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Grützmann K, Kraft T, Meinhardt M, Meier F, Westphal D, Seifert M. Network-based analysis of heterogeneous patient-matched brain and extracranial melanoma metastasis pairs reveals three homogeneous subgroups. Comput Struct Biotechnol J 2024; 23:1036-1050. [PMID: 38464935 PMCID: PMC10920107 DOI: 10.1016/j.csbj.2024.02.013] [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: 11/06/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Melanoma, the deadliest form of skin cancer, can metastasize to different organs. Molecular differences between brain and extracranial melanoma metastases are poorly understood. Here, promoter methylation and gene expression of 11 heterogeneous patient-matched pairs of brain and extracranial metastases were analyzed using melanoma-specific gene regulatory networks learned from public transcriptome and methylome data followed by network-based impact propagation of patient-specific alterations. This innovative data analysis strategy allowed to predict potential impacts of patient-specific driver candidate genes on other genes and pathways. The patient-matched metastasis pairs clustered into three robust subgroups with specific downstream targets with known roles in cancer, including melanoma (SG1: RBM38, BCL11B, SG2: GATA3, FES, SG3: SLAMF6, PYCARD). Patient subgroups and ranking of target gene candidates were confirmed in a validation cohort. Summarizing, computational network-based impact analyses of heterogeneous metastasis pairs predicted individual regulatory differences in melanoma brain metastases, cumulating into three consistent subgroups with specific downstream target genes.
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Affiliation(s)
- Konrad Grützmann
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Theresa Kraft
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Matthias Meinhardt
- Department of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, University Hospital Carl Gustav Carus Dresden, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
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Shi K, Chen Y, Liu R, Fu X, Guo H, Gao T, Wang S, Dou L, Wang J, Wu Y, Yu J, Yu H. NFIC mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to represses malignant phenotype of non-small cell lung cancer cells. Cancer Cell Int 2024; 24:223. [PMID: 38943137 PMCID: PMC11212411 DOI: 10.1186/s12935-024-03414-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/22/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Multiple genetic and epigenetic regulatory mechanisms are crucial in the development and tumorigenesis process. Transcriptional regulation often involves intricate relationships and networks with post-transcriptional regulatory molecules, impacting the spatial and temporal expression of genes. However, the synergistic relationship between transcription factors and N6-methyladenosine (m6A) modification in regulating gene expression, as well as their influence on the mechanisms underlying the occurrence and progression of non-small cell lung cancer (NSCLC), requires further investigation. The present study aimed to investigate the synergistic relationship between transcription factors and m6A modification on NSCLC. METHODS The transcription factor NFIC and its potential genes was screened by analyzing publicly available datasets (ATAC-seq, DNase-seq, and RNA-seq). The association of NFIC and its potential target genes were validated through ChIP-qPCR and dual-luciferase reporter assays. Additionally, the roles of NFIC and its potential genes in NSCLC were detected in vitro and in vivo through silencing and overexpression assays. RESULTS Based on multi-omics data, the transcription factor NFIC was identified as a potential tumor suppressor of NSCLC. NFIC was significantly downregulated in both NSCLC tissues and cells, and when NFIC was overexpressed, the malignant phenotype and total m6A content of NSCLC cells was suppressed, while the PI3K/AKT pathway was inactivated. Additionally, we discovered that NFIC inhibits the expression of METTL3 by directly binding to its promoter region, and METTL3 regulates the expression of KAT2A, a histone acetyltransferase, by methylating the m6A site in the 3'UTR of KAT2A mRNA in NSCLC cells. Intriguingly, NFIC was also found to negatively regulate the expression of KAT2A by directly binding to its promoter region. CONCLUSIONS Our findings demonstrated that NFIC suppresses the malignant phenotype of NSCLC cells by regulating gene expression at both the transcriptional and post-transcriptional levels. A deeper comprehension of the genetic and epigenetic regulatory mechanisms in tumorigenesis would be beneficial for the development of personalized treatment strategies.
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Affiliation(s)
- Kesong Shi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yani Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Ruihua Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Hua Guo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Tian Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Shu Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Jiemin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Jiale Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China.
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Zhang Z, Fang P, Zhu J, Sun G. ZNF623 contributes to breast carcinoma progress by recruiting CtBP1 to regulate NF-κB pathway. Biochem Biophys Res Commun 2024; 728:150314. [PMID: 38959528 DOI: 10.1016/j.bbrc.2024.150314] [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: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Breast cancer ranks among the most prevalent tumor types worldwide. Copy number amplification of chromosome 8q24 is frequently detected in breast cancer. ZNF623 is a relatively unexplored gene mapped to 8q24. Here, we explore the expression profile, prognostic significance, and biological action of ZNF623 in breast carcinogenesis. METHODS To evaluate the mRNA expression pattern and prognostic relevance of ZNF623 across different cancer types, we conducted bioinformatic analyses. The expression of the gene was suppressed using ZNF623 shRNAs/siRNAs and augmented through transfection with plasmids containing ZNF623 cDNA. Cell viability assay, clonogenic assay, and transwell migration assay were utilized to assess the proliferation, viability, and invasion capacity of breast cancer cell lines. Luciferase reporter assay served as a pivotal tool to ascertain the transcriptional activity of ZNF623. IP-MS and co-IP were employed to validate that ZNF623 interacted with CtBP1. ChIP analysis and ChIP-qPCR were conducted to assess the genes targeted by ZNF623/CtBP1 complex. Flow cytometry was conducted to evaluate the phosphorylation status of p65. RESULTS ZNF623 expression was notably elevated in breast cancer (BC). Prognostic analysis indicated higher expression of ZNF623 indicated worse survival. Functional experiments discovered that the upregulation of ZNF623 significantly enhanced both the proliferative and migratory capacities of breast cancer cells. Luciferase reporter assay indicated that ZNF623 was a transcription repressor. Immunoprecipitation coupled mass spectrometry analysis revealed a physical association between ZNF623 and CtBP1 in the interaction group. The conjoint analysis of ChIP-seq and TCGA DEG analysis revealed that the ZNF623/CtBP1 complex repressed a series of genes, such as negative regulation of the NF-kappaB signaling pathway. Flow cytometry analysis discovered that knockdown of ZNF623 decreased the phosphorylation level of p65, indicating that ZNF623 could regulate the activity of the NF-κB pathway. CONCLUSION ZNF623 predicts poor prognosis of BC and enhances breast cancer growth and metastasis. By recruiting CtBP1, ZNF623 could suppress NF-κB inhibitors, including COMMD1, NFKBIL1, PYCARD, and BRMS1, expression from the transcription level.
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Affiliation(s)
- Zihan Zhang
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China; Beijing Clinical Research Institute, Beijing, 100050, China
| | - Peiyang Fang
- Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jinging Zhu
- Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Guangyong Sun
- Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China; Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China.
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Shin Y, Kim S, An W. Promoter hypermethylation as a novel regulator of ANO1 expression and function in prostate cancer bone metastasis. Sci Rep 2024; 14:11595. [PMID: 38773164 PMCID: PMC11109272 DOI: 10.1038/s41598-024-62478-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Despite growing evidence implicating the calcium-activated chloride channel anoctamin1 (ANO1) in cancer metastasis, its direct impact on the metastatic potential of prostate cancer and the possible significance of epigenetic alteration in this process are not fully understood. Here, we show that ANO1 is minimally expressed in LNCap and DU145 prostate cancer cell lines with low metastatic potential but overexpressed in high metastatic PC3 prostate cancer cell line. The treatment of LNCap and DU145 cells with DNMT inhibitor 5-aza-2'-deoxycytidine (5-Aza-CdR) potentiates ANO1 expression, suggesting that DNA methylation is one of the mechanisms controlling ANO1 expression. Consistent with this notion, hypermethylation was detected at the CpG island of ANO1 promoter region in LNCap and DU145 cells, and 5-Aza-CdR treatment resulted in a drastic demethylation at promoter CpG methylation sites. Upon 5-Aza-CdR treatment, metastatic indexes, such as cell motility, invasion, and metastasis-related gene expression, were significantly altered in LNCap and DU145 cells. These 5-Aza-CdR-induced metastatic hallmarks were, however, almost completely ablated by stable knockdown of ANO1. These in vitro discoveries were further supported by our in vivo observation that ANO1 expression in xenograft mouse models enhances the metastatic dissemination of prostate cancer cells into tibial bone and the development of osteolytic lesions. Collectively, our results help elucidate the critical role of ANO1 expression in prostate cancer bone metastases, which is epigenetically modulated by promoter CpG methylation.
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Affiliation(s)
- Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Sungmin Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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Karati D, Mukherjee S, Roy S. Deciphering the molecular mechanistic paths describing the chemotherapeutic potential and epigenetic regulation of curcumin in lung cancer: a mini review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2715-2725. [PMID: 37982888 DOI: 10.1007/s00210-023-02838-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
In an uncontrolled inflammatory environment, the complex process of lung carcinogenesis occurs. Lung cancer remains the leading cause of cancer-related mortality worldwide. The average 5-year survival rate is still low despite significant advancements in our knowledge of lung carcinogenesis and the development of innovative therapies in recent decades. Research on adjuvant treatment, lung carcinogenesis pathways, and possible prognostic indicators has to be refocused using an innovative approach. The majority of lung cancers are discovered at an advanced stage when there is little chance of recovery. It has grown in popularity in recent years to supplement already available chemotherapeutic therapies with adjuvant herbal medications, which may lessen toxicity and adverse effects without sacrificing therapeutic efficiency. One such prospective contender is curcumin. In-depth research has been done on curcumin as a multi-target anti-tumor and anti-inflammatory molecule. A pharmacologically active polyphenol produced from turmeric is called curcumin. Over the past few decades, curcumin's therapeutic potential has been thoroughly studied, and data indicate that curcumin may play a part in a variety of biological processes, most notably its potent anticancer activity. Being a pleiotropic chemical, curcumin regulates a variety of molecules that are key players in many cell signaling pathways. It has been shown to stifle transformation, restrain proliferation, and trigger apoptosis. Curcumin can reduce the development of non-small cell LC by downregulating Circular RNA hsa_circ_0007580, which in turn controls the expression of integrin subunit beta 1 by adsorbing miR-384. Nevertheless, despite all these advantages, curcumin's effectiveness is still restricted because of its weak bioavailability, poor absorption within the systemic circulation, and quick removal from the body. In an effort to overcome these constraints, scientists from all around the world are working to develop a synthetic and improved curcuminoid by appropriately altering the parent skeleton structurally. These curcuminoids will simultaneously improve the physicochemical properties and efficacy. This review presents evidence from the most recent clinical trials coupled with the molecular mechanisms of curcumin in LC.
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Affiliation(s)
- Dipanjan Karati
- Department of Pharmaceutical Technology, School of Pharmacy, Techno India University, Kolkata, 700091, West Bengal, India
| | - Swarupananda Mukherjee
- Department of Pharmaceutical Technology, NSHM Knowledge Campus, Kolkata, 124 B.L. Saha Road, Kolkata, West Bengal, 700053, India
| | - Souvik Roy
- Department of Pharmaceutical Technology, NSHM Knowledge Campus, Kolkata, 124 B.L. Saha Road, Kolkata, West Bengal, 700053, India.
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Herst P, Carson G, Lewthwaite D, Eccles D, Schmidt A, Wilson A, Grasso C, O’Sullivan D, Neuzil J, McConnell M, Berridge M. Residual OXPHOS is required to drive primary and metastatic lung tumours in an orthotopic breast cancer model. Front Oncol 2024; 14:1362786. [PMID: 38751813 PMCID: PMC11094293 DOI: 10.3389/fonc.2024.1362786] [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: 12/29/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
Background Fast adaptation of glycolytic and mitochondrial energy pathways to changes in the tumour microenvironment is a hallmark of cancer. Purely glycolytic ρ0 tumour cells do not form primary tumours unless they acquire healthy mitochondria from their micro-environment. Here we explored the effects of severely compromised respiration on the metastatic capability of 4T1 mouse breast cancer cells. Methods 4T1 cell lines with different levels of respiratory capacity were generated; the Seahorse extracellular flux analyser was used to evaluate oxygen consumption rates, fluorescent confocal microscopy to assess the number of SYBR gold-stained mitochondrial DNA nucleoids, and the presence of the ATP5B protein in the cytoplasm and fluorescent in situ nuclear hybridization was used to establish ploidy. MinION nanopore RNA sequence analysis was used to compare mitochondrial DNA transcription between cell lines. Orthotopic injection was used to determine the ability of cells to metastasize to the lungs of female Balb/c mice. Results OXPHOS-deficient ATP5B-KO3.1 cells did not generate primary tumours. Severely OXPHOS compromised ρ0D5 cells generated both primary tumours and lung metastases. Cells generated from lung metastasis of both OXPHOS-competent and OXPHOS-compromised cells formed primary tumours but no metastases when re-injected into mice. OXPHOS-compromised cells significantly increased their mtDNA content, but this did not result in increased OXPHOS capacity, which was not due to decreased mtDNA transcription. Gene set enrichment analysis suggests that certain cells derived from lung metastases downregulate their epithelial-to-mesenchymal related pathways. Conclusion In summary, OXPHOS is required for tumorigenesis in this orthotopic mouse breast cancer model but even very low levels of OXPHOS are sufficient to generate both primary tumours and lung metastases.
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Affiliation(s)
- Patries Herst
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
- Department of Radiation Therapy, University of Otago, Wellington, New Zealand
| | - Georgia Carson
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Danielle Lewthwaite
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
- School of Biological Sciences , Victoria University of Wellington, Wellington, New Zealand
| | - David Eccles
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Alfonso Schmidt
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Andrew Wilson
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carole Grasso
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - David O’Sullivan
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Jiri Neuzil
- Institute of Biotechnology of the Czech Academy of Sciences, Prague-West, Czechia
- School of Pharmacy and Medical Science, Griffith University, Southport, QLD, Australia
| | - Melanie McConnell
- School of Biological Sciences , Victoria University of Wellington, Wellington, New Zealand
| | - Michael Berridge
- Department of Cancer Cell Biology, Malaghan Institute of Medical Research, Wellington, New Zealand
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Papadaki S, Piperi C. Impact of Histone Lysine Methyltransferase SUV4-20H2 on Cancer Onset and Progression with Therapeutic Potential. Int J Mol Sci 2024; 25:2498. [PMID: 38473745 DOI: 10.3390/ijms25052498] [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: 01/26/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Histone lysine methyltransferase SUV4-20H2, a member of the suppressor of variegation 4-20 homolog (SUV4-20) family, has a critical impact on the regulation of chromatin structure and gene expression. This methyltransferase establishes the trimethylation of histone H4 lysine 20 (H4K20me3), a repressive histone mark that affects several cellular processes. Deregulated SUV4-20H2 activity has been associated with altered chromatin dynamics, leading to the misregulation of key genes involved in cell cycle control, apoptosis and DNA repair. Emerging research evidence indicates that SUV4-20H2 acts as a potential epigenetic modifier, contributing to the development and progression of several malignancies, including breast, colon and lung cancer, as well as renal, hepatocellular and pancreatic cancer. Understanding the molecular mechanisms that underlie SUV4-20H2-mediated effects on chromatin structure and gene expression may provide valuable insights into novel therapeutic strategies for targeting epigenetic alterations in cancer. Herein, we discuss structural and functional aspects of SUV4-20H2 in cancer onset, progression and prognosis, along with current targeting options.
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Affiliation(s)
- Stela Papadaki
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece
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Maurya SK, Rehman AU, Zaidi MAA, Khan P, Gautam SK, Santamaria-Barria JA, Siddiqui JA, Batra SK, Nasser MW. Epigenetic alterations fuel brain metastasis via regulating inflammatory cascade. Semin Cell Dev Biol 2024; 154:261-274. [PMID: 36379848 PMCID: PMC10198579 DOI: 10.1016/j.semcdb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Brain metastasis (BrM) is a major threat to the survival of melanoma, breast, and lung cancer patients. Circulating tumor cells (CTCs) cross the blood-brain barrier (BBB) and sustain in the brain microenvironment. Genetic mutations and epigenetic modifications have been found to be critical in controlling key aspects of cancer metastasis. Metastasizing cells confront inflammation and gradually adapt in the unique brain microenvironment. Currently, it is one of the major areas that has gained momentum. Researchers are interested in the factors that modulate neuroinflammation during BrM. We review here various epigenetic factors and mechanisms modulating neuroinflammation and how this helps CTCs to adapt and survive in the brain microenvironment. Since epigenetic changes could be modulated by targeting enzymes such as histone/DNA methyltransferase, deacetylases, acetyltransferases, and demethylases, we also summarize our current understanding of potential drugs targeting various aspects of epigenetic regulation in BrM.
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Affiliation(s)
- Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Mohd Ali Abbas Zaidi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Shailendra K Gautam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | | | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA.
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Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024; 5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as a prime target in the discovery of novel therapeutics. Our review delves into the complexities of epigenetic regulation, exploring its profound effects on tumor initiation, metastatic behavior, metabolic pathways, and the tumor microenvironment. We place a particular emphasis on the dysregulation at each level of epigenetic modulation, including but not limited to, the aberrations in enzymes responsible for DNA methylation and histone modification, subunit loss or fusions in chromatin remodeling complexes, and the disturbances in higher-order chromatin structure. Finally, we also evaluate therapeutic approaches that leverage the growing understanding of chromatin dysregulation, offering new avenues for cancer treatment.
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Affiliation(s)
- Minzhi Gu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Bo Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yuan Fang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Jie Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiaohong Liu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xing Wang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Feihan Zhou
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Ruiling Xiao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiyuan Luo
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Lei You
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yupei Zhao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
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Amin R, Ha NH, Qiu T, Holewinski R, Lam KC, Lopès A, Liu H, Tran AD, Lee MP, Gamage ST, Andresson T, Goldszmid RS, Meier JL, Hunter KW. Loss of NAT10 disrupts enhancer organization via p300 mislocalization and suppresses transcription of genes necessary for metastasis progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577116. [PMID: 38410432 PMCID: PMC10896336 DOI: 10.1101/2024.01.24.577116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Acetylation of protein and RNA represent a critical event for development and cancer progression. NAT10 is the only known RNA acetylase that catalyzes the N4-actylcytidine (ac4C) modification of RNAs. Here, we show that the loss of NAT10 significantly decreases lung metastasis in allograft and genetically engineered mouse models of breast cancer. NAT10 interacts with a mechanosensitive, metastasis susceptibility protein complex at the nuclear pore. In addition to its canonical role in RNA acetylation, we find that NAT10 interacts with p300 at gene enhancers. NAT10 loss is associated with p300 mislocalization into heterochromatin regions. NAT10 depletion disrupts enhancer organization, leading to alteration of gene transcription necessary for metastatic progression, including reduced myeloid cell-recruiting chemokines that results in a less metastasis-prone tumor microenvironment. Our study uncovers a distinct role of NAT10 in enhancer organization of metastatic tumor cells and suggests its involvement in the tumor-immune crosstalk dictating metastatic outcomes.
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11
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Ajithkumar P, Vasantharajan SS, Pattison S, McCall JL, Rodger EJ, Chatterjee A. Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis. Int J Mol Sci 2024; 25:874. [PMID: 38255946 PMCID: PMC10815915 DOI: 10.3390/ijms25020874] [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: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Metastatic progression is a complex, multistep process and the leading cause of cancer mortality. There is growing evidence that emphasises the significance of epigenetic modification, specifically DNA methylation and histone modifications, in influencing colorectal (CRC) metastasis. Epigenetic modifications influence the expression of genes involved in various cellular processes, including the pathways associated with metastasis. These modifications could contribute to metastatic progression by enhancing oncogenes and silencing tumour suppressor genes. Moreover, specific epigenetic alterations enable cancer cells to acquire invasive and metastatic characteristics by altering cell adhesion, migration, and invasion-related pathways. Exploring the involvement of DNA methylation and histone modification is crucial for identifying biomarkers that impact cancer prediction for metastasis in CRC. This review provides a summary of the potential epigenetic biomarkers associated with metastasis in CRC, particularly DNA methylation and histone modifications, and examines the pathways associated with these biomarkers.
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Affiliation(s)
- Priyadarshana Ajithkumar
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sai Shyam Vasantharajan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand; (P.A.)
- School of Health Sciences and Technology, UPES University, Dehradun 248007, India
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12
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Kervarrec T, Pissaloux D, Tirode F, de la Fouchardière A, Sohier P, Frouin E, Hamard A, Houben R, Schrama D, Barlier A, Cribier B, Battistella M, Macagno N. Gene fusions in poroma, porocarcinoma and related adnexal skin tumours: An update. Histopathology 2024; 84:266-278. [PMID: 37609771 DOI: 10.1111/his.15023] [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: 06/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023]
Abstract
Poroma is a benign sweat gland tumour showing morphological features recapitulating the superficial portion of the eccrine sweat coil. A subset of poromas may transform into porocarcinoma, its malignant counterpart. Poroma and porocarcinoma are characterised by recurrent gene fusions involving YAP1, a transcriptional co-activator, which is controlled by the Hippo signalling pathway. The fusion genes frequently involve MAML2 and NUTM1, which are also rearranged in other cutaneous and extracutaneous neoplasms. We aimed to review the clinical, morphological and molecular features of this category of adnexal neoplasms with a special focus upon emerging differential diagnoses, and discuss how their systematic molecular characterisation may contribute to a standardisation of diagnosis, more accurate classification and, ultimately, refinement of their prognosis and therapeutic modalities.
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Affiliation(s)
- Thibault Kervarrec
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Department of Pathology, University Hospital of Tours, Tours, France
- 'Biologie des infections à polyomavirus' Team, UMR1282 INRAE, University of Tours, Tours, France
| | | | - Franck Tirode
- Department of Biopathology, Center Léon Bérard, Lyon, France
- Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée, University of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Arnaud de la Fouchardière
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Department of Biopathology, Center Léon Bérard, Lyon, France
- Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée, University of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Pierre Sohier
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Department of Pathology, Hôpital Cochin, AP-HP, AP-HP Centre - Université Paris Cité, Paris, France
- Faculté de Médecine, University Paris Cité, Paris, France
| | - Eric Frouin
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Department of Pathology, University Hospital of Poitiers, University of Poitiers, LITEC, Poitiers, France
| | - Aymeric Hamard
- Department of Pathology, University Hospital of Tours, Tours, France
| | - Roland Houben
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Anne Barlier
- Aix-Marseille Univ, INSERM, MMG, U1251, Marmara Institute, Marseille, France
- Laboratory of Molecular Biology, La Conception Hospital, Marseille, France
| | - Bernard Cribier
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Clinique Dermatologique, Hôpital Civil, Hôpitaux Universitaires, Université de Strasbourg, Strasbourg, France
| | - Maxime Battistella
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Department of Pathology, Hospital Saint-Louis, AP-HP, Université Paris Cité, INSERM U976, Paris, France
| | - Nicolas Macagno
- CARADERM, French Network of Rare Cutaneous Cancer, Lille, France
- Aix-Marseille Univ, INSERM, MMG, U1251, Marmara Institute, Marseille, France
- Department of Pathology, APHM, Timone University Hospital, Marseille, France
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13
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Pascual G, Majem B, Benitah SA. Targeting lipid metabolism in cancer metastasis. Biochim Biophys Acta Rev Cancer 2024; 1879:189051. [PMID: 38101461 DOI: 10.1016/j.bbcan.2023.189051] [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: 08/06/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
This review delves into the most recent research on the metabolic adaptability of cancer cells and examines how their metabolic functions can impact their progression into metastatic forms. We emphasize the growing significance of lipid metabolism and dietary lipids within the tumor microenvironment, underscoring their influence on tumor progression. Additionally, we present an outline of the interplay between metabolic processes and the epigenome of cancer cells, underscoring the importance regarding the metastatic process. Lastly, we examine the potential of targeting metabolism as a therapeutic approach in combating cancer progression, shedding light on innovative drugs/targets currently undergoing preclinical evaluation.
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Affiliation(s)
- Gloria Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Blanca Majem
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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14
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Wang Y, Wang H, Shao W, Chen Y, Gui Y, Hu C, Yi X, Huang L, Li S, Wang D. Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0276. [PMID: 38062748 PMCID: PMC10875281 DOI: 10.20892/j.issn.2095-3941.2023.0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/26/2023] [Indexed: 02/16/2024] Open
Abstract
OBJECTIVE Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression; however, the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain elusive. It is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic targets. METHODS We employed high-throughput sequencing-based high-throughput screening (HTS2) to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic regulators. Then, bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast cancer. RESULTS Utilizing these gene expression signatures, we classified the epigenetic regulators into five distinct clusters, each characterized by specific functions. We discovered functional similarities between BAZ2B and SETMAR, as well as CLOCK and CBX3. Moreover, we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene regulation. Notably, we constructed an epigenetic regulatory network based on the gene expression signatures, which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast cancer. CONCLUSIONS Our work deciphered the extensive regulation among hundreds of epigenetic regulators. The identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Yumei Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Haiyan Wang
- Department of Pathology, School of Medicine, Qinghai University, Xining 810001, China
| | - Wei Shao
- Omics Biosciences Inc, Beijing 100871, China
| | - Yuhui Chen
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yu Gui
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaohong Yi
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lijun Huang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Dong Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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15
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Hu Y, Shen F, Yang X, Han T, Long Z, Wen J, Huang J, Shen J, Guo Q. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity. Clin Epigenetics 2023; 15:161. [PMID: 37821906 PMCID: PMC10568863 DOI: 10.1186/s13148-023-01574-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as the fundamental drivers of carcinogenesis. However, recent research has shed light on the crucial role of epigenomic alterations in various cell types present within the tumor microenvironment, suggesting their potential contribution to tumor formation and progression. Despite these significant findings, the progress in understanding the epigenetic mechanisms regulating tumor heterogeneity has been impeded over the past few years due to the lack of appropriate technical tools and methodologies. RESULTS The emergence of single-cell sequencing has enhanced our understanding of the epigenetic mechanisms governing tumor heterogeneity by revealing the distinct epigenetic layers of individual cells (chromatin accessibility, DNA/RNA methylation, histone modifications, nucleosome localization) and the diverse omics (transcriptomics, genomics, multi-omics) at the single-cell level. These technologies provide us with new insights into the molecular basis of intratumoral heterogeneity and help uncover key molecular events and driving mechanisms in tumor development. CONCLUSION This paper provides a comprehensive review of the emerging analytical and experimental approaches of single-cell sequencing in various omics, focusing specifically on epigenomics. These approaches have the potential to capture and integrate multiple dimensions of individual cancer cells, thereby revealing tumor heterogeneity and epigenetic features. Additionally, this paper outlines the future trends of these technologies and their current technical limitations.
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Affiliation(s)
- Yuhua Hu
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Feng Shen
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Department of Neurosurgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Xi Yang
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Tingting Han
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Zhuowen Long
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Jiale Wen
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Junxing Huang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Jiangfeng Shen
- Department of Thoracic Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Qing Guo
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
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16
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Shi K, Sa R, Dou L, Wu Y, Dong Z, Fu X, Yu H. METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma. Clin Epigenetics 2023; 15:153. [PMID: 37742030 PMCID: PMC10517543 DOI: 10.1186/s13148-023-01568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Multiple genetic and epigenetic regulatory mechanisms play a vital role in tumorigenesis and development. Understanding the interplay between different epigenetic modifications and its contribution to transcriptional regulation in cancer is essential for precision medicine. Here, we aimed to investigate the interplay between N6-methyladenosine (m6A) modifications and histone modifications in lung adenocarcinoma (LUAD). RESULTS Based on the data from public databases, including chromatin property data (ATAC-seq, DNase-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), and gene expression data (RNA-seq), a m6A-related differentially expressed gene nerve growth factor inducible (VGF) was identified between LUAD tissues and normal lung tissues. VGF was significantly highly expressed in LUAD tissues and cells, and was associated with a worse prognosis for LUAD, silencing of VGF inhibited the malignant phenotype of LUAD cells by inactivating the PI3K/AKT/mTOR pathway. Through the weighted correlation network analysis (WGCNA) and integration of TCGA-LUAD RNA-seq and m6A methyltransferase METTL3-knockdown RNA-seq data, a significant positive correlation between METTL3 and VGF was observed. By using the MeRIP-qPCR and dual-luciferase reporter assays, we demonstrated that METTL3 knockdown decreased m6A modification level of VGF coding sequences in LUAD cells, the colorimetric m6A quantification assay also showed that METTL3 knockdown significantly decreased global m6A modification level in LUAD cells. Interestingly, we found that METTL3 knockdown also reduced VGF expression by increasing H3K36me3 modification at the VGF promoter. Further research revealed that METTL3 knockdown upregulated the expression of histone methylase SETD2, the major H3K36me3 methyltransferase, by methylating the m6A site in the 3'UTR of SETD2 mRNA in LUAD cells. CONCLUSIONS Overall, our results reveal that the expression of VGF in LUAD cells is regulated spatio-temporally by METTL3 through both transcriptional (via histone modifications) and post-transcriptional (via m6A modifications) mechanisms. The synergistic effect of these multiple epigenetic mechanisms provides new opportunities for the diagnosis and precision treatment of tumors.
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Affiliation(s)
- Kesong Shi
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Rula Sa
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Zhiqiang Dong
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China.
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Salimy S, Lanjanian H, Abbasi K, Salimi M, Najafi A, Tapak L, Masoudi-Nejad A. A deep learning-based framework for predicting survival-associated groups in colon cancer by integrating multi-omics and clinical data. Heliyon 2023; 9:e17653. [PMID: 37455955 PMCID: PMC10344710 DOI: 10.1016/j.heliyon.2023.e17653] [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: 04/30/2023] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Precise prognostic classification of patients and identifying survival subgroups and their associated genes can be important clinical references when designing treatment strategies for cancer patients. Multi-omics and data integration techniques are powerful tools to achieve this goal. This study aimed to introduce a machine learning method to integrate three types of biological data, and investigate the performance of two other methods, in identifying the survival dependency of patients. The data included TCGA RNA-seq gene expression, DNA methylation, and clinical data from 368 patients with colon cancer also we use an independent external validation data set, containing 232 samples. Three methods including, hyper-parameter optimized autoencoders (HPOAE), normal autoencoder, and penalized principal component analysis (PPCA) were used for simultaneous data integration and estimation under a COX hazards model. The HPOAE was thought to outperform other methods. The HPOAE had the Log Rank Mantel-Cox value of 14.27 ± 2, and a Breslow-Generalized Wilcoxon value of 13.13 ± 1. Ten miRNA, 11 methylated genes, and 28 mRNA all by (importance of marginal cutoff > 0.95) were identified. The study demonstrated that hsa-miR-485-5p targets both ZMYM1 and tp53, the latter of which has been previously associated with cancer in numerous studies. Furthermore, compared to other methods, the HPOAE exhibited a greater capacity for identifying survival subgroups and the genes associated with them in patients with colon cancer. However, all of the results were obtained by computational methods, and clinical and experimental studies are needed to validate these results.
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Affiliation(s)
- Siamak Salimy
- Laboratory of System Biology and Bioinformatics (LBB), Department of Bioinformatics, University of Tehran, Kish International Campus, Kish, Iran
| | - Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Karim Abbasi
- Laboratory of System Biology, Bioinformatics & Artificial Intelligent in Medicine (LBBai), Faculty of Mathematics and Computer Science, Kharazmi University, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Leili Tapak
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Department of Bioinformatics, University of Tehran, Kish International Campus, Kish, Iran
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18
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Rodger EJ, Gimenez G, Ajithkumar P, Stockwell PA, Almomani S, Bowden SA, Leichter AL, Ahn A, Pattison S, McCall JL, Schmeier S, Frizelle FA, Eccles MR, Purcell RV, Chatterjee A. An epigenetic signature of advanced colorectal cancer metastasis. iScience 2023; 26:106986. [PMID: 37378317 PMCID: PMC10291510 DOI: 10.1016/j.isci.2023.106986] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/12/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of morbidity and mortality worldwide. The majority of CRC deaths are caused by tumor metastasis, even following treatment. There is strong evidence for epigenetic changes, such as DNA methylation, accompanying CRC metastasis and poorer patient survival. Earlier detection and a better understanding of molecular drivers for CRC metastasis are of critical clinical importance. Here, we identify a signature of advanced CRC metastasis by performing whole genome-scale DNA methylation and full transcriptome analyses of paired primary cancers and liver metastases from CRC patients. We observed striking methylation differences between primary and metastatic pairs. A subset of loci showed coordinated methylation-expression changes, suggesting these are potentially epigenetic drivers that control the expression of critical genes in the metastatic cascade. The identification of CRC epigenomic markers of metastasis has the potential to enable better outcome prediction and lead to the discovery of new therapeutic targets.
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Affiliation(s)
- Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Peter A. Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Suzan Almomani
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sarah A. Bowden
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Anna L. Leichter
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Antonio Ahn
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sharon Pattison
- Department of Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - John L. McCall
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Frank A. Frizelle
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rachel V. Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Honorary Professor, School of Health Sciences and Technology, UPES University, India
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19
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Kravitz CJ, Yan Q, Nguyen DX. Epigenetic markers and therapeutic targets for metastasis. Cancer Metastasis Rev 2023; 42:427-443. [PMID: 37286865 PMCID: PMC10595046 DOI: 10.1007/s10555-023-10109-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
The last few years have seen an increasing number of discoveries which collectively demonstrate that histone and DNA modifying enzyme modulate different stages of metastasis. Moreover, epigenomic alterations can now be measured at multiple scales of analysis and are detectable in human tumors or liquid biopsies. Malignant cell clones with a proclivity for relapse in certain organs may arise in the primary tumor as a consequence of epigenomic alterations which cause a loss in lineage integrity. These alterations may occur due to genetic aberrations acquired during tumor progression or concomitant to therapeutic response. Moreover, evolution of the stroma can also alter the epigenome of cancer cells. In this review, we highlight current knowledge with a particular emphasis on leveraging chromatin and DNA modifying mechanisms as biomarkers of disseminated disease and as therapeutic targets to treat metastatic cancers.
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Affiliation(s)
- Carolyn J Kravitz
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT, 06520, USA.
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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21
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Curcumin: An epigenetic regulator and its application in cancer. Biomed Pharmacother 2022; 156:113956. [DOI: 10.1016/j.biopha.2022.113956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
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22
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Barakeh DH, Alsolme E, Alqubaishi F, Almutairi A, Alhabeeb L, Al Abdulmohsen S, Almohsen SS, Alayed D, AlAnazi SR, AlZahrani M, Binowayn AM, AlOtaibi SS, Alkhureeb FA, Al Shakweer W, Al-Hindi H, Alassiri A, Robinson HA, Abedalthagafi M. Clinicopathologic and genomic characterizations of brain metastases using a comprehensive genomic panel. Front Med (Lausanne) 2022; 9:947456. [PMID: 36507516 PMCID: PMC9729258 DOI: 10.3389/fmed.2022.947456] [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: 05/18/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Central nervous system (CNS) metastasis is the most common brain tumor type in adults. Compared to their primary tumors, these metastases undergo a variety of genetic changes to be able to survive and thrive in the complex tissue microenvironment of the brain. In clinical settings, the majority of traditional chemotherapies have shown limited efficacy against CNS metastases. However, the discovery of potential driver mutations, and the development of drugs specifically targeting affected signaling pathways, could change the treatment landscape of CNS metastasis. Genetic studies of brain tumors have so far focused mainly on common cancers in western populations. In this study, we performed Next Generation Sequencing (NGS) on 50 pairs of primary tumors, including but not limited to colorectal, breast, renal and thyroid tumors, along with their brain metastatic tumor tissue counterparts, from three different local tertiary centers in Saudi Arabia. We identified potentially clinically relevant mutations in brain metastases that were not detected in corresponding primary tumors, including mutations in the PI3K, CDK, and MAPK pathways. These data highlight the differences between primary cancers and brain metastases and the importance of acquiring and analyzing brain metastatic samples for further clinical management.
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Affiliation(s)
- Duna H. Barakeh
- Department of Pathology, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia,Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ebtehal Alsolme
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fatimah Alqubaishi
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Lamees Alhabeeb
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia,Department of Pathology, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Shahd S. Almohsen
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Doaa Alayed
- Department of Pathology, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | | | - Malak AlZahrani
- Department of Pathology, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | | | - Sarah S. AlOtaibi
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Wafa Al Shakweer
- Department of Pathology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Alassiri
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | - Malak Abedalthagafi
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia,Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA, United States,*Correspondence: Malak Abedalthagafi,
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23
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曾 银, 樊 嵘. [PCGF1 is highly expressed in rectal adenocarcinoma and silencing PCGF1 inhibits proliferation of rectal adenocarcinoma cells in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:1296-1302. [PMID: 36210701 PMCID: PMC9550553 DOI: 10.12122/j.issn.1673-4254.2022.09.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To investigate the expression of PCGF1 in rectal adenocarcinoma (READ) and the effect of PCGF1 silencing on proliferation READ cells in vitro. METHODS The UALCAN and ENCORI online databases were used to analyze the expression level of PCGF1 in READ tissues and normal tissues and its association with the clinicopathological parameters and survival outcomes of patients with READ. The expression levels of PCGF1 were detected in two READ cell lines and a normal rectal epithelial cell line (HcoEpiC cells) using qPCR and Western blotting. Lentiviral vectors were used to construct PCGF1-overexpressing and PCGF1-silenced cell lines, and the proliferative activity of the cells was assessed using CCK-8 assay. The effect of PCGF1 silencing on tumor proliferation in vivo was also evaluated by observing tumorigenicity of the cells in nude mice. RESULTS PCGF1 was highly expressed in READ tissue (P < 0.001), and its expression levels was correlated with READ stage, differentiation and lymph node metastasis (P < 0.001). A high PCGF1 expression level was associated with a poor survival outcome of READ patients (P < 0.05). In SW837 and SW1463 cells, PCGF1 silencing significantly lowered the proliferative activity of the cells both in vitro (P < 0.05) and in nude mice (P < 0.01). CONCLUSION PCGF1 is highly expressed in READ tissue and may potentially serve as a prognostic biomarker as well as a therapeutic target for READ.
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Affiliation(s)
- 银珍 曾
- 南方医科大学南方医院麻醉科,广东 广州 510515Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 嵘 樊
- 天津市西青医院中心实验室,天津 300380Central Laboratory, Tianjin Xiqing Hospital, Tianjin 300380, China
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24
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Wan L, Deng M, Zhang H. SR Splicing Factors Promote Cancer via Multiple Regulatory Mechanisms. Genes (Basel) 2022; 13:1659. [PMID: 36140826 PMCID: PMC9498594 DOI: 10.3390/genes13091659] [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: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Substantial emerging evidence supports that dysregulated RNA metabolism is associated with tumor initiation and development. Serine/Arginine-Rich proteins (SR) are a number of ultraconserved and structurally related proteins that contain a characteristic RS domain rich in arginine and serine residues. SR proteins perform a critical role in spliceosome assembling and conformational transformation, contributing to precise alternative RNA splicing. Moreover, SR proteins have been reported to participate in multiple other RNA-processing-related mechanisms than RNA splicing, such as genome stability, RNA export, and translation. The dysregulation of SR proteins has been reported to contribute to tumorigenesis through multiple mechanisms. Here we reviewed the different biological roles of SR proteins and strategies for functional rectification of SR proteins that may serve as potential therapeutic approaches for cancer.
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Affiliation(s)
- Ledong Wan
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou 310058, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Min Deng
- Department of Pathology, First Peoples Hospital Fuyang, Hangzhou 311400, China
| | - Honghe Zhang
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou 310058, China
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25
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Cai WL, Chen JFY, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. eLife 2022; 11:e78163. [PMID: 36043466 PMCID: PMC9584608 DOI: 10.7554/elife.78163] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/24/2022] [Indexed: 12/26/2022] Open
Abstract
Metastatic breast cancer remains a major cause of cancer-related deaths in women, and there are few effective therapies against this advanced disease. Emerging evidence suggests that key steps of tumor progression and metastasis are controlled by reversible epigenetic mechanisms. Using an in vivo genetic screen, we identified WDR5 as an actionable epigenetic regulator that is required for metastatic progression in models of triple-negative breast cancer. We found that knockdown of WDR5 in breast cancer cells independently impaired their tumorigenic as well as metastatic capabilities. Mechanistically, WDR5 promotes cell growth by increasing ribosomal gene expression and translation efficiency in a KMT2-independent manner. Consistently, pharmacological inhibition or degradation of WDR5 impedes cellular translation rate and the clonogenic ability of breast cancer cells. Furthermore, a combination of WDR5 targeting with mTOR inhibitors leads to potent suppression of translation and proliferation of breast cancer cells. These results reveal novel therapeutic strategies to treat metastatic breast cancer.
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Affiliation(s)
- Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical CenterPittsburghUnited States
- Department of Pathology, Yale UniversityNew HavenUnited States
| | | | - Huacui Chen
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Emily Wingrove
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Sarah J Kurley
- Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Lok Hei Chan
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Meiling Zhang
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Anna Arnal-Estape
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
| | - Minghui Zhao
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Amer Balabaki
- Department of Pathology, Yale UniversityNew HavenUnited States
| | - Wenxue Li
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Ethan D Krop
- Department of Pathology, Yale UniversityNew HavenUnited States
- Department of Biosciences, Rice University,HoustonUnited States
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann ArborAnn ArborUnited States
- Department of Medicine, Department of Biochemistry and Molecular Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Yansheng Liu
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Cancer Biology Institute, Department of Pharmacology, Yale UniversityWest HavenUnited States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Thomas F Westbrook
- Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Don X Nguyen
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Stem Cell Center, Yale School of MedicineNew HavenUnited States
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine,New HavenUnited States
| | - Qin Yan
- Department of Pathology, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
- Yale Stem Cell Center, Yale School of MedicineNew HavenUnited States
- Yale Center for Immuno-Oncology, Yale School of MedicineNew HavenUnited States
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26
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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27
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Casado-Pelaez M, Bueno-Costa A, Esteller M. Single cell cancer epigenetics. Trends Cancer 2022; 8:820-838. [PMID: 35821003 DOI: 10.1016/j.trecan.2022.06.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/02/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Bulk sequencing methodologies have allowed us to make great progress in cancer research. Unfortunately, these techniques lack the resolution to fully unravel the epigenetic mechanisms that govern tumor heterogeneity. Consequently, many novel single cell-sequencing methodologies have been developed over the past decade, allowing us to explore the epigenetic components that regulate different aspects of cancer heterogeneity, namely: clonal heterogeneity, tumor microenvironment (TME), spatial organization, intratumoral differentiation programs, metastasis, and resistance mechanisms. In this review, we explore the different sequencing techniques that enable researchers to study different aspects of epigenetics (DNA methylation, chromatin accessibility, histone modifications, DNA-protein interactions, and chromatin 3D architecture) at the single cell level, their potential applications in cancer, and their current technical limitations.
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Affiliation(s)
- Marta Casado-Pelaez
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Alberto Bueno-Costa
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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28
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Liang Y, Zhang B, Xue Z, Ye X, Liang B. Magnetic Immunosensor Coupled to Enzymatic Signal for Determination of Genomic DNA Methylation. BIOSENSORS 2022; 12:bios12030162. [PMID: 35323432 PMCID: PMC8946087 DOI: 10.3390/bios12030162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/18/2022]
Abstract
Aberrations of genomic DNA methylation have been confirmed to be involved in the evolution of human cancer and have thus gained the potential to be depicted as biomarkers for cancer diagnostics and prognostic predictions, which implicates an urgent need for detection of total genomic DNA methylation. In this work, we suggested an assay for the quantification of global DNA methylation, utilizing methylation specific antibody (5mC) modified magnetic beads (MBs) for immunorecognition and affinity enrichment. Subsequently, the captured DNA on the surface of MBs interacted with the glucose oxidase-conjugated DNA antibody whose catalytic reaction product was engaged in electrochemical detection of the overall level of DNA methylation on a PB-doped screen-printed electrode. With 15 pg of input DNA, which, to our best knowledge, is the lowest required amount of DNA without sodium bisulfite treatment or amplification, this test strategy was able to perceive as low as 5% methylation level within 70 min including the preparation of anti-5mC-MBs. We believe this detection technique offers a promising option to detect global DNA methylation in both academic and clinical scenarios.
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Affiliation(s)
- Yitao Liang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Bin Zhang
- Sir Run-Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China;
| | - Zexin Xue
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Xuesong Ye
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Bo Liang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
- Correspondence:
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29
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Zhang M, Liu ZZ, Aoshima K, Cai WL, Sun H, Xu T, Zhang Y, An Y, Chen JF, Chan LH, Aoshima A, Lang SM, Tang Z, Che X, Li Y, Rutter SJ, Bossuyt V, Chen X, Morrow JS, Pusztai L, Rimm DL, Yin M, Yan Q. CECR2 drives breast cancer metastasis by promoting NF-κB signaling and macrophage-mediated immune suppression. Sci Transl Med 2022; 14:eabf5473. [PMID: 35108062 PMCID: PMC9003667 DOI: 10.1126/scitranslmed.abf5473] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metastasis is the major cause of cancer-related deaths due to the lack of effective therapies. Emerging evidence suggests that certain epigenetic and transcriptional regulators drive cancer metastasis and could be targeted for metastasis treatment. To identify epigenetic regulators of breast cancer metastasis, we profiled the transcriptomes of matched pairs of primary breast tumors and metastases from human patients. We found that distant metastases are more immune inert with increased M2 macrophages compared to their matched primary tumors. The acetyl-lysine reader, cat eye syndrome chromosome region candidate 2 (CECR2), was the top up-regulated epigenetic regulator in metastases associated with an increased abundance of M2 macrophages and worse metastasis-free survival. CECR2 was required for breast cancer metastasis in multiple mouse models, with more profound effect in the immunocompetent setting. Mechanistically, the nuclear factor κB (NF-κB) family member v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA) recruits CECR2 to increase chromatin accessibility and activate the expression of their target genes. These target genes include multiple metastasis-promoting genes, such as TNC, MMP2, and VEGFA, and cytokine genes CSF1 and CXCL1, which are critical for immunosuppression at metastatic sites. Consistent with these results, pharmacological inhibition of CECR2 bromodomain impeded NF-κB-mediated immune suppression by macrophages and inhibited breast cancer metastasis. These results reveal that targeting CECR2 may be a strategy to treat metastatic breast cancer.
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Affiliation(s)
- Meiling Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Z. Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Keisuke Aoshima
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Laboratory of Comparative Pathology, Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Wesley L. Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Hongyin Sun
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tianrui Xu
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yangyi Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongyan An
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jocelyn F. Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lok Hei Chan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Asako Aoshima
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhenwei Tang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xuanlin Che
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yao Li
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sara J. Rutter
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Veerle Bossuyt
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jon S. Morrow
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Breast Medical Oncology, Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - David. L. Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingzhu Yin
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520, USA
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