatory networks in primary prostate tumours, critical for molecular stratification of the disease.
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Affiliation(s)
- Sebnem Ece Eksi
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA.
| | - Alex Chitsazan
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
| | - Zeynep Sayar
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA
| | - George V Thomas
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Pathology & Laboratory Medicine, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew J Fields
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Ryan P Kopp
- Department of Urology, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew C Adey
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA.
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308
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Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer. Cell Rep 2021; 37:110109. [PMID: 34910907 PMCID: PMC8889623 DOI: 10.1016/j.celrep.2021.110109] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 01/27/2023] Open
Abstract
This study addresses the roles of nuclear receptor corepressor 2 (NCOR2) in prostate cancer (PC) progression in response to androgen deprivation therapy (ADT). Reduced NCOR2 expression significantly associates with shorter disease-free survival in patients with PC receiving adjuvant ADT. Utilizing the CWR22 xenograft model, we demonstrate that stably reduced NCOR2 expression accelerates disease recurrence following ADT, associates with gene expression patterns that include neuroendocrine features, and induces DNA hypermethylation. Stably reduced NCOR2 expression in isogenic LNCaP (androgen-sensitive) and LNCaP-C4–2 (androgen-independent) cells revealed that NCOR2 reduction phenocopies the impact of androgen treatment and induces global DNA hypermethylation patterns. NCOR2 genomic binding is greatest in LNCaP-C4–2 cells and most clearly associates with forkhead box (FOX) transcription factor FOXA1 binding. NCOR2 binding significantly associates with transcriptional regulation most when in active enhancer regions. These studies reveal robust roles for NCOR2 in regulating the PC transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PC disease progression. Long et al. show that reduced levels of NCOR2 lead to accelerated prostate cancer recurrence during androgen withdrawal in a patient-derived xenograft model. NCOR2 reduction is characterized by incomplete response to androgen withdrawal, and recurrent tumors show increased neuroendocrine traits. These phenotypic changes are associated with hypermethylated enhancers.
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309
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Ghamlouch H, Boyle EM, Blaney P, Wang Y, Choi J, Williams L, Bauer M, Auclair D, Bruno B, Walker BA, Davies FE, Morgan GJ. Insights into high-risk multiple myeloma from an analysis of the role of PHF19 in cancer. J Exp Clin Cancer Res 2021; 40:380. [PMID: 34857028 PMCID: PMC8638425 DOI: 10.1186/s13046-021-02185-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/13/2021] [Indexed: 02/07/2023] Open
Abstract
Despite improvements in outcome, 15-25% of newly diagnosed multiple myeloma (MM) patients have treatment resistant high-risk (HR) disease with a poor survival. The lack of a genetic basis for HR has focused attention on the role played by epigenetic changes. Aberrant expression and somatic mutations affecting genes involved in the regulation of tri-methylation of the lysine (K) 27 on histone 3 H3 (H3K27me3) are common in cancer. H3K27me3 is catalyzed by EZH2, the catalytic subunit of the Polycomb Repressive Complex 2 (PRC2). The deregulation of H3K27me3 has been shown to be involved in oncogenic transformation and tumor progression in a variety of hematological malignancies including MM. Recently we have shown that aberrant overexpression of the PRC2 subunit PHD Finger Protein 19 (PHF19) is the most significant overall contributor to HR status further focusing attention on the role played by epigenetic change in MM. By modulating both the PRC2/EZH2 catalytic activity and recruitment, PHF19 regulates the expression of key genes involved in cell growth and differentiation. Here we review the expression, regulation and function of PHF19 both in normal and the pathological contexts of solid cancers and MM. We present evidence that strongly implicates PHF19 in the regulation of genes important in cell cycle and the genetic stability of MM cells making it highly relevant to HR MM behavior. A detailed understanding of the normal and pathological functions of PHF19 will allow us to design therapeutic strategies able to target aggressive subsets of MM.
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Affiliation(s)
- Hussein Ghamlouch
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA.
| | - Eileen M Boyle
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
- Applied Bioinformatics Laboratories (ABL), NYU Langone Medical Center, New York, NY, USA
| | - Yubao Wang
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Jinyoung Choi
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Louis Williams
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Daniel Auclair
- The Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - Benedetto Bruno
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Faith E Davies
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA.
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310
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White SM, Snyder MP, Yi C. Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic Acids Res 2021; 49:12196-12210. [PMID: 34850122 PMCID: PMC8643643 DOI: 10.1093/nar/gkab1105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/09/2021] [Accepted: 11/15/2021] [Indexed: 12/28/2022] Open
Abstract
The term 'super enhancers' (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of >600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis revealed that compared to classic SEs and regular enhancers, aSEs are tightly bound by a dense array of master lineage TFs, which serve as anchors to recruit additional TFs and co-factors in trans. In addition, aSEs are preferentially enriched for Cohesins, which likely involve in stabilizing long-distance interactions between aSEs and their distal target genes. Finally, we showed that aSEs can be reliably predicted using a single DNase-seq data or combined with Mediator and/or P300 ChIP-seq. Overall, our study demonstrates that aSEs represent a unique class of functionally important enhancer elements that distally regulate the transcription of highly expressed genes.
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Affiliation(s)
- Shannon M White
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chunling Yi
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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311
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Niu J, Qin B, Wang C, Chen C, Yang J, Shao H. Identification of Key Immune-Related Genes in the Progression of Septic Shock. Front Genet 2021; 12:668527. [PMID: 34804111 PMCID: PMC8595268 DOI: 10.3389/fgene.2021.668527] [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: 02/16/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Septic shock is the severe complication of sepsis, with a high mortality. The inflammatory response regulates the immune status and mediates the progression of septic shock. In this study, we aim to identify the key immune-related genes (IRGs) of septic shock and explore their potential mechanism. Methods: Gene expression profiles of septic shock blood samples and normal whole blood samples were retrieved from the Gene Expression Omnibus (GEO) and Genotype-Tissue Expression Portal (GTEx). The differential expression genes (DEGs) and septic shock-specific immune-related genes (SSSIRGs) were evaluated and identified, along with the immune components by "cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT, version x)" algorithm. Additionally, in order to explore the key regulatory network, the relationship among SSSIRGs, upstream transcription factors (TFs), and downstream signaling pathways were also identified by Gene Set Variation Analysis (GSVA) and co-expression analysis. Moreover, the Connectivity Map (CMap) analysis was applied to find bioactive small molecules against the members of regulation network while Chromatin Immunoprecipitation sequencing (ChIP-seq) and Assay for Targeting Accessible-Chromatin with high-throughput sequencing (ATAC-seq) data were used to validate the regulation mechanism of the network. Results: A total of 14,843 DEGs were found between 63 septic shock blood samples and 337 normal whole blood samples. Then, we identified septic shock-specific 839 IRGs as the intersection of DEGs and IRGs. Moreover, we uncovered the regulatory networks based on co-expression analysis and found 28 co-expression interaction pairs. In the regulation network, protein phosphatase 3, catalytic subunit, alpha isozyme (PPP3CA) may regulate late estrogen response, glycolysis and TNFα signaling via NFκB and HLA; Kirsten rat sarcoma viral oncogene homolog (KRAS) may be related to late estrogen response and HLA; and Toll-like receptor 8 (TLR8) may be associated with TNFα signaling via NFκB. And the regulation mechanisms between TFs and IRGs (TLR8, PPP3CA, and KRAS) were validated by ChIP-seq and ATAC-seq. Conclusion: Our data identify three SSSIRGs (TLR8, PPP3CA, and KRAS) as candidate therapeutic targets for septic shock and provide constructed regulatory networks in septic shock to explore its potential mechanism.
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Affiliation(s)
- Jingjing Niu
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Bingyu Qin
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Cunzhen Wang
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Chao Chen
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Jianxu Yang
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Huanzhang Shao
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
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312
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Liu J, Tokheim C, Lee JD, Gan W, North BJ, Liu XS, Pandolfi PP, Wei W. Genetic fusions favor tumorigenesis through degron loss in oncogenes. Nat Commun 2021; 12:6704. [PMID: 34795215 PMCID: PMC8602260 DOI: 10.1038/s41467-021-26871-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Chromosomal rearrangements can generate genetic fusions composed of two distinct gene sequences, many of which have been implicated in tumorigenesis and progression. Our study proposes a model whereby oncogenic gene fusions frequently alter the protein stability of the resulting fusion products, via exchanging protein degradation signal (degron) between gene sequences. Computational analyses of The Cancer Genome Atlas (TCGA) identify 2,406 cases of degron exchange events and reveal an enrichment of oncogene stabilization due to loss of degrons from fusion. Furthermore, we identify and experimentally validate that some recurrent fusions, such as BCR-ABL, CCDC6-RET and PML-RARA fusions, perturb protein stability by exchanging internal degrons. Likewise, we also validate that EGFR or RAF1 fusions can be stabilized by losing a computationally-predicted C-terminal degron. Thus, complementary to enhanced oncogene transcription via promoter swapping, our model of degron loss illustrates another general mechanism for recurrent fusion proteins in driving tumorigenesis.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jonathan D Lee
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Brian J North
- Department of Biomedical Sciences, Creighton University, Omaha, NE, 68178, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10124, Italy.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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313
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Su G, Wang W, Zhao X, Chen J, Zheng J, Liu M, Bi J, Guo D, Chen B, Zhao Z, Shi J, Zhang L, Lu W. Enhancer architecture-dependent multilayered transcriptional regulation orchestrates RA signaling-induced early lineage differentiation of ESCs. Nucleic Acids Res 2021; 49:11575-11595. [PMID: 34723340 PMCID: PMC8599802 DOI: 10.1093/nar/gkab1001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Signaling pathway-driven target gene transcription is critical for fate determination of embryonic stem cells (ESCs), but enhancer-dependent transcriptional regulation in these processes remains poorly understood. Here, we report enhancer architecture-dependent multilayered transcriptional regulation at the Halr1–Hoxa1 locus that orchestrates retinoic acid (RA) signaling-induced early lineage differentiation of ESCs. We show that both homeobox A1 (Hoxa1) and Hoxa adjacent long non-coding RNA 1 (Halr1) are identified as direct downstream targets of RA signaling and regulated by RARA/RXRA via RA response elements (RAREs). Chromosome conformation capture-based screens indicate that RA signaling promotes enhancer interactions essential for Hoxa1 and Halr1 expression and mesendoderm differentiation of ESCs. Furthermore, the results also show that HOXA1 promotes expression of Halr1 through binding to enhancer; conversely, loss of Halr1 enhances interaction between Hoxa1 chromatin and four distal enhancers but weakens interaction with chromatin inside the HoxA cluster, leading to RA signaling-induced Hoxa1 overactivation and enhanced endoderm differentiation. These findings reveal complex transcriptional regulation involving synergistic regulation by enhancers, transcription factors and lncRNA. This work provides new insight into intrinsic molecular mechanisms underlying ESC fate determination during RA signaling-induced early differentiation.
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Affiliation(s)
- Guangsong Su
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Wenbin Wang
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Xueyuan Zhao
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jun Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jian Zheng
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Man Liu
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jinfang Bi
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Dianhao Guo
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Bohan Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Zhongfang Zhao
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jiandang Shi
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Lei Zhang
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Wange Lu
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
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314
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Hu C, Yang L, Wang Y, Zhou S, Luo J, Gu Y. Ginsenoside Rh2 reduces m6A RNA methylation in cancer via the KIF26B-SRF positive feedback loop. J Ginseng Res 2021; 45:734-743. [PMID: 34764728 PMCID: PMC8569326 DOI: 10.1016/j.jgr.2021.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
Background The underlying mechanisms of the potential tumor-suppressive effects of ginsenoside Rh2 are complex. N6-methyladenosine (m6A) RNA methylation is usually dysregulated in cancer. This study explored the regulatory effect of ginsenoside Rh2 on m6A RNA methylation in cancer. Methods: m6A RNA quantification and gene-specific m6A RIP-qPCR assays were applied to assess total and gene-specific m6A RNA levels. Co-immunoprecipitation, fractionation western blotting, and immunofluorescence staining were performed to detect protein interactions and distribution. QRT-PCR, dual-luciferase, and ChIP-qPCR assays were conducted to check the transcriptional regulation. Results Ginsenoside Rh2 reduces m6A RNA methylation and KIF26B expression in a dose-dependent manner in some cancers. KIF26B interacts with ZC3H13 and CBLL1 in the cytoplasm of cancer cells and enhances their nuclear distribution. KIF26B inhibition reduces m6A RNA methylation level in cancer cells. SRF bound to the KIF26B promoter and activated its transcription. SRF mRNA m6A abundance significantly decreased upon KIF26B silencing. SRF knockdown suppressed cancer cell proliferation and growth both in vitro and in vivo, the effect of which was partly rescued by KIF26B overexpression. Conclusion: ginsenoside Rh2 reduces m6A RNA methylation via downregulating KIF26B expression in some cancer cells. KIF26B elevates m6A RNA methylation via enhancing ZC3H13/CBLL1 nuclear localization. KIF26B-SRF forms a positive feedback loop facilitating tumor growth.
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Affiliation(s)
- Chunmei Hu
- Department of Otolaryngology-Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Linhan Yang
- Outpatient Department, Chengdu Aurora Huan Hua Xiang, Chengdu, Sichuan, China
| | - Yi Wang
- Department of Specialty of Geriatric Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Shijie Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
- Corresponding author. State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, Sichuan, China
| | - Jing Luo
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Corresponding author. Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Yi Gu
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Corresponding author. Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
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315
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Hammal F, de Langen P, Bergon A, Lopez F, Ballester B. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res 2021; 50:D316-D325. [PMID: 34751401 PMCID: PMC8728178 DOI: 10.1093/nar/gkab996] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches 4.8M peaks, 423 TRs across 694 datasets. Also, this ReMap release is enriched by two new regulatory catalogs for Mus musculus and Drosophila melanogaster. First, the Mouse regulatory catalog consists of 123M peaks across 648 TRs as a result of the integration and validation of 5503 ChIP-seq datasets. Second, the Drosophila melanogaster catalog contains 16.6M peaks across 550 TRs from the integration of 1205 datasets. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers. Finally, ReMap 2022 comes with a new Cis Regulatory Module identification method, improved quality controls, faster search results, and better user experience with an interactive tour and video tutorials on browsing and filtering ReMap catalogs.
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316
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Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br J Cancer 2021; 125:1408-1419. [PMID: 34526665 PMCID: PMC8575955 DOI: 10.1038/s41416-021-01545-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/04/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Integration of human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC), yet the tumorigenicity of cis genomic changes at integration sites remains largely understudied. METHODS Combining multi-omics data from The Cancer Genome Atlas with patient-matched long-read sequencing of HPV integration sites, we developed a strategy for using HPV integration events to identify and prioritise novel candidate ICC target genes (integration-detected genes (IDGs)). Four IDGs were then chosen for in vitro functional studies employing small interfering RNA-mediated knockdown in cell migration, proliferation and colony formation assays. RESULTS PacBio data revealed 267 unique human-HPV breakpoints comprising 87 total integration events in eight tumours. Candidate IDGs were filtered based on the following criteria: (1) proximity to integration site, (2) clonal representation of integration event, (3) tumour-specific expression (Z-score) and (4) association with ICC survival. Four candidates prioritised based on their unknown function in ICC (BNC1, RSBN1, USP36 and TAOK3) exhibited oncogenic properties in cervical cancer cell lines. Further, annotation of integration events provided clues regarding potential mechanisms underlying altered IDG expression in both integrated and non-integrated ICC tumours. CONCLUSIONS HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.
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317
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Astudillo P. An emergent Wnt5a/YAP/TAZ regulatory circuit and its possible role in cancer. Semin Cell Dev Biol 2021; 125:45-54. [PMID: 34764023 DOI: 10.1016/j.semcdb.2021.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 12/29/2022]
Abstract
Wnt5a is a ligand that plays several roles in development, homeostasis, and disease. A growing body of evidence indicates that Wnt5a is involved in cancer progression. Despite extensive research in this field, our knowledge about how Wnt5a is precisely involved in cancer is still incomplete. It is usually thought that certain combinations of Frizzled receptors and co-receptors might explain the observed effects of Wnt5a either as a tumor suppressor or by promoting migration and invasion. While accepting this 'receptor context' model, this review proposes that Wnt5a is integrated within a larger regulatory circuit involving β-catenin, YAP/TAZ, and LATS1/2. Remarkably, WNT5A and YAP1 are transcriptionally regulated by the Hippo and Wnt pathways, respectively, and might form a regulatory circuit acting through LATS kinases and secreted Wnt/β-catenin inhibitors, including Wnt5a itself. Therefore, understanding the precise role of Wnt5a and YAP in cancer requires a systems biology perspective.
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Affiliation(s)
- Pablo Astudillo
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile.
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318
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Nath A, Rayabaram J, Ijee S, Bagchi A, Chaudhury AD, Roy D, Chambayil K, Singh J, Nakamura Y, Velayudhan SR. Comprehensive Analysis of microRNAs in Human Adult Erythropoiesis. Cells 2021; 10:3018. [PMID: 34831239 PMCID: PMC8616439 DOI: 10.3390/cells10113018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs, which play an important role in various cellular and developmental processes. The study of miRNAs in erythropoiesis is crucial to uncover the cellular pathways that are modulated during the different stages of erythroid differentiation. Using erythroid cells derived from human CD34+ hematopoietic stem and progenitor cells (HSPCs)and small RNA sequencing, our study unravels the various miRNAs involved in critical cellular pathways in erythroid maturation. We analyzed the occupancy of erythroid transcription factors and chromatin accessibility in the promoter and enhancer regions of the differentially expressed miRNAs to integrate miRNAs in the transcriptional circuitry of erythropoiesis. Analysis of the targets of the differentially expressed miRNAs revealed novel pathways in erythroid differentiation. Finally, we described the application of Clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) based editing of miRNAs to study their function in human erythropoiesis.
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Affiliation(s)
- Aneesha Nath
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Janakiram Rayabaram
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Abhirup Bagchi
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
| | - Debanjan Roy
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
- Manipal Academy of Higher Education, Manipal 576119, India
| | - Karthik Chambayil
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Jyoti Singh
- National Centre for Cell Science, University of Pune Campus, Pune 411007, India;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan;
| | - Shaji R. Velayudhan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
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319
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Zhang H, Lu T, Liu S, Yang J, Sun G, Cheng T, Xu J, Chen F, Yen K. Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. NAR Genom Bioinform 2021; 3:lqab094. [PMID: 34729473 PMCID: PMC8557372 DOI: 10.1093/nargab/lqab094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Tn5 transposase, which can efficiently tagment the genome, has been widely adopted as a molecular tool in next-generation sequencing, from short-read sequencing to more complex methods such as assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we systematically map Tn5 insertion characteristics across several model organisms, finding critical parameters that affect its insertion. On naked genomic DNA, we found that Tn5 insertion is not uniformly distributed or random. To uncover drivers of these biases, we used a machine learning framework, which revealed that DNA shape cooperatively works with DNA motif to affect Tn5 insertion preference. These intrinsic insertion preferences can be modeled using nucleotide dependence information from DNA sequences, and we developed a computational pipeline to correct for these biases in ATAC-seq data. Using our pipeline, we show that bias correction improves the overall performance of ATAC-seq peak detection, recovering many potential false-negative peaks. Furthermore, we found that these peaks are bound by transcription factors, underscoring the biological relevance of capturing this additional information. These findings highlight the benefits of an improved understanding and precise correction of Tn5 insertion preference.
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Affiliation(s)
- Houyu Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shan Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jianyu Yang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jin Xu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Kuangyu Yen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
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320
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Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer. Nat Commun 2021; 12:6377. [PMID: 34737261 PMCID: PMC8568894 DOI: 10.1038/s41467-021-26612-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
Endocrine therapies for prostate cancer inhibit the androgen receptor (AR) transcription factor. In most cases, AR activity resumes during therapy and drives progression to castration-resistant prostate cancer (CRPC). However, therapy can also promote lineage plasticity and select for AR-independent phenotypes that are uniformly lethal. Here, we demonstrate the stem cell transcription factor Krüppel-like factor 5 (KLF5) is low or absent in prostate cancers prior to endocrine therapy, but induced in a subset of CRPC, including CRPC displaying lineage plasticity. KLF5 and AR physically interact on chromatin and drive opposing transcriptional programs, with KLF5 promoting cellular migration, anchorage-independent growth, and basal epithelial cell phenotypes. We identify ERBB2 as a point of transcriptional convergence displaying activation by KLF5 and repression by AR. ERBB2 inhibitors preferentially block KLF5-driven oncogenic phenotypes. These findings implicate KLF5 as an oncogene that can be upregulated in CRPC to oppose AR activities and promote lineage plasticity.
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321
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Hadar A, Kapitansky O, Ganaiem M, Sragovich S, Lobyntseva A, Giladi E, Yeheskel A, Avitan A, Vatine GD, Gurwitz D, Ivashko-Pachima Y, Gozes I. Introducing ADNP and SIRT1 as new partners regulating microtubules and histone methylation. Mol Psychiatry 2021; 26:6550-6561. [PMID: 33967268 DOI: 10.1038/s41380-021-01143-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Activity-dependent neuroprotective protein (ADNP) is essential for brain formation and function. As such, de novo mutations in ADNP lead to the autistic ADNP syndrome and somatic ADNP mutations may drive Alzheimer's disease (AD) tauopathy. Sirtuin 1 (SIRT1) is positively associated with aging, the major risk for AD. Here, we revealed two key interaction sites for ADNP and SIRT1. One, at the microtubule end-binding protein (EB1 and EB3) Tau level, with EB1/EB3 serving as amplifiers for microtubule dynamics, synapse formation, axonal transport, and protection against tauopathy. Two, on the DNA/chromatin site, with yin yang 1, histone deacetylase 2, and ADNP, sharing a DNA binding motif and regulating SIRT1, ADNP, and EB1 (MAPRE1). This interaction was linked to sex- and age-dependent altered histone modification, associated with ADNP/SIRT1/WD repeat-containing protein 5, which mediates the assembly of histone modification complexes. Single-cell RNA and protein expression analyses as well as gene expression correlations placed SIRT1-ADNP and either MAPRE1 (EB1), MAPRE3 (EB3), or both in the same mouse and human cell; however, while MAPRE1 seemed to be similarly regulated to ADNP and SIRT1, MAPRE3 seemed to deviate. Finally, we demonstrated an extremely tight correlation for the gene transcripts described above, including related gene products. This correlation was specifically abolished in affected postmortem AD and Parkinson's disease brain select areas compared to matched controls, while being maintained in blood samples. Thus, we identified an ADNP-SIRT1 complex that may serve as a new target for the understanding of brain degeneration.
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Affiliation(s)
- Adva Hadar
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Weizmann Institute of Science, Rehovot, Israel
| | - Oxana Kapitansky
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Maram Ganaiem
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Sragovich
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Alexandra Lobyntseva
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Eliezer Giladi
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Adva Yeheskel
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aliza Avitan
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, The Regenerative Medicine and Stem Cell (RMSC) Research Center and the Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Gad D Vatine
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, The Regenerative Medicine and Stem Cell (RMSC) Research Center and the Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Yanina Ivashko-Pachima
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Illana Gozes
- The Elton Laboratory for Neuroendocrinology, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel. .,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.
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322
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Li Y, Qiu X, Wang X, Liu H, Geck RC, Tewari AK, Xiao T, Font-Tello A, Lim K, Jones KL, Morrow M, Vadhi R, Kao PL, Jaber A, Yerrum S, Xie Y, Chow KH, Cejas P, Nguyen QD, Long HW, Liu XS, Toker A, Brown M. FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance. Nat Cell Biol 2021; 23:1187-1198. [PMID: 34737445 DOI: 10.1038/s41556-021-00781-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/26/2021] [Indexed: 12/20/2022]
Abstract
How cancer cells adapt to evade the therapeutic effects of drugs targeting oncogenic drivers is poorly understood. Here we report an epigenetic mechanism leading to the adaptive resistance of triple-negative breast cancer (TNBC) to fibroblast growth factor receptor (FGFR) inhibitors. Prolonged FGFR inhibition suppresses the function of BRG1-dependent chromatin remodelling, leading to an epigenetic state that derepresses YAP-associated enhancers. These chromatin changes induce the expression of several amino acid transporters, resulting in increased intracellular levels of specific amino acids that reactivate mTORC1. Consistent with this mechanism, addition of mTORC1 or YAP inhibitors to FGFR blockade synergistically attenuated the growth of TNBC patient-derived xenograft models. Collectively, these findings reveal a feedback loop involving an epigenetic state transition and metabolic reprogramming that leads to adaptive therapeutic resistance and provides potential therapeutic strategies to overcome this mechanism of resistance.
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Affiliation(s)
- Yihao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hui Liu
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Renee C Geck
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen L Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Murry Morrow
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Raga Vadhi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pei-Lun Kao
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aliya Jaber
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Smitha Yerrum
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kin-Hoe Chow
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Quang-Dé Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex Toker
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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323
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Huang R, Wang S, Zhu R, Xian S, Huang Z, Cheng L, Zhang J. Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:728242. [PMID: 34708039 PMCID: PMC8542800 DOI: 10.3389/fcell.2021.728242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Spinal cord injury (SCI) is a severe neurological deficit affecting both young and older people worldwide. The potential role of key enhancer RNAs (eRNAs) in SCI remains elusive, which is a prominent challenge in the trauma repair process. This study aims to investigate the roles of key eRNAs, transcription factors (TFs), signaling pathways, and small-molecule inhibitors in SCI using multi-omics bioinformatics analysis. Methods: Microarray data of peripheral blood mononuclear cell (PBMC) samples from 27 healthy volunteers and 25 chronic-phase SCI patients were retrieved from the Gene Expression Omnibus database. Differentially expressed transcription factors (DETFs), differentially expressed enhancer RNAs (DEeRNAs), and differentially expressed target genes (DETGs) were identified using the Linear Models for Microarray Data (limma) package. Fraction of immune cells was estimated using CIBERSORT algorithm. Gene Set Variation Analysis (GSVA) was applied to identify the downstream signaling pathways. The eRNA regulatory network was constructed based on the correlation results. Connectivity Map (CMap) database was used to find potential drugs for SCI patients. The cellular communication analysis was performed to explore the molecular regulation mechanism of SCI based on single-cell RNA sequencing (scRNA-seq) data. Chromatin immunoprecipitation sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data were used to validate the key regulatory mechanisms. scRNA-seq dataset was used to validate the cell subtype localization of the key eRNAs. Results: In total, 21 DETFs, 24 DEeRNAs, and 829 DETGs were identified. A regulatory network of 13 DETFs, six DEeRNAs, seven DETGs, two hallmark pathways, two immune cells, and six immune pathways was constructed. The link of Splicing factor proline and glutamine rich (SFPQ) (TF) and vesicular overexpressed in cancer prosurvival protein 1 (VOPP1) (eRNA) (R = 0.990, p < 0.001, positive), VOPP1 (eRNA) and epidermal growth factor receptor (EGFR) (target gene) (R = 0.974, p < 0.001, positive), VOPP1, and T helper (Th) cells (R = -0.987, p < 0.001, negative), and VOPP1 and hallmark coagulation (R = 0.937, p < 0.001, positive) was selected. Trichostatin A was considered the best compound target to SCI-related eRNAs (specificity = 0.471, p < 0.001). Conclusion: VOPP1, upregulated by SFPQ, strengthened the transient expression of EGFR. Th cells and coagulation were the potential downstream pathways of VOPP1. This regulatory network and potential inhibitors provide novel diagnostic biomarkers and therapeutic targets for SCI.
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Affiliation(s)
- Runzhi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Rui Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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324
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Zhang L, Li H, Qiu Y, Liu Y, Liu X, Wang W. Screening and cellular validation of prognostic genes regulated by super enhancers in oral squamous cell carcinoma. Bioengineered 2021; 12:10073-10088. [PMID: 34709988 PMCID: PMC8810015 DOI: 10.1080/21655979.2021.1997089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the leading cause of death in patients with head and neck cancer. Reliable biomarkers to guide treatment decisions for OSCC remain scarce. The purpose of this study was to identify novel prognostic markers regulated by super enhancers in OSCC. Eight modules were obtained by weighted gene co-expression network analysis (WGCNA), among which MEblue module had the highest correlation with tumor stage, alcohol consumption and smoking. There were 41 genes regulated by super enhancers in MEblue module. Functional analysis showed that 41 super enhancer-regulated genes were involved in cancer progression. A total of twenty transcription factors of the 41 genes were predicted. Prognostic analysis of the 41 genes and the top 5 transcription factors showed that patients with high expression of AHCY, KCMF1, MANBAL and TFDP1 had a poor prognosis. Immunohistochemical analysis showed that AHCY, KCMF1 and MANBAL were highly expressed in OSCC tissue. Cellular experiment demonstrated that TFDP1 promoted AHCY, KCMF1 and MANBAL expression by binding to the super enhancers of these genes. Knockdown of TFDP1, AHCY, KCMF1 and MANBAL inhibited the proliferation of OSCC cells. In conclusion, AHCY, KCMF1 and MANBAL were recognized as super enhancer-regulated prognostic biomarkers regulated by TFDP1 in OSCC.
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Affiliation(s)
- Liru Zhang
- Department of Stomatology, Second Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, China
| | - Huanju Li
- Department of Surgery, Gucheng County Hospital, Hengshui, Hebei 253800, China
| | - Yongle Qiu
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Yuanhang Liu
- Department of Stomatology, Second Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, China
| | - Xin Liu
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Wenjing Wang
- Department of Stomatology, Fourth Affiliated Hospital, Hebei Medical University, Shijiazhuang, Hebei 050017, China
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325
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Li GS, Yang LJ, Chen G, Huang SN, Fang YY, Huang WJ, Lu W, He J, Liu HC, Li LY, Mo BY, Lu HP. Laryngeal Squamous Cell Carcinoma: Clinical Significance and Potential Mechanism of Cell Division Cycle 45. Cancer Biother Radiopharm 2021; 37:300-312. [PMID: 34672813 DOI: 10.1089/cbr.2020.4314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Cell division cycle 45 (CDC45) plays an important role in the occurrence and development of numerous carcinomas, but its effect in laryngeal squamous cell carcinoma (LSCC) remains unclear. Materials and Methods: The messenger RNA and protein expression levels of CDC45 in LSCC were evaluated with a t test and the standard mean difference (SMD). The ability of CDC45 expression to distinguish the LSCC was assessed through receiver operating characteristic (ROC) curves. Gene set enrichment analysis (GSEA), protein-protein interaction, public databases, and online tools were used to explore the potential molecular mechanism of CDC45 in LSCC. Results: A high expression of CDC45 was identified in LSCC (SMD = 2.61, 95% confidence interval [1.62-3.61]). Through ROC curves, the expression of CDC45 makes it feasible to distinguish the LSCC group from the non-LSCC counterpart. CDC45 was relevant to the progression-free interval of LSCC patients (log-rank p = 0.03). GSEAs show that CDC45 is related to the cell cycle. CDC45, CDC6, KIF2C, and AURKB were identified as hub genes of LSCC. E2F1 may be the regulatory transcription factor of CDC45. Conclusions: High expression of CDC45 likely demonstrates carcinogenic effects in LSCC, and CDC45 is a potential target in screening and treatment of LSCC.
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Affiliation(s)
- Guo-Sheng Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Lin-Jie Yang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Su-Ning Huang
- Department of Radiotherapy, Guangxi Medical University Cancer Hospital, Nanning, P.R. China
| | - Ye-Ying Fang
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Wei-Jian Huang
- Department of Pathology, Redcross Hospital of Yulin, Yulin, P.R. China
| | - Wei Lu
- Department of Pathology, Nanning Second People's Hospital, Third Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Juan He
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - He-Chuan Liu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Lin-Yi Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Bin-Yu Mo
- Department of Otolaryngology, Liuzhou People's Hospital, Liuzhou, P.R. China
| | - Hui-Ping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
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326
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Wang X, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z, Zhang Y, Li Z, Zhang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang P, Cejas P, Lim K, Long H, Brown M, Liu XS. In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. Cell 2021; 184:5357-5374.e22. [PMID: 34582788 PMCID: PMC9136996 DOI: 10.1016/j.cell.2021.09.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/14/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that deletion of the E3 ubiquitin ligase Cop1 in cancer cells decreases secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, enhances anti-tumor immunity, and strengthens ICB response. Transcriptomics, epigenomics, and proteomics analyses revealed that Cop1 functions through proteasomal degradation of the C/ebpδ protein. The Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. In addition, deletion of the E3 ubiquitin ligase Cop1 in cancer cells stabilizes C/ebpδ to suppress expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy in TNBC by regulating chemokine secretion and macrophage infiltration in the tumor microenvironment.
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Affiliation(s)
- Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shengqing Stan Gu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Binbin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Qin Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yihao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicole Traugh
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ziyi Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Boning Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingxin Fu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jun Chu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui 230038, China
| | - Peng Jiang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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327
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Regulatory association of long noncoding RNAs and chromatin accessibility facilitates erythroid differentiation. Blood Adv 2021; 5:5396-5409. [PMID: 34644394 PMCID: PMC9153002 DOI: 10.1182/bloodadvances.2021005167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/13/2021] [Indexed: 01/17/2023] Open
Abstract
Erythroid differentiation is a dynamic process regulated by multiple factors, while the interaction between long non-coding RNAs and chromatin accessibility and its influence on erythroid differentiation remains unclear. To elucidate this interaction, we employed hematopoietic stem cells, multipotent progenitor cells, common myeloid progenitor cells, megakaryocyte-erythroid progenitor cells, and erythroblasts from human cord blood as an erythroid differentiation model to explore the coordinated regulatory functions of lncRNAs and chromatin accessibility by integrating RNA-Seq and ATAC-Seq data. We revealed that the integrated network of chromatin accessibility and lncRNAs exhibits stage-specific changes throughout the erythroid differentiation process, and that the changes at the EB stage of maturation are dramatic. We identified a subset of stage-specific lncRNAs and transcription factors (TFs) that associate with chromatin accessibility during erythroid differentiation, in which lncRNAs are key regulators of terminal erythroid differentiation via a lncRNA-TF-gene network. LncRNA PCED1B-AS1 was revealed to regulate terminal erythroid differentiation by coordinating GATA1 dynamically binding to the chromatin and interacting with cytoskeleton network during erythroid differentiation. DANCR, another lncRNA that is highly expressed at the MEP stage, was verified to promote erythroid differentiation by compromising megakaryocyte differentiation and coordinating with chromatin accessibility and TFs, such as RUNX1. Overall, our results identified the associated network of lncRNAs and chromatin accessibility in erythropoiesis and provide novel insights into erythroid differentiation and abundant resources for further study.
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328
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Zhang Y, Long X, Ruan X, Wei Q, Zhang L, Wo L, Huang D, Lin L, Wang D, Xia L, Zhao Q, Liu J, Zhao Q, He M. SIRT2-mediated deacetylation and deubiquitination of C/EBPβ prevents ethanol-induced liver injury. Cell Discov 2021; 7:93. [PMID: 34642310 PMCID: PMC8511299 DOI: 10.1038/s41421-021-00326-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
Protein acetylation has emerged to play pivotal roles in alcoholic liver disease (ALD). Sirutin 2 (SIRT2) is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase involved in the regulation of aging, metabolism, and stress. However, the role of SIRT2 in ALD remains unclear. Here, we report that the SIRT2-mediated deacetylation-deubiquitination switch of CCAAT/enhancer-binding protein beta (C/EBPβ) prevents ALD. Our results showed that hepatic SIRT2 protein expression was negatively correlated with the severity of alcoholic liver injury in ALD patients. Liver-specific SIRT2 deficiency sensitized mice to ALD, whereas transgenic SIRT2 overexpression in hepatocytes significantly prevented ethanol-induced liver injury via normalization of hepatic steatosis, lipid peroxidation, and hepatocyte apoptosis. Mechanistically, we identified C/EBPβ as a critical substrate of SIRT2 implicated in ALD. SIRT2-mediated deacetylation at lysines 102 and 211 decreased C/EBPβ ubiquitination, resulting in enhanced protein stability and subsequently increased transcription of C/EBPβ-target gene LCN2. Importantly, hepatic deacetylated C/EBPβ and LCN2 compensation reversed SIRT2 deletion-induced ALD aggravation in mice. Furthermore, C/EBPβ protein expression was positively correlated with SIRT2 and LCN2 expression in the livers of ALD patients and was inversely correlated with ALD development. Therefore, activating SIRT2-C/EBPβ-LCN2 signaling pathway is a potential therapy for ALD.
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Affiliation(s)
- Yingting Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xidai Long
- Department of Pathology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xin Ruan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Wei
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Zhang
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lulu Wo
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongdong Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longshuai Lin
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Difei Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Xia
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinghua Zhao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Junling Liu
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ming He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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329
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Wang Q, Zhong W, Deng L, Lin Q, Lin Y, Liu H, Xu L, Lu L, Chen Y, Huang J, Jiang M, Xiao H, Zhang J, Li H, Lin Y, Song C, Lin Y. The Expression and Prognostic Value of SUMO1-Activating Enzyme Subunit 1 and Its Potential Mechanism in Triple-Negative Breast Cancer. Front Cell Dev Biol 2021; 9:729211. [PMID: 34621746 PMCID: PMC8490707 DOI: 10.3389/fcell.2021.729211] [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: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 01/23/2023] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is the most invasive and metastatic subtype of breast cancer. SUMO1-activating enzyme subunit 1 (SAE1), an E1-activating enzyme, is indispensable for protein SUMOylation. SAE1 has been found to be a relevant biomarker for progression and prognosis in several tumor types. However, the role of SAE1 in TNBC remains to be elucidated. Methods: In the research, the mRNA expression of SAE1 was analyzed via the cancer genome atlas (TCGA) and gene expression omnibus (GEO) database. Cistrome DB Toolkit was used to predict which transcription factors (TFs) are most likely to increase SAE1 expression in TNBC. The correlation between the expression of SAE1 and the methylation of SAE1 or quantity of tumor-infiltrating immune cells was further invested. Single-cell analysis, using CancerSEA, was performed to query which functional states are associated with SAE1 in different cancers in breast cancer at the single-cell level. Next, weighted gene coexpression network (WGCNA) was applied to reveal the highly correlated genes and coexpression networks of SAE1 in TNBC patients, and a prognostic model containing SAE1 and correlated genes was constructed. Finally, we also examined SAE1 protein expression of 207 TNBC tissues using immunohistochemical (IHC) staining. Results: The mRNA and protein expression of SAE1 were increased in TNBC tissues compared with adjacent normal tissues, and the protein expression of SAE1 was significantly associated with overall survival (OS) and disease-free survival (DFS). Correlation analyses revealed that SAE1 expression was positively correlated with forkhead box M1 (FOXM1) TFs and negatively correlated with SAE1 methylation site (cg14042711) level. WGCNA indicated that the genes coexpressed with SAE1 belonged to the green module containing 1,176 genes. Through pathway enrichment analysis of the module, 1,176 genes were found enriched in cell cycle and DNA repair. Single-cell analysis indicated that SAE1 and its coexpression genes were associated with cell cycle, DNA damage, DNA repair, and cell proliferation. Using the LASSO COX regression, a prognostic model including SAE1 and polo-like kinase 1 (PLK1) was built to accurately predict the likelihood of DFS in TNBC patients. Conclusion: In conclusion, we comprehensively analyzed the mRNA and protein expression, prognosis, and interaction genes of SAE1 in TNBC and constructed a prognostic model including SAE1 and PLK1. These results might be important for better understanding of the role of SAE1 in TNBC. In addition, DNA methyltransferase and TFs inhibitor treatments targeting SAE1 might improve the survival of TNBC patients.
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Affiliation(s)
- Qingshui Wang
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Fujian Provincial Key Laboratory of Hepatic Drug Research, Fuzhou, China
| | - Wenting Zhong
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lin Deng
- Department of General Surgery, The 900th Hospital of the Joint Logistics Support Force, Fuzhou, China
| | - Qili Lin
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Youyu Lin
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hongxia Liu
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Luyun Xu
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lingfang Lu
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yajuan Chen
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jianping Huang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Han Xiao
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jie Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, China
| | - He Li
- Department of General Surgery, The 900th Hospital of the Joint Logistics Support Force, Fuzhou, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, China
| | - Chuangui Song
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, China
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
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330
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Jungwirth E, Panzitt K, Marschall HU, Thallinger GG, Wagner M. Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. Hepatol Commun 2021; 5:1721-1736. [PMID: 34558825 PMCID: PMC8485886 DOI: 10.1002/hep4.1749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/25/2021] [Indexed: 12/24/2022] Open
Abstract
Farnesoid X receptor (FXR) is a nuclear receptor that controls gene regulation of different metabolic pathways and represents an upcoming drug target for various liver diseases. Several data sets on genome-wide FXR binding in different species and conditions exist. We have previously reported that these data sets are heterogeneous and do not cover the full spectrum of potential FXR binding sites. Here, we report the first meta-analysis of all publicly available FXR chromatin immunoprecipitation sequencing (ChIP-seq) data sets from mouse, rat, and human across different conditions using a newly generated analysis pipeline. All publicly available single data sets were biocurated in a standardized manner and compared on every relevant level from raw reads to affected functional pathways. Individual murine data sets were then virtually merged into a single unique "FXR binding atlas" spanning all potential binding sites across various conditions. Comparison of the single biocurated data sets showed that the overlap of FXR binding sites between different species is modest and ranges from 48% (mouse-human) to 55% (mouse-rat). Moreover, in vivo data among different species are more similar than human in vivo data compared to human in vitro data. The consolidated murine global FXR binding atlas virtually increases sequencing depth and allows recovering more and novel potential binding sites and signaling pathways that were missed in the individual data sets. The FXR binding atlas is publicly searchable (https://fxratlas.tugraz.at). Conclusion: Published single FXR ChIP-seq data sets and large-scale integrated omics data sets do not cover the full spectrum of FXR binding. Combining different individual data sets and creating an "FXR super-binding atlas" enhances understanding of FXR signaling capacities across different conditions. This is important when considering the potential wide spectrum for drugs targeting FXR in liver diseases.
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Affiliation(s)
- Emilian Jungwirth
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria.,Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
| | - Katrin Panzitt
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg LaboratorySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Gerhard G Thallinger
- Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
| | - Martin Wagner
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
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331
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Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK, Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens L, Dreijerink KMA, Ellis L, Alaiwi SA, Seo JH, Baca S, Beltran H, Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM, Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N, Drapkin B, Liu XS, Freedman M, Haffner MC, Corey E, Brown M, Long HW. Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun 2021; 12:5775. [PMID: 34599169 PMCID: PMC8486778 DOI: 10.1038/s41467-021-26042-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyze cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single-cell analysis of human clinical samples exhibits a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall, our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy. Neuroendocrine carcinomas (NECs) arise from different anatomic sites, but have similar histological and clinical features. Here, the authors show that the epigenetic landscape of a range of NECs converges towards a common epigenetic state, while distinct subtypes occur within neuroendocrine prostate cancer contributing to intratumor heterogeneity in clinical samples.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain.
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neel Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lodewijk Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Leigh Ellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Sylvan Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Francesca Khani
- Weill Cornell Medical Center, Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, New York, NY, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joaquim Bellmunt
- Beth Israel Deaconess Medical Center and PSMAR-IMIM Lab. Harvard Medical School, Boston, Massachusetts, USA
| | - Colm Morrisey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Anna Farago
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Benjamin Drapkin
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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332
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Blanco E, González-Ramírez M, Di Croce L. Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. Sci Rep 2021; 11:19545. [PMID: 34599234 PMCID: PMC8486768 DOI: 10.1038/s41598-021-98889-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu, and the source code is freely distributed at https://github.com/eblancoga/seqcode.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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333
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Feng C, Li Y, Li K, Lyu Y, Zhu W, Jiang H, Wen H. PFKFB4 is overexpressed in clear-cell renal cell carcinoma promoting pentose phosphate pathway that mediates Sunitinib resistance. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:308. [PMID: 34593007 PMCID: PMC8482632 DOI: 10.1186/s13046-021-02103-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/12/2021] [Indexed: 01/16/2023]
Abstract
Background Kinases play critical role in clear-cell renal cell carcinoma (ccRCC). We aim to exploit novel kinase that is both protumorigenic and drugable in ccRCC. Methods Reproduction of public datasets with validation using microarray was performed to identify candidate gene. Functionality was studied using multi-omics with validation in vitro and in vivo. Results 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 (PFKFB4) was differentially expressed showing significantly higher expression in tumor than in normal kidney. PFKFB4 overexpression was associated with advanced tumor grade, stage and worsened prognosis. PFKFB4-knockdown significantly impaired fitness in cell proliferation, migration and wound healing. Despite being recurrently deleted on 3p, PFKFN4 mRNA remained actively transcribed by HIF1α. Metabolomics showed overexpressed PFKFB4 showed enriched metabolites in pentose phosphate pathway (PPP). Phosphoproteomics and immunoprecipitation showed PFKFB4 also phosphorylated NCOA3 which interacted with FBP1 to counteract overactive PPP flux, forming a regulatory loop. PFKFB4-knockdown overcame resistance to Sunitinib in vitro and in vivo both in xenograft and tail-vein injection murine models. Conclusion We concluded PFKFB4 was associated with PPP activity and the fine-tuning of which was mediated by its phosphorylation of NCOA3. Targeting PFKFB4 held promise to combat resistance to Sunitinib. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02103-5.
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Affiliation(s)
- Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Yuqing Li
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Kunping Li
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Yinfeng Lyu
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Wenhui Zhu
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China. .,Institute of Urology, Fudan University, 200040, Shanghai, PR China.
| | - Hui Wen
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China. .,Institute of Urology, Fudan University, 200040, Shanghai, PR China.
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334
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Kotarba G, Taracha-Wisniewska A, Miller M, Dabrowski M, Wilanowski T. Transcription factors Krüppel-like factor 4 and paired box 5 regulate the expression of the Grainyhead-like genes. PLoS One 2021; 16:e0257977. [PMID: 34570823 PMCID: PMC8476022 DOI: 10.1371/journal.pone.0257977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Genes from the Grainyhead-like (GRHL) family code for transcription factors necessary for the development and maintenance of various epithelia. These genes are also very important in the development of many types of cancer. However, little is known about the regulation of expression of GRHL genes. Previously, there were no systematic analyses of the promoters of GRHL genes or transcription factors that bind to these promoters. Here we report that the Krüppel-like factor 4 (KLF4) and the paired box 5 factor (PAX5) bind to the regulatory regions of the GRHL genes and regulate their expression. Ectopic expression of KLF4 or PAX5 alters the expression of GRHL genes. In KLF4-overexpressing HEK293 cells, the expression of GRHL1 and GRHL3 genes was upregulated by 32% and 60%, respectively, whereas the mRNA level of GRHL2 gene was lowered by 28% when compared to the respective controls. The levels of GRHL1 and GRHL3 expression were decreased by 30% or 33% in PAX5-overexpressing HEK293 cells. The presence of minor frequency allele of single nucleotide polymorphism rs115898376 in the promoter of the GRHL1 gene affected the binding of KLF4 to this site. The evidence presented here suggests an important role of KLF4 and PAX5 in the regulation of expression of GRHL1-3 genes.
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Affiliation(s)
- Grzegorz Kotarba
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | | | - Michal Miller
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Wilanowski
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
- * E-mail:
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335
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Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res 2021; 50:D1408-D1416. [PMID: 34570217 PMCID: PMC8728305 DOI: 10.1093/nar/gkab853] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.
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Affiliation(s)
- Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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336
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Kupkova K, Shetty SJ, Haque R, Petri WA, Auble DT. Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism. Clin Epigenetics 2021; 13:182. [PMID: 34565452 PMCID: PMC8474848 DOI: 10.1186/s13148-021-01173-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Stunting is a condition in which a child does not reach their full growth potential due to chronic undernutrition. It arises during the first 2 years of a child's life and is associated with developmental deficiencies and life-long health problems. Current interventions provide some benefit, but new approaches to prevention and treatment grounded in a molecular understanding of stunting are needed. Epigenetic analyses are critical as they can provide insight into how signals from a poor environment lead to changes in cell function. RESULTS Here we profiled histone H3 acetylation on lysine 27 (H3K27ac) in peripheral blood mononuclear cells (PBMCs) of 18-week-old (n = 14) and 1-year-old children (n = 22) living in an urban slum in Dhaka, Bangladesh. We show that 18-week-old children destined to become stunted have elevated levels of H3K27ac overall, functional analysis of which indicates activation of the immune system and stress response pathways as a primary response to a poor environment with high pathogen load. Conversely, overt stunting at 1-year-of age is associated with globally reduced H3K27ac that is indicative of metabolic rewiring and downregulation of the immune system and DNA repair pathways that are likely secondary responses to chronic exposure to a poor environment with limited nutrients. Among processes altered in 1-year-old children, we identified one-carbon metabolism, the significance of which is supported by integrative analysis with results from histone H3 trimethylation on lysine 4 (H3K4me3). Together, these results suggest altered one-carbon metabolism in this population of stunted children. CONCLUSIONS The epigenomes of stunted children undergo two global changes in H3K27ac within their first year of life, which are associated with probable initial hyperactive immune responses followed by reduced metabolic capacity. Limitation of one-carbon metabolites may play a key role in the development of stunting. Trial registration ClinicalTrials.gov NCT01375647. Registered 17 June 2011, retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01375647 .
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Rashidul Haque
- Laboratory Sciences Division, International Centre for Diarrhoeal Disease Research, Dhaka, 1000, Bangladesh
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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337
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Fernandez Lahore G, Förster M, Johannesson M, Sabatier P, Lönnblom E, Aoun M, He Y, Nandakumar KS, Zubarev RA, Holmdahl R. Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. Nat Commun 2021; 12:5565. [PMID: 34552089 PMCID: PMC8458462 DOI: 10.1038/s41467-021-25828-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023] Open
Abstract
Complex autoimmune diseases are sexually dimorphic. An interplay between predisposing genetics and sex-related factors probably controls the sex discrepancy in the immune response, but the underlying mechanisms are unclear. Here we positionally identify a polymorphic estrogen receptor binding site that regulates Cd2 expression, leading to female-specific differences in T cell-dependent mouse models of autoimmunity. Female mice with reduced Cd2 expression have impaired autoreactive T cell responses. T cells lacking Cd2 costimulation upregulate inhibitory Lag-3. These findings help explain sexual dimorphism in human autoimmunity, as we find that CD2 polymorphisms are associated with rheumatoid arthritis and 17-β-estradiol-regulation of CD2 is conserved in human T cells. Hormonal regulation of CD2 might have implications for CD2-targeted therapy, as anti-Cd2 treatment more potently affects T cells in female mice. These results demonstrate the relevance of sex-genotype interactions, providing strong evidence for CD2 as a sex-sensitive predisposing factor in autoimmunity.
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Affiliation(s)
- Gonzalo Fernandez Lahore
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Michael Förster
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Martina Johannesson
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Erik Lönnblom
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Mike Aoun
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Yibo He
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Kutty Selva Nandakumar
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- SMU-KI United Medical Inflammation Centre, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - Rikard Holmdahl
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden.
- The Second Affiliated Hospital of Xi'an Jiaotong University (Xibei Hospital), 710004, Xi'an, China.
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338
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Wang T, Song J, Qu M, Gao X, Zhang W, Wang Z, Zhao L, Wang Y, Li B, Li J, Yang J. Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition. Front Cell Dev Biol 2021; 9:723676. [PMID: 34513844 PMCID: PMC8427514 DOI: 10.3389/fcell.2021.723676] [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: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022] Open
Abstract
Cells of all tissues in the human body share almost the exact same DNA sequence, but the epigenomic landscape can be drastically distinct. To improve our understanding of the epigenetic abnormalities in prostate-related diseases, it is important to use the epigenome of normal prostate as a reference. Although previous efforts have provided critical insights into the genetic and transcriptomic features of the normal prostate, a comprehensive epigenome map has been lacking. To address this need, we conducted a Roadmap Epigenomics legacy project integrating six histone marks (H3K4me1, H3K4me3, H3K9me3, H3K36me3, H3K27me3, and H3K27ac) with complete DNA methylome, transcriptome, and chromatin accessibility data to produce a comprehensive epigenome map of normal prostate tissue. Our epigenome map is composed of 18 chromatin states each with unique signatures of DNA methylation, chromatin accessibility, and gene expression. This map provides a high-resolution comprehensive annotation of regulatory regions of the prostate, including 105,593 enhancer and 70,481 promoter elements, which account for 5.3% of the genome. By comparing with other epigenomes, we identified 7,580 prostate-specific active enhancers associated with prostate development. Epigenomic annotation of GWAS SNPs associated with prostate cancers revealed that two out of nine SNPs within prostate enhancer regions destroyed putative androgen receptor (AR) binding motif. A notable SNP rs17694493, might decouple AR's repressive effect on CDKN2B-AS1 and cell cycle regulation, thereby playing a causal role in predisposing cancer risk. The comprehensive epigenome map of the prostate is valuable for investigating prostate-related diseases.
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Affiliation(s)
- Tao Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Juan Song
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wenhui Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ziwei Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lin Zhao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bing Li
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Li
- Department of Bioinformatics, Center for Translational Medicine, Second Military Medical University, Shanghai, China
| | - Jinjian Yang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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339
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Ayaz G, Turan G, Olgun ÇE, Kars G, Karakaya B, Yavuz K, Demiralay ÖD, Can T, Muyan M, Yaşar P. A prelude to the proximity interaction mapping of CXXC5. Sci Rep 2021; 11:17587. [PMID: 34475492 PMCID: PMC8413330 DOI: 10.1038/s41598-021-97060-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
CXXC5 is a member of the zinc-finger CXXC family proteins that interact with unmodified CpG dinucleotides through a conserved ZF-CXXC domain. CXXC5 is involved in the modulation of gene expressions that lead to alterations in diverse cellular events. However, the underlying mechanism of CXXC5-modulated gene expressions remains unclear. Proteins perform their functions in a network of proteins whose identities and amounts change spatiotemporally in response to various stimuli in a lineage-specific manner. Since CXXC5 lacks an intrinsic transcription regulatory function or enzymatic activity but is a DNA binder, CXXC5 by interacting with proteins could act as a scaffold to establish a chromatin state restrictive or permissive for transcription. To initially address this, we utilized the proximity-dependent biotinylation approach. Proximity interaction partners of CXXC5 include DNA and chromatin modifiers, transcription factors/co-regulators, and RNA processors. Of these, CXXC5 through its CXXC domain interacted with EMD, MAZ, and MeCP2. Furthermore, an interplay between CXXC5 and MeCP2 was critical for a subset of CXXC5 target gene expressions. It appears that CXXC5 may act as a nucleation factor in modulating gene expressions. Providing a prelude for CXXC5 actions, our results could also contribute to a better understanding of CXXC5-mediated cellular processes in physiology and pathophysiology.
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Affiliation(s)
- Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey. .,Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Gizem Turan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Çağla Ece Olgun
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Burcu Karakaya
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Kerim Yavuz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Öykü Deniz Demiralay
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Tolga Can
- Department of Computer Engineering Middle, East Technical University, 06800, Ankara, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey. .,Cansyl Laboratories, Middle East Technical University, 06800, Ankara, Turkey.
| | - Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.,Epigenetics and Stem Cell Biology Laboratory, Single Cell Dynamics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
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340
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Hernández-Oliveras A, Izquierdo-Torres E, Hernández-Martínez G, Zarain-Herzberg Á, Santiago-García J. Transcriptional and epigenetic landscape of Ca 2+-signaling genes in hepatocellular carcinoma. J Cell Commun Signal 2021; 15:433-445. [PMID: 33398721 PMCID: PMC8222487 DOI: 10.1007/s12079-020-00597-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Calcium (Ca2+) signaling has a major role in regulating a wide range of cellular mechanisms, including gene expression, proliferation, metabolism, cell death, muscle contraction, among others. Recent evidence suggests that ~ 1600 genes are related to the Ca2+ signaling. Some of these genes' expression is altered in several pathological conditions, including different cancer types, and epigenetic mechanisms are involved. However, their expression and regulation in hepatocellular carcinoma (HCC) and the liver are barely known. Here, we aimed to explore the expression of genes involved in the Ca2+-signaling in HCC, liver regeneration, and hepatocyte differentiation, and whether their expression is regulated by epigenetic mechanisms such as DNA methylation and histone posttranslational modifications (HPM). Results show that several Ca2+-signaling genes' expression is altered in HCC samples; among these, a subset of twenty-two correlate with patients' survival. DNA methylation correlates with eight of these genes' expression, and Guadecitabine, a hypomethylating agent, regulates the expression of seven down-regulated and three up-regulated genes in HepG2 cells. The down-regulated genes displayed a marked decrease of euchromatin histone marks, whereas up-regulated genes displayed gain in these marks. Additionally, the expression of these genes is modulated during liver regeneration and showed similar profiles between in vitro differentiated hepatocytes and liver-derived hepatocytes. In conclusion, some components of the Ca2+-signaling are altered in HCC and displayed a correlation with patients' survival. DNA methylation and HMP are an attractive target for future investigations to regulate their expression. Ca2+-signaling could be an important regulator of cell proliferation and differentiation in the liver.
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Affiliation(s)
- Andrés Hernández-Oliveras
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
| | - Eduardo Izquierdo-Torres
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Guadalupe Hernández-Martínez
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Juan Santiago-García
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Luis Castelazo Ayala S/N, Xalapa, Veracruz, 91190 Mexico
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Chumpitaz-Diaz L, Samee MAH, Pollard KS. Systematic identification of non-canonical transcription factor motifs. BMC Mol Cell Biol 2021; 22:44. [PMID: 34465294 PMCID: PMC8408965 DOI: 10.1186/s12860-021-00382-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Sequence-specific transcription factors (TFs) recognize motifs of related nucleotide sequences at their DNA binding sites. Upon binding at these sites, TFs regulate critical molecular processes such as gene expression. It is widely assumed that a TF recognizes a single “canonical” motif, although recent studies have identified additional “non-canonical” motifs for some TFs. A comprehensive approach to identify non-canonical DNA binding motifs and the functional importance of those motifs’ matches in the human genome is necessary for fully understanding the mechanisms of TF-regulated molecular processes in human cells. To address this need, we developed a statistical pipeline for in vitro HT-SELEX data that identifies and characterizes the distributions of non-canonical TF motifs in a stringent manner. Analyzing ~170 human TFs’ HT-SELEX data, we found non-canonical motifs for 19 TFs (11%). These non-canonical motifs occur independently of the TFs’ canonical motifs. Non-canonical motif occurrences in the human genome show similar evolutionary conservation to canonical motif occurrences, explain TF binding in locations without canonical motifs, and occur within gene promoters and epigenetically marked regulatory sequences in human cell lines and tissues. Our approach and collection of non-canonical motifs expand current understanding of functionally relevant DNA binding sites for human TFs.
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Affiliation(s)
| | - Md Abul Hassan Samee
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston,, TX, USA.
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA. .,Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, CA, USA. .,Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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342
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Chen ZX, Li GS, Yang LH, Liu HC, Qin GM, Shen L, He WY, Gan TQ, Li JJ. Upregulation of BIRC5 plays essential role in esophageal squamous cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6941-6960. [PMID: 34517565 DOI: 10.3934/mbe.2021345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers in the world, the detection and prognosis of which are still unsatisfactory. Thus, it is essential to explore the factors that may identify ESCC and evaluate the prognosis of ESCC patients. RESULTS Both protein and mRNA expression levels of BIRC5 are upregulated in ESCC group rather than non-ESCC group (standardized mean difference > 0). BIRC5 mRNA expression is related to the age, tumor location, lymph node stage and clinical stage of ESCC patients (p < 0.05). BIRC5 expression makes it feasible to distinguish ESCC from non-ESCC (area under the curve > 0.9), and its high expression is related to poor prognosis of ESCC patients (restrictive survival time difference = -0.036, p < 0.05). BIRC5 may play an important role in ESCC by influencing the cell cycle pathway, and CDK1, MAD2L and CDC20 may be the hub genes of this pathway. The transcription factors-MAZ and TFPD1 -are likely to regulate the transcription of BIRC5, which may be one of the factors for the high expression of BIRC5 in ESCC. CONCLUSIONS The current study shows that upregulation of BIRC5 may have essential clinical value in ESCC, and contributes to the understanding of the pathogenesis of ESCC.
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Affiliation(s)
- Zu-Xuan Chen
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Guo-Sheng Li
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Li-Hua Yang
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - He-Chuan Liu
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Guang-Mei Qin
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Lang Shen
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Wei-Ying He
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Ting-Qing Gan
- Department of Medical Oncology, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Jian-Jun Li
- Department of General Surgery, Second Affiliated Hospital of Guangxi Medical University, 166 DaxueXi Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
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343
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Zheng L, Xu H, Di Y, Chen L, Liu J, Kang L, Gao L. ELK4 promotes the development of gastric cancer by inducing M2 polarization of macrophages through regulation of the KDM5A-PJA2-KSR1 axis. J Transl Med 2021; 19:342. [PMID: 34372882 PMCID: PMC8353876 DOI: 10.1186/s12967-021-02915-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/27/2021] [Indexed: 02/09/2023] Open
Abstract
Background We tried to elaborate the molecular mechanism of ETS-like transcription factor 4 (ELK4) affecting gastric cancer (GC) progression through M2 polarization of macrophages mediated by lysine-specific demethylase 5A (KDM5A)-Praja2 (PJA2)-kinase suppressor of ras 1 (KSR1) axis. Methods GC expression dataset was obtained from GEO database, and the downstream regulatory mechanism of ELK4 was predicted. Tumor-associated macrophages (TAMs) were isolated from GC tissues. The interaction among ELK4, KDM5A, PJA2 and KSR1 was analyzed by dual luciferase reporter gene, ChIP and Co-IP assays. The stability of KSR1 protein was detected by cycloheximide (CHX) treatment. After TAMs were co-cultured with HGC-27 cells, HGC-27 cell biological processes were assessed through gain- and loss-of function assays. Tumorigenicity was detected by tumorigenicity test in nude mice. Results In GC and TAMs, ELK4, KDM5A and KSR1 were highly expressed, while PJA2 was lowly expressed. M2 polarization of macrophages promoted the development of GC. ELK4 activated KDM5A by transcription and promoted macrophage M2 polarization. KDM5A inhibited the expression of PJA2 by removing H3K4me3 of PJA2 promoter, which promoted M2 polarization of macrophages. PJA2 reduced KSR1 by ubiquitination. ELK4 promoted the proliferative, migrative and invasive potentials of GC cells as well as the growth of GC xenografts by regulating KSR1. Conclusion ELK4 may reduce the PJA2-dependent inhibition of KSR1 by transcriptional activation of KDM5A to promote M2 polarization of macrophages, thus promoting the development of GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02915-1.
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Affiliation(s)
- Lei Zheng
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Hongmei Xu
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Ya Di
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Lanlan Chen
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Jiao Liu
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Liying Kang
- Department of Oncology, Tianjin Wuqing District People's Hospital, Tianjin, 301700, People's Republic of China
| | - Liming Gao
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China.
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Coronel L, Riege K, Schwab K, Förste S, Häckes D, Semerau L, Bernhart SH, Siebert R, Hoffmann S, Fischer M. Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. Nucleic Acids Res 2021; 49:7437-7456. [PMID: 34197623 PMCID: PMC8287911 DOI: 10.1093/nar/gkab575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/25/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7’s role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Silke Förste
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Lena Semerau
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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345
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Yaşar P, Kars G, Yavuz K, Ayaz G, Oğuztüzün Ç, Bilgen E, Suvacı Z, Çetinkol ÖP, Can T, Muyan M. A CpG island promoter drives the CXXC5 gene expression. Sci Rep 2021; 11:15655. [PMID: 34341443 PMCID: PMC8329181 DOI: 10.1038/s41598-021-95165-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5' untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5'-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G-C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.
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Affiliation(s)
- Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Epigenetics and Stem Cell Biology Laboratory, Single Cell Dynamics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Kerim Yavuz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Çerağ Oğuztüzün
- Department of Computer Engineering, Bilkent University, Ankara, 06800, Turkey
| | - Ecenaz Bilgen
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | - Zeynep Suvacı
- Department of Chemistry, Middle East Technical University, Ankara, 06800, Turkey
| | | | - Tolga Can
- Department of Computer Engineering, Middle East Technical University, Ankara, 06800, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.
- Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey.
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346
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Servetto A, Kollipara R, Formisano L, Lin CC, Lee KM, Sudhan DR, Gonzalez-Ericsson PI, Chatterjee S, Guerrero-Zotano A, Mendiratta S, Akamatsu H, James N, Bianco R, Hanker AB, Kittler R, Arteaga CL. Nuclear FGFR1 Regulates Gene Transcription and Promotes Antiestrogen Resistance in ER + Breast Cancer. Clin Cancer Res 2021; 27:4379-4396. [PMID: 34011560 PMCID: PMC8338892 DOI: 10.1158/1078-0432.ccr-20-3905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 01/09/2023]
Abstract
PURPOSE FGFR1 overexpression has been associated with endocrine resistance in ER+ breast cancer. We found FGFR1 localized in the nucleus of breast cancer cells in primary tumors resistant to estrogen suppression. We investigated a role of nuclear FGFR1 on gene transcription and antiestrogen resistance. EXPERIMENTAL DESIGN Tumors from patients treated with letrozole were subjected to Ki67 and FGFR1 IHC. MCF7 cells were transduced with FGFR1(SP-)(NLS) to promote nuclear FGFR1 overexpression. FGFR1 genomic activity in ER+/FGFR1-amplified breast cancer cells ± FOXA1 siRNA or ± the FGFR tyrosine kinase inhibitor (TKI) erdafitinib was examined by chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq). The nuclear and chromatin-bound FGFR1 interactome was investigated by mass spectrometry (MS). RESULTS High nuclear FGFR1 expression in ER+ primary tumors positively correlated with post-letrozole Ki67 values. Nuclear FGFR1 overexpression influenced gene transcription and promoted resistance to estrogen suppression and to fulvestrant in vivo. A gene expression signature induced by nuclear FGFR1 correlated with shorter survival in the METABRIC cohort of patients treated with antiestrogens. ChIP-Seq revealed FGFR1 occupancy at transcription start sites, overlapping with active transcription histone marks. MS analysis of the nuclear FGFR1 interactome identified phosphorylated RNA-Polymerase II and FOXA1, with FOXA1 RNAi impairing FGFR1 recruitment to chromatin. Treatment with erdafitinib did not impair nuclear FGFR1 translocation and genomic activity. CONCLUSIONS These data suggest nuclear FGFR1 contributes to endocrine resistance by modulating gene transcription in ER+ breast cancer. Nuclear FGFR1 activity was unaffected by FGFR TKIs, thus supporting the development of treatment strategies to inhibit nuclear FGFR1 in ER+/FGFR1 overexpressing breast cancer.
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Affiliation(s)
- Alberto Servetto
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Rahul Kollipara
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Luigi Formisano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Chang-Ching Lin
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Kyung-Min Lee
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Dhivya R. Sudhan
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | | | - Sumanta Chatterjee
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | | | - Saurabh Mendiratta
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Hiroaki Akamatsu
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Nicholas James
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Manoa, Hawaii
| | - Roberto Bianco
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ariella B. Hanker
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Ralf Kittler
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas
| | - Carlos L. Arteaga
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas Texas.,Corresponding Author: Carlos L. Arteaga, The University of Texas Southwestern Medical Center Simmons Comprehensive Cancer Center, 5323 Harry Hines Boulevard, Dallas, TX 75390–8590. E-mail:
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347
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Cui Y, Li JS, Li W. From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-seq Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:519-521. [PMID: 34273562 PMCID: PMC9039543 DOI: 10.1016/j.gpb.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
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348
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Liu Y, Liu X, Gu Y, Lu H. A novel RNA binding protein-associated prognostic model to predict overall survival in hepatocellular carcinoma patients. Medicine (Baltimore) 2021; 100:e26491. [PMID: 34398005 PMCID: PMC8294901 DOI: 10.1097/md.0000000000026491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is 1 of the deadliest malignancies worldwide. Despite significant advances in diagnosis and treatment, the mortality rate from HCC persists at a substantial level. Construction of a prognostic model that can reliably predict HCC patients' overall survival is urgently needed.Two RNA-seq dataset (the Cancer Genome Atlas and International Cancer Genome Consortium) and 1 microarray dataset (GSE14520) were included in our study. RNA-binding proteins (RBPs) in HCC patients was examined by differentially expressed genes analysis, functional enrichment analysis and protein-protein interaction network analysis. Subsequently, the Cancer Genome Atlas dataset was randomly divided into training and testing cohort with a prognostic model developed in the training cohort. In order to evaluate the prognostic value of the model, a comprehensive survival assessment was conducted.Five RBPs (ribosomal protein L10-like, enhancer of zeste homolog 2 (EZH2), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A), zinc finger protein 239, interferon-induced protein with tetratricopeptide repeats 1) were used to construct the model. The model accurately predicted the prognosis of liver cancer patients in both the training cohort and validation cohort. HCC patients could be assigned into a high-risk group and a low-risk group by this model, and the overall survival of these 2 groups was significantly different (P < .05). Furthermore, the risk scores obtained by this model were highly correlated with immune cell infiltration.The prognostic model helps to identify HCC patients at high risk of mortality, which optimizes decision-making for individualized treatment.
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Affiliation(s)
- Ye Liu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xiaohong Liu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Yang Gu
- Department of General Surgery, Wuhan University Zhongnan Hospital, Wuhan, China
| | - Haofeng Lu
- Department of Hepatobiliary and Pancreatic, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
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349
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Jones RE, Andrews R, Holmans P, Hill M, Taylor PR. Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer's disease. Sci Rep 2021; 11:14935. [PMID: 34294785 PMCID: PMC8298495 DOI: 10.1038/s41598-021-94324-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic association studies have identified multiple variants at the SPI1 locus that modify risk and age of onset for Alzheimer's Disease (AD). Reports linking risk variants to gene expression suggest that variants denoting higher SPI1 expression are likely to have an earlier AD onset, and several other AD risk genes contain PU.1 binding sites in the promoter region. Overall, this suggests the level of SPI1 may alter microglial phenotype potentially impacting AD. This study determined how the microglial transcriptome was altered following modest changes to Spi1 expression in primary mouse microglia. RNA-sequencing was performed on microglia with reduced or increased Spi1/PU.1 expression to provide an unbiased approach to determine transcriptomic changes affected by Spi1. In summary, a reduction in microglial Spi1 resulted in the dysregulation of transcripts encoding proteins involved in DNA replication pathways while an increased Spi1 results in an upregulation of genes associated with immune response pathways. Additionally, a subset of 194 Spi1 dose-sensitive genes was identified and pathway analysis suggests that several innate immune and interferon response pathways are impacted by the concentration of Spi1. Together these results suggest Spi1 levels can alter the microglial transcriptome and suggests interferon pathways may be altered in individuals with AD related Spi1 risk SNPs.
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Affiliation(s)
- Ruth E Jones
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Robert Andrews
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Matthew Hill
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Philip R Taylor
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK.
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350
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Liang F, Zhang C, Guo H, Gao SH, Yang FY, Zhou GB, Wang GZ. Comprehensive analysis of BTN3A1 in cancers: mining of omics data and validation in patient samples and cellular models. FEBS Open Bio 2021; 11:2586-2599. [PMID: 34293829 PMCID: PMC8409294 DOI: 10.1002/2211-5463.13256] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/21/2021] [Indexed: 11/11/2022] Open
Abstract
Butyrophilin 3A1 (BTN3A1), a major histocompatibility complex‐associated gene that encodes a membrane protein with two extracellular immunoglobulin domains and an intracellular B30.2 domain, is critical in T‐cell activation and adaptive immune response. Here, the expression of BTN3A1 in cancers was analyzed in eight databases comprising 86 733 patients of 33 cancers, and the findings were validated in patient samples and cell models. We showed that BTN3A1 was expressed in most cancers, and its expression level was strongly correlated with clinical outcome of 13 cancers. Mutations of BTN3A1 were detected, and the mutations were distributed throughout the entire gene. Gene set enrichment analysis showed that BTN3A1 co‐expression genes and interacting proteins were enriched in immune regulation‐related pathways. BTN3A1 was associated with tumor‐infiltrating immune cells and was co‐expressed with multiple immune checkpoints in patients with breast cancer (BRCA) and non‐small cell lung cancer (NSCLC). We reported that BTN3A1 was downregulated in 46 of 65 (70.8%) NSCLCs, and its expression level was inversely associated with clinical outcome of the patients. BTN3A1 in tumor samples was lower than in counterpart normal tissues in 31 of 38 (81.6%) BRCAs. Bioinformatics analyses showed that BTN3A1 could be a target gene of transcription factor Spi‐1 proto‐oncogene (SPI1), and our ‘wet’ experiments showed that ectopic expression of SPI1 upregulated, whereas silencing of SPI1 downregulated, BTN3A1 expression in cells. These results suggest that BTN3A1 may function as a tumor suppressor and may serve as a potential prognostic biomarker in NSCLCs and BRCAs.
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Affiliation(s)
- Fan Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Guo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - San-Hui Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fu-Ying Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guang-Biao Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gui-Zhen Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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