1
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Chen K, Shuen TWH, Chow PKH. The association between tumour heterogeneity and immune evasion mechanisms in hepatocellular carcinoma and its clinical implications. Br J Cancer 2024; 131:420-429. [PMID: 38760445 PMCID: PMC11300599 DOI: 10.1038/s41416-024-02684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. The emergence of combination therapy, atezolizumab (anti-PDL1, immune checkpoint inhibitor) and bevacizumab (anti-VEGF) has revolutionised the management of HCC. Despite this breakthrough, the best overall response rate with first-line systemic therapy is only about 30%, owing to intra-tumoural heterogeneity, complex tumour microenvironment and the lack of predictive biomarkers. Many groups have attempted to classify HCC based on the immune microenvironment and have consistently observed better outcomes in immunologically "hot" HCC. We summarised possible mechanisms of tumour immune evasion based on the latest literature and the rationale for combination/sequential therapy to improve treatment response. Lastly, we proposed future strategies and therapies to overcome HCC immune evasion to further improve treatment outcomes of HCC.
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Affiliation(s)
- Kaina Chen
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Timothy W H Shuen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Pierce K H Chow
- Duke-NUS Medical School, Singapore, Singapore.
- Department of Hepato-pancreato-biliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore, Singapore.
- Program in Translational and Clinical Liver Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.
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2
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Gantner BN, Palma FR, Kayzuka C, Lacchini R, Foltz DR, Backman V, Kelleher N, Shilatifard A, Bonini MG. Histone oxidation as a new mechanism of metabolic control over gene expression. Trends Genet 2024:S0168-9525(24)00134-3. [PMID: 38910033 DOI: 10.1016/j.tig.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The emergence of aerobic respiration created unprecedented bioenergetic advantages, while imposing the need to protect critical genetic information from reactive byproducts of oxidative metabolism (i.e., reactive oxygen species, ROS). The evolution of histone proteins fulfilled the need to shield DNA from these potentially damaging toxins, while providing the means to compact and structure massive eukaryotic genomes. To date, several metabolism-linked histone post-translational modifications (PTMs) have been shown to regulate chromatin structure and gene expression. However, whether and how PTMs enacted by metabolically produced ROS regulate adaptive chromatin remodeling remain relatively unexplored. Here, we review novel mechanistic insights into the interactions of ROS with histones and their consequences for the control of gene expression regulation, cellular plasticity, and behavior.
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Affiliation(s)
- Benjamin N Gantner
- Department of Medicine, Division of Endocrinology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Flavio R Palma
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cezar Kayzuka
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil; Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vadim Backman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Bioengineering, McCormick School of Engineering, Northwestern University, Chicago, IL, USA
| | - Neil Kelleher
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcelo G Bonini
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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3
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Atmaca HN, Gun S, Onal M, Tural S. Promoter methylation status of RASSF1A and RASSF2A tumor suppressor genes in endometrial endometrioid carcinomas. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-13. [PMID: 38830238 DOI: 10.1080/15257770.2024.2356744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
We aimed to investigate the promoter methylation status of RASSF1A and RASSF2A tumor suppressor genes in endometrial endometrioid carcinomas with p53 wild type and mismatch repair proficient. Genomic DNAs were isolated from 50 specimens (15 formalin-fixed paraffin embedded tumor tissues, 15 paired blood samples and 20 normal endometrial tissues). Bisulfide modification and methylation-specific polymerase chain reaction were performed. As a result of the study, while no significance was found for RASSF1A gene (p = 0.08), a statistically significance was found for RASSF2A gene (p < 0.001), RASSF2A gene methylation status was also found higher in high grade tumors, advanced age (≥50) and nonsmokers groups. Our results indicate that RASSF2A gene may play a role in the carcinogenesis of endometrioid and it could be potential biomarker for early detection for endometrioid carcinoma. Further and larger investigations are needed to confirm our results.
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Affiliation(s)
- Habibe Nur Atmaca
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Türkiye
| | - Seda Gun
- Department of Pathology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Türkiye
| | - Mesut Onal
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Türkiye
| | - Sengul Tural
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Türkiye
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4
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Qin CM, Wei XW, Wu JY, Liu XQ, Lin Y. Decreased NSD2 impairs stromal cell proliferation in human endometrium via reprogramming H3K36me2. Reproduction 2024; 167:e230254. [PMID: 38236723 PMCID: PMC10895284 DOI: 10.1530/rep-23-0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024]
Abstract
In brief The proliferation of the endometrium is regulated by histone methylation. This study shows that decreased NSD2 impairs proliferative-phase endometrial stromal cell proliferation in patients with recurrent implantation failure via epigenetic reprogramming of H3K36me2 methylation on the promoter region of MCM7. Abstract Recurrent implantation failure (RIF) is a formidable challenge in assisted reproductive technology because of its unclear molecular mechanism. Impaired human endometrial stromal cell (HESC) proliferation disrupts the rhythm of the menstrual cycle, resulting in devastating disorders between the embryo and the endometrium. The molecular function of histone methylation enzymes in modulating HESC proliferation remains largely uncharacterized. Herein, we found that the levels of histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2) and the dimethylation of lysine 36 on histone H3 are decreased significantly in the proliferative-phase endometrium of patients with RIF. Knockdown of NSD2 in an HESC cell line markedly impaired cell proliferation and globally reduced H3K36me2 binding to chromatin, leading to altered expression of many genes. Transcriptomic analyses revealed that cell cycle-related gene sets were downregulated in the endometrium of patients with RIF and in NSD2‑knockdown HESCs. Furthermore, RNA-sequencing and CUT&Tag sequencing analysis suggested that NSD2 knockdown reduced the binding of H3K36me2 to the promoter region of cell cycle marker gene MCM7 (encoding minichromosome maintenance complex component 7) and downregulated its expression. The interaction of H3K36me2 with the MCM7 promoter was verified using chromatin immunoprecipitation-quantitative real-time PCR. Our results demonstrated a unifying epigenome-scale mechanism by which decreased NSD2 impairs endometrial stromal cell proliferation in the proliferative-phase endometrium of patients with RIF.
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Affiliation(s)
- Chuan-Mei Qin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Wei Wei
- Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Yi Wu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Qing Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Lin
- Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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5
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Zhang C, Zeng J, Ye C, Tian K, Xian Z. Construction and validation of a chromatin regulator-related gene signature for prognostic and therapeutic significance of clear cell renal cell carcinoma. Transl Cancer Res 2024; 13:150-172. [PMID: 38410230 PMCID: PMC10894348 DOI: 10.21037/tcr-23-1383] [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: 08/03/2023] [Accepted: 11/29/2023] [Indexed: 02/28/2024]
Abstract
Background Epigenetic alterations driven by chromatin regulators (CRs) are well-recognized cancer hallmarks. Growing evidence suggests that the imbalance of CRs may lead to the occurrence of various diseases including tumors. However, the role and prognostic value of CRs in clear cell renal cell carcinoma (ccRCC) remain undefined. Methods Consensus clustering analysis was used to identify different subtypes. Univariate and multivariate Cox regression analysis were performed to identify prognosis-related CRs and constructed a risk model. Transcriptome sequencing was used to verify gene expression levels. Kaplan-Meier survival analysis was used to compare overall survival (OS) between high- and low-risk groups. The area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was used to evaluate the performance of the model. The ESTIMATE algorithm and single-sample gene set enrichment analysis (ssGSEA) were executed to evaluate the immune characteristics of samples. Correlation analysis was used to assess the relationship between risk score and immune checkpoint genes, the relationship between expression levels of CRs and immune cell infiltration and drug therapeutic response. Finally, we also compared differences in drug sensitivity between low- and high-risk groups. Results We identified three CRs-related subtypes with different characteristics. A prognostic model was built with four CRs and can precisely predict the OS of patients in different risk groups. The model has good stability and applicability and was further verified in the internal and external dataset. The transcriptomic levels of the four CRs were also validated, and the risk score was an independent prognostic factor for ccRCC. Obvious differences in the immune microenvironment and the expression levels of immune checkpoints were observed in low- and high-risk group. Higher immune activity and immune cell infiltration were found in the high-risk group. Besides, the expression levels of CRs were associated with drug therapeutic response. Patients with high-risk score may be more sensitive to gemcitabine, vinblastine, paclitaxel, axitinib, sunitinib, and temsirolimus. Conclusions CRs were strongly associated with the occurrence and development of ccRCC. Targeting CRs may become a new therapeutic strategy for ccRCC. Besides, CRs-related gene signature can predict the prognosis and therapeutic significance of ccRCC, which provides an important reference for clinical decision-making.
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Affiliation(s)
- Changzheng Zhang
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jiayi Zeng
- Department of Urology, Guangdong Provincial People’s Hospital’s Nanhai Hospital, Foshan, China
| | - Chujin Ye
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Kaiwen Tian
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhiyong Xian
- Department of Urology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Urology, Guangdong Provincial People’s Hospital’s Nanhai Hospital, Foshan, China
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6
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Zhou Y, Wang A, Sun X, Zhang R, Zhao L. Survival prognosis model for elderly women with epithelial ovarian cancer based on the SEER database. Front Oncol 2023; 13:1257615. [PMID: 37841445 PMCID: PMC10570503 DOI: 10.3389/fonc.2023.1257615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Objectives We aimed to analyze the risk factors of elderly women with epithelial ovarian cancer (EOC) using data on the SEER database, and to generate a nomogram model their 1-, 3-, and 5-year prognoses. The resulting nomogram model should be useful for clinical diagnoses and treatment. Methods We collected clinical data of women older than 70 years with epithelial ovarian cancer (diagnosed on the basis of surgical pathology) from the SEER database including datasets between 2010 and 2019. We randomly grouped the data into two groups (7:3 ratio) using the R language software. We divided the independent prognostic factors obtained by univariate and multi-factor Cox regression analyses into training and validation sets, and we plotted the same independent prognostic factors in a nomogram model of overall survival (OS) at 1, 3, and 5 years. We used the C-index, calibration curve, and area under the curve to validate the nomograms. We further evaluated the model and its clinical applicability using decision curve analyses. Results We identified age, race, marital status, histological type, AJCC staging, differentiation degree, unilateral and bilateral tumor involvement, number of positive lymph nodes, chemotherapy, surgery, sequence of systemic treatment versus surgery, and time from diagnosis to treatment as independent prognostic factors for elderly women with EOC (P < 0.5). The C-indexes were 0.749 and 0.735 in the training and validation sets, respectively; the ROC curves showed that the AUC of each prognostic factor was greater than 0.7; and, the AUC values predicted by the line plot were similar in the training and validation sets. The decision curves suggest that this line plot model has a high clinical value for predicting overall survivals at 1, 3, and 5 years in elderly women with EOC. Conclusion The nomogram model in this study can provide an accurate assessment of the overall survival of women older than 70 years with EOC at the time of the first treatment, and it provides a basis for individualized clinical treatment.
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Affiliation(s)
- Yingping Zhou
- The First Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
| | - Aifen Wang
- The First Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
| | - Xin Sun
- The First Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
| | - Rong Zhang
- The First Department of General Surgery, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
| | - Luwen Zhao
- The First Department of Gynecology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China
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7
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Zeng C, Song X, Zhang Z, Cai Q, Cai J, Horbinski C, Hu B, Cheng SY, Zhang W. Dissection of transcriptomic and epigenetic heterogeneity of grade 4 gliomas: implications for prognosis. Acta Neuropathol Commun 2023; 11:133. [PMID: 37580817 PMCID: PMC10426201 DOI: 10.1186/s40478-023-01619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Grade 4 glioma is the most aggressive and currently incurable brain tumor with a median survival of one year in adult patients. Elucidating novel transcriptomic and epigenetic contributors to the molecular heterogeneity underlying its aggressiveness may lead to improved clinical outcomes. METHODS To identify grade 4 glioma -associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with grade 4 gliomas and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms. RESULTS Despite global reduction, the majority of differential 5hmC features showed higher modification levels in grade 4 gliomas as compared to normal controls. In addition, the bi-directional correlations between 5hmC modifications over promoter regions or gene bodies and gene expression were greatly disturbed in grade 4 gliomas regardless of IDH1 mutation status. Phenotype-associated co-regulated 5hmC-5hmC modules and 5hmC-mRNA modules not only are enriched with different molecular pathways that are indicative of the pathogenesis of grade 4 gliomas, but also are of prognostic significance comparable to IDH1 mutation status. Lastly, the best-performing 5hmC model can predict patient survival at a much higher accuracy (c-index = 74%) when compared to conventional prognostic factor IDH1 (c-index = 57%), capturing the molecular characteristics of tumors that are independent of IDH1 mutation status and gene expression-based molecular subtypes. CONCLUSIONS The 5hmC-based prognostic model could offer a robust tool to predict survival in patients with grade 4 gliomas, potentially outperforming existing prognostic factors such as IDH1 mutations. The crosstalk between 5hmC and gene expression revealed another layer of complexity underlying the molecular heterogeneity in grade 4 gliomas, offering opportunities for identifying novel therapeutic targets.
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Affiliation(s)
- Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Xiao Song
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Qinyun Cai
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Jiajun Cai
- Huashan Hospital, Fudan University, 12 Wulumuqi Rd., Shanghai, 200040, China
| | - Craig Horbinski
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Bo Hu
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA.
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Zhao J, Lu R, Jin C, Li S, Chen Y, Huang Q, Li X, Meng W, Wu H, Wen T, Mo X. Gene expression networks involved in multiple cellular programs coexist in individual hepatocellular cancer cells. Heliyon 2023; 9:e18305. [PMID: 37539322 PMCID: PMC10393770 DOI: 10.1016/j.heliyon.2023.e18305] [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: 10/28/2022] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
The gene expression networks of a single cell can be used to reveal cell type- and condition-specific patterns that account for cell states, cell identity, and its responses to environmental changes. We applied single cell sequencing datasets to define mRNA patterns and visualized potential cellular capacities among hepatocellular cancer cells. The expressing numbers and levels of genes were highly heterogenous among the cancer cells. The cellular characteristics were dependent strongly on the expressing numbers and levels of genes, especially oncogenes and anti-oncogenes, in an individual cancer cell. The transcriptional activations of oncogenes and anti-oncogenes were strongly linked to inherent multiple cellular programs, some of which oppose and contend against other processes, in a cancer cell. The gene expression networks of multiple cellular programs proliferation, differentiation, apoptosis, autophagy, epithelial-mesenchymal transition, ATP production, and neurogenesis coexisted in an individual cancer cell. The findings give rise a hypothesis that a cancer cell expresses balanced combinations of genes and undergoes a given biological process by rapidly transmuting gene expressing networks.
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9
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Possible regulation of ganglioside GD3 synthase gene expression with DNA methylation in human glioma cells. Glycoconj J 2023; 40:323-332. [PMID: 36897478 DOI: 10.1007/s10719-023-10108-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/02/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023]
Abstract
Gangliosides are expressed in nervous systems and some neuroectoderm-derived tumors at high levels and play pivotal roles. However, mechanisms for the regulation of glycosyltransferase genes responsible for the ganglioside synthesis are not well understood. In this study, we analyzed DNA methylation patterns of promoter regions of GD3 synthase (ST8SIA1) as well as mRNA levels and ganglioside expression using human glioma cell lines. Among 5 cell lines examined, 4 lines showed changes in the expression levels of related genes after treatment with 5-aza-dC. LN319 showed up-regulation of St8sia1 and increased b-series gangliosides after 5-aza-dC treatment, and an astrocytoma cell line, AS showed high expression of ST8SIA1 and b-series gangliosides persistently before and after 5-Aza-2'-deoxycytidine treatment. Using these 2 cell lines, DNA methylation patterns of the promoter regions of the gene were analyzed by bisulfite-sequencing. Consequently, 2 regions that were methylated before 5-Aza-2'-deoxycytidine treatment were demethylated in LN319 after the treatment, while those regions were persistently demethylated in AS. These 2 regions corresponded with sites defined as promoter regions by Luciferase assay. Taken together, it was suggested that ST8SIA1 gene is regulated by DNA methylation at the promoter regions, leading to the regulation of tumor phenotypes.
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10
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Asif H, Foley G, Simon M, Roque D, Kim JJ. Analysis of endometrial carcinoma TCGA reveals differences in DNA methylation in tumors from Black and White women. Gynecol Oncol 2023; 170:1-10. [PMID: 36580834 PMCID: PMC10023328 DOI: 10.1016/j.ygyno.2022.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Racial disparities exist in cancer patients both in incidence and death rates. In endometrial cancer, Black patients are reported to have higher incidence of aggressive endometrial cancer subtypes and higher death rates than White women. To date, diagnostic and prognostic biomarkers associated with race-specific methylation driven genes have yet to be identified. The objective of this study was to explore DNA methylation patterns in endometrial tumor samples from White and Black women. METHODS Differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs) were identified in White tumor samples compared to Black tumor samples using Endometrial Carcinoma (EC) methylation and clinical data from The Cancer Genome Atlas (TCGA). Survival analysis was performed using survival R package and results were visualized using Kaplan-Meier plots. To access the correlation between changes in methylation and gene expression, we downloaded raw RNA-sequencing by Expectation-Maximization (RSEM) counts data from The Cancer Genome Atlas (TCGA) using TCGABiolinks package (v2.18.0). RESULTS Our analysis revealed 704 differentially methylated CpGs in tumors from Black and White women. These differentially methylated genes showed strong negative correlation with gene expression and statistically significant enrichment in regulatory regions such as DNase I hypersensitivity sites (DHSs) and transcription factor binding sites (TFBSs). Increased variability in methylation occurred in genes such as the insulin signaling pathway in Black tumor samples. CONCLUSION By using two independent statistical method based on means (DMR, DMCs) and variances (DVCs) on the endometrial carcinoma TCGA data, we showed that endometrial tumors from Black women are hypomethylated and more hypervariable than tumors from White women. In-depth investigation of these methylation driven markers can aid in successful management of endometrial cancer disparities and improved overall survival in Black and White populations.
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Affiliation(s)
- Huma Asif
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, USA
| | - Grace Foley
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, USA
| | - Melissa Simon
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, USA
| | - Dario Roque
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, USA
| | - J Julie Kim
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, USA.
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11
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Zhang Y, Zhang Y, Song C, Zhao X, Ai B, Wang Y, Zhou L, Zhu J, Feng C, Xu L, Wang Q, Sun H, Fang Q, Xu X, Li E, Li C. CRdb: a comprehensive resource for deciphering chromatin regulators in human. Nucleic Acids Res 2023; 51:D88-D100. [PMID: 36318256 PMCID: PMC9825595 DOI: 10.1093/nar/gkac960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes.
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Affiliation(s)
- Yimeng Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
| | | | | | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liwei Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hong Sun
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Qiaoli Fang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Xiaozheng Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South
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12
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Wu Q, Tian R, Liu J, Ou C, Li Y, Fu X. Deciphering comprehensive features of tumor microenvironment controlled by chromatin regulators to predict prognosis and guide therapies in uterine corpus endometrial carcinoma. Front Immunol 2023; 14:1139126. [PMID: 36936912 PMCID: PMC10022674 DOI: 10.3389/fimmu.2023.1139126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Dysregulation of chromatin regulators (CRs) can perturb the tumor immune microenvironment, but the underlying mechanism remains unclear. We focused on uterine corpus endometrial carcinoma (UCEC) and used gene expression data from TCGA-UCEC to investigate this mechanism. Methods We used weighted gene co-expression network analysis (WGCNA) and consensus clustering algorithm to classify UCEC patients into Cluster_L and Cluster_H. TME-associated CRs were identified using WGCNA and differential gene expression analysis. A CR risk score (CRRS) was constructed using univariate Cox and LASSO-Cox regression analyses. A nomogram was developed based on CRRS and clinicopathologic factors to predict patients' prognosis. Results Lower CRRS was associated with lower grade, more benign molecular subtypes, and improved survival. Patients with low CRRS showed abundant immune infiltration, a higher mutation burden, fewer CNVs, and better response to immunotherapy. Moreover, low CRRS patients were more sensitive to 24 chemotherapeutic agents. Conclusion A comprehensive assessment of CRRS could identify immune activation and improve the efficacy of UCEC treatments.
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Affiliation(s)
- Qihui Wu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Ruotong Tian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaxin Liu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Chunlin Ou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
| | - Yimin Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
| | - Xiaodan Fu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
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13
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Cao L, Zeng B, Wang Y, Wang X, Qin Y, Zhang C, Wu M, Wang J, Zhang X, Ma L. Integrated Clinical and Prognostic Analysis of the m 6A RNA Methylation Regulator YTHDF3 in Pan-Cancer and its Correlation with Cancer Cell Proliferation. J Cancer 2022; 13:3623-3639. [PMID: 36606187 PMCID: PMC9809312 DOI: 10.7150/jca.78403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/05/2022] [Indexed: 12/03/2022] Open
Abstract
Background: N6-methyladenosine (m6A) is the most abundant and extensive chemical modification of mammalian RNA molecules. Although numerous studies have investigated m6A methylation-related genes, to the best of our knowledge, none have examined the expression patterns of YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) across cancers. Methods: Using various publicly available datasets, we searched for a potential carcinogenic role of YTHDF3 in 33 tumor types. Furthermore, the clinicopathological parameters, clinical prognostic value, enrichment analysis, mutations, microsatellite instability (MSI), tumor mutation burden (TMB), levels of infiltrating cells, and related immune checkpoint genes were included. Finally, we performed a validation analysis using existing clinical samples and proliferation-related functional experiments. Results: YTHDF3 is highly expressed in most cancer types and associated with patient prognosis in certain tumors. The ROC analysis suggested that YTHDF3 has high diagnostic value in 13 types of cancer. Furthermore, we found that the genes associated with YTHDF3 were enriched for translation initiation and mRNA metabolic processes. The results of the GSEA enrichment suggest that YTHDF3 may be associated with different pathways in cells in various tumor types. We further analyzed the correlations between YTHDF3 expression and MSI, TMB, and immune checkpoint genes. YTHDF3 also possibly exerts important antitumor immunotherapy effects. Additionally, the results of the immune analysis using TIMER showed that high YTHDF3 expression levels in pan-cancer tissues were related to an immunosuppressive microenvironment. Finally, we experimentally demonstrated that both overexpression and downregulation of YTHDF3 can affect cancer cell proliferation rates. Conclusion: YTHDF3 is a promising biomarker for cancer diagnosis. This study provides the first comprehensive pan-cancer report on YTHDF3 and increases our understanding of its oncogenic role in different tumors.
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Affiliation(s)
- Leiqun Cao
- Anhui University of Science and Technology School of Medicine, Huainan, Anhui, 232001, China.,Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Bingjie Zeng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yulan Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xianzhao Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yueyang Qin
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Congcong Zhang
- Anhui University of Science and Technology School of Medicine, Huainan, Anhui, 232001, China.,Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mengyi Wu
- Shanghai University of Traditional Chineses Medicine, Shanghai, 201203, China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,✉ Corresponding authors: Xiao Zhang, No. 241, West Huaihai Rd, Shanghai, 200030, China. . Lifang Ma, No. 241, West Huaihai Rd, Shanghai, 200030, China.
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China.,✉ Corresponding authors: Xiao Zhang, No. 241, West Huaihai Rd, Shanghai, 200030, China. . Lifang Ma, No. 241, West Huaihai Rd, Shanghai, 200030, China.
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14
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Comprehensive Analysis of Histone Modifications in Hepatocellular Carcinoma Reveals Different Subtypes and Key Prognostic Models. JOURNAL OF ONCOLOGY 2022; 2022:5961603. [PMID: 35957801 PMCID: PMC9359864 DOI: 10.1155/2022/5961603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Histone modification, an important epigenetic mechanism, is related to the carcinogenesis of hepatocellular carcinoma (HCC). In three datasets, we screened 88 epigenetic-dysregulated PCGs (epi-PCGs) , which were significantly associated with HCC survival and could cluster HCC into three molecular subtypes. These subtypes were associated with prognosis, immunomodulatory alterations, and response to different treatment strategies. Based on 88 epi-PCGs in the TCGA training set, a risk prediction model composed of 4 epi-PCGs was established. The model was closely related to the clinicopathological features and showed a strong predictive ability in different clinical subgroups. In addition, the risk prediction model was an independent prognostic factor for patients with HCC. The significance of epi-PCGs in HCC is revealed by our data analysis.
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15
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Recalde M, Gárate-Rascón M, Herranz JM, Elizalde M, Azkona M, Unfried JP, Boix L, Reig M, Sangro B, Fernández-Barrena MG, Fortes P, Ávila MA, Berasain C, Arechederra M. DNA Methylation Regulates a Set of Long Non-Coding RNAs Compromising Hepatic Identity during Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14092048. [PMID: 35565178 PMCID: PMC9102946 DOI: 10.3390/cancers14092048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Hepatocarcinogenesis is a long process which implies the loss of hepatic functions. Our effort is to understand the mechanisms implicated in this pathological process in order to contribute to the development of new diagnostic markers and therapeutic targets. In this study we have identified a set of lncRNAs significantly downregulated in hepatocellular carcinoma (HCC) in correlation with the grade of tumor dedifferentiation and patients’ worse prognosis. Mechanistically, our results show that they are related with hepatic differentiation and at least a subset of those lncRNAs are essential to ensure the expression of other hepato-specific genes required for liver function. Moreover, we demonstrate that the expression of these lncRNAs in HCC is silenced by DNA methylation. All in all, we uncover connected epigenetic alterations involved in the progression of liver cancer and identify potential new biomarkers. Abstract Background: Long noncoding RNAs (lncRNAs) are emerging as key players in cancer, including hepatocellular carcinoma (HCC). Here we identify the mechanism implicated in the HCC inhibition of a set of lncRNAs, and their contribution to the process of hepatocarcinogenesis. Methods and Results: The top-ranked 35 lncRNAs downregulated in HCC (Top35 LNDH) were validated in several human HCC cohorts. We demonstrate that their inhibition is associated with promoter hypermethylation in HCC compared to control tissue, and in HCC human cell lines compared to primary hepatocytes. Moreover, demethylating treatment of HCC human cell lines induced the expression of these lncRNAs. The Top35 LNDH were preferentially expressed in the adult healthy liver compared to other tissues and fetal liver and were induced in well-differentiated HepaRG cells. Remarkably, their knockdown compromised the expression of other hepato-specific genes. Finally, the expression of the Top35 LNDH positively correlates with the grade of tumor differentiation and, more importantly, with a better patient prognosis. Conclusions: Our results demonstrate that the selected Top35 LNDH are not only part of the genes that compose the hepatic differentiated signature but participate in its establishment. Moreover, their downregulation through DNA methylation occurs during the process of hepatocarcinogenesis compromising hepatocellular differentiation and HCC patients’ prognosis.
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Affiliation(s)
- Miriam Recalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Gárate-Rascón
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - José María Herranz
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
| | - María Elizalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Azkona
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - Juan P. Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - Loreto Boix
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - María Reig
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Bruno Sangro
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Hepatology Unit, Navarra University Clinic, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Puri Fortes
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Matías A. Ávila
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Carmen Berasain
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
| | - María Arechederra
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
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Jin Y, Liu T, Luo H, Liu Y, Liu D. Targeting Epigenetic Regulatory Enzymes for Cancer Therapeutics: Novel Small-Molecule Epidrug Development. Front Oncol 2022; 12:848221. [PMID: 35419278 PMCID: PMC8995554 DOI: 10.3389/fonc.2022.848221] [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: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulation of the epigenetic enzyme-mediated transcription of oncogenes or tumor suppressor genes is closely associated with the occurrence, progression, and prognosis of tumors. Based on the reversibility of epigenetic mechanisms, small-molecule compounds that target epigenetic regulation have become promising therapeutics. These compounds target epigenetic regulatory enzymes, including DNA methylases, histone modifiers (methylation and acetylation), enzymes that specifically recognize post-translational modifications, chromatin-remodeling enzymes, and post-transcriptional regulators. Few compounds have been used in clinical trials and exhibit certain therapeutic effects. Herein, we summarize the classification and therapeutic roles of compounds that target epigenetic regulatory enzymes in cancer treatment. Finally, we highlight how the natural compounds berberine and ginsenosides can target epigenetic regulatory enzymes to treat cancer.
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Affiliation(s)
- Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Tianjia Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Haoming Luo
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yangyang Liu
- Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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17
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Lin L, Shi K, Zhou S, Cai MC, Zhang C, Sun Y, Zang J, Cheng L, Ye K, Ma P, Shen P, Zhang M, Cheng Y, Qi C, Li Y, Yin X, Zheng Y, Tan L, Zhuang G, Zang R. SOX17 and PAX8 constitute an actionable lineage-survival transcriptional complex in ovarian cancer. Oncogene 2022; 41:1767-1779. [DOI: 10.1038/s41388-022-02210-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 12/22/2022]
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Lin HY, Wu HJ, Chen SY, Hou MF, Lin CS, Chu PY. Epigenetic therapy combination of UNC0638 and CI-994 suppresses breast cancer via epigenetic remodeling of BIRC5 and GADD45A. Biomed Pharmacother 2022; 145:112431. [PMID: 34798471 DOI: 10.1016/j.biopha.2021.112431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND There is currently a growing interest in the roles of epigenetic mechanisms in the diagnosis, prognosis, and therapies associated with precision oncology for breast cancer (BC). This study aimed to demonstrate the clinical significance of euchromatic histone lysine methyltransferase 2 (EHMT2), histone deacetylase 1 (HDAC1) and HDAC2 in BC, to evaluate the antitumor effectiveness of a combination of the selective inhibitors UNC0638 and CI-994 (U+C), and to clarify the underlying mechanisms. METHODS Multi-omic analysis was used to study the clinical significance of the biomarkers of interest. The effects of U+C treatment were evaluated by detecting cell viability, cell cycle, apoptosis, and representative gene expressions. RNA-Seq and Gene Set Enrichment Analysis (GSEA) were employed to identify over-represented genes associated with the treatment. Chromatin immunoprecipitation and qPCR (ChIP-qPCR) assay were applied to verify epigenetic profiling on the identified promoters. RESULTS The significance of elevated expressions of EHMT2, HDAC1, and HDAC2 in tumor tissue and BC basal-like subtype in predicting a poor prognosis was noted. The U+C combined treatment showed an enhanced suppressive effect as compared to single agent treatment, perturbed the cell cycle, induced apoptosis, reduced expressions of the genes representing anti-apoptosis, stemness, drug resistance and basal-like state, while increasing luminal-like state genes. In addition, the combined U+C treatment suppressed xenograft tumor growth. The epigenetic reprogramming of histones was identified in the down-regulated BIRC5 and upregulated GADD45A. CONCLUSION These findings demonstrate that selectively targeting EHMT2, HDAC1, and HDAC2 by concurrent U+C treatment suppresses BC tumor progression via epigenetic remodeling of BIRC5 and GADD45A.
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Affiliation(s)
- Hung-Yu Lin
- College of Medicine, National Chung Hsing University, Taichung 402, Taiwan; Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan.
| | - Hsing-Ju Wu
- College of Medicine, National Chung Hsing University, Taichung 402, Taiwan; Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan; Department of Biology, National Changhua University of Education, Changhua 500, Taiwan.
| | - Si-Yun Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan.
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
| | - Chang-Shen Lin
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Department of Biological Sciences, National Sun Yet-sen University, Kaohsiung 804, Taiwan.
| | - Pei-Yi Chu
- College of Medicine, National Chung Hsing University, Taichung 402, Taiwan; Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan; School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan; Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
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Natu A, Singh A, Gupta S. Hepatocellular carcinoma: Understanding molecular mechanisms for defining potential clinical modalities. World J Hepatol 2021; 13:1568-1583. [PMID: 34904030 PMCID: PMC8637668 DOI: 10.4254/wjh.v13.i11.1568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/12/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
Liver cancer is the sixth most commonly occurring cancer and costs millions of lives per year. The diagnosis of hepatocellular carcinoma (HCC) has relied on scanning techniques and serum-based markers such as α-fetoprotein. These measures have limitations due to their detection limits and asymptomatic conditions during the early stages, resulting in late-stage cancer diagnosis where targeted chemotherapy or systemic treatment with sorafenib is offered. However, the aid of conventional therapy for patients in the advanced stage of HCC has limited outcomes. Thus, it is essential to seek a new treatment strategy and improve the diagnostic techniques to manage the disease. Researchers have used the omics profile of HCC patients for sub-classification of tissues into different groups, which has helped us with prognosis. Despite these efforts, a promising target for treatment has not been identified. The hurdle in this situation is genetic and epigenetic variations in the tumor, leading to disparities in response to treatment. Understanding reversible epigenetic changes along with clinical traits help to define new markers for patient categorization and design personalized therapy. Many clinical trials of inhibitors of epigenetic modifiers (also known as epi-drugs) are in progress. Epi-drugs like azacytidine or belinostat are already approved for other cancer treatments. Furthermore, epigenetic changes have also been observed in drug-resistant HCC tumors. In such cases, combinatorial treatment of epi-drugs with systemic therapy or trans-arterial chemoembolization might re-sensitize resistant cells.
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Affiliation(s)
- Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
| | - Anjali Singh
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
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20
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Lee J, Gillam L, Visvanathan K, Hansford JR, McCarthy MC. Clinical Utility of Precision Medicine in Pediatric Oncology: A Systematic Review. JCO Precis Oncol 2021; 5:1088-1102. [DOI: 10.1200/po.20.00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Precision medicine uses advanced molecular techniques to guide the use of targeted therapeutic drugs and is an emerging paradigm in pediatric oncology. Clinical evidence related to the efficacy of many novel targeted drugs, however, is currently very limited given the rarity of pediatric cancer and the lack of published evidence for the use of these drugs in children. This systematic review aimed to evaluate the existing evidence for the feasibility and clinical efficacy of precision medicine in pediatric oncology. METHODS A systematic review was conducted using the PubMed, Medline, and Embase databases. Clinical trials and observational studies, which used molecular assays such as whole-exome sequencing to identify molecular targets that guided the allocation of targeted cancer drugs and reported clinical outcomes, were included in this review. RESULTS Twenty-one clinical trials and observational studies were identified, collectively enrolling 1,408 pediatric patients across nine countries. Therapeutic targets were found in 647 patients (46.0%); however, only 175 of these patients (27.0%) received a targeted drug. Objective responses were recorded for 73 (41.7%) of these 175 patients, only 5.2% of the total sample. Inconsistent outcome reporting and limited comparison with conventional treatment hindered evaluation of the clinical utility of precision medicine. CONCLUSION Precision medicine can feasibly identify molecular targets in a clinical setting. However, the inaccessibility of targeted drugs is a significant barrier, restricting the exploration of its therapeutic potential in pediatric oncology. Future clinical trials should endeavor to link the molecular testing results with access to targeted drugs and standardize outcome reporting to advance understanding of the benefits of this novel paradigm in improving patient outcomes.
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Affiliation(s)
- Justin Lee
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
| | - Lynn Gillam
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
- Department of Human Bioethics, University of Melbourne, Melbourne, VIC, Australia
| | - Keshini Visvanathan
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jordan R. Hansford
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Maria C. McCarthy
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC, Australia
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
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21
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Galloy M, Lachance C, Cheng X, Distéfano-Gagné F, Côté J, Fradet-Turcotte A. Approaches to Study Native Chromatin-Modifying Complex Activities and Functions. Front Cell Dev Biol 2021; 9:729338. [PMID: 34604228 PMCID: PMC8481805 DOI: 10.3389/fcell.2021.729338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
The modification of histones-the structural components of chromatin-is a central topic in research efforts to understand the mechanisms regulating genome expression and stability. These modifications frequently occur through associations with multisubunit complexes, which contain active enzymes and additional components that orient their specificity and read the histone modifications that comprise epigenetic signatures. To understand the functions of these modifications it is critical to study the enzymes and substrates involved in their native contexts. Here, we describe experimental approaches to purify native chromatin modifiers complexes from mammalian cells and to produce recombinant nucleosomes that are used as substrates to determine the activity of the complex. In addition, we present a novel approach, similar to the yeast anchor-away system, to study the functions of essential chromatin modifiers by quickly inducing their depletion from the nucleus. The step-by-step protocols included will help standardize these approaches in the research community, enabling convincing conclusions about the specificities and functions of these crucial regulators of the eukaryotic genome.
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Affiliation(s)
- Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Félix Distéfano-Gagné
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
| | - Amelie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Université Laval, Québec, QC, Canada
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22
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Sasca D, Guezguez B, Kühn MWM. Next generation epigenetic modulators to target myeloid neoplasms. Curr Opin Hematol 2021; 28:356-363. [PMID: 34267079 DOI: 10.1097/moh.0000000000000673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE OF REVIEW Comprehensive sequencing studies aimed at determining the genetic landscape of myeloid neoplasms have identified epigenetic regulators to be among the most commonly mutated genes. Detailed studies have also revealed a number of epigenetic vulnerabilities. The purpose of this review is to outline these vulnerabilities and to discuss the new generation of drugs that exploit them. RECENT FINDINGS In addition to deoxyribonucleic acid-methylation, novel epigenetic dependencies have recently been discovered in various myeloid neoplasms and many of them can be targeted pharmacologically. These include not only chromatin writers, readers, and erasers but also chromatin movers that shift nucleosomes to allow access for transcription. Inhibitors of protein-protein interactions represent a novel promising class of drugs that allow disassembly of oncogenic multiprotein complexes. SUMMARY An improved understanding of disease-specific epigenetic vulnerabilities has led to the development of second-generation mechanism-based epigenetic drugs against myeloid neoplasms. Many of these drugs have been introduced into clinical trials and synergistic drug combination regimens have been shown to enhance efficacy and potentially prevent drug resistance.
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Affiliation(s)
- Daniel Sasca
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
| | - Borhane Guezguez
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
- German Cancer Research Center (DKFZ), Heidelberg
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Michael W M Kühn
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University Mainz, Mainz
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23
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Yang J, He Z, Chen C, Li S, Qian J, Zhao J, Fang R. Toxoplasma gondii Infection Inhibits Histone Crotonylation to Regulate Immune Response of Porcine Alveolar Macrophages. Front Immunol 2021; 12:696061. [PMID: 34322124 PMCID: PMC8312545 DOI: 10.3389/fimmu.2021.696061] [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: 04/16/2021] [Accepted: 06/18/2021] [Indexed: 01/01/2023] Open
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can infect almost all warm-blooded animals, causing serious public health problems. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which is first identified on histones and has been proved relevant to procreation regulation, transcription activation, and cell signaling pathway. However, the biological functions of histone crotonylation have not yet been reported in macrophages infected with T. gondii. As a result, a total of 1,286 Kcr sites distributed in 414 proteins were identified and quantified, demonstrating the existence of crotonylation in porcine alveolar macrophages. According to our results, identified histones were overall downregulated. HDAC2, a histone decrotonylase, was found to be significantly increased, which might be the executor of histone Kcr after parasite infection. In addition, T. gondii infection inhibited the crotonylation of H2B on K12, contributing on the suppression of epigenetic regulation and NF-κB activation. Nevertheless, the reduction of histone crotonylation induced by parasite infection could promote macrophage proliferation via activating PI3K/Akt signaling pathway. The present findings point to a comprehensive understanding of the biological functions of histone crotonylation in porcine alveolar macrophages, thereby providing a certain research basis for the mechanism research on the immune response of host cells against T. gondii infection.
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Affiliation(s)
- Jing Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhengming He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengjie Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Senyang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiahui Qian
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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24
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Coughlan AY, Testa G. Exploiting epigenetic dependencies in ovarian cancer therapy. Int J Cancer 2021; 149:1732-1743. [PMID: 34213777 PMCID: PMC9292863 DOI: 10.1002/ijc.33727] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023]
Abstract
Ovarian cancer therapy has remained fundamentally unchanged for 50 years, with surgery and chemotherapy still the frontline treatments. Typically asymptomatic until advanced stages, ovarian cancer is known as “the silent killer.” Consequently, it has one of the worst 5‐year survival rates, as low as 30%. The most frequent driver mutations are found in well‐defined tumor suppressors, such as p53 and BRCA1/2. In recent years, it has become clear that, like the majority of other cancers, many epigenetic regulators are altered in ovarian cancer, including EZH2, SMARCA2/4 and ARID1A. Disruption of epigenetic regulators often leads to loss of transcriptional control, aberrant cell fate trajectories and disruption of senescence, apoptotic and proliferation pathways. These mitotically inherited epigenetic alterations are particularly promising targets for therapy as they are largely reversible. Consequently, many drugs targeting chromatin modifiers and other epigenetic regulators are at various stages of clinical trials for other cancers. Understanding the mechanisms by which ovarian cancer‐specific epigenetic processes are disrupted in patients can allow for informed targeting of epigenetic pathways tailored for each patient. In recent years, there have been groundbreaking new advances in disease modeling through ovarian cancer organoids; these models, alongside single‐cell transcriptomic and epigenomic technologies, allow the elucidation of the epigenetic pathways deregulated in ovarian cancer. As a result, ovarian cancer therapy may finally be ready to advance to next‐generation treatments. Here, we review the major developments in ovarian cancer, including genetics, model systems and technologies available for their study and the implications of applying epigenetic therapies to ovarian cancer.
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Affiliation(s)
- Aisling Y Coughlan
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
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25
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Sharma S, Mukherjee AK, Roy SS, Bagri S, Lier S, Verma M, Sengupta A, Kumar M, Nesse G, Pandey DP, Chowdhury S. Human telomerase is directly regulated by non-telomeric TRF2-G-quadruplex interaction. Cell Rep 2021; 35:109154. [PMID: 34010660 PMCID: PMC7611063 DOI: 10.1016/j.celrep.2021.109154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) remains suppressed in most normal somatic cells. Resulting erosion of telomeres leads eventually to replicative senescence. Reactivation of hTERT maintains telomeres and triggers progression of >90% of cancers. However, any direct causal link between telomeres and telomerase regulation remains unclear. Here, we show that the telomere-repeat-binding-factor 2 (TRF2) binds hTERT promoter G-quadruplexes and recruits the polycomb-repressor EZH2/PRC2 complex. This is causal for H3K27 trimethylation at the hTERT promoter and represses hTERT in cancer as well as normal cells. Two highly recurrent hTERT promoter mutations found in many cancers, including ∼83% glioblastoma multiforme, that are known to destabilize hTERT promoter G-quadruplexes, showed loss of TRF2 binding in patient-derived primary glioblastoma multiforme cells. Ligand-induced G-quadruplex stabilization restored TRF2 binding, H3K27-trimethylation, and hTERT re-suppression. These results uncover a mechanism of hTERT regulation through a telomeric factor, implicating telomere-telomerase molecular links important in neoplastic transformation, aging, and regenerative therapy.
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Affiliation(s)
- Shalu Sharma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Shuvra Shekhar Roy
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Silje Lier
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Meenakshi Verma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manish Kumar
- Imaging Facility, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Gaute Nesse
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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26
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Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in multiple myeloma. Blood Adv 2021; 4:5616-5630. [PMID: 33186461 DOI: 10.1182/bloodadvances.2020002566] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Multiple myeloma (MM) is a hematologic malignancy produced by a clonal expansion of plasma cells and characterized by abnormal production and secretion of monoclonal antibodies. This pathology exhibits an enormous heterogeneity resulting not only from genetic alterations but also from several epigenetic dysregulations. Here we provide evidence that Che-1/AATF (Che-1), an interactor of RNA polymerase II, promotes MM proliferation by affecting chromatin structure and sustaining global gene expression. We found that Che-1 depletion leads to a reduction of "active chromatin" by inducing a global decrease of histone acetylation. In this context, Che-1 directly interacts with histones and displaces histone deacetylase class I members from them. Strikingly, transgenic mice expressing human Che-1 in plasma cells develop MM with clinical features resembling those observed in the human disease. Finally, Che-1 downregulation decreases BRD4 chromatin accumulation to further sensitize MM cells to bromodomain and external domain inhibitors. These findings identify Che-1 as a promising target for MM therapy, alone or in combination with bromodomain and external domain inhibitors.
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27
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Mabe NW, Garcia NMG, Wolery SE, Newcomb R, Meingasner RC, Vilona BA, Lupo R, Lin CC, Chi JT, Alvarez JV. G9a Promotes Breast Cancer Recurrence through Repression of a Pro-inflammatory Program. Cell Rep 2021; 33:108341. [PMID: 33147463 PMCID: PMC7656293 DOI: 10.1016/j.celrep.2020.108341] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/30/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Dysregulated gene expression is a common feature of cancer and may underlie some aspects of tumor progression, including tumor relapse. Here, we show that recurrent mammary tumors exhibit global changes in gene expression and histone modifications and acquire dependence on the G9a histone methyltransferase. Genetic ablation of G9a delays tumor recurrence, and pharmacologic inhibition of G9a slows the growth of recurrent tumors. Mechanistically, G9a activity is required to silence pro-inflammatory cytokines, including tumor necrosis factor (TNF), through H3K9 methylation at gene promoters. G9a inhibition induces re-expression of these cytokines, leading to p53 activation and necroptosis. Recurrent tumors upregulate receptor interacting protein kinase-3 (RIPK3) expression and are dependent upon RIPK3 activity. High RIPK3 expression renders recurrent tumors sensitive to necroptosis following G9a inhibition. These findings demonstrate that G9a-mediated silencing of pro-necroptotic proteins is a critical step in tumor recurrence and suggest that G9a is a targetable dependency in recurrent breast cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Nina Marie G Garcia
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Shayna E Wolery
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Rachel Newcomb
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Ryan C Meingasner
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Brittany A Vilona
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Ryan Lupo
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Chao-Chieh Lin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - James V Alvarez
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA.
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28
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Zhu A, Hopkins KM, Friedman RA, Bernstock JD, Broustas CG, Lieberman HB. DNMT1 and DNMT3B regulate tumorigenicity of human prostate cancer cells by controlling RAD9 expression through targeted methylation. Carcinogenesis 2021; 42:220-231. [PMID: 32780107 PMCID: PMC7905840 DOI: 10.1093/carcin/bgaa088] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is the second most common type of cancer and the second leading cause of cancer death in American men. RAD9 stabilizes the genome, but prostate cancer cells and tumors often have high quantities of the protein. Reduction of RAD9 level within prostate cancer cells decreases tumorigenicity of nude mouse xenographs and metastasis phenotypes in culture, indicating that RAD9 overproduction is essential for the disease. In prostate cancer DU145 cells, CpG hypermethylation in a transcription suppressor site of RAD9 intron 2 causes high-level gene expression. Herein, we demonstrate that DNA methyltransferases DNMT1 and DNMT3B are highly abundant in prostate cancer cells DU145, CWR22, LNCaP and PC-3; yet, these DNMTs bind primarily to the transcription suppressor in DU145, the only cells where methylation is critical for RAD9 regulation. For DU145 cells, DNMT1 or DNMT3B shRNA reduced RAD9 level and tumorigenicity, and RAD9 ectopic expression restored this latter activity in the DNMT knockdown cells. High levels of RAD9, DNMT1, DNMT3B and RAD9 transcription suppressor hypermethylation were significantly correlated in prostate tumors, and not in normal prostate tissues. Based on these results, we propose a novel model where RAD9 is regulated epigenetically by DNMT1 and DNMT3B, via targeted hypermethylation, and that consequent RAD9 overproduction promotes prostate tumorigenesis.
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Affiliation(s)
- Aiping Zhu
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kevin M Hopkins
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Joshua D Bernstock
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Constantinos G Broustas
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Howard B Lieberman
- Center for Radiological Research, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
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29
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Ghasemi S, Xu S, Nabavi SM, Amirkhani MA, Sureda A, Tejada S, Lorigooini Z. Epigenetic targeting of cancer stem cells by polyphenols (cancer stem cells targeting). Phytother Res 2021; 35:3649-3664. [PMID: 33619811 DOI: 10.1002/ptr.7059] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022]
Abstract
Epigenetic alterations are one of the main factors that disrupt the expression of genes and consequently, they have an important role in the carcinogenicity and the progression of different cancers. Cancer stem cells (CSCs) are accountable for the recurrence, metastasis, and therapeutic failure of cancer. The noticeable and specific pathways in CSCs can be organized by epigenetic mechanisms such as DNA methylation, chromatin remodeling, regulatory RNAs, among others. Since epigenetics modifications can be changed and reversed, it is a possible tool for cancer control and treatment. Epigenetic therapies against CSCs are emerging as a very new strategy with a good future expectation to treat cancer patients. Phenolic compounds are a vast group of substances with anticarcinogenic functions, antiinflammatory, and antioxidative activities. It seems these characteristics are related to neutralizing CSCs development, their microenvironment, and metabolism through epigenetic mechanisms. In the current work, the types of epigenetic changes known in these cells are introduced. In addition, some studies about the use of polyphenols acting through a variety of epigenetic mechanisms to counteract these cells will be reviewed. The reported results seem to indicate that the use of these phenolic compounds may be useful for CSCs defeat.
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Affiliation(s)
- Sorayya Ghasemi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.,Cancer Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Suowen Xu
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York, USA
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Amir Amirkhani
- Stem Cell and Regenerative Medicine Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress, University of Balearic Islands & Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain.,CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Tejada
- CIBEROBN (Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, Madrid, Spain.,Laboratory of neurophysiology. Biology Department, University of Balearic Islands & Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Zahra Lorigooini
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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30
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Yang G, Yuan Y, Yuan H, Wang J, Yun H, Geng Y, Zhao M, Li L, Weng Y, Liu Z, Feng J, Bu Y, Liu L, Wang B, Zhang X. Histone acetyltransferase 1 is a succinyltransferase for histones and non-histones and promotes tumorigenesis. EMBO Rep 2021; 22:e50967. [PMID: 33372411 PMCID: PMC7857430 DOI: 10.15252/embr.202050967] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Lysine succinylation (Ksucc) is an evolutionarily conserved and widespread post-translational modification. Histone acetyltransferase 1 (HAT1) is a type B histone acetyltransferase, regulating the acetylation of both histone and non-histone proteins. However, the role of HAT1 in succinylation modulation remains unclear. Here, we employ a quantitative proteomics approach to study succinylation in HepG2 cancer cells and find that HAT1 modulates lysine succinylation on various proteins including histones and non-histones. HAT1 succinylates histone H3 on K122, contributing to epigenetic regulation and gene expression in cancer cells. Moreover, HAT1 catalyzes the succinylation of PGAM1 on K99, resulting in its increased enzymatic activity and the stimulation of glycolytic flux in cancer cells. Clinically, HAT1 is significantly elevated in liver cancer, pancreatic cancer, and cholangiocarcinoma tissues. Functionally, HAT1 succinyltransferase activity and the succinylation of PGAM1 by HAT1 play critical roles in promoting tumor progression in vitro and in vivo. Thus, we conclude that HAT1 is a succinyltransferase for histones and non-histones in tumorigenesis.
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Affiliation(s)
- Guang Yang
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Ying Yuan
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Hongfeng Yuan
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Jiapei Wang
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Haolin Yun
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Yu Geng
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Man Zhao
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Linhan Li
- Jingjie PTM BioLab Co. Ltd.Hangzhou Economic and Technological Development AreaHangzhouChina
| | - Yejing Weng
- Jingjie PTM BioLab Co. Ltd.Hangzhou Economic and Technological Development AreaHangzhouChina
| | - Zixian Liu
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Jinyan Feng
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Yanan Bu
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Lei Liu
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Bingnan Wang
- Jingjie PTM BioLab Co. Ltd.Hangzhou Economic and Technological Development AreaHangzhouChina
| | - Xiaodong Zhang
- Department of Cancer ResearchInstitute of Molecular BiologyCollege of Life SciencesNankai UniversityTianjinChina
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31
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Shang W, Wang Y, Liang X, Li T, Shao W, Liu F, Cui X, Wang Y, Lv L, Chai L, Qu L, Zheng L, Jia J. SETDB1 promotes gastric carcinogenesis and metastasis via upregulation of CCND1 and MMP9 expression. J Pathol 2021; 253:148-159. [PMID: 33044755 DOI: 10.1002/path.5568] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 09/20/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
SETDB1 is a histone lysine methyltransferase that has critical roles in cancers. However, its potential role in gastric cancer (GC) remains obscure. Here, we mainly investigate the clinical significance and the possible role of SETDB1 in GC. We find that SETDB1 expression is upregulated in GC tissues and its high-level expression was a predictor of poor prognosis in patients. Overexpression of SETDB1 promoted cell proliferation and metastasis, while SETDB1 suppression had an opposite effect both in vitro and in vivo. Mechanistically, SETDB1 was shown to interact with ERG to promote the transcription of cyclin D1 (CCND1) and matrix metalloproteinase 9 (MMP9) through binding to their promoter regions. In addition, the expression of SETDB1 was also enhanced by the transcription factor TCF4 at the transcriptional level in GC. Furthermore, SETDB1 expression was found to be induced by Helicobacter pylori (H. pylori) infection in a TCF4-dependent manner. Taken together, our results indicate that SETDB1 is aberrantly overexpressed in GC and plays key roles in gastric carcinogenesis and metastasis via upregulation of CCND1 and MMP9. Our work also suggests that SETDB1 could be a potential oncogenic factor and a therapeutic target for GC. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Wenjing Shang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Yue Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Xiuming Liang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Shandong University-Karolinska Institute Collaborative Laboratory for Cancer Research, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Tongyu Li
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Wei Shao
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Fen Liu
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Xiujie Cui
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Yuanyuan Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lin Lv
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Li Chai
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lingxin Qu
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lixin Zheng
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Shandong University-Karolinska Institute Collaborative Laboratory for Cancer Research, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
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32
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Wei Z, Liu X, Cheng C, Yu W, Yi P. Metabolism of Amino Acids in Cancer. Front Cell Dev Biol 2021; 8:603837. [PMID: 33511116 PMCID: PMC7835483 DOI: 10.3389/fcell.2020.603837] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Metabolic reprogramming has been widely recognized as a hallmark of malignancy. The uptake and metabolism of amino acids are aberrantly upregulated in many cancers that display addiction to particular amino acids. Amino acids facilitate the survival and proliferation of cancer cells under genotoxic, oxidative, and nutritional stress. Thus, targeting amino acid metabolism is becoming a potential therapeutic strategy for cancer patients. In this review, we will systematically summarize the recent progress of amino acid metabolism in malignancy and discuss their interconnection with mammalian target of rapamycin complex 1 (mTORC1) signaling, epigenetic modification, tumor growth and immunity, and ferroptosis. Finally, we will highlight the potential therapeutic applications.
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Affiliation(s)
- Zhen Wei
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Brain Science and Advanced Technology Institute, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunming Cheng
- Department of Radiation Oncology, James Comprehensive Cancer Center and College of Medicine at The Ohio State University, Columbus, OH, United States
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Fernández-Barrena MG, Arechederra M, Colyn L, Berasain C, Avila MA. Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg. JHEP Rep 2020; 2:100167. [PMID: 33134907 PMCID: PMC7585149 DOI: 10.1016/j.jhepr.2020.100167] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly tumour whose causative agents are generally well known, but whose pathogenesis remains poorly understood. Nevertheless, key genetic alterations are emerging from a heterogeneous molecular landscape, providing information on the tumorigenic process from initiation to progression. Among these molecular alterations, those that affect epigenetic processes are increasingly recognised as contributing to carcinogenesis from preneoplastic stages. The epigenetic machinery regulates gene expression through intertwined and partially characterised circuits involving chromatin remodelers, covalent DNA and histone modifications, and dedicated proteins reading these modifications. In this review, we summarise recent findings on HCC epigenetics, focusing mainly on changes in DNA and histone modifications and their carcinogenic implications. We also discuss the potential drugs that target epigenetic mechanisms for HCC treatment, either alone or in combination with current therapies, including immunotherapies.
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Key Words
- 5acC, 5-acetylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5-hydoxymethyl cytosine
- 5mC, 5-methylcytosine
- Acetyl-CoA, acetyl coenzyme A
- BER, base excision repair
- BRD, bromodomain
- CDA, cytidine deaminase
- CGI, CpG island
- CIMP, CGI methylator phenotype
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- DNMT, DNA methyltransferase
- DNMTi, DNMT inhibitor
- Epigenetics
- FAD, flavin adenine dinucleotide
- HAT, histone acetyltransferases
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HDACi, HDAC inhibitor
- HDM, histone demethylase
- HMT, histone methyltransferase
- Hepatocellular carcinoma
- KMT, lysine methyltransferase
- LSD/KDM, lysine specific demethylases
- NAFLD, non-alcoholic fatty liver disease
- NK, natural killer
- NPC, nasopharyngeal carcinoma
- PD-L1, programmed cell death ligand-1
- PD1, programmed cell death protein 1
- PHD, plant homeodomain
- PTM, post-translational modification
- SAM, S-adenosyl-L-methionine
- TDG, thymidine-DNA-glycosylase
- TERT, telomerase reverse transcriptase
- TET, ten-eleven translocation
- TME, tumour microenvironment
- TSG, tumour suppressor gene
- Therapy
- UHRF1, ubiquitin like with PHD and ring finger domains 1
- VEGF, vascular endothelial growth factor
- ncRNAs, non-coding RNAs
- α-KG, α-ketoglutarate
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Affiliation(s)
- Maite G. Fernández-Barrena
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Arechederra
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Leticia Colyn
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Matias A. Avila
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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Potluri V, Shandil RK, Gavara R, Sambasivam G, Campo B, Wittlin S, Narayanan S. Discovery of FNDR-20123, a histone deacetylase inhibitor for the treatment of Plasmodium falciparum malaria. Malar J 2020; 19:365. [PMID: 33046062 PMCID: PMC7549214 DOI: 10.1186/s12936-020-03421-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Emergence of anti-malarial drug resistance and perpetual increase in malaria incidence necessitates the development of novel anti-malarials. Histone deacetylases (HDAC) has been shown to be a promising target for malaria, despite this, there are no HDAC inhibitors in clinical trials for malaria treatment. This can be attributed to the poor pharmacokinetics, bioavailability and selectivity of the HDAC inhibitors. Methods A collection of HDAC inhibitors were screened for anti-malarial activity, and the best candidate was profiled in parasite-killing kinetics, growth inhibition of sensitive and multi-drug resistant (MDR) strains and against gametocytes. Absorption, distribution, metabolism and excretion pharmacokinetics (ADME-PK) parameters of FNDR-20123 were determined, and in vivo efficacy was studied in a mouse model for Plasmodium falciparum infection. Results A compound library of HDAC inhibitors (180 in number) was screened for anti-malarial activity, of which FNDR-20123 was the most potent candidate. The compound had been shown to inhibit Plasmodium HDAC with IC50 of 31 nM and human HDAC with IC50 of 3 nM. The IC50 obtained for P. falciparum in asexual blood-stage assay was 42 nM. When compared to atovaquone and pyrimethamine, the killing profiles of FNDR-20123 were better than atovaquone and comparable to pyrimethamine. The IC50 values for the growth inhibition of sensitive and MDR strains were similar, indicating that there is no cross-resistance and a low risk of resistance development. The selected compound was also active against gametocytes, indicating a potential for transmission control: IC50 values being 190 nM for male and > 5 µM for female gametocytes. FNDR-20123 is a stable candidate in human/mouse/rat liver microsomes (> 75% remaining post 2-h incubation), exhibits low plasma protein binding (57% in humans) with no human Ether-à-go–go-Related Gene (hERG) liability (> 100 µM), and does not inhibit any of the cytochrome P450 (CYP) isoforms tested (IC50 > 25 µM). It also shows negligible cytotoxicity to HepG-2 and THP-1 cell lines. The oral pharmacokinetics in rats at 100 mg/kg body weight shows good exposures (Cmax = 1.1 µM) and half-life (T1/2 = 5.5 h). Furthermore, a 14-day toxicokinetic study at 100 mg/kg daily dose did not show any abnormality in body weight or gross organ pathology. FNDR-20123 is also able to reduce parasitaemia significantly in a mouse model for P. falciparum infection when dosed orally and subcutaneously. Conclusion FNDR-20123 may be a suitable candidate for the treatment of malaria, which can be further developed.
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Affiliation(s)
- Vijay Potluri
- Foundation for Neglected Disease Research, Bengaluru, India
| | | | - R Gavara
- Anthem Biosciences Private Limited, Bengaluru, India
| | | | - Brice Campo
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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35
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Yang Z, Jiang H. A chromatin perspective on metabolic and genotoxic impacts on hematopoietic stem and progenitor cells. Cell Mol Life Sci 2020; 77:4031-4047. [PMID: 32318759 PMCID: PMC7541408 DOI: 10.1007/s00018-020-03522-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Fate determination in self-renewal and differentiation of hematopoietic stem and progenitor cells (HSCs and HPCs) is ultimately controlled by gene expression, which is profoundly influenced by the global and local chromatin state. Cellular metabolism directly influences the chromatin state through the dynamic regulation of the enzymatic activities that modify DNA and histones, but also generates genotoxic metabolites that can damage DNA and thus pose threat to the genome integrity. On the other hand, mechanisms modulating the chromatin state impact metabolism by regulating the expression and activities of key metabolic enzymes. Moreover, through regulating either DNA damage response directly or expression of genes involved in this process, chromatin modulators play active and crucial roles in guarding the genome integrity, breaching of which results in defective HSPC function. Therefore, HSPC function is regulated by the dynamic and two-way interactions between metabolism and chromatin. Here, we review recent advances that provide a chromatin perspective on the major impacts the metabolic and genotoxic factors can have on HSPC function and fate determination.
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Affiliation(s)
- Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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36
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Soncini D, Orecchioni S, Ruberti S, Minetto P, Martinuzzi C, Agnelli L, Todoerti K, Cagnetta A, Miglino M, Clavio M, Contini P, Varaldo R, Bergamaschi M, Guolo F, Passalacqua M, Nencioni A, Monacelli F, Gobbi M, Neri A, Abbadessa G, Eathiraj S, Schwartz B, Bertolini F, Lemoli RM, Cea M. The new small tyrosine kinase inhibitor ARQ531 targets acute myeloid leukemia cells by disrupting multiple tumor-addicted programs. Haematologica 2020; 105:2420-2431. [PMID: 33054082 PMCID: PMC7556675 DOI: 10.3324/haematol.2019.224956] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/10/2019] [Indexed: 11/17/2022] Open
Abstract
Tyrosine kinases have been implicated in promoting tumorigenesis of several human cancers. Exploiting these vulnerabilities has been shown to be an effective anti-tumor strategy as demonstrated for example by the Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib, for treatment of various blood cancers. Here, we characterize a new multiple kinase inhibitor, ARQ531, and evaluate its mechanism of action in preclinical models of acute myeloid leukemia. Treatment with ARQ531, by producing global signaling pathway deregulation, resulted in impaired cell cycle progression and survival in a large panel of leukemia cell lines and patient-derived tumor cells, regardless of the specific genetic background and/or the presence of bone marrow stromal cells. RNA-seq analysis revealed that ARQ531 constrained tumor cell proliferation and survival through Bruton's tyrosine kinase and transcriptional program dysregulation, with proteasome-mediated MYB degradation and depletion of short-lived proteins that are crucial for tumor growth and survival, including ERK, MYC and MCL1. Finally, ARQ531 treatment was effective in a patient-derived leukemia mouse model with significant impairment of tumor progression and survival, at tolerated doses. These data justify the clinical development of ARQ531 as a promising targeted agent for the treatment of patients with acute myeloid leukemia.
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Affiliation(s)
- Debora Soncini
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Samantha Ruberti
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Paola Minetto
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Claudia Martinuzzi
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Luca Agnelli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Katia Todoerti
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonia Cagnetta
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Maurizio Miglino
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Marino Clavio
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Contini
- Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Riccardo Varaldo
- Division of Hematology and Hematopoietic Stem Cell Transplantation Unit, Ospedale Policlinico San Martino, Genoa, Italy
| | - Micaela Bergamaschi
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Fabio Guolo
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Mario Passalacqua
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
| | - Alessio Nencioni
- Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Fiammetta Monacelli
- Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
| | - Marco Gobbi
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | | | | | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto M. Lemoli
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Michele Cea
- Chair of Hematology, Department of Internal Medicine and Specialities (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, Herceg Z. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res 2020; 30:1517-1532. [PMID: 32963031 PMCID: PMC7605261 DOI: 10.1101/gr.268292.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
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Affiliation(s)
- Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
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38
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Cao N, Yu Y, Zhu H, Chen M, Chen P, Zhuo M, Mao Y, Li L, Zhao Q, Wu M, Ye M. SETDB1 promotes the progression of colorectal cancer via epigenetically silencing p21 expression. Cell Death Dis 2020; 11:351. [PMID: 32393761 PMCID: PMC7214465 DOI: 10.1038/s41419-020-2561-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
SETDB1, a histone H3K9 methyltransferase, has been reported to be upregulated in a variety of tumors and promotes cancer development. However, the exact pathogenesis of SETDB1 in human colorectal cancer (CRC) is hitherto unknown. Here, we showed that SETDB1 expression was highly amplified in CRC. Functionally, SETDB1 downregulation in SW480 and HCT116 cells reduced cell proliferation, migration, invasion, and increased CRC cells apoptosis. In contrast, SETDB1 overexpression promoted CRC cells proliferation, migration, and invasion. High expression of SETDB1 was associated with a more aggressive phenotype in vitro. Flow cytometry showed that cell cycle was arrested in G1 phase after SETDB1 silencing. Furthermore, depletion of SETDB1 in vivo suppressed CRC cells proliferation. Mechanistically, p21 was identified as the target of SETDB1. After transfected with siSETDB1, expression of p21 was distinctly increased. In contrast, expression of p21 was significantly decreased after overexpression SETDB1. We also showed that SETDB1 could be involved in the regulation of epithelial–mesenchymal transition (EMT) in HCT116 cells. Moreover, we confirmed that SETDB1 could regulate the activity of p21 promoter by dual-luciferase repoter assay, and proved that SETDB1 could bind to the promoter of p21 and regulate its H3K9me3 enrichment level by ChIP-PCR experiment. Finally, we verified that silencing of SETDB1 inhibited CRC tumorigenesis in vivo. In conclusion, our results indicate that SETDB1 is a major driver of CRC development and might provide a new therapeutic target for the clinical treatment of CRC.
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Affiliation(s)
- Nan Cao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Yali Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Hua Zhu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Meng Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Ping Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Mingxing Zhuo
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Yujuan Mao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Lianyun Li
- College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China
| | - Min Wu
- College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Mei Ye
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China. .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, Hubei, 430071, China.
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39
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Tsuchiya Y, Umemura Y, Yagita K. Circadian clock and cancer: From a viewpoint of cellular differentiation. Int J Urol 2020; 27:518-524. [PMID: 32223039 DOI: 10.1111/iju.14231] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/27/2020] [Indexed: 12/18/2022]
Abstract
The circadian clock controls and adapts diverse physiological and behavioral processes according to Earth's 24-h cycle of environmental changes. The master pacemaker of the mammalian circadian clock resides in the hypothalamic suprachiasmatic nucleus, but almost all cells throughout the body show circadian oscillations in gene expression patterns and associated functions. Recent studies have shown that the circadian clock gradually develops during embryogenesis. Embryonic stem cells and induced pluripotent stem cells do not show circadian oscillations of gene expression, but gradually develop circadian clock oscillation during differentiation; thus, the developmental program of circadian clock emergence appears closely associated with cellular differentiation. Like embryonic stem cells, certain cancer cell types also lack the circadian clock. Given this similarity between embryonic stem cells and cancer cells, interest is growing in the contributions of circadian clock dysfunction to dedifferentiation and cancer development. In this review, we summarize recent advances in our understanding of circadian clock emergence during ontogenesis, and discuss possible associations with cellular differentiation and carcinogenesis. Considering the multiple physiological functions of circadian rhythms, circadian abnormalities might contribute to a host of diseases, including cancer. Insights on circadian function could lead to the identification of biomarkers for cancer diagnosis and prognosis, as well as novel targets for treatment.
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Affiliation(s)
- Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuhiro Umemura
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
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40
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Li Z, Tang J, Wen W, Wu W, Wang J, Xu J, Yu Y, He Z, Pan X, Wei H, Zhu Y, Hu S, Cao J, Shen H, Que J, Wang W, Zhu Q, Chen L. Systematic analysis of genetic variants in cancer-testis genes identified two novel lung cancer susceptibility loci in Chinese population. J Cancer 2020; 11:1985-1993. [PMID: 32194810 PMCID: PMC7052880 DOI: 10.7150/jca.40002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/25/2019] [Indexed: 12/29/2022] Open
Abstract
Cancer-testis (CT) genes played important roles in the progression of malignant tumors and were recognized as promising therapeutic targets. However, the roles of genetic variants in CT genes in lung cancer susceptibility have not been well depicted. This study aimed to evaluate the associations between genetic variants in CT genes and lung cancer risk in Chinese population. A total of 22,556 qualified SNPs from 268 lung cancer associated CT genes were initially evaluated based on our previous lung cancer GWAS (Genome-wide association studies) with 2,331 cases and 3,077 controls. As a result, 17 candidate SNPs were further genotyped in 1,056 cases and 1,053 controls using Sequenom platform. Two variants (rs6941653, OPRM1, T > C, screening: OR = 1.24, 95%CI: 1.12-1.38, P = 2.40×10-5; validation: OR = 1.18, 95%CI: 1.01-1.37, P = 0.039 and rs402969, NLRP8, C > T, screening: OR = 1.15, 95%CI: 1.04-1.26, P = 0.006; validation: OR = 1.16, 95%CI: 1.02-1.33, P = 0.028) were identified as novel lung cancer susceptibility variants. Stratification analysis indicated that the effect of rs6941653 was stronger in lung squamous cell carcinoma (OR = 1.36) than that in lung adenocarcinoma (OR = 1.15, I2 = 77%, P = 0.04). Finally, functional annotations, differential gene expression analysis, pathway and gene ontology analyses were performed to suggest the potential functions of our identified variants and genes. In conclusion, this study identified two novel lung cancer risk variants in Chinese population and provided deeper insight into the roles of CT genes in lung tumorigenesis.
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Affiliation(s)
- Zhihua Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jianwei Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wei Wen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Weibing Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jun Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jing Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zhicheng He
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xianglong Pan
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Haixing Wei
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yining Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shuo Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jing Cao
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, International Joint Research Center, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center of Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Quan Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
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Yang MW, Tao LY, Jiang YS, Yang JY, Huo YM, Liu DJ, Li J, Fu XL, He R, Lin C, Liu W, Zhang JF, Hua R, Li Q, Jiang SH, Hu LP, Tian GA, Zhang XX, Niu N, Lu P, Shi J, Xiao GG, Wang LW, Xue J, Zhang ZG, Sun YW. Perineural Invasion Reprograms the Immune Microenvironment through Cholinergic Signaling in Pancreatic Ductal Adenocarcinoma. Cancer Res 2020; 80:1991-2003. [PMID: 32098780 DOI: 10.1158/0008-5472.can-19-2689] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/09/2020] [Accepted: 02/21/2020] [Indexed: 12/29/2022]
Abstract
Perineural invasion is a common feature of pancreatic ductal adenocarcinoma (PDAC). Here, we investigated the effect of perineural invasion on the microenvironment and how this affects PDAC progression. Transcriptome expression profiles of PDAC tissues with different perineural invasion status were compared, and the intratumoral T-cell density and levels of neurotransmitters in these tissues were assessed. Perineural invasion was associated with impaired immune responses characterized by decreased CD8+ T and Th1 cells, and increased Th2 cells. Acetylcholine levels were elevated in severe perineural invasion. Acetylcholine impaired the ability of PDAC cells to recruit CD8+ T cells via HDAC1-mediated suppression of CCL5. Moreover, acetylcholine directly inhibited IFNγ production by CD8+ T cells in a dose-dependent manner and favored Th2 over Th1 differentiation. Furthermore, hyperactivation of cholinergic signaling enhanced tumor growth by suppressing the intratumoral T-cell response in an orthotopic PDAC model. Conversely, blocking perineural invasion with bilateral subdiaphragmatic vagotomy in tumor-bearing mice was associated with an increase in CD8+ T cells, an elevated Th1/Th2 ratio, and improved survival. In conclusion, perineural invasion-triggered cholinergic signaling favors tumor growth by promoting an immune-suppressive microenvironment characterized by impaired CD8+ T-cell infiltration and a reduced Th1/Th2 ratio. SIGNIFICANCE: These findings provide a promising therapeutic strategy to modulate the immunosuppressive microenvironment of pancreatic ductal adenocarcinoma with severe perineural invasion.
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Affiliation(s)
- Min-Wei Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ling-Ye Tao
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yong-Sheng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jian-Yu Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yan-Miao Huo
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - De-Jun Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jiao Li
- Department of Hepatobiliary Pancreas Surgery, Shanghai East Hospital, Tong Ji University School of Medicine, Shanghai, P.R. China
| | - Xue-Liang Fu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ruizhe He
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Chaoyi Lin
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Wei Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jun-Feng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Rong Hua
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Guang-Ang Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiao-Xin Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ningning Niu
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ping Lu
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Juanjuan Shi
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Gary G Xiao
- Department of Pharmacy at School of Chemical Engineering, Dalian University of Technology, Dalian, P.R. China.,Functional Genomics and Proteomics Laboratories, Osteoporosis Research Center, Creighton University Medical Center, Omaha, Nebraska
| | - Li-Wei Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai, P.R. China
| | - Jing Xue
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Yong-Wei Sun
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
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42
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Gan Y, Li N, Xin Y, Zou G. TriPCE: A Novel Tri-Clustering Algorithm for Identifying Pan-Cancer Epigenetic Patterns. Front Genet 2020; 10:1298. [PMID: 32010182 PMCID: PMC6974616 DOI: 10.3389/fgene.2019.01298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022] Open
Abstract
Epigenetic alteration is a fundamental characteristic of nearly all human cancers. Tumor cells not only harbor genetic alterations, but also are regulated by diverse epigenetic modifications. Identification of epigenetic similarities across different cancer types is beneficial for the discovery of treatments that can be extended to different cancers. Nowadays, abundant epigenetic modification profiles have provided a great opportunity to achieve this goal. Here, we proposed a new approach TriPCE, introducing tri-clustering strategy to integrative pan-cancer epigenomic analysis. The method is able to identify coherent patterns of various epigenetic modifications across different cancer types. To validate its capability, we applied the proposed TriPCE to analyze six important epigenetic marks among seven cancer types, and identified significant cross-cancer epigenetic similarities. These results suggest that specific epigenetic patterns indeed exist among these investigated cancers. Furthermore, the gene functional analysis performed on the associated gene sets demonstrates strong relevance with cancer development and reveals consistent risk tendency among these investigated cancer types.
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Affiliation(s)
- Yanglan Gan
- School of Computer Science and Technology, Donghua University, Shanghai, China
| | - Ning Li
- School of Computer Science and Technology, Donghua University, Shanghai, China
| | - Yongchang Xin
- School of Computer Science and Technology, Donghua University, Shanghai, China
| | - Guobing Zou
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
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43
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Nawaz M, Malik I, Hameed M, Hussain Kuthu Z, Zhou J. Modifications of histones in parasites as drug targets. Vet Parasitol 2020; 278:109029. [PMID: 31978703 DOI: 10.1016/j.vetpar.2020.109029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
Post-translational modifications of histones and histone modifying enzymes play important roles in gene regulations and other physiological processes in parasites. Inhibitors of such modifying enzymes could be useful as novel therapeutics against parasitic diseases or as chemical probes for investigation of epigenetics. Development of parasitic histone modulators has got rapid expansion in the last few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Some of these compounds have been widely used in humans targeting cancer and are found non-toxic. This review summarizes the antiparasitic activities of histone and histone modifying enzymes inhibitors evaluated in last few years. As the current chemotherapy against parasites is still not satisfactory, therefore, such compounds represents good starting points for the discovery of effective antiparasitic drugs.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Irfan Malik
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Mudassar Hameed
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zulfiqar Hussain Kuthu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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44
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Li Y, Klase Z, Sardo L. Visualizing Chromatin Modifications in Isolated Nuclei. Methods Mol Biol 2020; 2175:23-31. [PMID: 32681481 DOI: 10.1007/978-1-0716-0763-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Modifications in chromatin structure are traditionally monitored by biochemical assays that provide average measurements of static events in a population of cells. Microscopy provides a method by which single cells or nuclei can be observed. Traditionally, microscopy has been used to image the nucleus by the application of immunostaining to chemically fixed samples or the use of exogenously expressed fluorescent proteins. This method represents an approach to observe changes in endogenous proteins relating to chromatin structure in real time. Here we describe a method for isolating transcriptionally and enzymatically active nuclei from live cells and visualizing events using fluorescently labeled antibodies. This method allows the observation of real time changes in chromatin architecture and can be used to observe the effects of drugs on nuclei while under microscopic observation.
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Affiliation(s)
- Yuan Li
- Department of Infectious Diseases and Vaccines, MRL, Merck & Co. Inc., West Point, PA, USA
| | - Zachary Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA.
| | - Luca Sardo
- Department of Infectious Diseases and Vaccines, MRL, Merck & Co. Inc., West Point, PA, USA
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45
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TRPS1 Is a Lineage-Specific Transcriptional Dependency in Breast Cancer. Cell Rep 2019; 25:1255-1267.e5. [PMID: 30380416 PMCID: PMC6366939 DOI: 10.1016/j.celrep.2018.10.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 10/03/2018] [Indexed: 12/14/2022] Open
Abstract
Perturbed epigenomic programs play key roles in tumorigenesis, and chromatin modulators are candidate therapeutic targets in various human cancer types. To define singular and shared dependencies on DNA and histone modifiers and transcription factors in poorly differentiated adult and pediatric cancers, we conducted a targeted shRNA screen across 59 cell lines of 6 cancer types. Here, we describe the TRPS1 transcription factor as a strong breast cancer-specific hit, owing largely to lineage-restricted expression. Knockdown of TRPS1 resulted in perturbed mitosis, apoptosis, and reduced tumor growth. Integrated analysis of TRPS1 transcriptional targets, chromatin binding, and protein interactions revealed that TRPS1 is associated with the NuRD repressor complex. These findings uncover a transcriptional network that is essential for breast cancer cell survival and propagation. Witwicki et al. use a targeted shRNA screening strategy to identify transcriptional and epigenomic dependencies in poorly differentiated human cancers. TRPS1 is a lineage-specific transcription factor that is required for mitosis in breast cancer cells. TRPS1 is associated with the NuRD complex, and it regulates cell adhesion, cytoskeleton, and G2-M phase-related genes.
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46
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Lenting K, van den Heuvel CNAM, van Ewijk A, ElMelik D, de Boer R, Tindall E, Wei G, Kusters B, te Dorsthorst M, ter Laan M, Huynen MA, Leenders WP. Mapping actionable pathways and mutations in brain tumours using targeted RNA next generation sequencing. Acta Neuropathol Commun 2019; 7:185. [PMID: 31747973 PMCID: PMC6865071 DOI: 10.1186/s40478-019-0826-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 01/28/2023] Open
Abstract
Many biology-based precision drugs are available that neutralize aberrant molecular pathways in cancer. Molecular heterogeneity and the lack of reliable companion diagnostic biomarkers for many drugs makes targeted treatment of cancer inaccurate for many individuals. Identifying actionable hyperactive biological pathways in individual cancers may improve this situation. To achieve this we applied a novel targeted RNA next generation sequencing (t/RNA-NGS) technique to surgically obtained glioma tissues. The test combines mutation detection with analysis of biological pathway activities that are involved in tumour behavior in many cancer types (e.g. tyrosine kinase signaling, angiogenesis signaling, immune response, metabolism), via quantitative measurement of transcript levels and splice variants of hundreds of genes. We here present proof of concept that the technique, which uses molecular inversion probes, generates a histology-independent molecular diagnosis and identifies classifiers that are strongly associated with conventional histopathology diagnoses and even with patient prognosis. The test not only confirmed known glioma-associated molecular aberrations but also identified aberrant expression levels of actionable genes and mutations that have so far been considered not to be associated with glioma, opening up the possibility of drug repurposing for individual patients. Its cost-effectiveness makes t/RNA-NGS to an attractive instrument to aid oncologists in therapy decision making.
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47
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Yamamoto T, Fujimura A, Wei FY, Shinojima N, Kuroda JI, Mukasa A, Tomizawa K. 2-Methylthio Conversion of N6-Isopentenyladenosine in Mitochondrial tRNAs by CDK5RAP1 Promotes the Maintenance of Glioma-Initiating Cells. iScience 2019; 21:42-56. [PMID: 31654853 PMCID: PMC6820277 DOI: 10.1016/j.isci.2019.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022] Open
Abstract
2-Methylthio-N6-isopentenyl modification of adenosine (ms2i6A) is an evolutionally conserved modification found in mitochondrial (mt)-tRNAs. Cdk5 regulatory subunit-associated protein 1 (CDK5RAP1) specifically converts N6-isopentenyladenosine (i6A) to ms2i6A at position A37 of four mt-DNA-encoded tRNAs, and the modification regulates efficient mitochondrial translation and energy metabolism in mammals. Here, we report that the ms2 conversion mediated by CDK5RAP1 in mt-tRNAs is required to sustain glioma-initiating cell (GIC)-related traits. CDK5RAP1 maintained the self-renewal capacity, undifferentiated state, and tumorigenic potential of GICs. This regulation was not related to the translational control of mt-proteins. CDK5RAP1 abrogated the antitumor effect of i6A by converting i6A to ms2i6A and protected GICs from excessive autophagy triggered by i6A. The elevated activity of CDK5RAP1 contributed to the amelioration of the tumor-suppressive effect of i6A and promoted GIC maintenance. This work demonstrates that CDK5RAP1 is crucial for the detoxification of endogenous i6A and that GICs readily utilize this mechanism for survival. CDK5RAP1 is required to sustain the growth of GICs through ms2 modification of i6A Deficit of CDK5RAP1 inhibits the growth of GIC through i6A accumulation CDK5RAP1 detoxifies i6A by conversion into ms2i6A in the mitochondria of GICs Mitochondria serve as antidotal machinery against i6A in GICs
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Affiliation(s)
- Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Jun-Ichiro Kuroda
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan.
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48
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Wingelhofer B, Somervaille TCP. Emerging Epigenetic Therapeutic Targets in Acute Myeloid Leukemia. Front Oncol 2019; 9:850. [PMID: 31552175 PMCID: PMC6743337 DOI: 10.3389/fonc.2019.00850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 01/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous malignancy for which treatment options have been largely limited to cytotoxic chemotherapy for the past four decades. Next-generation sequencing and other approaches have identified a spectrum of genomic and epigenomic alterations that contribute to AML initiation and maintenance. The key role of epigenetic modifiers and the reversibility of epigenetic changes have paved the way for evaluation of a new set of drug targets, and facilitated the design of novel candidate treatment strategies. More recently, seven new targeted therapies have been FDA-approved demonstrating successful implementation of the past decades' research. In this review, we will summarize the most recent advances in targeted therapeutics designed for a focused group of key epigenetic regulators in AML, outline their mechanism of action and their current status in clinical development. Furthermore, we will discuss promising new approaches for epigenetic targeted treatment in AML which are currently being tested in pre-clinical trials.
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Affiliation(s)
| | - Tim C. P. Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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49
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Ru B, Sun J, Tong Y, Wong CN, Chandra A, Tang ATS, Chow LKY, Wun WL, Levitskaya Z, Zhang J. CR2Cancer: a database for chromatin regulators in human cancer. Nucleic Acids Res 2019; 46:D918-D924. [PMID: 29036683 PMCID: PMC5753221 DOI: 10.1093/nar/gkx877] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining. We collected and integrated genomic, transcriptomic, proteomic, clinical and functional information for over 400 CRs across multiple cancer types. We also built diverse types of CR-associated relations, including cancer type dependent (CR-target and miRNA-CR) and independent (protein-protein interaction and drug-target) ones. Furthermore, we manually curated around 6000 items of aberrant molecular alterations and interactions of CRs in cancer development from 5007 publications. CR2Cancer provides a user-friendly web interface to conveniently browse, search and download data of interest. We believe that this database would become a valuable resource for cancer epigenetics investigation and potential clinical application. CR2Cancer is freely available at http://cis.hku.hk/CR2Cancer.
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Affiliation(s)
- Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Aditi Chandra
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Acacia Tsz So Tang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Larry Ka Yue Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Wai Lam Wun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Zarina Levitskaya
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
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50
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Vlaming H, McLean CM, Korthout T, Alemdehy MF, Hendriks S, Lancini C, Palit S, Klarenbeek S, Kwesi‐Maliepaard EM, Molenaar TM, Hoekman L, Schmidlin TT, Altelaar AFM, van Welsem T, Dannenberg J, Jacobs H, van Leeuwen F. Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO J 2019; 38:e101564. [PMID: 31304633 PMCID: PMC6627229 DOI: 10.15252/embj.2019101564] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
DOT1L methylates histone H3K79 and is aberrantly regulated in MLL-rearranged leukemia. Inhibitors have been developed to target DOT1L activity in leukemia, but cellular mechanisms that regulate DOT1L are still poorly understood. We have identified the histone deacetylase Rpd3 as a negative regulator of budding yeast Dot1. At its target genes, the transcriptional repressor Rpd3 restricts H3K79 methylation, explaining the absence of H3K79me3 at a subset of genes in the yeast genome. Similar to the crosstalk in yeast, inactivation of the murine Rpd3 homolog HDAC1 in thymocytes led to an increase in H3K79 methylation. Thymic lymphomas that arise upon genetic deletion of Hdac1 retained the increased H3K79 methylation and were sensitive to reduced DOT1L dosage. Furthermore, cell lines derived from Hdac1Δ/Δ thymic lymphomas were sensitive to a DOT1L inhibitor, which induced apoptosis. In summary, we identified an evolutionarily conserved crosstalk between HDAC1 and DOT1L with impact in murine thymic lymphoma development.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMAUSA
| | - Chelsea M McLean
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tessy Korthout
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mir Farshid Alemdehy
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Hendriks
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Cesare Lancini
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sander Palit
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Thom M Molenaar
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Thierry T Schmidlin
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
- Proteomics FacilityNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tibor van Welsem
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jan‐Hermen Dannenberg
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Genmab B.V.Antibody SciencesUtrechtThe Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Fred van Leeuwen
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
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