1
|
Vai A, Noberini R, Ghirardi C, Rodrigues de Paula D, Carminati M, Pallavi R, Araújo N, Varga-Weisz P, Bonaldi T. Improved Mass Spectrometry-Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles. Mol Cell Proteomics 2024; 23:100799. [PMID: 38866077 PMCID: PMC11277384 DOI: 10.1016/j.mcpro.2024.100799] [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: 08/03/2023] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024] Open
Abstract
Histone posttranslational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry is the most powerful, comprehensive, and unbiased method to study histone PTMs. However, typical mass spectrometry-based protocols for histone PTM analysis do not allow the identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allow the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.
Collapse
Affiliation(s)
- Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Dieggo Rodrigues de Paula
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Michele Carminati
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Rani Pallavi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy
| | - Nathália Araújo
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Patrick Varga-Weisz
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; School of Biological Sciences, University of Essex, Colchester, UK
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCSS, Milan, Italy; Department of Oncology and Hematology-Oncology (DIPO), University of Milan, Milan, Italy.
| |
Collapse
|
2
|
Chen C, Zhu Y, Zhang H, Xiao L. Prognostic Effects of RASSF1A, BRCA1, APC, and p16 Promoter Methylation in Ovarian Cancer: A Meta-Analysis. Gynecol Obstet Invest 2024:1-13. [PMID: 38615670 DOI: 10.1159/000538673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION DNA methylation plays an important role in the carcinogenesis, progression, and prognosis of various human cancers. RASSF1A, BRCA1, APC, and p16 are the frequently methylated genes among patients with ovarian cancer. Therefore, our study aimed to better determine the prognostic and cancer characteristics effects of RASSF1A, BRCA1, APC, and p16 promoter methylation in ovarian cancer patients. METHODS Databases such as PubMed, Web of Science, EMBASE, CNKI, and WanFang were searched for published studies up to March 4, 2024. The outcomes are shown as OR and HR with their 95% CIs. Then, the random or fixed-effect model was performed to evaluate the effect sizes. RESULTS Finally, 27 articles were included in this meta-analysis. No significant relationships were observed between RASSF1A, BRCA1, and APC promoter methylation and the clinical prognostic (including overall survival and progression-free survival) and cancer characteristics (including ascites, lymph node metastasis, and pelvic peritoneal metastasis) in ovarian cancer. p16 promoter methylation was significantly related to poor progression-free survival (PFS) (HR = 1.52, 95% CI = 1.14-2.04) and overall survival (OS) (HR = 1.39, 95% CI = 1.06, to 1.83) in univariate and poor PFS in multivariate Cox regression models (HR = 1.42, 95% CI = 1.05-1.92). Besides, our results indicated that the clinical stage was associated with inferior OS while there was no significant association between tumor grade and OS. CONCLUSION RASSF1A, BRCA1, and APC promoter methylation were not significantly associated with clinical prognostic and cancer characteristics. p16 may be a useful biomarker for predicting PFS in ovarian cancer. Furthermore, the clinical stage was significantly associated with OS. In further research, more prospective and multicenter validation studies remain needed.
Collapse
Affiliation(s)
- Cheng Chen
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ying Zhu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Haibo Zhang
- Central Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lan Xiao
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
3
|
Endale HT, Mariye YF, Negash HK, Hassen FS, Asrat WB, Mengstie TA, Tesfaye W. MiRNA in cervical cancer: Diagnosis to therapy: Systematic review. Heliyon 2024; 10:e24398. [PMID: 38317930 PMCID: PMC10839805 DOI: 10.1016/j.heliyon.2024.e24398] [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: 05/25/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Cancers are one of the most public health problems worldwide. Among them, cervical cancer (CC) is the fourth most prevalent cancer with 604 000 new cases and 342 000 deaths. Mostly, it is associated with Human papillomavirus (HPV). It has been caused by the aggregation of genetic and epigenetic modifications in cervical epithelial cells. Although genetic mutations are given great attention for the carcinogenesis of CC, epigenetic changes have emerged as a hotspot area for CC biomarkers research with great implications for early diagnosis, prognosis, and treatment response prediction of the disease. Recently, there are several studies focused on miRNAs as biomarkers of cervical cancer. However, the precise function of miRNAs in the development of cervical cancer is not still completely understood, particularly when it comes to unconventional sampling materials like cervical mucus and plasma serum. Hence, this review article will give a summary of the miRNAs profiles that emerge at different stages of cervical cancer progression and their downstream effects on target genes and associated signaling pathways. Finally, these results may provide insight into the use of miRNAs as biomarkers for the prediction or diagnosis of cervical cancer or the development of miRNA-based therapeutics against cervical cancer.
Collapse
Affiliation(s)
- Hiwot Tezera Endale
- Department of Biochemistry, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| | - Yitbarek Fantahun Mariye
- Department of Obstetrics & Gynecology, School of Medicine, College of Medicine & Health Sciences, Addis Ababa University, Ethiopia
| | - Habtu Kifle Negash
- Department of Human Anatomy, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| | - Fethiya Seid Hassen
- Department of Biochemistry, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| | - Wastina Bitewlign Asrat
- Department of Biochemistry, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| | - Tiget Ayelgn Mengstie
- Department of Biochemistry, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| | - Winta Tesfaye
- Department of Human Physiology, School of Medicine, College of Medicine & Health Sciences, University of Gondar, Ethiopia
| |
Collapse
|
4
|
Zhang X, Zhong Y, Liu L, Jia C, Cai H, Yang J, Wu B, Lv Z. Fasting regulates mitochondrial function through lncRNA PRKCQ-AS1-mediated IGF2BPs in papillary thyroid carcinoma. Cell Death Dis 2023; 14:827. [PMID: 38092752 PMCID: PMC10719255 DOI: 10.1038/s41419-023-06348-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Recurring evidence suggests that fasting has extensive antitumor effects in various cancers, including papillary thyroid carcinoma (PTC). However, the underlying mechanism of this relationship with PTC is unknown. In this study, we study the effect of fasting on glycolysis and mitochondrial function in PTC. We find that fasting impairs glycolysis and reduces mitochondrial dysfunction in vitro and in vivo and also fasting in vitro and fasting mimicking diets (FMD) in vivo significantly increase the expression of lncRNA-protein kinase C theta antisense RNA 1 (PRKCQ-AS1), during the inhibition of TPC cell glycolysis and mitochondrial function. Moreover, lncRNA PRKCQ-AS1 was significantly lower in PTC tissues and cells. In addition, PRKCQ-AS1 overexpression increased PTC cell glycolysis and mitochondrial function; PRKCQ-AS1 knockdown has the opposite effect. On further mechanistic analysis, we identified that PRKCQ-AS1 physically interacts with IGF2BPs and enhances protein arginine methyltransferases 7 (PRMT7) mRNA, which is the key player in regulating glycolysis and mitochondrial function in PTC. Hence, PRKCQ-AS1 inhibits tumor growth while regulating glycolysis and mitochondrial functions via IGF2BPs/PRMT7 signaling. These results indicate that lncRNA PRKCQ-AS1 is a key downstream target of fasting and is involved in PTC metabolic reprogramming. Further, the PRKCQ-AS1/IGF2BPs/PRMT7 axis is an ideal therapeutic target for PTC diagnosis and treatment.
Collapse
Affiliation(s)
- Xiaoping Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai hospital Affiliated with Jinan University, Jinan University, 519000, Guangdong, China.
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China.
| | - Yong Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Lin Liu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Haidong Cai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Jianshe Yang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China
| | - Bo Wu
- Center of Thyroid, Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 200233, Shanghai, China.
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, 200072, Shanghai, China.
| |
Collapse
|
5
|
Gil-Martín E, Ramos E, López-Muñoz F, Egea J, Romero A. Potential of melatonin to reverse epigenetic aberrations in oral cancer: new findings. EXCLI JOURNAL 2023; 22:1280-1310. [PMID: 38234969 PMCID: PMC10792176 DOI: 10.17179/excli2023-6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
It is now an accepted principle that epigenetic alterations cause cellular dyshomeostasis and functional changes, both of which are essential for the initiation and completion of the tumor cycle. Oral carcinogenesis is no exception in this regard, as most of the tumors in the different subsites of the oral cavity arise from the cross-reaction between (epi)genetic inheritance and the huge challenge of environmental stressors. Currently, the biochemical machinery is put at the service of the tumor program, halting the cell cycle, triggering uncontrolled proliferation, driving angiogenesis and resistance to apoptosis, until the archetypes of the tumor phenotype are reached. Melatonin has the ability to dynamically affect the epigenetic code. It has become accepted that melatonin can reverse (epi)genetic aberrations present in oral and other cancers, suggesting the possibility of enhancing the oncostatic capacity of standard multimodal treatments by incorporating this indolamine as an adjuvant. First steps in this direction confirm the potential of melatonin as a countermeasure to mitigate the detrimental side effects of conventional first-line radiochemotherapy. This single effect could produce synergies of extraordinary clinical importance, allowing doses to be increased and treatments not to be interrupted, ultimately improving patients' quality of life and prognosis. Motivated by the urgency of improving the medical management of oral cancer, many authors advocate moving from in vitro and preclinical research, where the bulk of melatonin cancer research is concentrated, to systematic randomized clinical trials on large cohorts. Recognizing the challenge to improve the clinical management of cancer, our motivation is to encourage comprehensive and robust research to reveal the clinical potential of melatonin in oral cancer control. To improve the outcome and quality of life of patients with oral cancer, here we provide the latest evidence of the oncolytic activity that melatonin can achieve by manipulating epigenetic patterns in oronasopharyngeal tissue.
Collapse
Affiliation(s)
- Emilio Gil-Martín
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, 36310 Vigo, Spain
| | - Eva Ramos
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Francisco López-Muñoz
- Faculty of Health, Camilo José Cela University of Madrid (UCJC), 28692 Madrid, Spain
- Neuropsychopharmacology Unit, Hospital 12 de Octubre Research Institute, 28041 Madrid, Spain
| | - Javier Egea
- Unidad de Investigación, Hospital Santa Cristina, Instituto de Investigación Sanitaria Princesa (IIS-IP), 28006 Madrid, Spain
| | - Alejandro Romero
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| |
Collapse
|
6
|
Sinha R, Dvorak M, Ganesan A, Kalesinskas L, Niemeyer CM, Flotho C, Sakamoto KM, Lacayo N, Patil RV, Perriman R, Cepika AM, Liu YL, Kuo A, Utz PJ, Khatri P, Bertaina A. Epigenetic Profiling of PTPN11 Mutant JMML Hematopoietic Stem and Progenitor Cells Reveals an Aberrant Histone Landscape. Cancers (Basel) 2023; 15:5204. [PMID: 37958378 PMCID: PMC10650722 DOI: 10.3390/cancers15215204] [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: 10/05/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a deadly pediatric leukemia driven by RAS pathway mutations, of which >35% are gain-of-function in PTPN11. Although DNA hypermethylation portends severe clinical phenotypes, the landscape of histone modifications and chromatin profiles in JMML patient cells have not been explored. Using global mass cytometry, Epigenetic Time of Flight (EpiTOF), we analyzed hematopoietic stem and progenitor cells (HSPCs) from five JMML patients with PTPN11 mutations. These data revealed statistically significant changes in histone methylation, phosphorylation, and acetylation marks that were unique to JMML HSPCs when compared with healthy controls. Consistent with these data, assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis revealed significant alterations in chromatin profiles at loci encoding post-translational modification enzymes, strongly suggesting their mis-regulated expression. Collectively, this study reveals histone modification pathways as an additional epigenetic abnormality in JMML patient HSPCs, thereby uncovering a new family of potential druggable targets for the treatment of JMML.
Collapse
Affiliation(s)
- Roshani Sinha
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Mai Dvorak
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Ananthakrishnan Ganesan
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Larry Kalesinskas
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Charlotte M. Niemeyer
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Christian Flotho
- Department of Pediatric Hematology and Oncology, University of Freiburg Medical Centre, 79098 Freiburg im Breisgau, Germany; (C.M.N.); (C.F.)
| | - Kathleen M. Sakamoto
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Norman Lacayo
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| | - Rachana Vinay Patil
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Rhonda Perriman
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alma-Martina Cepika
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Yunying Lucy Liu
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
| | - Alex Kuo
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Paul J. Utz
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Purvesh Khatri
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.G.); (L.K.); (A.K.); (P.J.U.); (P.K.)
| | - Alice Bertaina
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; (R.S.); (R.V.P.); (R.P.); (A.-M.C.); (Y.L.L.)
- Bass Center for Childhood Cancer and Blood Disorders at Lucile Packard Children’s Hospital, Palo Alto, CA 94304, USA; (K.M.S.); (N.L.)
| |
Collapse
|
7
|
Szczepanek J, Tretyn A. MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications. Biomolecules 2023; 13:1590. [PMID: 38002272 PMCID: PMC10669115 DOI: 10.3390/biom13111590] [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: 09/21/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.
Collapse
Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, ul. Wilenska 4, 87-100 Torun, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, ul. Lwowska 1, 87-100 Torun, Poland;
| |
Collapse
|
8
|
Chai H, Pan C, Zhang M, Huo H, Shan H, Wu J. Histone methyltransferase SETD1A interacts with notch and promotes notch transactivation to augment ovarian cancer development. BMC Cancer 2023; 23:96. [PMID: 36707804 PMCID: PMC9883963 DOI: 10.1186/s12885-023-10573-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND High expression of SETD1A, a histone methyltransferase that specifically methylates H3K4, acted as a key oncogene in several human cancers. However, the function and underlying molecular mechanism of SETD1A in ovarian cancer (OV) remain markedly unknown. METHODS The expression of SETD1A in OV were detected by Western blot and analyzed online, and the prognosis of STED1A in OV were analyzed online. The protein and mRNA levels were determined by Western blot and RT-qPCR. The cell proliferatin, migration and invasion were measured by CCK-8 and transwell assays. The protein interaction was detected by co-IP assay. The interaction between protein and DNA was performed by ChIP assay. The tumor growth in vivo was performed by xenograft tumor model. RESULTS SETD1A was overexpressed in OV and a predictor of poor prognosis. Overexpression of SETD1A augmented the abilities of cell proliferation, migration, and invasion in MRG1 and OVCAR5 cells. In comparison, SETD1A knockdown suppressed cell growth, migration, and invasion in SKOV3 and Caov3 cells. Specifically, SETD1A enhanced Notch signaling by promoting the expression of Notch target genes, such as Hes1, Hey1, Hey2, and Heyl. Mechanistically, SETD1A interacted with Notch1 and methylated H3K4me3 at Notch1 targets to enhance Notch signaling. In addition, restoration of Notch1 in SETD1A-knockdown OV cells recovered cell proliferation, migration and invasion, which was inhibited by SETD1A knockdown. Furthermore, reduction of SETD1A suppressed tumorigenesis in vivo. CONCLUSION In conclusion, our results highlighted the key role of SETD1A in OV development and proved that SETD1A promotes OV development by enhancing Notch1 signaling, indicating that SETD1A may be a novel target for OV treatment.
Collapse
Affiliation(s)
- Hongjuan Chai
- grid.412523.30000 0004 0386 9086Department of Gynecology and Obstetrics, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Chunpeng Pan
- grid.412523.30000 0004 0386 9086Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- grid.263761.70000 0001 0198 0694Department of Forensic Sciences, Soochow University, Suzhou, China
| | - Haizhong Huo
- grid.412523.30000 0004 0386 9086Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Haiyan Shan
- grid.89957.3a0000 0000 9255 8984Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, 242, Guangji Road, 215000 Suzhou, China
| | - Jugang Wu
- grid.412523.30000 0004 0386 9086Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| |
Collapse
|
9
|
Kumar A, Maurya P, Hayes JJ. Post-Translation Modifications and Mutations of Human Linker Histone Subtypes: Their Manifestation in Disease. Int J Mol Sci 2023; 24:ijms24021463. [PMID: 36674981 PMCID: PMC9860689 DOI: 10.3390/ijms24021463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Linker histones (LH) are a critical component of chromatin in addition to the canonical histones (H2A, H2B, H3, and H4). In humans, 11 subtypes (7 somatic and 4 germinal) of linker histones have been identified, and their diverse cellular functions in chromatin structure, DNA replication, DNA repair, transcription, and apoptosis have been explored, especially for the somatic subtypes. Delineating the unique role of human linker histone (hLH) and their subtypes is highly tedious given their high homology and overlapping expression patterns. However, recent advancements in mass spectrometry combined with HPLC have helped in identifying the post-translational modifications (PTMs) found on the different LH subtypes. However, while a number of PTMs have been identified and their potential nuclear and non-nuclear functions explored in cellular processes, there are very few studies delineating the direct relevance of these PTMs in diseases. In addition, recent whole-genome sequencing of clinical samples from cancer patients and individuals afflicted with Rahman syndrome have identified high-frequency mutations and therefore broadened the perspective of the linker histone mutations in diseases. In this review, we compile the identified PTMs of hLH subtypes, current knowledge of the relevance of hLH PTMs in human diseases, and the correlation of PTMs coinciding with mutations mapped in diseases.
Collapse
Affiliation(s)
- Ashok Kumar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
- Correspondence:
| | - Preeti Maurya
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
| |
Collapse
|
10
|
De Palma FDE, Carbonnier V, Salvatore F, Kroemer G, Pol JG, Maiuri MC. Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers. Cancers (Basel) 2022; 14:cancers14235980. [PMID: 36497462 PMCID: PMC9738797 DOI: 10.3390/cancers14235980] [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: 09/27/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Long non-coding RNAs may constitute epigenetic biomarkers for the diagnosis, prognosis, and therapeutic response of a variety of tumors. In this context, we aimed at assessing the diagnostic and prognostic value of the recently described long intergenic non-coding RNA 01087 (LINC01087) in human cancers. (2) Methods: We studied the expression of LINC01087 across 30 oncological indications by interrogating public resources. Data extracted from the TCGA and GTEx databases were exploited to plot receiver operating characteristic curves (ROC) and determine the diagnostic performance of LINC01087. Survival data from TCGA and KM-Plotter directories allowed us to graph Kaplan-Meier curves and evaluate the prognostic value of LINC01087. To investigate the function of LINC01087, gene ontology (GO) annotation and Kyoto Encyclopedia of Gene and Genomes (KEGG) enrichment analyses were performed. Furthermore, interactions between LINC01087 and both miRNA and mRNA were studied by means of bioinformatics tools. (3) Results: LINC01087 was significantly deregulated in 7 out of 30 cancers, showing a predominant upregulation. Notably, it was overexpressed in breast (BC), esophageal (ESCA), and ovarian (OV) cancers, as well as lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD), and uterine carcinosarcoma (UCS). By contrast, LINC01087 displayed downregulation in testicular germ cell tumors (TGCT). ROC curve analyses identified LINC01087 as a potential diagnostic indicator in BC, ESCA, OV, STAD, and TGCT. Moreover, high and low expression of LINC01087 predicted a favorable prognosis in BC and papillary cell carcinoma, respectively. In silico analyses indicated that deregulation of LINC01087 in cancer was associated with a modulation of genes related to ion channel, transporter, and peptide receptor activity. (4) Conclusions: the quantification of an altered abundance of LINC01087 in tissue specimens might be clinically useful for the diagnosis and prognosis of some hormone-related tumors, including BC, OV, and TGCT, as well as other cancer types such as ESCA and STAD. Moreover, our study revealed the potential of LINC01087 (and perhaps other lncRNAs) to regulate neuroactive molecules in cancer.
Collapse
Affiliation(s)
- Fatima Domenica Elisa De Palma
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Vincent Carbonnier
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Napoli, Italy
- Centro Interuniversitario per Malattie Multigeniche e Multifattoriali e Loro Modelli Animali (Federico II, 80131, Napoli, Tor Vergata, Rome and “G. D’Annunzio”, Chieti-Pescara), 80131 Napoli, Italy
| | - Guido Kroemer
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, 75004 Paris, France
| | - Jonathan G. Pol
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
| | - Maria Chiara Maiuri
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, 80131 Napoli, Italy
- Équipe Labellisée par la Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Institut Universitaire de France, 75005 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Correspondence: (J.G.P.); (M.C.M.)
| |
Collapse
|
11
|
Robusti G, Vai A, Bonaldi T, Noberini R. Investigating pathological epigenetic aberrations by epi-proteomics. Clin Epigenetics 2022; 14:145. [PMID: 36371348 PMCID: PMC9652867 DOI: 10.1186/s13148-022-01371-y] [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: 05/12/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetics includes a complex set of processes that alter gene activity without modifying the DNA sequence, which ultimately determines how the genetic information common to all the cells of an organism is used to generate different cell types. Dysregulation in the deposition and maintenance of epigenetic features, which include histone posttranslational modifications (PTMs) and histone variants, can result in the inappropriate expression or silencing of genes, often leading to diseased states, including cancer. The investigation of histone PTMs and variants in the context of clinical samples has highlighted their importance as biomarkers for patient stratification and as key players in aberrant epigenetic mechanisms potentially targetable for therapy. Mass spectrometry (MS) has emerged as the most powerful and versatile tool for the comprehensive, unbiased and quantitative analysis of histone proteoforms. In recent years, these approaches-which we refer to as "epi-proteomics"-have demonstrated their usefulness for the investigation of epigenetic mechanisms in pathological conditions, offering a number of advantages compared with the antibody-based methods traditionally used to profile clinical samples. In this review article, we will provide a critical overview of the MS-based approaches that can be employed to study histone PTMs and variants in clinical samples, with a strong focus on the latest advances in this area, such as the analysis of uncommon modifications and the integration of epi-proteomics data into multi-OMICs approaches, as well as the challenges to be addressed to fully exploit the potential of this novel field of research.
Collapse
Affiliation(s)
- Giulia Robusti
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Alessandro Vai
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Tiziana Bonaldi
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milan, Italy
| | - Roberta Noberini
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| |
Collapse
|
12
|
Anticarcinogenic Effects of Isothiocyanates on Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms232213834. [PMID: 36430307 PMCID: PMC9693344 DOI: 10.3390/ijms232213834] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, accounting for about 90% of cases. Sorafenib, lenvatinib, and the combination of atezolizumab and bevacizumab are considered first-line treatments for advanced HCC. However, clinical application of these drugs has also caused some adverse reactions such as hypertension, elevated aspartate aminotransferases, and proteinuria. At present, natural products and their derivatives have drawn more and more attention due to less side effects as cancer treatments. Isothiocyanates (ITCs) are one type of hydrolysis products from glucosinolates (GLSs), secondary plant metabolites found exclusively in cruciferous vegetables. Accumulating evidence from encouraging in vitro and in vivo animal models has demonstrated that ITCs have multiple biological activities, especially their potentially health-promoting activities (antibacterial, antioxidant, and anticarcinogenic effects). In this review, we aim to comprehensively summarize the chemopreventive, anticancer, and chemosensitizative effects of ITCs on HCC, and explain the underlying molecular mechanisms.
Collapse
|
13
|
Xie B, Peng F, He F, Cheng Y, Cheng J, Zhou Z, Mao W. DNA methylation influences the CTCF-modulated transcription of RASSF1A in lung cancer cells. Cell Biol Int 2022; 46:1900-1914. [PMID: 35989484 DOI: 10.1002/cbin.11868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/30/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022]
Abstract
Ras-association domain family 1A (RASSF1A) is one of the most methylated genes in lung cancer (LC). We investigate whether the high DNA methylation level of RASSF1A can relieve the resistance of RASSF1A to LC by inhibiting RASSF1A's transcription factor binding to RASSF1A. RASSF1A expression in tissues and cells was tested utilizing quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot. RASSF1A expression and RASSF1A methylation level in LC cells exposed to 5-Aza-dc were assessed by qRT-PCR and quantitative methylation-specific PCR. The association between CTCF and RASSF1A was assessed using hTFtarget, ChIP, and luciferase reporter gene analysis. The effects of 5-Aza-dc, CTCF, and RASSF1A on cell biological behaviors and epithelial-mesenchymal transition (EMT)-related markers were assessed by cell function experiments and Western blot. Moreover, we constructed the xenograft tumor and pulmonary nodule metastasis models, and assessed tumor volume and weight. RASSF1A expression and pulmonary nodule metastasis were tested utilizing qRT-PCR, Western blot, and H&E staining. RASSF1A was under-expressed in LC tissues and cells. 5-Aza-dc enhanced RASSF1A level and weakened RASSF1A methylation level in LC cells. RASSF1A silencing neutralized 5-Aza-dc-mediated repressing effects on LC cell biological function and EMT. The loss of CTCF binding to RASSF1A in LC cells was associated with DNA methylation. The effect of 5-Aza-dc on RASSF1A level, LC cell malignant behaviors, and EMT-related factors were strengthened by CTCF upregulation. RASSF1A overexpression suppressed LC tumor growth and pulmonary nodule metastasis in vivo. DNA methylation blocked the modulation of RASSF1A expression by CTCF and relieved the resistance of RASSF1A to LC.
Collapse
Affiliation(s)
- Bin Xie
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Feng Peng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Fengping He
- Central Laboratory, Yue Bei People's Hospital, Shaoguan, China
| | - Yixing Cheng
- Department of Respiratory Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou, Zhejiang, China
| | - Jiangtao Cheng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Zhibing Zhou
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wei Mao
- Department of Respiratory Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou, Zhejiang, China
| |
Collapse
|
14
|
Ghosh A, Lahiri A, Mukherjee S, Roy M, Datta A. Prevention of inorganic arsenic induced squamous cell carcinoma of the skin in Swiss albino mice by black tea through epigenetic modulation. Heliyon 2022; 8:e10341. [PMID: 36061029 PMCID: PMC9429555 DOI: 10.1016/j.heliyon.2022.e10341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/16/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022] Open
|
15
|
Zhao Q, Hu W, Xu J, Zeng S, Xi X, Chen J, Wu X, Hu S, Zhong T. Comprehensive Pan-Cancer Analysis of Senescence With Cancer Prognosis and Immunotherapy. Front Mol Biosci 2022; 9:919274. [PMID: 35911954 PMCID: PMC9334796 DOI: 10.3389/fmolb.2022.919274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Senescence is a double-edged sword in tumorigenesis and affects the immunotherapy response through the modulation of the host’s immune system. However, there is currently a lack of comprehensive analysis of the senescence-related genes (SRGs) in human cancers, and the predictive role of senescence in cancer immunotherapy response has not been explored. The multi-omics approaches were performed in this article to conduct a systematic pan-cancer genomic analysis of SRGs in cancer. In addition, we calculated the generic senescence score (SS) to quantify the senescence levels in cancers and explored the correlations of SS with cancer prognosis, biological processes, and tumor microenvironment (TME). The gene signatures were deregulated in multiple cancers and indicated a context-dependent correlation with prognosis, tumor-immune evasion, and response to therapy across various tumor types. Further analysis disclosed that SS was positively associated with the infiltration levels of immune suppressive cells, including induced Tregs (iTregs), central memory Ts (Tcms), and natural Tregs (nTregs), and negatively associated with immune killer cells, including natural killers (NKs) and mucosal-associated invariant Ts (MAITs). Moreover, the SS was significantly correlated with tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs), immune-related genes, and immune checkpoints and had a predictive value of immunotherapy response. Thus, the expression of SRGs was involved in resistance to several anticancer drugs. Our work illustrates the characterization of senescence across various malignancies and highlights the potential of senescence as a biomarker of the response to immunotherapy.
Collapse
Affiliation(s)
- Qinfei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weiquan Hu
- Department of Joint Surgery, Ganzhou People’s Hospital, Ganzhou, China
| | - Jing Xu
- Department of Orthopaedic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaoying Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuxiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jing Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiangsheng Wu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Suping Hu
- Department of Emergency, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- *Correspondence: Tianyu Zhong,
| |
Collapse
|
16
|
Luteolin Causes 5'CpG Demethylation of the Promoters of TSGs and Modulates the Aberrant Histone Modifications, Restoring the Expression of TSGs in Human Cancer Cells. Int J Mol Sci 2022; 23:ijms23074067. [PMID: 35409426 PMCID: PMC8999529 DOI: 10.3390/ijms23074067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer progression is linked to abnormal epigenetic alterations such as DNA methylation and histone modifications. Since epigenetic alterations, unlike genetic changes, are heritable and reversible, they have been considered as interesting targets for cancer prevention and therapy by dietary compounds such as luteolin. In this study, epigenetic modulatory behaviour of luteolin was analysed on HeLa cells. Various assays including colony forming and migration assays, followed by biochemical assays of epigenetic enzymes including DNA methyltransferase, histone methyl transferase, histone acetyl transferase, and histone deacetylases assays were performed. Furthermore, global DNA methylation and methylation-specific PCR for examining the methylation status of CpG promoters of various tumour suppressor genes (TSGs) and the expression of these TSGs at transcript and protein level were performed. It was observed that luteolin inhibited migration and colony formation in HeLa cells. It also modulated DNA methylation at promoters of TSGs and the enzymatic activity of DNMT, HDAC, HMT, and HAT and reduced the global DNA methylation. Decrease in methylation resulted in the reactivation of silenced tumour suppressor genes including FHIT, DAPK1, PTEN, CDH1, SOCS1, TIMPS, VHL, TP53, TP73, etc. Hence, luteolin-targeted epigenetic alterations provide a promising approach for cancer prevention and intervention.
Collapse
|
17
|
TIAN S, LIU R, QIAN X, GUO X, ZHANG K. [Extraction and isolation of histones from paraffin-embedded tissues and quantitative analysis of post-translational modifications]. Se Pu 2021; 39:1094-1101. [PMID: 34505431 PMCID: PMC9404118 DOI: 10.3724/sp.j.1123.2021.06018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 11/25/2022] Open
Abstract
Histone post-translational modifications (HPTMs) have been believed to play crucial roles in the regulation of gene transcription. Thus, aberrant modification of histone can contribute to the occurrence and development of diseases such as tumors. To date, formalin fixed paraffin-embedded (FFPE) clinical tissues are believed to be one of the most valuable sample resources in the study of human diseases. Therefore, it is of great significance to reveal the molecular mechanism of cancer and discover the markers of tumor. Proteomics, based on high performance liquid chromatograph-tandem mass spectrometry (HPLC-MS/MS), has become a powerful tool for HPTM identification. However, HPTM analysis of FFPE samples is yet to be explored; it has not been reported in China to our best knowledge. In this study, a new method based on HPLC-MS/MS was developed for the extraction and separation of histone proteins and analysis and quantification of HPTMs in FFPE tissues. First, the strategy for the extraction and separation of histone proteins from FFPE samples were optimized. After comparing the extraction efficiency of two different methods, which include the acid extraction of histone and extraction of total protein, a novel method was developed for histone extraction, separation, and HPTMs analysis by integrating dewaxed hydration treatment of FFPE tissues with protein extraction and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation. Furthermore, the effects of operation parameters on histone extraction and HPTM identification were investigated, including number of paraffin embedded sections and chemical derivation of histone proteins. Thereafter, the identification and quantification of HPTMs were performed using reversed-phase HPLC-MS/MS in data independent acquisition (DIA) mode. Finally, the optimized methods were applied to quantitative analysis of HPTMs in FFPE tissues. A variety of HPTMs were identified; they included lysine methylation, acetylation, crotonylation, etc. Therefore, the spectrum of HPTMs on global level was set for human breast cancer and paracancerous tissues from two cases of FFPE clinical tissues. The sites holding differential HPTM level in cancer and paracancerous tissues were further obtained by quantifying the individual HPTMs. Thus, the relationship between HPTM level and tumor was discussed. Abnormal HPTM sites were characterized using cluster analysis, thus their similar tendency was found. For example, abnormal HPTM sites such as H3K9me3, H3K9ac, and H3K27me3 in cancers are associated with epigenetic regulation. It indicated that different epigenetic events might occur in cancer and paracancerous tissues. Interestingly, we found that the level of H4K20me3 were both significantly down-regulated in the two cancer tissues. HPTM had been thought to be a potential biomarker in breast cancer; therefore, these positive results indicated that our method is effective for HPTMs of clinical FFPE samples. Our study provides a useful tool for the isolation and analysis of HPTMs in clinical FFPE samples, showing the potential for the detection of epigenetic biomarker in cancer.
Collapse
|
18
|
Lawal B, Tseng SH, Olugbodi JO, Iamsaard S, Ilesanmi OB, Mahmoud MH, Ahmed SH, Batiha GES, Wu ATH. Pan-Cancer Analysis of Immune Complement Signature C3/C5/C3AR1/C5AR1 in Association with Tumor Immune Evasion and Therapy Resistance. Cancers (Basel) 2021; 13:4124. [PMID: 34439277 PMCID: PMC8394789 DOI: 10.3390/cancers13164124] [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: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/08/2023] Open
Abstract
Despite the advances in our understanding of the genetic and immunological basis of cancer, cancer remains a major public health burden with an ever-increasing incidence rate globally. Nevertheless, increasing evidence suggests that the components of the complement system could regulate the tumor microenvironment (TME) to promote cancer progression, recurrence, and metastasis. In the present study, we used an integrative multi-omics analysis of clinical data to explore the relationships between the expression levels of and genetic and epigenetic alterations in C3, C5, C3AR1, and C5AR1 and tumor immune evasion, therapy response, and patient prognosis in various cancer types. We found that the complements C3, C5, C3AR1, and C5AR1 have deregulated expression in human malignancies and are associated with activation of immune-related oncogenic processes and poor prognosis of cancer patients. Furthermore, we found that the increased expression levels of C3, C5, C3AR1, and C5AR1 were primarily predicted by copy number variation and gene methylation and were associated with dysfunctional T-cell phenotypes. Single nucleotide variation in the gene signature co-occurred with multiple oncogenic mutations and is associated with the progression of onco-immune-related diseases. Further correlation analysis revealed that C3, C5, C3AR1, and C5AR1 were associated with tumor immune evasion via dysfunctional T-cell phenotypes with a lesser contribution of T-cell exclusion. Lastly, we also demonstrated that the expression levels of C3, C5, C3AR1, and C5AR1 were associated with context-dependent chemotherapy, lymphocyte-mediated tumor killing, and immunotherapy outcomes in different cancer types. In conclusion, the complement components C3, C5, C3AR1, and C5AR1 serve as attractive targets for strategizing cancer immunotherapy and response follow-up.
Collapse
Affiliation(s)
- Bashir Lawal
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan;
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Sung-Hui Tseng
- Department of Physical Medicine and Rehabilitation, Taipei Medical University Hospital, Taipei 11031, Taiwan;
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | | | - Sitthichai Iamsaard
- Department of Anatomy, Faculty of Medicine and Research Institute for Human High Performance and Health Promotion (HHP&HP), Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Omotayo B. Ilesanmi
- Department of Biochemistry, Faculty of Science, Federal University Otuoke, Ogbia 23401, Bayelsa State, Nigeria;
| | - Mohamed H. Mahmoud
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Sahar H. Ahmed
- Medical Laboratory Technology Department, Faculty of Applied Medical Science, Misr University For Science &Technology, Cairo 3245310, Egypt;
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheira, Egypt;
| | - Alexander T. H. Wu
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
- Taipei Heart Institute (THI), Taipei Medical University, Taipei 11031, Taiwan
| |
Collapse
|
19
|
Wu J, Chai H, Shan H, Pan C, Xu X, Dong W, Yu J, Gu Y. Histone Methyltransferase SETD1A Induces Epithelial-Mesenchymal Transition to Promote Invasion and Metastasis Through Epigenetic Reprogramming of Snail in Gastric Cancer. Front Cell Dev Biol 2021; 9:657888. [PMID: 34164392 PMCID: PMC8215546 DOI: 10.3389/fcell.2021.657888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/03/2021] [Indexed: 01/15/2023] Open
Abstract
Aberrant epigenetic modification induces oncogene expression and promotes cancer development. The histone lysine methyltransferase SETD1A, which specifically methylates histone 3 lysine 4 (H3K4), is involved in tumor growth and metastasis, and its ectopic expression has been detected in aggressive malignancies. Our previous study reported that SETD1A promotes gastric cancer (GC) proliferation and tumorigenesis. However, the function and molecular mechanisms of SETD1A in GC metastasis remain to be elucidated. In this study, we found that overexpression of SETD1A promoted GC migration and invasion, whereas knockdown of SETD1A suppressed GC migration and invasion in vitro. Moreover, knockdown of SETD1A suppressed GC epithelial-mesenchymal transition (EMT) by increasing the expression of epithelial marker E-cadherin and decreasing the expression of mesenchymal markers, including N-cadherin, Fibronectin, Vimentin, and α-smooth muscle actin (α-SMA). Mechanistically, knockdown of SETD1A reduced the EMT key transcriptional factor snail expression. SETD1A was recruited to the promoter of snail, where SETD1A could methylate H3K4. However, knockdown of SETD1A decreased the methylation of H3K4 on the snail promoter. Furthermore, SETD1A could be a coactivator of snail to induce EMT gene expression. Rescue of snail restored SETD1A knockdown-induced GC migration and invasion inhibition. In addition, knockdown of SETD1A suppressed GC metastasis in vivo. In summary, our data revealed that SETD1A mediated the EMT process and induced metastasis through epigenetic reprogramming of snail.
Collapse
Affiliation(s)
- Jugang Wu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongjuan Chai
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiyan Shan
- Department of Obstetrics and Gynecology, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Chunpeng Pan
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Xu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenpei Dong
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiwei Yu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Gu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
20
|
Guo Q, Hua Y. The assessment of circulating cell-free DNA as a diagnostic tool for breast cancer: an updated systematic review and meta-analysis of quantitative and qualitative ssays. Clin Chem Lab Med 2021; 59:1479-1500. [PMID: 33951758 DOI: 10.1515/cclm-2021-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This updated meta-analysis aimed to assess the diagnostic accuracy of circulating cell-free DNA (cfDNA) in breast cancer (BC). CONTENT An extensive systematic search was performed in PubMed, Scopus, Embase, and Science Direct databases to retrieve all related literature. Various diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), diagnostic odds ratio (DOR), and area under the curve (AUC) of summary receiver operating characteristic (sROC) curve, were also calculated using bivariate linear mixed models. SUMMARY In this meta-analysis, 57 unique articles (130 assays) on 4246 BC patients and 2,952 controls, were enrolled. For quantitative approaches, pooled SE, SP, PLR, NLR, DOR, and AUC were obtained as 0.80, 0.88, 6.7, 0.23, 29, and 0.91, respectively. Moreover, for qualitative approaches, pooled SE and SP for diagnostic performance were obtained as 0.36 and 0.98, respectively. In addition, PLR was 14.9 and NLR was 0.66. As well, the combined DOR was 23, and the AUC was 0.79. OUTLOOK Regardless of promising SE and SP, analysis of LRs suggested that quantitative assays are not robust enough neither for BC confirmation nor for its exclusion. On the other hand, qualitative assays showed satisfying performance only for confirming the diagnosis of BC, but not for its exclusion. Furthermore, qualitative cfDNA assays showed a better diagnostic performance in patients at the advanced stage of cancer, which represented no remarkable clinical significance as a biomarker for early detection.
Collapse
Affiliation(s)
- Qingfeng Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| | - Yuming Hua
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| |
Collapse
|
21
|
Pasyukova EG, Symonenko AV, Rybina OY, Vaiserman AM. Epigenetic enzymes: A role in aging and prospects for pharmacological targeting. Ageing Res Rev 2021; 67:101312. [PMID: 33657446 DOI: 10.1016/j.arr.2021.101312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
The development of interventions aimed at improving healthspan is one of the priority tasks for the academic and public health authorities. It is also the main objective of a novel branch in biogerontological research, geroscience. According to the geroscience concept, targeting aging is an effective way to combat age-related disorders. Since aging is an exceptionally complex process, system-oriented integrated approaches seem most appropriate for such an interventional strategy. Given the high plasticity and adaptability of the epigenome, epigenome-targeted interventions appear highly promising in geroscience research. Pharmaceuticals targeted at mechanisms involved in epigenetic control of gene activity are actively developed and implemented to prevent and treat various aging-related conditions such as cardiometabolic, neurodegenerative, inflammatory disorders, and cancer. In this review, we describe the roles of epigenetic mechanisms in aging; characterize enzymes contributing to the regulation of epigenetic processes; particularly focus on epigenetic drugs, such as inhibitors of DNA methyltransferases and histone deacetylases that may potentially affect aging-associated diseases and longevity; and discuss possible caveats associated with the use of epigenetic drugs.
Collapse
Affiliation(s)
- Elena G Pasyukova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Alexander V Symonenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Olga Y Rybina
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia; Federal State Budgetary Educational Institution of Higher Education «Moscow Pedagogical State University», M. Pirogovskaya Str. 1/1, Moscow, 119991, Russia
| | | |
Collapse
|
22
|
A novel proteomics approach to epigenetic profiling of circulating nucleosomes. Sci Rep 2021; 11:7256. [PMID: 33790358 PMCID: PMC8012598 DOI: 10.1038/s41598-021-86630-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 12/26/2022] Open
Abstract
Alteration of epigenetic modifications plays an important role in human cancer. Notably, the dysregulation of histone post-translational modifications (PTMs) has been associated with several cancers including colorectal cancer (CRC). However, the signature of histone PTMs on circulating nucleosomes is still not well described. We have developed a fast and robust enrichment method to isolate circulating nucleosomes from plasma for further downstream proteomic analysis. This method enabled us to quantify the global alterations of histone PTMs from 9 CRC patients and 9 healthy donors. Among 54 histone proteoforms identified and quantified in plasma samples, 13 histone PTMs were distinctive in CRC. Notably, methylation of histone H3K9 and H3K27, acetylation of histone H3 and citrullination of histone H2A1R3 were upregulated in plasma of CRC patients. A comparative analysis of paired samples identified 3 common histone PTMs in plasma and tumor tissue including the methylation and acetylation state of lysine 27 of histone H3. Moreover, we highlight for the first time that histone H2A1R3 citrulline is a modification upregulated in CRC patients. This new method presented herein allows the detection and quantification of histone variants and histone PTMs from circulating nucleosomes in plasma samples and could be used for biomarker discovery of cancer.
Collapse
|
23
|
Noberini R, Robusti G, Bonaldi T. Mass spectrometry-based characterization of histones in clinical samples: applications, progresses, and challenges. FEBS J 2021; 289:1191-1213. [PMID: 33415821 PMCID: PMC9291046 DOI: 10.1111/febs.15707] [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: 09/01/2020] [Revised: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post-translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody-based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS-based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS-based approaches currently available for histone PTM profiling, we will focus on the 'bottom-up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples.
Collapse
Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| |
Collapse
|
24
|
Romanowska K, Sobecka A, Rawłuszko-Wieczorek AA, Suchorska WM, Golusiński W. Head and Neck Squamous Cell Carcinoma: Epigenetic Landscape. Diagnostics (Basel) 2020; 11:diagnostics11010034. [PMID: 33375464 PMCID: PMC7823717 DOI: 10.3390/diagnostics11010034] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous carcinoma (HNSCC) constitutes the sixth most prevalent cancer worldwide. The molecular pathogenesis of HNSCC includes disorders in cell cycle, intercellular signaling, proliferation, squamous cell differentiation and apoptosis. In addition to the genetic mutations, changes in HNSCC are also characterized by the accumulation of epigenetic alterations such as DNA methylation, histone modifications, non-coding RNA activity and RNA methylation. In fact, some of them may promote cancer formation and progression by controlling the gene expression machinery, hence, they could be used as biomarkers in the clinical surveillance of HNSCC or as targets for therapeutic strategies. In this review, we focus on the current knowledge regarding epigenetic modifications observed in HNSCC and its predictive value for cancer development.
Collapse
Affiliation(s)
- Kamila Romanowska
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
- Correspondence:
| | - Agnieszka Sobecka
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
| | | | - Wiktoria M. Suchorska
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
| | - Wojciech Golusiński
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
| |
Collapse
|
25
|
Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
26
|
Komar D, Juszczynski P. Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 2020; 12:147. [PMID: 33054831 PMCID: PMC7556946 DOI: 10.1186/s13148-020-00941-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background With the discovery that more than half of human cancers harbor mutations in chromatin proteins, deregulation of epigenetic mechanisms has been recognized a hallmark of malignant transformation. Post-translational modifications (PTMs) of histone proteins, as main components of epigenetic regulatory machinery, are also broadly accepted as therapeutic target. Current “epigenetic” therapies target predominantly writers, erasers and readers of histone acetylation and (to a lesser extent) methylation, leaving other types of PTMs largely unexplored. One of them is the phosphorylation of serine 10 on histone H3 (H3S10ph). Main body H3S10ph is emerging as an important player in the initiation and propagation of cancer, as it facilitates cellular malignant transformation and participates in fundamental cellular functions. In normal cells this histone mark dictates the hierarchy of additional histone modifications involved in the formation of protein binding scaffolds, transcriptional regulation, blocking repressive epigenetic information and shielding gene regions from heterochromatin spreading. During cell division, this mark is essential for chromosome condensation and segregation. It is also involved in the function of specific DNA–RNA hybrids, called R-loops, which modulate transcription and facilitate chromosomal instability. Increase in H3S10ph is observed in numerous cancer types and its abundance has been associated with inferior prognosis. Many H3S10-kinases, including MSK1/2, PIM1, CDK8 and AURORA kinases, have been long considered targets in cancer therapy. However, since these proteins also participate in other critical processes, including signal transduction, apoptotic signaling, metabolic fitness and transcription, their chromatin functions are often neglected. Conclusions H3S10ph and enzymes responsible for deposition of this histone modification are important for chromatin activity and oncogenesis. Epigenetic-drugs targeting this axis of modifications, potentially in combination with conventional or targeted therapy, provide a promising angle in search for knowledge-driven therapeutic strategies in oncology.
Collapse
Affiliation(s)
- Dorota Komar
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland.
| | - Przemyslaw Juszczynski
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland
| |
Collapse
|
27
|
Wu J, Chai H, Li F, Ren Q, Gu Y. SETD1A augments sorafenib primary resistance via activating YAP in hepatocellular carcinoma. Life Sci 2020; 260:118406. [PMID: 32918976 DOI: 10.1016/j.lfs.2020.118406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/24/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
AIMS Sorafenib, the approved first-line chemotherapy drug for HCC (Hepatocellular Carcinoma), remains the key treatment agent which effectively improves the survival rate of advanced HCC patients. However, the sorafenib primary resistance limits the application of sorafenib for HCC treatment. The aims of current study are to explore the role and mechanism of SETD1A (Histone Lysine Methyltransferase SET Domain Containing 1A) in sorafenib primary resistance. MAIN METHODS The SETD1A expression in HCC was analyzed by Gene Expression Profiling Interactive Analysis. The survival of HCC patients was analyzed by Kaplan-Meier Plotter. Western Blot and Real-time qPCR were performed to measure the protein and mRNA levels, respectively. Cell counting kit-8 assay and colony formation assay were performed to determine cell viability and proliferation. Propidium Iodide and Trypan Blue staining assays were performed to investigate cell death. KEY FINDINGS Here, we showed that the expression of SETD1A was markedly upregulated in both HCC cell lines and tumor tissues compared to normal hepatocytes and corresponding non-tumor liver tissues, respectively. Regardless of whether treated with sorafenib, the patients who had higher level of SETD1A underwent lower survival rate of overall. In addition, SETD1A expression was positively correlated with the IC50 of sorafenib treated HCC cell lines. Furthermore, we indicated that knockdown of SETD1 augmented proliferation inhibition and cell death induced by sorafenib. SETD1A deficiency impaired YAP (Yes-associated protein) phosphorylation and activation. YAP activation contributed to SETD1A mediated sorafenib primary resistance. SIGNIFICANCE The current study demonstrated that SETD1A enhanced YAP activation to induce sorafenib primary resistance in HCC.
Collapse
Affiliation(s)
- Jugang Wu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Hongjuan Chai
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Feng Li
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Qing Ren
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Department of Gynecology and Obstetrics, Hainan West Central Hospital (Shanghai Ninth People's Hospital, Hainan Branch), Shanghai JiaoTong University School of Medicine, Hainan, China.
| | - Yan Gu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.
| |
Collapse
|
28
|
Shah SG, Mandloi T, Kunte P, Natu A, Rashid M, Reddy D, Gadewal N, Gupta S. HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. Epigenetics Chromatin 2020; 13:31. [PMID: 32746900 PMCID: PMC7398201 DOI: 10.1186/s13072-020-00354-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/28/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetics research is progressing in basic, pre-clinical and clinical studies using various model systems. Hence, updating the knowledge and integration of biological data emerging from in silico, in vitro and in vivo studies for different epigenetic factors is essential. Moreover, new drugs are being discovered which target various epigenetic proteins, tested in pre-clinical studies, clinical trials and approved by the FDA. It brings distinct challenges as well as opportunities to update the existing HIstome database for implementing and applying enormous data for biomedical research. RESULTS HISTome2 focuses on the sub-classification of histone proteins as variants and isoforms, post-translational modifications (PTMs) and modifying enzymes for humans (Homo sapiens), rat (Rattus norvegicus) and mouse (Mus musculus) on one interface for integrative analysis. It contains 232, 267 and 350 entries for histone proteins (non-canonical/variants and canonical/isoforms), PTMs and modifying enzymes respectively for human, rat, and mouse. Around 200 EpiDrugs for various classes of epigenetic modifiers, their clinical trial status, and pharmacological relevance have been provided in HISTome2. The additional features like 'Clustal omega' for multiple sequence alignment, link to 'FireBrowse' to visualize TCGA expression data and 'TargetScanHuman' for miRNA targets have been included in the database. CONCLUSION The information for multiple organisms and EpiDrugs on a common platform will accelerate the understanding and future development of drugs. Overall, HISTome2 has significantly increased the extent and diversity of its content which will serve as a 'knowledge Infobase' for biologists, pharmacologists, and clinicians. HISTome2: The HISTone Infobase is freely available on http://www.actrec.gov.in/histome2/ .
Collapse
Affiliation(s)
- Sanket G. Shah
- 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, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Tushar Mandloi
- Bioinformatics Centre, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
| | - Pooja Kunte
- 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, MH 410210 India
- Present Address: Diabetes Unit, King Edward Memorial Hospital Research Centre, Rasta Peth, Pune, Maharashtra 411 011 India
| | - 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, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Mudasir Rashid
- 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, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Divya Reddy
- 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, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
- Present Address: Stowers Institute for Medical Research, Kansas City, MO 64110 USA
| | - Nikhil Gadewal
- Bioinformatics Centre, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 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, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| |
Collapse
|
29
|
Banday S, Farooq Z, Ganai SA, Altaf M. Therapeutic strategies against hDOT1L as a potential drug target in MLL-rearranged leukemias. Clin Epigenetics 2020; 12:73. [PMID: 32450905 PMCID: PMC7249331 DOI: 10.1186/s13148-020-00860-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Therapeutic intervention of proteins participating in chromatin-mediated signaling with small-molecules is a novel option to reprogram expression networks for restraining disease states. Protein methyltransferases form the prominent family of such proteins regulating gene expression via epigenetic mechanisms thereby representing novel targets for pharmacological intervention. Disruptor of telomeric silencing, hDot1L is the only non-SET domain containing histone methyltransferase that methylates histone H3 at lysine 79. H3K79 methylation mediated by hDot1L plays a crucial role in mixed lineage leukemia (MLL) pathosis. MLL fusion protein mediated mistargeting of DOT1L to aberrant gene locations results in ectopic H3K79 methylation culminating in aberrant expression of leukemogenic genes like HOXA9 and MEIS1. hDOT1L has thus been proposed as a potential target for therapeutic intervention in MLL. This review presents the general overview of hDOT1L and its functional role in distinct biological processes. Furthermore, we discuss various therapeutic strategies against hDOT1L as a promising drug target to vanquish therapeutically challenging MLL.
Collapse
Affiliation(s)
- Shahid Banday
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, 190006, India
| | - Zeenat Farooq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, 190006, India
| | - Shabir Ahmad Ganai
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, 190006, India.,Present Address: Division of Basic Sciences and Humanities, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir, 193201, India
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, 190006, India. .,Centre for Interdisciplinary Research and Innovations, University of Kashmir, Hazratbal, Srinagar, 190006, India.
| |
Collapse
|
30
|
Wu J, Chai H, Xu X, Yu J, Gu Y. Histone methyltransferase SETD1A interacts with HIF1α to enhance glycolysis and promote cancer progression in gastric cancer. Mol Oncol 2020; 14:1397-1409. [PMID: 32291851 PMCID: PMC7266269 DOI: 10.1002/1878-0261.12689] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/03/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
Growing tumors alter their metabolic profiles to support the increased cell proliferation. SETD1A, a histone lysine methyltransferase which specifically methylates H3K4, plays important roles in both normal cell and cancer cell functions. However, the function of SETD1A in gastric cancer (GC) progression and its role in GC metabolic reprogramming are still largely unknown. In the current study, we discovered that the expression of SETD1A was higher in GC tumor specimens compared to surrounding nontumor tissues. Upregulation of SETD1A increased GC cell proliferation, whereas downregulation of SETD1A inhibited GC cell proliferation. Furthermore, knockdown of SETD1A reduced glucose uptake and production of lactate and suppressed glycolysis by decreasing the expression of glycolytic genes, including GLUT1, HK2, PFK2, PKM2, LDHA, and MCT4. Mechanistically, SETD1A interacted with HIF1α to strengthen its transactivation, indicating that SETD1A promotes glycolysis through coactivation of HIF1α. SETD1A and HIF1α were recruited to the promoter of HK2 and PFK2, where SETD1A could methylate H3K4. However, knockdown of SETD1A decreased the methylation of H3K4 on HK2 and PFK2 promoter and reduced HIF1α recruitment necessary to promote transcription of glycolytic genes. Inhibition of HIF1α decelerated SETD1A‐enhanced GC cell growth. In additional, there was a linear correlation between SETD1A and several key glycolytic genes in human GC specimens obtained from TCGA dataset. Thus, our results demonstrated that SETD1A interacted with HIF1α to promote glycolysis and accelerate GC progression, implicating that SETD1A may be a potential molecular target for GC treatment.
Collapse
Affiliation(s)
- Jugang Wu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, China
| | - Hongjuan Chai
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, China
| | - Xin Xu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, China
| | - Jiwei Yu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, China
| | - Yan Gu
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, China
| |
Collapse
|
31
|
Chemopreventive and Therapeutic Efficacy of Cinnamomum zeylanicum L. Bark in Experimental Breast Carcinoma: Mechanistic In Vivo and In Vitro Analyses. Molecules 2020; 25:molecules25061399. [PMID: 32204409 PMCID: PMC7144360 DOI: 10.3390/molecules25061399] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022] Open
Abstract
Comprehensive oncology research suggests an important role of phytochemicals or whole plant foods in the modulation of signaling pathways associated with anticancer action. The goal of this study is to assess the anticancer activities of Cinnamomum zeylanicum L. using rat, mouse, and cell line breast carcinoma models. C. zeylanicum (as bark powder) was administered in the diet at two concentrations of 0.1% (w/w) and 1% (w/w) during the whole experiment in chemically induced rat mammary carcinomas and a syngeneic 4T1 mouse model. After autopsy, histopathological and molecular evaluations of mammary gland tumors in rodents were carried out. Moreover, in vitro analyses using MCF-7 and MDA-MB-231 cells were performed. The dominant metabolites present in the tested C. zeylanicum essential oil (with relative content over 1%) were cinnamaldehyde, cinnamaldehyde dimethyl acetal, cinnamyl acetate, eugenol, linalool, eucalyptol, limonene, o-cymol, and α-terpineol. The natural mixture of mentioned molecules demonstrated significant anticancer effects in our study. In the mouse model, C. zeylanicum at a higher dose (1%) significantly decreased tumor volume by 44% when compared to controls. In addition, treated tumors showed a significant dose-dependent decrease in mitotic activity index by 29% (0.1%) and 45.5% (1%) in comparison with the control group. In rats, C. zeylanicum in both doses significantly reduced the tumor incidence by 15.5% and non-significantly suppressed tumor frequency by more than 30% when compared to controls. An evaluation of the mechanism of anticancer action using valid oncological markers showed several positive changes after treatment with C. zeylanicum. Histopathological analysis of treated rat tumor specimens showed a significant decrease in the ratio of high-/low-grade carcinomas compared to controls. In treated rat carcinomas, we found caspase-3 and Bax expression increase. On the other hand, we observed a decrease in Bcl-2, Ki67, VEGF, and CD24 expressions and MDA levels. Assessment of epigenetic changes in rat tumor cells in vivo showed a significant decrease in lysine methylation status of H3K4m3 and H3K9m3 in the high-dose treated group, a dose-dependent increase in H4K16ac levels (H4K20m3 was not changed), down-regulations of miR21 and miR155 in low-dose cinnamon groups (miR22 and miR34a were not modulated), and significant reduction of the methylation status of two out of five gene promoters-ATM and TIMP3 (PITX2, RASSF1, PTEN promoters were not changed). In vitro study confirmed results of animal studies, in that the essential oil of C. zeylanicum displayed significant anticancer efficacy in MCF-7 and MDA-MB-231 cells (using MTS, BrdU, cell cycle, annexin V/PI, caspase-3/7, Bcl-2, PARP, and mitochondrial membrane potential analyses). As a conclusion, C. zeylanicum L. showed chemopreventive and therapeutic activities in animal breast carcinoma models that were also significantly confirmed by mechanistic evaluations in vitro and in vivo.
Collapse
|
32
|
Lai JJ, Cruz FM, Rock KL. Immune Sensing of Cell Death through Recognition of Histone Sequences by C-Type Lectin-Receptor-2d Causes Inflammation and Tissue Injury. Immunity 2019; 52:123-135.e6. [PMID: 31859049 DOI: 10.1016/j.immuni.2019.11.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/10/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022]
Abstract
The immune system monitors the health of cells and is stimulated by necrosis. Here we examined the receptors and ligands driving this response. In a targeted screen of C-type lectin receptors, a Clec2d reporter responded to lysates from necrotic cells. Biochemical purification identified histones, both free and bound to nucleosomes or neutrophil extracellular traps, as Clec2d ligands. Clec2d recognized poly-basic sequences in histone tails and this recognition was sensitive to post-translational modifications of these sequences. As compared with WT mice, Clec2d-/- mice exhibited reduced proinflammatory responses to injected histones, and less tissue damage and improved survival in a hepatotoxic injury model. In macrophages, Clec2d localized to the plasma membrane and endosomes. Histone binding to Clec2d did not stimulate kinase activation or cytokine production. Rather, histone-bound DNA stimulated endosomal Tlr9-dependent responses in a Clec2d-dependent manner. Thus, Clec2d binds to histones released upon necrotic cell death, with functional consequences to inflammation and tissue damage.
Collapse
Affiliation(s)
- Jiann-Jyh Lai
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
33
|
Perri AM, Agosti V, Olivo E, Concolino A, Angelis MD, Tammè L, Fiumara CV, Cuda G, Scumaci D. Histone proteomics reveals novel post-translational modifications in breast cancer. Aging (Albany NY) 2019; 11:11722-11755. [PMID: 31816600 PMCID: PMC6932915 DOI: 10.18632/aging.102577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 11/26/2019] [Indexed: 04/28/2023]
Abstract
Histones and their variants are subjected to several post-translational modifications (PTMs). Histones PTMs play an important role in the regulation of gene expression and are critical for the development and progression of many types of cancer, including breast cancer. In this study, we used two-dimensional TAU/SDS electrophoresis, coupled with mass spectrometry for a comprehensive profiling of histone PTMs in breast cancer cell lines.Proteomic approach allowed us to identify 85 histone PTMs, seventeen of which are not reported in the UniProt database. Western blot analysis was performed to confirm a peculiar pattern of PTMs in the sporadic and hereditary breast cancer cell lines compared to normal cells. Overlapping mass spectrometry data with western blotting results, we identified, for the first time to our knowledge, a tyrosine phosphorylation on histone H1, which is significantly higher in breast cancer cells. Additionally, by inhibiting specific signaling paths, such as PI3K, PPARγ and FAK pathways, we established a correlation between their regulation and the presence of new histone PTMs. Our results may provide new insight on the possible implication of these modifications in breast cancer and may offer new perspectives for future clinical applications.
Collapse
Affiliation(s)
- Angela Mena Perri
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Valter Agosti
- Laboratory of Molecular Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy, CIS for Genomics and Molecular Pathology, Magna Graecia University, Catanzaro, Italy
| | - Erika Olivo
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Antonio Concolino
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - MariaTeresa De Angelis
- Stem Cell Laboratory, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine University “Magna Graecia” of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Laura Tammè
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Claudia Vincenza Fiumara
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Giovanni Cuda
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Domenica Scumaci
- Laboratory of Proteomics, Research Center on Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro, Italy
| |
Collapse
|
34
|
Samec M, Liskova A, Koklesova L, Mestanova V, Franekova M, Kassayova M, Bojkova B, Uramova S, Zubor P, Janikova K, Danko J, Samuel SM, Büsselberg D, Kubatka P. Fluctuations of Histone Chemical Modifications in Breast, Prostate, and Colorectal Cancer: An Implication of Phytochemicals as Defenders of Chromatin Equilibrium. Biomolecules 2019; 9:E829. [PMID: 31817446 PMCID: PMC6995638 DOI: 10.3390/biom9120829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Natural substances of plant origin exert health beneficiary efficacy due to the content of various phytochemicals. Significant anticancer abilities of natural compounds are mediated via various processes such as regulation of a cell's epigenome. The potential antineoplastic activity of plant natural substances mediated by their action on posttranslational histone modifications (PHMs) is currently a highly evaluated area of cancer research. PHMs play an important role in maintaining chromatin structure and regulating gene expression. Aberrations in PHMs are directly linked to the process of carcinogenesis in cancer such as breast (BC), prostate (PC), and colorectal (CRC) cancer, common malignant diseases in terms of incidence and mortality among both men and women. This review summarizes the effects of plant phytochemicals (isolated or mixtures) on cancer-associated PHMs (mainly modulation of acetylation and methylation) resulting in alterations of chromatin structure that are related to the regulation of transcription activity of specific oncogenes, which are crucial in the development of BC, PC, and CRC. Significant effectiveness of natural compounds in the modulation of aberrant PHMs were confirmed by a number of in vitro or in vivo studies in preclinical cancer research. However, evidence concerning PHMs-modulating abilities of plant-based natural substances in clinical trials is insufficient.
Collapse
Affiliation(s)
- Marek Samec
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Alena Liskova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Veronika Mestanova
- Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Maria Franekova
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Monika Kassayova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Bianka Bojkova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Sona Uramova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Pavol Zubor
- OBGY Health & Care, Ltd., 01026 Zilina, Slovakia;
| | - Katarina Janikova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Jan Danko
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Samson Mathews Samuel
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Peter Kubatka
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| |
Collapse
|
35
|
Thakur GK, Sharma T, Krishna Latha T, Banerjee BD, Shah HK, Guleria K. High Resolution Based Quantitative Determination of Methylation Status of CDH1 and VIM Gene in Epithelial Ovarian Cancer. Asian Pac J Cancer Prev 2019; 20:2923-2928. [PMID: 31653136 PMCID: PMC6982649 DOI: 10.31557/apjcp.2019.20.10.2923] [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: 01/31/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA promoter methylation is widely explored epigenetic phenomena, known to effect gene expression and further perturbation in cellular homeostasis. Myriad of studies have leveraged promoter methylation and its potential as biomarker for various types of cancer. Aim of present study is to investigate promoter methylation of CDH1 and VIM gene and etiology of epithelial ovarian cancer (EOC). METHODS Most of previous studies were qualitative; we have quantitatively assessed methylation levels in 50 EOC cases and control each through high recognition melt (HRM) technique. RESULTS At 10 % cutoff for CDH1 94% of EOC cases were found to be methylated with mean methylation of 45±13.8, whereas for control mean methylation was found to be 7.3±3.7 amongst 16 % methylation positive control samples. For VIM methylation was detected in 96% of cases with mean of 50.44±11.7 in EOC and in 12% methylation positive samples for control mean methylation was 6.24±4.3. CONCLUSION In short HRM based DNA methylation can serve as a robust and sensitive diagnostic method for promoter methylation detection and as a biomarker for early epithelial ovarian cancer detection.
Collapse
Affiliation(s)
- Gaurav Kr Thakur
- Environmental and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| | - Tusha Sharma
- Environmental and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| | - T Krishna Latha
- Environmental and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| | - B D Banerjee
- Environmental and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| | - Harendra Kr Shah
- Environmental and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| | - Kiran Guleria
- Department of Obst and Gynae, University College of Medical Sciences (Delhi University) and GTB Hospital, Dilshad Garden, Delhi, India
| |
Collapse
|
36
|
Histone acetylation in refractory sudden sensorineural hearing loss patients after intratympanic methylprednisolone perfusion. The Journal of Laryngology & Otology 2019; 133:895-902. [PMID: 31506109 DOI: 10.1017/s0022215119001865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE To examine the relationship between the therapeutic effect of intratympanic methylprednisolone perfusion and histone acetylation in refractory sudden sensorineural hearing loss. METHODS Thirty-four refractory sudden sensorineural hearing loss patients were enrolled and treated with intratympanic methylprednisolone perfusion. Pure tone average, acetylated histone H3, acetylated histone H4 and histone deacetylase 2 (HDAC2) were measured in peripheral blood mononuclear cells before and after intratympanic methylprednisolone perfusion. Sixteen healthy volunteers were recruited to obtain normal reference values. RESULTS Pure tone average in sudden sensorineural hearing loss patients improved from 84.14 ± 13.54 dB to 73.56 ± 18.45 dB after intratympanic methylprednisolone perfusion. Up-regulations in HDAC2 protein level, and down-regulations in histone H3 and H4 acetylation were observed in the intratympanic methylprednisolone perfusion sensitive group (pure tone average gain of 15 dB or more), while no significant changes were observed in the intratympanic methylprednisolone perfusion insensitive group (pure tone average gain of less than 15 dB). CONCLUSION Intratympanic methylprednisolone perfusion can improve hearing in a considerable number of refractory sudden sensorineural hearing loss patients. The therapeutic effect is closely related to reduced histone acetylation.
Collapse
|
37
|
Xia L, Zhang W, Gao L. Clinical and prognostic effects ofCDKN2A,CDKN2BandCDH13promoter methylation in ovarian cancer: a study using meta-analysis and TCGA data. Biomarkers 2019; 24:700-711. [PMID: 31382782 DOI: 10.1080/1354750x.2019.1652685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Liang Xia
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Wenzhu Zhang
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Li Gao
- Department of Gynecology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| |
Collapse
|
38
|
Sang Y, Deng Y. Current insights into the epigenetic mechanisms of skin cancer. Dermatol Ther 2019; 32:e12964. [PMID: 31081988 DOI: 10.1111/dth.12964] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 12/23/2022]
Abstract
Skin cancer is a manifestation of tumors. The different types of skin cancer are named according to their source of tumor cells. Currently, there are three main types of skin cancer. They are squamous cell carcinoma, basal cell carcinoma, and melanoma. Their epidemiological characteristics, clinical classifications, and treatment methods are somewhat different. The epigenetic modifications are also different in these three types of skin cancer. Epigenetics is the change in gene expression and function and the generation of a heritable phenotype without changing the DNA sequence. The phenomenon of epigenetics involves a variety of processes, including the methylation of DNA and RNA, histone modifications, RNAi, and chromatin remodeling. Researchers have found that DNA, RNA, histone, and chromatin level modifications cause heritable changes in gene expression patterns. This review will introduce the role of epigenetics in skin cancer from the three following angles: DNA methylation, histone modifications, and RNA methylation.
Collapse
Affiliation(s)
- Yanqi Sang
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, People's Republic of China
| |
Collapse
|
39
|
Gurova KV. Chromatin Stability as a Target for Cancer Treatment. Bioessays 2019; 41:e1800141. [PMID: 30566250 PMCID: PMC6522245 DOI: 10.1002/bies.201800141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/29/2018] [Indexed: 12/14/2022]
Abstract
In this essay, I propose that DNA-binding anti-cancer drugs work more via chromatin disruption than DNA damage. Success of long-awaited drugs targeting cancer-specific drivers is limited by the heterogeneity of tumors. Therefore, chemotherapy acting via universal targets (e.g., DNA) is still the mainstream treatment for cancer. Nevertheless, the problem with targeting DNA is insufficient efficacy due to high toxicity. I propose that this problem stems from the presumption that DNA damage is critical for the anti-cancer activity of these drugs. DNA in cells exists as chromatin, and many DNA-targeting drugs alter chromatin structure by destabilizing nucleosomes and inducing histone eviction from chromatin. This effect has been largely ignored because DNA damage is seen as the major reason for anti-cancer activity. I discuss how DNA-binding molecules destabilize chromatin, why this effect is more toxic to tumoral than normal cells, and why cells die as a result of chromatin destabilization.
Collapse
Affiliation(s)
- Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263. Tel 1-716-845-4760,
| |
Collapse
|
40
|
Liu Z, Gao Y, Li X. Cancer epigenetics and the potential of epigenetic drugs for treating solid tumors. Expert Rev Anticancer Ther 2018; 19:139-149. [PMID: 30470148 DOI: 10.1080/14737140.2019.1552139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Epigenetic modification without DNA sequence mutation plays an important role in cancer development. Some small molecular inhibitors targeting key epigenetic molecules have been approved by the Food and Drug Administration to treat hematological malignancies. However, the anticancer effects of these drugs on solid tumors are not satisfactory, and the mechanisms of action remain largely unknown. Areas covered: The review summarizes the latest research on cancer epigenetics and discusses the potentials and limitations of using epigenetic drugs to treat solid tumors. An analysis of possible reasons for epigenetic drug treatment failure in solid tumors in some clinical trials is discussed along with prospects for future development. Expert commentary: Next-generation small molecule inhibitors will target novel epigenetic regulators with high cancer specificity. Combined modalities exploiting epigenetic drugs with chemo-/radiotherapy, molecular-targeting drugs, and immunotherapy will be able to effectively treat solid tumors in the near future.
Collapse
Affiliation(s)
- Zhenghui Liu
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Yingxue Gao
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Xiong Li
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| |
Collapse
|
41
|
Srivastava A, Creek DJ. Discovery and Validation of Clinical Biomarkers of Cancer: A Review Combining Metabolomics and Proteomics. Proteomics 2018; 19:e1700448. [PMID: 30353665 DOI: 10.1002/pmic.201700448] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/11/2018] [Indexed: 12/19/2022]
Abstract
Early detection and diagnosis of cancer can allow timely medical intervention, which greatly improves chances of survival and enhances quality of life. Biomarkers play an important role in assisting clinicians and health care providers in cancer diagnosis and treatment follow-up. In spite of years of research and the discovery of thousands of candidate cancer biomarkers, only a few have transitioned to routine usage in the clinic. This review highlights advances in proteomics technologies that have enabled high rates of discovery of candidate cancer biomarkers and evaluates integration with other omics technologies to improve their progress through to validation and clinical translation. Furthermore, it gauges the role of metabolomics technology in cancer biomarker research and assesses it as a complementary tool in aiding cancer biomarker discovery and validation.
Collapse
Affiliation(s)
- Anubhav Srivastava
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| | - Darren John Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, 3052, Australia
| |
Collapse
|
42
|
Singer F, Irmisch A, Toussaint NC, Grob L, Singer J, Thurnherr T, Beerenwinkel N, Levesque MP, Dummer R, Quagliata L, Rothschild SI, Wicki A, Beisel C, Stekhoven DJ. SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. BMC Med Inform Decis Mak 2018; 18:89. [PMID: 30373609 PMCID: PMC6206832 DOI: 10.1186/s12911-018-0680-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/18/2018] [Indexed: 12/18/2022] Open
Abstract
Background Molecular precision oncology is an emerging practice to improve cancer therapy by decreasing the risk of choosing treatments that lack efficacy or cause adverse events. However, the challenges of integrating molecular profiling into routine clinical care are manifold. From a computational perspective these include the importance of a short analysis turnaround time, the interpretation of complex drug-gene and gene-gene interactions, and the necessity of standardized high-quality workflows. In addition, difficulties faced when integrating molecular diagnostics into clinical practice are ethical concerns, legal requirements, and limited availability of treatment options beyond standard of care as well as the overall lack of awareness of their existence. Methods To the best of our knowledge, we are the first group in Switzerland that established a workflow for personalized diagnostics based on comprehensive high-throughput sequencing of tumors at the clinic. Our workflow, named SwissMTB (Swiss Molecular Tumor Board), links genetic tumor alterations and gene expression to therapeutic options and clinical trial opportunities. The resulting treatment recommendations are summarized in a clinical report and discussed in a molecular tumor board at the clinic to support therapy decisions. Results Here we present results from an observational pilot study including 22 late-stage cancer patients. In this study we were able to identify actionable variants and corresponding therapies for 19 patients. Half of the patients were analyzed retrospectively. In two patients we identified resistance-associated variants explaining lack of therapy response. For five out of eleven patients analyzed before treatment the SwissMTB diagnostic influenced treatment decision. Conclusions SwissMTB enables the analysis and clinical interpretation of large numbers of potentially actionable molecular targets. Thus, our workflow paves the way towards a more frequent use of comprehensive molecular diagnostics in Swiss hospitals. Electronic supplementary material The online version of this article (10.1186/s12911-018-0680-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Franziska Singer
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Jochen Singer
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Thomas Thurnherr
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Niko Beerenwinkel
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Luca Quagliata
- Department of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4056, Basel, Switzerland
| | - Sacha I Rothschild
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Andreas Wicki
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Daniel J Stekhoven
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.
| |
Collapse
|
43
|
Celano M, Mio C, Sponziello M, Verrienti A, Bulotta S, Durante C, Damante G, Russo D. Targeting post-translational histone modifications for the treatment of non-medullary thyroid cancer. Mol Cell Endocrinol 2018; 469:38-47. [PMID: 28579118 DOI: 10.1016/j.mce.2017.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/25/2017] [Accepted: 05/30/2017] [Indexed: 02/07/2023]
Abstract
Genomic and epigenetic alterations are now being exploited as molecular targets in cancer treatment. Abnormalities involving the post-translational modification of histones have been demonstrated in thyroid cancer, and they are regarded as promising molecular targets for novel drug treatment of tumors that are resistant to conventional therapies. After a brief overview of the histone modifications most commonly associated with human malignancies, we will review recently published preclinical and clinical findings regarding the use of histone-activity modulators in thyroid cancers. Particular attention will be focused on their use as re-differentiating or anti-proliferating agents, the differential effects observed when they are used alone and in combination with other targeted drugs, and current prospects for their use in the treatment of thyroid cancer.
Collapse
Affiliation(s)
- Marilena Celano
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy
| | - Marialuisa Sponziello
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Antonella Verrienti
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Cosimo Durante
- Department of Internal Medicine and Medical Specialties, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| |
Collapse
|
44
|
Ismail T, Lee HK, Kim C, Kwon T, Park TJ, Lee HS. KDM1A microenvironment, its oncogenic potential, and therapeutic significance. Epigenetics Chromatin 2018; 11:33. [PMID: 29921310 PMCID: PMC6006565 DOI: 10.1186/s13072-018-0203-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The lysine-specific histone demethylase 1A (KDM1A) was the first demethylase to challenge the concept of the irreversible nature of methylation marks. KDM1A, containing a flavin adenine dinucleotide (FAD)-dependent amine oxidase domain, demethylates histone 3 lysine 4 and histone 3 lysine 9 (H3K4me1/2 and H3K9me1/2). It has emerged as an epigenetic developmental regulator and was shown to be involved in carcinogenesis. The functional diversity of KDM1A originates from its complex structure and interactions with transcription factors, promoters, enhancers, oncoproteins, and tumor-associated genes (tumor suppressors and activators). In this review, we discuss the microenvironment of KDM1A in cancer progression that enables this protein to activate or repress target gene expression, thus making it an important epigenetic modifier that regulates the growth and differentiation potential of cells. A detailed analysis of the mechanisms underlying the interactions between KDM1A and the associated complexes will help to improve our understanding of epigenetic regulation, which may enable the discovery of more effective anticancer drugs.
Collapse
Affiliation(s)
- Tayaba Ismail
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Hyun-Kyung Lee
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Chowon Kim
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Taejoon Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Tae Joo Park
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
| | - Hyun-Shik Lee
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea.
| |
Collapse
|
45
|
Cao Z, Wei L, Zhu W, Yao X. Meta-analysis of CDKN2A methylation to find its role in prostate cancer development and progression, and also to find the effect of CDKN2A expression on disease-free survival (PRISMA). Medicine (Baltimore) 2018; 97:e0182. [PMID: 29561434 PMCID: PMC5895353 DOI: 10.1097/md.0000000000010182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Reduction of cyclin-dependent kinase inhibitor 2A (CDKN2A) (p16 and p14) expression through DNA methylation has been reported in prostate cancer (PCa). This meta-analysis was conducted to assess the difference of p16 and p14 methylation between PCa and different histological types of nonmalignant controls and the correlation of p16 or p14 methylation with clinicopathological features of PCa. METHODS According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement criteria, articles were searched in PubMed, Embase, EBSCO, Wanfang, and CNKI databases. The strength of correlation was calculated by the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). Trial sequential analysis (TSA) was used to estimate the required population information for significant results. RESULTS A total of 20 studies published from 1997 to 2017 were identified in this meta-analysis, including 1140 PCa patients and 530 cases without cancer. Only p16 methylation in PCa was significantly higher than in benign prostatic lesions (OR = 4.72, P = .011), but had a similar level in PCa and adjacent tissues or high-grade prostatic intraepithelial neoplasias (HGPIN). TSA revealed that this analysis on p16 methylation is a false positive result in cancer versus benign prostatic lesions (the estimated required information size of 5116 participants). p16 methylation was not correlated with PCa in the urine and blood. Besides, p16 methylation was not linked to clinical stage, prostate-specific antigen (PSA) level, and Gleason score (GS) of patients with PCa. p14 methylation was not correlated with PCa in tissue and urine samples. No correlation was observed between p14 methylation and clinical stage or GS. CDKN2A mutation and copy number alteration were not associated with prognosis of PCa in overall survival and disease-free survival. CDKN2A expression was not correlated with the prognosis of PCa in overall survival (492 cases) (P > .1), while CDKN2A expression was significantly associated with a poor disease-free survival (P < .01). CONCLUSION CDKN2A methylation may not be significantly associated with the development, progression of PCa. Although CDKN2A expression had an unfavorable prognosis in disease-free survival. More studies are needed to confirm our results.
Collapse
Affiliation(s)
| | - Lijuan Wei
- Department of Respiratory Medicine, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang, China
| | | | | |
Collapse
|
46
|
Ye M, Huang T, Ying Y, Li J, Yang P, Ni C, Zhou C, Chen S. Detection of 14-3-3 sigma (σ) promoter methylation as a noninvasive biomarker using blood samples for breast cancer diagnosis. Oncotarget 2018; 8:9230-9242. [PMID: 27999208 PMCID: PMC5354727 DOI: 10.18632/oncotarget.13992] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/12/2016] [Indexed: 12/19/2022] Open
Abstract
As a tumor suppressor gene, 14-3-3 σ has been reported to be frequently methylated in breast cancer. However, the clinical effect of 14-3-3 σ promoter methylation remains to be verified. This study was performed to assess the clinicopathological significance and diagnostic value of 14-3-3 σ promoter methylation in breast cancer. 14-3-3 σ promoter methylation was found to be notably higher in breast cancer than in benign lesions and normal breast tissue samples. We did not observe that 14-3-3 σ promoter methylation was linked to the age status, tumor grade, clinic stage, lymph node status, histological subtype, ER status, PR status, HER2 status, or overall survival of patients with breast cancer. The combined sensitivity, specificity, AUC (area under the curve), positive likelihood ratios (PLR), negative likelihood ratios (NLR), diagnostic odds ratio (DOR), and post-test probability values (if the pretest probability was 30%) of 14-3-3 σ promoter methylation in blood samples of breast cancer patients vs. healthy subjects were 0.69, 0.99, 0.86, 95, 0.31, 302, and 98%, respectively. Our findings suggest that 14-3-3 σ promoter methylation may be associated with the carcinogenesis of breast cancer and that the use of 14-3-3 σ promoter methylation might represent a useful blood-based biomarker for the clinical diagnosis of breast cancer.
Collapse
Affiliation(s)
- Meng Ye
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| | - Tao Huang
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| | - Ying Ying
- Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, People's Republic of China
| | - Jinyun Li
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| | - Ping Yang
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China.,Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Chao Ni
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China.,Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Chongchang Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Si Chen
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| |
Collapse
|
47
|
Vadla R, Haldar D. Mammalian target of rapamycin complex 2 (mTORC2) controls glycolytic gene expression by regulating Histone H3 Lysine 56 acetylation. Cell Cycle 2018; 17:110-123. [PMID: 29143563 DOI: 10.1080/15384101.2017.1404207] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer cells, but the mechanisms are not well understood. The mammalian target of rapamycin complex 2 (mTORC2) controls cell growth and proliferation and plays a critical role in metabolic reprogramming in glioma. mTORC2 regulates cellular processes such as cell survival, metabolism, and proliferation by phosphorylation of AGC kinases. Components of mTORC2 are shown to localize to the nucleus, but whether mTORC2 modulates epigenetic modifications to regulate gene expression is not known. Here, we identified histone H3 lysine 56 acetylation (H3K56Ac) is regulated by mTORC2 and show that global H3K56Ac levels were downregulated on mTORC2 knockdown but not on mTORC1 knockdown. mTORC2 promotes H3K56Ac in a tuberous sclerosis complex 1/2 (TSC1/2) mediated signaling pathway. We show that knockdown of sirtuin6 (SIRT6) prevented H3K56 deacetylation in mTORC2 depleted cells. Using glioma model consisting of U87EGFRvIII cells, we established that mTORC2 promotes H3K56Ac in glioma. Finally, we show that mTORC2 regulates the expression of glycolytic genes by regulating H3K56Ac levels at the promoters of these genes in glioma cells and depletion of mTOR leads to increased recruitment of SIRT6 to these promoters. Collectively, these results identify mTORC2 signaling pathway positively promotes H3K56Ac through which it may mediate metabolic reprogramming in glioma.
Collapse
Affiliation(s)
- Raghavendra Vadla
- a Centre for DNA Fingerprinting and Diagnostics , Survey Nos. 728, 729, 730 & 734, Opposite Uppal Water Tank, Beside BSNL T E Building, Uppal, Hyderabad 500039 , Ranga Reddy District , India.,b Graduate Studies , Manipal University , Manipal , India
| | - Devyani Haldar
- a Centre for DNA Fingerprinting and Diagnostics , Survey Nos. 728, 729, 730 & 734, Opposite Uppal Water Tank, Beside BSNL T E Building, Uppal, Hyderabad 500039 , Ranga Reddy District , India
| |
Collapse
|
48
|
Liu G. CDH1 promoter methylation in patients with cervical carcinoma: a systematic meta-analysis with trial sequential analysis. Future Oncol 2017; 14:51-63. [PMID: 29237293 DOI: 10.2217/fon-2017-0267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This study was performed to evaluate the correlation between CDH1 promoter methylation and cervical cancer. METHODS Trial sequential analysis was conducted to evaluate the required information size. RESULTS A total of 15 studies with 950 cervical cancers and 829 controls were identified. CDH1 promoter methylation was higher in cervical cancer than in cervical intraepithelial neoplasia lesions and normal cervical tissues. Subgroup analysis of ethnicity showed that CDH1 promoter methylation correlated with cervical cancer in Caucasians, but not in Asians. CDH1 promoter methylation was higher in cervical cancer cytology samples than in normal cytology samples. It was higher in squamous cell carcinoma than adenocarcinoma, but was not correlated with tumor stage, grade and overall survival. CONCLUSION CDH1 promoter methylation may be correlated with cervical cancer carcinogenesis, especially for Caucasians. It was associated with histological subtypes. Trial sequential analysis showed that more studies are needed.
Collapse
Affiliation(s)
- Guanyuan Liu
- Department of Gynaecology & Obstetrics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, No. 8 Workers Stadium South Road, Beijing 100020, China
| |
Collapse
|
49
|
Ovchinnikov VY, Antonets DV, Gulyaeva LF. The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs. J Bioinform Comput Biol 2017; 16:1750029. [PMID: 29301444 DOI: 10.1142/s0219720017500299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) play important roles in the regulation of gene expression at the post-transcriptional level. Many exogenous compounds or xenobiotics may affect microRNA expression. It is a well-established fact that xenobiotics with planar structure like TCDD, benzo(a)pyrene (BP) can bind aryl hydrocarbon receptor (AhR) followed by its nuclear translocation and transcriptional activation of target genes. Another chemically diverse group of xenobiotics including phenobarbital, DDT, can activate the nuclear receptor CAR and in some cases estrogen receptors ESR1 and ESR2. We hypothesized that such chemicals can affect miRNA expression through the activation of AHR, CAR, and ESRs. To prove this statement, we used in silico methods to find DRE, PBEM, ERE potential binding sites for these receptors, respectively. We have predicted AhR, CAR, and ESRs binding sites in 224 rat, 201 mouse, and 232 human promoters of miRNA-coding genes. In addition, we have identified a number of miRNAs with predicted AhR, CAR, and ESRs binding sites that are known as oncogenes and as tumor suppressors. Our results, obtained in silico, open a new strategy for ongoing experimental studies and will contribute to further investigation of epigenetic mechanisms of carcinogenesis.
Collapse
Affiliation(s)
- Vladimir Y Ovchinnikov
- 1 Laboratory of Molecular Mechanisms of Pathological Processes, The Federal Research Center Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation
| | - Denis V Antonets
- 2 Laboratory of Complex Systems Modeling, A.P. Ershov Institute of Informatics Systems, Prospekt Lavrentyeva 6, Novosibirsk 630090, Russian Federation.,3 AcademGene LLC, Prospekt Lavrentyeva 6, Novosibirsk 630090, Russian Federation
| | - Lyudmila F Gulyaeva
- 4 Laboratory of Molecular Mechanisms of Carcinogenesis, Research Institute of Molecular Biology and Biophysics, Timakov St., 2/12, Novosibirsk 630117, Russian Federation.,5 Natural Science Department, Novosibirsk State University, Pirogova St., 2, Novosibirsk 630090, Russian Federation
| |
Collapse
|
50
|
Wang H, Cui M, Zhang S, He J, Song L, Chen Y. Relationship between RAS Association Domain Family Protein 1A Promoter Methylation and the Clinicopathological Characteristics in Patients with Ovarian Cancer: A Systematic Meta-Analysis. Gynecol Obstet Invest 2017; 83:349-357. [PMID: 29130987 DOI: 10.1159/000484245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/13/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND To investigate the relationship between RAS association domain family protein 1A (RASSF1A) promoter methylation and the clinical features, and the survival of ovarian cancer patients. METHODS A comprehensive literature search was conducted in the PubMed, Embase, EBSCO, and Cochrane Library databases. The overall ORs with their 95% CIs were calculated in this meta-analysis. RESULTS Finally 17 relevant publications with 1,108 ovarian cancer samples were available for the current meta-analysis. RASSF1A promoter methylation had a significantly higher level in ovarian cancer than in low malignant potential (LMP) tumors. No significant relationship was observed between RASSF1A promoter methylation and the clinicopathological characteristics in ovarian cancer. Two studies reported that RASSF1A promoter methylation was not correlated with the survival of patients with ovarian cancer. CONCLUSIONS Our findings suggest that the use of RASSF1A promoter methylation could distinguish ovarian cancer and LMP tumors. -RASSF1A promoter methylation may not be correlated with the clinical features and the survival of ovarian cancer patients. More studies with large sample sizes are essential in the future.
Collapse
Affiliation(s)
- Hong Wang
- Department of Obstetrics and Gynaecology, Affiliated Hospital of Beihua University, Jilin, China
| | - Manhua Cui
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Shuangli Zhang
- Department of Obstetrics and Gynaecology, 307 Hospital of the people's Liberation Army, Beijing, China
| | - Jie He
- Department of Obstetrics and Gynaecology, Affiliated Hospital of Beihua University, Jilin, China
| | - Li Song
- Department of Obstetrics and Gynaecology, Affiliated Hospital of Beihua University, Jilin, China
| | - Ying Chen
- Department of Obstetrics and Gynaecology, Affiliated Hospital of Beihua University, Jilin, China
| |
Collapse
|