1
|
Ooki A, Osumi H, Yoshino K, Yamaguchi K. Potent therapeutic strategy in gastric cancer with microsatellite instability-high and/or deficient mismatch repair. Gastric Cancer 2024; 27:907-931. [PMID: 38922524 PMCID: PMC11335850 DOI: 10.1007/s10120-024-01523-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Gastric cancer (GC) is a common malignancy that presents challenges in patient care worldwide. The mismatch repair (MMR) system is a highly conserved DNA repair mechanism that protects genome integrity during replication. Deficient MMR (dMMR) results in an increased accumulation of genetic errors in microsatellite sequences, leading to the development of a microsatellite instability-high (MSI-H) phenotype. Most MSI-H/dMMR GCs arise sporadically, mainly due to MutL homolog 1 (MLH1) epigenetic silencing. Unlike microsatellite-stable (MSS)/proficient MMR (pMMR) GCs, MSI-H/dMMR GCs are relatively rare and represent a distinct subtype with genomic instability, a high somatic mutational burden, favorable immunogenicity, different responses to treatment, and prognosis. dMMR/MSI-H status is a robust predictive biomarker for treatment with immune checkpoint inhibitors (ICIs) due to high neoantigen load, prominent tumor-infiltrating lymphocytes, and programmed cell death ligand 1 (PD-L1) overexpression. However, a subset of MSI-H/dMMR GC patients does not benefit from immunotherapy, highlighting the need for further research into predictive biomarkers and resistance mechanisms. This review provides a comprehensive overview of the clinical, molecular, immunogenic, and therapeutic aspects of MSI-H/dMMR GC, with a focus on the impact of ICIs in immunotherapy and their potential as neoadjuvant therapies. Understanding the complexity and diversity of the molecular and immunological profiles of MSI-H/dMMR GC will drive the development of more effective therapeutic strategies and molecular targets for future precision medicine.
Collapse
Affiliation(s)
- Akira Ooki
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan.
| | - Hiroki Osumi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Koichiro Yoshino
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| |
Collapse
|
2
|
Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [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: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
Collapse
Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| |
Collapse
|
3
|
Li A, Li M, Wang J, Zhou J, Yang T, Fan M, Zhang K, Gao H, Ren H, Chen M. MECOM: a bioinformatics and experimentally identified marker for the diagnosis and prognosis of lung adenocarcinoma. Biomark Med 2024; 18:79-91. [PMID: 38440890 DOI: 10.2217/bmm-2023-0600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Objective: We aimed to explore the clinical value of MDS1 and EVI1 complex locus (MECOM) in lung adenocarcinoma (LUAD). Methods: Bioinformatics and experimental validation confirmed MECOM expression levels in LUAD. The value of MECOM was analyzed by receiver operating characteristic (ROC) curve and Cox regression analysis. Results: Serum MECOM levels were lower in LUAD and correlated with gender, TNM stage, tumor size, lymph node metastasis and distant metastasis. The ROC curve showed that the area under the curve of MECOM was 0.804 for LUAD and, of note, could reach 0.889 for advanced LUAD; specificity was up to 90%. Conclusion: MECOM may contribute to independently identifying LUAD patients, particularly in advanced stages.
Collapse
Affiliation(s)
- Anqi Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jing Wang
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
| | - Jiejun Zhou
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tian Yang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Fan
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kun Zhang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hengxing Gao
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hui Ren
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwei Chen
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
| |
Collapse
|
4
|
Di Donato M, Di Zazzo E, Salvati A, Sorrentino C, Giurato G, Fiore D, Proto MC, Rienzo M, Casamassimi A, Gazzerro P, Bifulco M, Castoria G, Weisz A, Nassa G, Abbondanza C. RIZ2 at the crossroad of the EGF/EGFR signaling in colorectal cancer. J Transl Med 2023; 21:736. [PMID: 37853459 PMCID: PMC10585774 DOI: 10.1186/s12967-023-04621-6] [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: 08/03/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most deadly and fourth most diagnosed cancer worldwide. Despite the progress in early diagnosis and advanced therapeutic options, CRC shows a poor prognosis with a 5 year survival rate of ~ 45%. PRDM2/RIZ, a member of PR/SET domain family (PRDM), expresses two main molecular variants, the PR-plus isoform (RIZ1) and the PR-minus (RIZ2). The imbalance in their expression levels in favor of RIZ2 is observed in many cancer types. The full length RIZ1 has been extensively investigated in several cancers where it acts as a tumor suppressor, whereas few studies have explored the RIZ2 oncogenic properties. PRDM2 is often target of frameshift mutations and aberrant DNA methylation in CRC. However, little is known about its role in CRC. METHODS We combined in-silico investigation of The Cancer Genome Atlas (TCGA) CRC datasets, cellular and molecular assays, transcriptome sequencing and functional annotation analysis to assess the role of RIZ2 in human CRC. RESULTS Our in-silico analysis on TCGA datasets confirmed that PRDM2 gene is frequently mutated and transcriptionally deregulated in CRC and revealed that a RIZ2 increase is highly correlated with a significant RIZ1 downregulation. Then, we assayed several CRC cell lines by qRT-PCR analysis for the main PRDM2 transcripts and selected DLD1 cell line, which showed the lowest RIZ2 levels. Therefore, we overexpressed RIZ2 in these cells to mimic TCGA datasets analysis results and consequently to assess the PRDM2/RIZ2 role in CRC. Data from RNA-seq disclosed that RIZ2 overexpression induced profound changes in CRC cell transcriptome via EGF pathway deregulation, suggesting that RIZ2 is involved in the EGF autocrine regulation of DLD1 cell behavior. Noteworthy, the forced RIZ2 expression increased cell viability, growth, colony formation, migration and organoid formation. These effects could be mediated by the release of high EGF levels by RIZ2 overexpressing DLD1 cells. CONCLUSIONS Our findings add novel insights on the putative RIZ2 tumor-promoting functions in CRC, although additional efforts are warranted to define the underlying molecular mechanism.
Collapse
Affiliation(s)
- Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
| | - Carmela Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | | | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| |
Collapse
|
5
|
Liu N, Zhang J, Chen W, Ma W, Wu T. The RNA methyltransferase METTL16 enhances cholangiocarcinoma growth through PRDM15-mediated FGFR4 expression. J Exp Clin Cancer Res 2023; 42:263. [PMID: 37817227 PMCID: PMC10566113 DOI: 10.1186/s13046-023-02844-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND RNA N6-Methyladenosine (m6A) modification is implicated in the progression of human cancers including cholangiocarcinoma (CCA). METTL16 is recently identified as a new RNA methyltransferase responsible for m6A modification, although the role of METTL16 in CCA has not yet been examined. The current study aims to investigate the effect and mechanism of the RNA methyltransferase METTL16 in CCA. METHODS The expression of METTL16 in CCA was examined by analyzing publicly available datasets or by IHC staining on tumor samples. siRNA or CRISPR/Cas9-mediated loss of function studies were performed in vitro and in vivo to investigate the oncogenic role of METTL16 in CCA. MeRIP-Seq was carried out to identify the downstream target of METTL16. ChIP-qPCR, immunoprecipitation, and immunoblots were used to explore the regulation mechanisms for METTL16 expression in CCA. RESULTS We observed that the expression of METTL16 was noticeably increased in human CCA tissues. Depletion of METTL16 significantly inhibited CCA cell proliferation and decreased tumor progression. PRDM15 was identified as a key target of METTL16 in CCA cells. Mechanistically, our data showed that METTL16 regulated PRDM15 protein expression via YTHDF1-dependent translation. Accordingly, we observed that restoration of PRDM15 expression could rescue the deficiency of CCA cell proliferation/colony formation induced by METTL16 depletion. Our subsequent analyses revealed that METTL16-PRDM15 signaling regulated the expression of FGFR4 in CCA cells. Specifically, we observed that PRDM15 protein was associated with the FGFR4 promoter to regulate its expression. Furthermore, we showed that the histone acetyltransferase p300 cooperated with the transcription factor YY1 to regulate METTL16 gene expression via histone H3 lysine 27 (H3K27) acetylation in CCA cells. CONCLUSIONS This study describes a novel METTL16-PRDM15-FGFR4 signaling axis which is crucial for CCA growth and may have important therapeutic implications. We showed that depletion of METTL16 significantly inhibited CCA cell proliferation and decreased tumor progression.
Collapse
Affiliation(s)
- Nianli Liu
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Jinqiang Zhang
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Weina Chen
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Avenue, SL-79, New Orleans, LA, 70112, USA.
| |
Collapse
|
6
|
Zhang S, Yao HF, Li H, Su T, Jiang SH, Wang H, Zhang ZG, Dong FY, Yang Q, Yang XM. Transglutaminases are oncogenic biomarkers in human cancers and therapeutic targeting of TGM2 blocks chemoresistance and macrophage infiltration in pancreatic cancer. Cell Oncol (Dordr) 2023; 46:1473-1492. [PMID: 37246171 DOI: 10.1007/s13402-023-00824-7] [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] [Accepted: 05/02/2023] [Indexed: 05/30/2023] Open
Abstract
PURPOSE Transglutaminases (TGs) are multifunctional enzymes exhibiting transglutaminase crosslinking, as well as atypical GTPase/ATPase and kinase activities. Here, we used an integrated comprehensive analysis to assess the genomic, transcriptomic and immunological landscapes of TGs across cancers. METHODS Gene expression and immune cell infiltration patterns across cancers were obtained from The Cancer Genome Atlas (TCGA) database and Gene Set Enrichment Analysis (GSEA) datasets. Western blotting, immunofluorescence staining, enzyme-linked immunosorbent assays, and orthotopic xenograft models were used to validate our database-derived results. RESULTS We found that the overall expression of TGs (designated as the TG score) is significantly upregulated in multiple cancers and related to a worse patient survival. The expression of TG family members can be regulated through multiple mechanisms at the genetic, epigenetic and transcriptional levels. The expression of transcription factors crucial for epithelial-to-mesenchymal transition (EMT) is commonly correlated with the TG score in many cancer types. Importantly, TGM2 expression displays a close connection with chemoresistance to a wide range of chemotherapeutic drugs. We found that TGM2 expression, F13A1 expression and the overall TG score were positively correlated with the infiltration of immune cells in all cancer types tested. Functional and clinical verification revealed that a higher TGM2 expression is linked with a worse patient survival, an increased IC50 value of gemcitabine, and a higher abundance of tumor-infiltrating macrophages in pancreatic cancer. Mechanistically, we found that increased C-C motif chemokine ligand 2 (CCL2) release mediated by TGM2 contributes to macrophage infiltration into the tumor microenvironment. CONCLUSIONS Our results reveal the relevance and molecular networks of TG genes in human cancers and highlight the importance of TGM2 in pancreatic cancer, which may provide promising directions for immunotherapy and for addressing chemoresistance.
Collapse
Affiliation(s)
- Shan Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hong-Fei Yao
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200217, People's Republic of China
| | - Hui Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Tong Su
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hao Wang
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 1800 Yuntai Road, Pudong District, Shanghai, 200123, China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Fang-Yuan Dong
- Department of Gastroenterology, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, People's Republic of China.
| | - Qin Yang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| |
Collapse
|
7
|
Hanquier JN, Sanders K, Berryhill CA, Sahoo FK, Hudmon A, Vilseck JZ, Cornett EM. Identification of non-histone substrates of the lysine methyltransferase PRDM9. J Biol Chem 2023; 299:104651. [PMID: 36972790 PMCID: PMC10164904 DOI: 10.1016/j.jbc.2023.104651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Lysine methylation is a dynamic, post-translational mark that regulates the function of histone and non-histone proteins. Many of the enzymes that mediate lysine methylation, known as lysine methyltransferases (KMTs), were originally identified to modify histone proteins but have also been discovered to methylate non-histone proteins. In this work, we investigate the substrate selectivity of the lysine methyltransferase PRDM9 to identify both potential histone and non-histone substrates. Though normally expressed in germ cells, PRDM9 is significantly upregulated across many cancer types. The methyltransferase activity of PRDM9 is essential for double-strand break formation during meiotic recombination. PRDM9 has been reported to methylate histone H3 at lysine residues 4 and 36; however, PRDM9 KMT activity had not previously been evaluated on non-histone proteins. Using lysine-oriented peptide (K-OPL) libraries to screen potential substrates of PRDM9, we determined that PRDM9 preferentially methylates peptide sequences not found in any histone protein. We confirmed PRDM9 selectivity through in vitro KMT reactions using peptides with substitutions at critical positions. A multisite λ-dynamics computational analysis provided a structural rationale for the observed PRDM9 selectivity. The substrate selectivity profile was then used to identify putative non-histone substrates, which were tested by peptide spot array, and a subset were further validated at the protein level by in vitro KMT assays on recombinant proteins. Finally, one of the non-histone substrates, CTNNBL1, was found to be methylated by PRDM9 in cells.
Collapse
Affiliation(s)
- Jocelyne N Hanquier
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Kenidi Sanders
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Christine A Berryhill
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Firoj K Sahoo
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Andy Hudmon
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A
| | - Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, U.S.A.
| |
Collapse
|
8
|
Di Zazzo E, Rienzo M, Casamassimi A, De Rosa C, Medici N, Gazzerro P, Bifulco M, Abbondanza C. Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation. J Transl Med 2023; 21:217. [PMID: 36964555 PMCID: PMC10039509 DOI: 10.1186/s12967-023-04066-x] [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: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND T cell activation and programming from their naïve/resting state, characterized by widespread modifications in chromatin accessibility triggering extensive changes in transcriptional programs, is orchestrated by several cytokines and transcription regulators. PRDM1 and PRDM2 encode for proteins with PR/SET and zinc finger domains that control several biological processes, including cell differentiation, through epigenetic regulation of gene expression. Different transcripts leading to main protein isoforms with (PR +) or without (PR-) the PR/SET domain have been described. Although many studies have established the critical PRDM1 role in hematopoietic cell differentiation, maintenance and/or function, the single transcript contribution has not been investigated before. Otherwise, very few evidence is currently available on PRDM2. Here, we aimed to analyze the role of PRDM1 and PRDM2 different transcripts as mediators of T lymphocyte activation. METHODS We analyzed the transcription signature of the main variants from PRDM1 (BLIMP1a and BLIMP1b) and PRDM2 (RIZ1 and RIZ2) genes, in human T lymphocytes and Jurkat cells overexpressing PRDM2 cDNAs following activation through different signals. RESULTS T lymphocyte activation induced an early increase of RIZ2 and RIZ1 followed by BLIMP1b increase and finally by BLIMP1a increase. The "first" and the "second" signals shifted the balance towards the PR- forms for both genes. Interestingly, the PI3K signaling pathway modulated the RIZ1/RIZ2 ratio in favor of RIZ1 while the balance versus RIZ2 was promoted by MAPK pathway. Cytokines mediating different Jak/Stat signaling pathways (third signal) early modulated the expression of PRDM1 and PRDM2 and the relationship of their different transcripts confirming the early increase of the PR- transcripts. Different responses of T cell subpopulations were also observed. Jurkat cells showed that the acute transient RIZ2 increase promoted the balancing of PRDM1 forms towards BLIMP1b. The stable forced expression of RIZ1 or RIZ2 induced a significant variation in the expression of key transcription factors involved in T lymphocyte differentiation. The BLIMP1a/b balance shifted in favor of BLIMP1a in RIZ1-overexpressing cells and of BLIMP1b in RIZ2-overexpressing cells. CONCLUSIONS This study provides the first characterization of PRDM2 in T-lymphocyte activation/differentiation and novel insights on PRDM1 and PRDM2 transcription regulation during initial activation phases.
Collapse
Affiliation(s)
- Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, 86100, Campobasso, Italy
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Nicola Medici
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084, Salerno, Fisciano (SA), Italy
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131, Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| |
Collapse
|
9
|
Zhao LN, Guccione E, Kaldis P. Proof-of-Concept Method to Study Uncharacterized Methyltransferases Using PRDM15. Int J Mol Sci 2023; 24:ijms24021327. [PMID: 36674842 PMCID: PMC9861158 DOI: 10.3390/ijms24021327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The PRDM family of methyltransferases has been implicated in cellular proliferation and differentiation and is deregulated in human diseases, most notably in cancer. PRDMs are related to the SET domain family of methyltransferases; however, from the 19 PRDMs only a few PRDMs with defined enzymatic activities are known. PRDM15 is an uncharacterized transcriptional regulator, with significant structural disorder and lack of defined small-molecule binding pockets. Many aspects of PRDM15 are yet unknown, including its structure, substrates, reaction mechanism, and its methylation profile. Here, we employ a series of computational approaches for an exploratory investigation of its potential substrates and reaction mechanism. Using the knowledge of PRDM9 and current knowledge of PRDM15 as basis, we tried to identify genuine substrates of PRDM15. We start from histone-based peptides and learn that the native substrates of PRDM15 may be non-histone proteins. In the future, a combination of sequence-based approaches and signature motif analysis may provide new leads. In summary, our results provide new information about the uncharacterized methyltransferase, PRDM15.
Collapse
Affiliation(s)
- Li-Na Zhao
- Department of Clinical Sciences, Lund University, P.O. Box 50332, SE-202 13 Malmö, Sweden
- Correspondence:
| | - Ernesto Guccione
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philipp Kaldis
- Department of Clinical Sciences, Lund University, P.O. Box 50332, SE-202 13 Malmö, Sweden
- Lund University Diabetes Center (LUDC), Lund University, Jan Waldenströms Gata 35, SE-214 28 Malmö, Sweden
| |
Collapse
|
10
|
Yu Y, Liu T, Yu G, Wang H, Du Z, Chen Y, Yang N, Cao K, Liu C, Wan Z, Shen H, Gao F, Yang Y, Zhang W. PRDM15 interacts with DNA-PK-Ku complex to promote radioresistance in rectal cancer by facilitating DNA damage repair. Cell Death Dis 2022; 13:978. [PMID: 36402747 PMCID: PMC9675803 DOI: 10.1038/s41419-022-05402-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
Neoadjuvant radiotherapy is a standard treatment for locally advanced rectal cancer, however, resistance to chemoradiotherapy is one of the main obstacles to improving treatment outcomes. The goal of this study was to explore the role of PRDM15 involved in the radioresistance of colorectal cancer and to clarify the underlying mechanism. In present study, we demonstrated that, after DNA damage, PRDM15 was upregulated and localized to DNA damage sites, co-localizing with γ-H2AX. Knockdown of PRDM15 inhibited DNA damage repair and increased radiosensitivity in colorectal cancer cells. Mechanistically, PRDM15 promoted DNA repair by interacting with DNA-PKcs and Ku70/Ku80 complex. In preclinical models of rectal cancer, knockdown of PRDM15 sensitized cell derived xenograft and patient derived xenograft to radiotherapy. In 80 rectal cancer patients treated with neoadjuvant chemoradiotherapy, higher PRDM15 expression was observed associated with weaker tumor regression and poorer prognosis. Our findings revealed that inhibiting PRDM15 was potent to overcome radioresistance through abrogating DNA repair in colorectal cancer cells. Additionally, the expression level of PRDM15 could be applied to predict radiotherapy responsiveness and the outcome of neoadjuvant radiotherapy in rectal cancer patients.
Collapse
Affiliation(s)
- Yue Yu
- grid.73113.370000 0004 0369 1660Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tingting Liu
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Guanyu Yu
- grid.73113.370000 0004 0369 1660Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Hang Wang
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Zhipeng Du
- grid.73113.370000 0004 0369 1660Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China ,grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang China
| | - Yuanyuan Chen
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Nan Yang
- Pharmacy Department, Qingdao Special Servicemen Recuperation Center of CPLA Navy, Qingdao, 266071 China
| | - Kun Cao
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Chunlei Liu
- grid.512114.20000 0004 8512 7501Chifeng Municipal Hospital, Chifeng Clinical Medical School of Inner Mongolia Medical University, Chifeng, 024000 China
| | - Zhijie Wan
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Hui Shen
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Fu Gao
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yanyong Yang
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Wei Zhang
- grid.73113.370000 0004 0369 1660Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| |
Collapse
|
11
|
Post-transcriptional regulation of factors important for the germ line. Curr Top Dev Biol 2022; 146:49-78. [PMID: 35152986 DOI: 10.1016/bs.ctdb.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Echinoderms are a major model system for many general aspects of biology, including mechanisms of gene regulation. Analysis of transcriptional regulation (Gene regulatory networks, direct DNA-binding of proteins to specific cis-elements, and transgenesis) has contributed to our understanding of how an embryo works. This chapter looks at post-transcriptional gene regulation in the context of how the primordial germ cells are formed, and how the factors essential for this process are regulated. Important in echinoderms, as in many embryos, is that key steps of fate determination are made post-transcriptionally. This chapter highlights these steps uncovered in sea urchins and sea stars, and links them to a general theme of how the germ line may regulate its fate differently than many of the embryo's somatic cell lineages.
Collapse
|
12
|
Li M, Ren H, Zhang Y, Liu N, Fan M, Wang K, Yang T, Chen M, Shi P. MECOM/PRDM3 and PRDM16 Serve as Prognostic-Related Biomarkers and Are Correlated With Immune Cell Infiltration in Lung Adenocarcinoma. Front Oncol 2022; 12:772686. [PMID: 35174083 PMCID: PMC8841357 DOI: 10.3389/fonc.2022.772686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background The MDS1 and EVI1 complex locus (MECOM, also called PRDM3) and PR domain containing 16 (PRDM16) are two highly related zinc finger transcription factors associated with many malignancies. However, the mechanisms of MECOM and PRDM16 in prognosis and tumor immune infiltration in lung adenocarcinoma (LUAD) remain uncertain. Methods The Cancer Genome Atlas (TCGA), Oncomine, UALCAN, GEPIA, and TIMER databases were searched to determine the relationship between the expression of MECOM and PRDM16, clinicopathological features, immune infiltration, and prognosis in LUAD. Coexpressed genes of the two genes were investigated by CBioPortal, and the potential mechanism of MECOM- and PRDM16-related genes was elucidated by GO and KEGG analyses. STRING database was utilized to further construct the protein-protein interaction network of the coexpressed genes, and the hub genes were identified by Cytoscape. Finally, qRT-PCR was performed to identify the mRNA levels of the target genes in LUAD. Results mRNA levels of MECOM and PRDM16 were downregulated in LUAD (p < 0.05), and the low expression of the two genes was associated with the age, gender, smoking duration, tissue subtype, poor stage, nodal metastasis status, TP53 mutation, and prognosis in LUAD (p < 0.05). MECOM and PRDM16 were also found to be correlated with the expression of a variety of immune cell subsets and their markers. KEGG analysis showed that both of them were mainly enriched in the cell cycle, cellular senescence, DNA replication, and p53 signaling pathway. Importantly, the mRNA levels of the two genes were also found to be decreased in the clinical samples of LUAD by qRT-PCR. Conclusion MECOM and PRDM16 may serve as potential prognostic biomarkers which govern immune cell recruitment to LUAD.
Collapse
Affiliation(s)
- Meng Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hui Ren
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yanpeng Zhang
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Na Liu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Fan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tian Yang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
| | - Puyu Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
| |
Collapse
|
13
|
IMAI K, TANIGUCHI H. Therapeutic siRNA targeting the cancer cell stemness regulator PRDI-BF1 and RIZ domain zinc finger protein 14. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:325-335. [PMID: 35908955 PMCID: PMC9363597 DOI: 10.2183/pjab.98.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
PRDI-BF1 and RIZ (PR) domain zinc finger protein 14 (PRDM14), first reported in 2007 to be overexpressed in breast cancer, plays an important role in breast cancer proliferation. Subsequent studies reported that PRDM14 is expressed in embryonic stem cells, primordial germ cells, and various cancers. PRDM14 was reported to confer stemness properties to cancer cells. These properties induce cancer initiation, cancer progression, therapeutic resistance, distant metastasis, and recurrence in refractory tumors. Therefore, PRDM14 may be an ideal therapeutic target for various types of tumors. Silencing PRDM14 expression using PRDM14-specific siRNA delivered through an innovative intravenous drug delivery system reduced the size of inoculated tumors, incidence of distant metastases, and increased overall survival in nude mice without causing adverse effects. Therapeutic siRNA targeting PRDM14 is now being evaluated in a human phase I clinical trial for patients with refractory breast cancer, including triple-negative breast cancer.
Collapse
Affiliation(s)
- Kohzoh IMAI
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroaki TANIGUCHI
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
14
|
Yan Q. The Yin-Yang Dynamics in Cancer Pharmacogenomics and Personalized Medicine. Methods Mol Biol 2022; 2547:141-163. [PMID: 36068463 DOI: 10.1007/978-1-0716-2573-6_6] [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] [Indexed: 06/15/2023]
Abstract
The enormous heterogeneity of cancer systems has made it very challenging to overcome drug resistance and adverse reactions to achieve personalized therapies. Recent developments in systems biology, especially the perception of cancer as the complex adaptive system (CAS), may help meet the challenges by deciphering the interactions at various levels from the molecular, cellular, tissue-organ, to the whole organism. The ubiquitous Yin-Yang interactions among the coevolving components, including the genes and proteins, decide their spatiotemporal features at various stages from cancer initiation to metastasis. The Yin-Yang imbalances across different systems levels, from genetic mutations to tumor cells adaptation, have been related to the intra- and inter-tumoral heterogeneity in the micro- and macro-environments. At the molecular and cellular levels, dysfunctional Yin-Yang dynamics in the cytokine networks, mitochondrial activities, redox systems, apoptosis, and metabolism can contribute to tumor cell growth and escape of immune surveillance. Up to the organism and system levels, the Yin-Yang imbalances in the cancer microenvironments can lead to different phenotypes from breast cancer to leukemia. These factors may be considered the systems-based biomarkers and treatment targets. The features of adaptation and nonlinearity in Yin-Yang dynamical interactions should be addressed by individualized drug combinations, dosages, intensities, timing, and frequencies at different cancer stages. The comprehensive "Yin-Yang dynamics" framework would enable powerful approaches for personalized and systems medicine strategies.
Collapse
|
15
|
Rienzo M, Di Zazzo E, Casamassimi A, Gazzerro P, Perini G, Bifulco M, Abbondanza C. PRDM12 in Health and Diseases. Int J Mol Sci 2021; 22:ijms222112030. [PMID: 34769459 PMCID: PMC8585061 DOI: 10.3390/ijms222112030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
PRDM12 is a member of the PRDI-BF1 (positive regulatory domain I-binding factor 1) homologous domain (PRDM)-containing protein family, a subfamily of Kruppel-like zinc finger proteins, controlling key processes in the development of cancer. PRDM12 is expressed in a spatio-temporal manner in neuronal systems where it exerts multiple functions. PRDM12 is essential for the neurogenesis initiation and activation of a cascade of downstream pro-neuronal transcription factors in the nociceptive lineage. PRDM12 inactivation, indeed, results in a complete absence of the nociceptive lineage, which is essential for pain perception. Additionally, PRDM12 contributes to the early establishment of anorexigenic neuron identity and the maintenance of high expression levels of pro-opiomelanocortin, which impacts on the program bodyweight homeostasis. PRDMs are commonly involved in cancer, where they act as oncogenes/tumor suppressors in a “Yin and Yang” manner. PRDM12 is not usually expressed in adult normal tissues but its expression is re-activated in several cancer types. However, little information is currently available on PRDM12 expression in cancers and its mechanism of action has not been thoroughly described. In this review, we summarize the recent findings regarding PRDM12 by focusing on four main biological processes: neurogenesis, pain perception, oncogenesis and cell metabolism. Moreover, we wish to highlight the importance of future studies focusing on the PRDM12 signaling pathway(s) and its role in cancer onset and progression.
Collapse
Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
- Correspondence:
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Salerno, Italy;
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
| |
Collapse
|
16
|
Usher ET, Namitz KEW, Cosgrove MS, Showalter SA. Probing multiple enzymatic methylation events in real time with NMR spectroscopy. Biophys J 2021; 120:4710-4721. [PMID: 34592262 PMCID: PMC8595733 DOI: 10.1016/j.bpj.2021.09.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Post-translational modification (PTM) of proteins is of critical importance to the regulation of many cellular processes in eukaryotic organisms. One of the most well-studied protein PTMs is methylation, wherein an enzyme catalyzes the transfer of a methyl group from a cofactor to a lysine or arginine side chain. Lysine methylation is especially abundant in the histone tails and is an important marker for denoting active or repressed genes. Given their relevance to transcriptional regulation, the study of methyltransferase function through in vitro experiments is an important stepping stone toward understanding the complex mechanisms of regulated gene expression. To date, most methyltransferase characterization strategies rely on the use of radioactive cofactors, detection of a methyl transfer byproduct, or discontinuous-type assays. Although such methods are suitable for some applications, information about multiple methylation events and kinetic intermediates is often lost. Herein, we describe the use of two-dimensional NMR to monitor mono-, di-, and trimethylation in a single reaction tube. To do so, we incorporated 13C into the donor methyl group of the enzyme cofactor S-adenosyl methionine. In this way, we may study enzymatic methylation by monitoring the appearance of distinct resonances corresponding to mono-, di-, or trimethyl lysine without the need to isotopically enrich the substrate. To demonstrate the capabilities of this method, we evaluated the activity of three lysine methyltransferases, Set7, MWRAD2 (MLL1 complex), and PRDM9, toward the histone H3 tail. We monitored mono- or multimethylation of histone H3 tail at lysine 4 through sequential short two-dimensional heteronuclear single quantum coherence experiments and fit the resulting progress curves to first-order kinetic models. In summary, NMR detection of PTMs in one-pot, real-time reaction using facile cofactor isotopic enrichment shows promise as a method toward understanding the intricate mechanisms of methyltransferases and other enzymes.
Collapse
Affiliation(s)
- Emery T Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Michael S Cosgrove
- SUNY Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, New York
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania.
| |
Collapse
|
17
|
Li W, Wu H, Sui S, Wang Q, Xu S, Pang D. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way. Front Cell Dev Biol 2021; 9:736935. [PMID: 34595180 PMCID: PMC8476812 DOI: 10.3389/fcell.2021.736935] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
Collapse
Affiliation(s)
- Wei Li
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Hao Wu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shiyao Sui
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Qin Wang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shouping Xu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Da Pang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| |
Collapse
|
18
|
Zhang H, Liu M, Wang X, Ren Y, Kim YM, Wang X, Lu X, Pang H, Liu G, Gu Y, Sun M, Shi Y, Zhang C, Zhang Y, Zhang J, Li S, Zhang L. Genomic Copy Number Variants in CML Patients With the Philadelphia Chromosome (Ph+): An Update. Front Genet 2021; 12:697009. [PMID: 34447409 PMCID: PMC8383316 DOI: 10.3389/fgene.2021.697009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Submicroscopic segmental imbalances detected by array-comparative genomic hybridization (array-CGH) were discovered to be common in chronic myeloid leukemia (CML) patients with t(9;22) as the sole chromosomal anomaly. To confirm the findings of the previous study and expand the investigation, additional CML patients with t(9;22) as the sole chromosomal anomaly were recruited and copy number variants (CNVs) were searched for. Methods Karyotyping tests were performed on 106 CML patients during January 2010-September 2019 in our Genetics Laboratory. Eighty-four (79.2%) patients had the Philadelphia (Ph) chromosome as the sole chromosomal anomaly. Only 49(58.3%) of these 84 patients had sufficient marrow or leukemia blood materials to additionally be included in the array-CGH analysis. Fluorescence in situ hybridization (FISH) was carried out to confirm the genes covered by the deleted or duplicated regions of the CNVs. Results 11(22.4%) out of the 49 patients were found to have one to three somatic segmental somatic segmental (CNVs), including fourteen deletions and three duplications. The common region associated with deletions was on 9q33.3-34.12. Identified in five (45.5%) of the 11 positive patients with segmental CNVs, the deletions ranged from 106 kb to 4.1 Mb in size. Two (18.2%) cases had a deletion in the ABL1-BCR fusion gene on der (9), while three (27.3%) cases had a deletion in the ASS1 gene. The remaining CNVs were randomly distributed on different autosomes. Conclusion Subtle genomic CNVs are relatively common in CML patients without cytogenetically visible additional chromosomal aberrations (ACAs). Long-term studies investigating the potential impact on patient prognosis and treatment outcome is underway.
Collapse
Affiliation(s)
- Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China
| | - Meng Liu
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China.,Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Xiaoxue Wang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China.,Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Yuan Ren
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China.,Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Young Mi Kim
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hui Pang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Guangming Liu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Yue Gu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Respiratory and Intensive Care Medicine, The First Hospital of Jilin University, Changchun, China
| | - Mingran Sun
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Hematology and Oncology, Anshan Hospital of First Hospital of China Medical University, Shenyang, Anshan, China
| | - Yunpeng Shi
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chuan Zhang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Gansu Province Medical Genetics Center, Gansu Provincial Maternal and Child Health Care Hospital, Lanzhou, China
| | - Yaowen Zhang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Neurology, The Second Hospital of Jilin University, Changchun, China
| | - Jianqin Zhang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Pediatric Respiratory, Dalian Children's Hospital, Dalian, China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Lijun Zhang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, China
| |
Collapse
|
19
|
Onizuka H, Masui K, Amano K, Kawamata T, Yamamoto T, Nagashima Y, Shibata N. Metabolic Reprogramming Drives Pituitary Tumor Growth through Epigenetic Regulation of TERT. Acta Histochem Cytochem 2021; 54:87-96. [PMID: 34276102 PMCID: PMC8275863 DOI: 10.1267/ahc.21-00007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary adenomas are common, benign brain tumors. Some tumors show aggressive phenotypes including early recurrence, local invasion and distant metastasis, but the underlying mechanism to drive the progression of pituitary tumors has remained to be clarified. Aerobic glycolysis known as the Warburg effect is one of the emerging hallmarks of cancer, which has an impact on the tumor biology partly through epigenetic regulation of the tumor-promoting genes. Here, we demonstrate metabolic reprogramming in pituitary tumors contributes to tumor cell growth with epigenetic changes such as histone acetylation. Notably, a shift in histone acetylation increases the expression of telomerase reverse transcriptase (TERT) oncogene, which drives metabolism-dependent cell proliferation in pituitary tumors. These indicate that epigenetic changes could be the specific biomarker for predicting the behavior of pituitary tumors and exploitable as a novel target for the aggressive types of the pituitary tumors.
Collapse
Affiliation(s)
- Hiromi Onizuka
- Department of Surgical Pathology, Tokyo Women’s Medical University
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Kenta Masui
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Kosaku Amano
- Department of Neurosurgery, Tokyo Women’s Medical University
| | | | - Tomoko Yamamoto
- Department of Surgical Pathology, Tokyo Women’s Medical University
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women’s Medical University
| | - Noriyuki Shibata
- Division of Pathological Neuroscience, Department of Pathology, Tokyo Women’s Medical University
| |
Collapse
|
20
|
Identification of key classification features of early cervical squamous cell carcinoma. Comput Biol Chem 2021; 93:107531. [PMID: 34217008 DOI: 10.1016/j.compbiolchem.2021.107531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022]
Abstract
Despite the tremendous progress in molecular analysis of pan-cancer, little is known regarding molecular classification of cervical squamous cell carcinoma. In this study, we adopted a multi-omics approach to identify potential key classification features of cervical squamous cell carcinoma. Specifically, we analyzed mRNA, and microRNA (miRNA) expression data, as well as DNA methylation and copy number variation in cervical squamous cell carcinoma cases, using datasets obtained from The Cancer Genome Atlas (TCGA). Moreover, we identified molecules in each dimension, as well as integrated and clustered filtered classification features, and used them to distinguish different subtypes. The resulting key classification features were used to establish a classification model for cervical squamous cell carcinoma. Our results revealed two cervical squamous cell carcinoma subtypes, with significant differences across clinical survival levels, as well as 8 key classification features of cervical squamous cell carcinomas. These findings are expected to provide important references for early classification of cervical squamous cell carcinoma and identification of classification markers.
Collapse
|
21
|
Bleu M, Mermet-Meillon F, Apfel V, Barys L, Holzer L, Bachmann Salvy M, Lopes R, Amorim Monteiro Barbosa I, Delmas C, Hinniger A, Chau S, Kaufmann M, Haenni S, Berneiser K, Wahle M, Moravec I, Vissières A, Poetsch T, Ahrné E, Carte N, Voshol J, Bechter E, Hamon J, Meyerhofer M, Erdmann D, Fischer M, Stachyra T, Freuler F, Gutmann S, Fernández C, Schmelzle T, Naumann U, Roma G, Lawrenson K, Nieto-Oberhuber C, Cobos-Correa A, Ferretti S, Schübeler D, Galli GG. PAX8 and MECOM are interaction partners driving ovarian cancer. Nat Commun 2021; 12:2442. [PMID: 33903593 PMCID: PMC8076227 DOI: 10.1038/s41467-021-22708-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The transcription factor PAX8 is critical for the development of the thyroid and urogenital system. Comprehensive genomic screens furthermore indicate an additional oncogenic role for PAX8 in renal and ovarian cancers. While a plethora of PAX8-regulated genes in different contexts have been proposed, we still lack a mechanistic understanding of how PAX8 engages molecular complexes to drive disease-relevant oncogenic transcriptional programs. Here we show that protein isoforms originating from the MECOM locus form a complex with PAX8. These include MDS1-EVI1 (also called PRDM3) for which we map its interaction with PAX8 in vitro and in vivo. We show that PAX8 binds a large number of genomic sites and forms transcriptional hubs. At a subset of these, PAX8 together with PRDM3 regulates a specific gene expression module involved in adhesion and extracellular matrix. This gene module correlates with PAX8 and MECOM expression in large scale profiling of cell lines, patient-derived xenografts (PDXs) and clinical cases and stratifies gynecological cancer cases with worse prognosis. PRDM3 is amplified in ovarian cancers and we show that the MECOM locus and PAX8 sustain in vivo tumor growth, further supporting that the identified function of the MECOM locus underlies PAX8-driven oncogenic functions in ovarian cancer.
Collapse
Affiliation(s)
- Melusine Bleu
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fanny Mermet-Meillon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Verena Apfel
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Louise Barys
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Laura Holzer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Rui Lopes
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Cecile Delmas
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Hinniger
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Suzanne Chau
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Markus Kaufmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Simon Haenni
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Karolin Berneiser
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maria Wahle
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ivana Moravec
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Vissières
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tania Poetsch
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Erik Ahrné
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nathalie Carte
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Johannes Voshol
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Elisabeth Bechter
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jacques Hamon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marco Meyerhofer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Erdmann
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Matteo Fischer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Therese Stachyra
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Felix Freuler
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sascha Gutmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - César Fernández
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tobias Schmelzle
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Kate Lawrenson
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | | | - Amanda Cobos-Correa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Stephane Ferretti
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, University of Basel, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Giorgio Giacomo Galli
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
22
|
Taniguchi H, Natori Y, Miyagi Y, Hayashi K, Nagamura F, Kataoka K, Imai K. Treatment of primary and metastatic breast and pancreatic tumors upon intravenous delivery of a PRDM14-specific chimeric siRNA/nanocarrier complex. Int J Cancer 2021; 149:646-656. [PMID: 33783816 DOI: 10.1002/ijc.33579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/10/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023]
Abstract
PRDM14 is highly expressed in several cancers but is not detected in normal tissues. It confers cancer stem cell-like properties, including chemoresistance and distant metastasis, to cancer cells. Herein, we aimed to develop a highly effective therapy against advanced stage cancer based on intravenously delivered PRDM14-targeted siRNA. First, we examined PRDM14 expression and gene amplification in breast and pancreatic tumors and cell lines. PRDM14 was expressed in breast cancer, including the triple-negative subtype, and pancreatic cancer. PRDM14 was amplified in 23.8% of patients with PRDM14+ breast cancer. Next, we investigated the inoculated tumor growth and distant metastasis following PRDM14 depletion by administering mice with PRDM14-specific chimeric siRNA combined with a novel branched PEGylated poly-L-ornithine (PLO)-based intravenous drug delivery system, designated PRDM14 unit polyion complex (uPIC) (n = 6/group). Inhibition of PRDM14 expression with PRDM14 uPIC by systemic intravenous injection effectively reduced tumor size and metastasis in vivo, thereby improving survival. Finally, pharmacokinetic/toxicokinetic analyses were performed on PRDM14 uPIC, which was intravenously administered to rats (n = 10-15/group) and cynomolgus monkeys (n = 3-5/group), twice weekly for 4 weeks. This revealed that PRDM14 uPIC was relatively nontoxic and the siRNA exposure in serum was greater than that predicted by the administered dose ratio when delivered as a uPIC. Taken together, our study indicated that PRDM14 uPIC is highly effective in suppressing malignant features of solid cancers and does not cause severe toxicity, making it a promising therapeutic agent for cancer treatment.
Collapse
Affiliation(s)
- Hiroaki Taniguchi
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan.,Research and Development Center for Precision Medicine, University of Tsukuba, Innovation Medical Research Institute, Ibaraki, Japan
| | - Yukikazu Natori
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan.,BioThinkTank Co. Ltd., Nishi-ku Yokohama, Kanagawa, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, Kawasaki City, Kanagawa Prefecture, Japan
| | - Fumitaka Nagamura
- Translational Research Center, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, Kawasaki City, Kanagawa Prefecture, Japan.,Institute for Future Initiatives, The University of Tokyo, Tokyo, Japan
| | - Kohzoh Imai
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|
23
|
Di Tullio F, Schwarz M, Zorgati H, Mzoughi S, Guccione E. The duality of PRDM proteins: epigenetic and structural perspectives. FEBS J 2021; 289:1256-1275. [PMID: 33774927 DOI: 10.1111/febs.15844] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/26/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
PRDF1 and RIZ1 homology domain containing (PRDMs) are a subfamily of Krüppel-like zinc finger proteins controlling key processes in metazoan development and in cancer. PRDMs exhibit unique dualities: (a) PR domain/ZNF arrays-their structure combines a SET-like domain known as a PR domain, typically found in methyltransferases, with a variable array of C2H2 zinc fingers (ZNF) characteristic of DNA-binding transcription factors; (b) transcriptional activators/repressors-their physiological function is context- and cell-dependent; mechanistically, some PRDMs have a PKMT activity and directly catalyze histone lysine methylation, while others are rather pseudomethyltransferases and act by recruiting transcriptional cofactors; (c) oncogenes/tumor suppressors-their pathological function depends on the specific PRDM isoform expressed during tumorigenesis. This duality is well known as the 'Yin and Yang' of PRDMs and involves a complex regulation of alternative splicing or alternative promoter usage, to generate full-length or PR-deficient isoforms with opposing functions in cancer. In conclusion, once their dualities are fully appreciated, PRDMs represent a promising class of targets in oncology by virtue of their widespread upregulation across multiple tumor types and their somatic dispensability, conferring a broad therapeutic window and limited toxic side effects. The recent discovery of a first-in-class compound able to inhibit PRDM9 activity has paved the way for the identification of further small molecular inhibitors able to counteract PRDM oncogenic activity.
Collapse
Affiliation(s)
- Federico Di Tullio
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan Schwarz
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Habiba Zorgati
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Mzoughi
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
24
|
Rienzo M, Sorrentino A, Di Zazzo E, Di Donato M, Carafa V, Marino MM, De Rosa C, Gazzerro P, Castoria G, Altucci L, Casamassimi A, Abbondanza C. Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. Front Oncol 2021; 10:583533. [PMID: 33585202 PMCID: PMC7880127 DOI: 10.3389/fonc.2020.583533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Positive Regulatory Domain (PRDM) gene family members commonly express two main molecular variants, the PR-plus isoform usually acting as tumor suppressor and the PR-minus one functioning as oncogene. Accordingly, PRDM2/RIZ encodes for RIZ1 (PR-plus) and RIZ2 (PR-minus). In human cancers, genetic or epigenetic modifications induce RIZ1 silencing with an expression level imbalance in favor of RIZ2 that could be relevant for tumorigenesis. Additionally, in estrogen target cells and tissues, estradiol increases RIZ2 expression level with concurrent increase of cell proliferation and survival. Several attempts to study RIZ2 function in HeLa or MCF-7 cells by its over-expression were unsuccessful. Thus, we over-expressed RIZ2 in HEK-293 cells, which are both RIZ1 and RIZ2 positive but unresponsive to estrogens. The forced RIZ2 expression increased cell viability and growth, prompted the G2-to-M phase transition and organoids formation. Accordingly, microarray analysis revealed that RIZ2 regulates several genes involved in mitosis. Consistently, RIZ silencing in both estrogen-responsive MCF-7 and -unresponsive MDA-MB-231 cells induced a reduction of cell proliferation and an increase of apoptosis rate. Our findings add novel insights on the putative RIZ2 tumor-promoting functions, although additional attempts are warranted to depict the underlying molecular mechanism.
Collapse
Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Michela Marino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| |
Collapse
|
25
|
Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov 2021; 20:265-286. [PMID: 33469207 DOI: 10.1038/s41573-020-00108-x] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Protein lysine methylation is a crucial post-translational modification that regulates the functions of both histone and non-histone proteins. Deregulation of the enzymes or 'writers' of protein lysine methylation, lysine methyltransferases (KMTs), is implicated in the cause of many diseases, including cancer, mental health disorders and developmental disorders. Over the past decade, significant advances have been made in developing drugs to target KMTs that are involved in histone methylation and epigenetic regulation. The first of these inhibitors, tazemetostat, was recently approved for the treatment of epithelioid sarcoma and follicular lymphoma, and several more are in clinical and preclinical evaluation. Beyond chromatin, the many KMTs that regulate protein synthesis and other fundamental biological processes are emerging as promising new targets for drug development to treat diverse diseases.
Collapse
Affiliation(s)
- Kamakoti P Bhat
- Department of Biology, Stanford University, Stanford, CA, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
26
|
Cui Y, Hunt A, Li Z, Birkin E, Lane J, Ruge F, Jiang WG. Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer. Comput Struct Biotechnol J 2020; 19:261-278. [PMID: 33425256 PMCID: PMC7779375 DOI: 10.1016/j.csbj.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
DEAD/H box helicases are implicated in lung cancer but have not been systematically investigated for their clinical significance and function. In this study, we aimed to evaluate the potential of DEAD/H box helicases as prognostic biomarkers and therapeutic targets in lung cancer by integrated bioinformatic analysis of multivariate large-scale databases. Survival and differential expression analysis of these helicases enabled us to identify four biomarkers with the most significant alterations. These were found to be the negative prognostic factors DDX11, DDX55 and DDX56, and positive prognostic factor DDX5. Pathway enrichment analysis indicates that MYC signalling is negatively associated with expression levels of the DDX5 gene while positively associated with that of DDX11, DDX55 and DDX56. High expression levels of the DDX5 gene is associated with low mutation levels of TP53 and MUC16, the two most frequently mutated genes in lung cancer. In contrast, high expression levels of DDX11, DDX55 and DDX56 genes are associated with high levels of TP53 and MUC16 mutation. The tumour-infiltrated CD8 + T and B cells positively correlate with levels of DDX5 gene expression, while negatively correlate with that of the other three DEAD box helicases, respectively. Moreover, the DDX5-associated miRNA profile is distinguished from the miRNA profiles of DDX11, DDX55 and DDX56, although each DDX has a different miRNA signature. The identification of these four DDX helicases as biomarkers will be valuable for prognostic prediction and targeted therapeutic development in lung cancer.
Collapse
Affiliation(s)
- Yuxin Cui
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Adam Hunt
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Zhilei Li
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, PR China
| | - Emily Birkin
- Cardiff & Vale University Health Board, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Jane Lane
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Fiona Ruge
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Wen G Jiang
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| |
Collapse
|
27
|
Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
Collapse
|
28
|
Structural and functional annotation of PR/SET Domain (PRDM) protein family: In-silico study elaborating role of PRDM12 mutation in congenital insensitivity to pain. Comput Biol Chem 2020; 89:107382. [PMID: 33010785 DOI: 10.1016/j.compbiolchem.2020.107382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 08/11/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Congenital insensitivity to pain (CIP), classified as a type of hereditary sensory and autonomic neuropathies, is a rare disease in which the affected individuals fail to perceive sensation of pain. One of the PR/SET Domain Proteins, PRDM12, has been identified in recent past as a candidate gene for congenital insensitivity to pain. In the present study, we performed whole exome sequencing in a Pakistani family with CIP phenotype to ascertain the causative mutation. We identified a previously described alanine repeat duplication in PRDM12 (Ala353_Ala359dup) in this family. After this, we performed structural annotations for PR/SET Domain (PRDM) containing protein family to prognosticate the potential hypothetical structure of PRDM proteins with physical and chemical parameters. Out of nineteen members of this family, four members (PRDM5, PRDM8, PRDM12 and PRDM13) were specially focused because of their role in neurological disorders. Predictions about structure and interactions of these proteins revealed novel interacting molecules and pathways. Detailed in silico analysis of PRDM12 was performed to elaborate importance of its domain structure in interaction with other proteins and its role in pain insensitivity phenotype. These results have substantially enhanced our understanding regarding the etiology of congenital pain insensitivity and would stimulate further research on therapy and prevention.
Collapse
|
29
|
Iwanaga R, Truong BT, Hsu JY, Lambert KA, Vyas R, Orlicky D, Shellman YG, Tan AC, Ceol C, Artinger KB. Loss of prdm1a accelerates melanoma onset and progression. Mol Carcinog 2020; 59:1052-1063. [PMID: 32562448 PMCID: PMC7864383 DOI: 10.1002/mc.23236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/04/2020] [Indexed: 12/19/2022]
Abstract
Melanoma is an aggressive, deadly skin cancer derived from melanocytes, a neural crest cell derivative. Melanoma cells mirror the developmental program of neural crest cells in that they exhibit the same gene expression patterns and utilize similar cellular mechanisms, including increased cell proliferation, epithelial-mesenchymal transition, and migration. Here we studied the role of neural crest regulator PRDM1 in melanoma onset and progression. In development, Prdm1a functions to promote neural crest progenitor fate, and in melanoma, we found that PRDM1 has reduced copy number and is recurrently deleted in both zebrafish and humans. When examining expression of neural crest and melanocyte development genes, we show that sox10 progenitor expression is high in prdm1a-/- mutants, while more differentiated melanocyte markers are reduced, suggesting that normally Prdm1a is required for differentiation. Data mining of human melanoma datasets indicates that high PRDM1 expression in human melanoma is correlated with better patient survival and decreased PRDM1 expression is common in metastatic tumors. When one copy of prdm1a is lost in the zebrafish melanoma model Tg(mitfa:BRAFV600E );p53-/- ;prdm1a+/- , melanoma onset occurs more quickly, and the tumors that form have a larger area with increased expression of sox10. These data demonstrate a novel role for PRDM1 as a tumor suppressor in melanoma.
Collapse
Affiliation(s)
- Ritsuko Iwanaga
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Brittany T. Truong
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Jessica Y. Hsu
- Pharmacology Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Karoline A. Lambert
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Rajesh Vyas
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - David Orlicky
- Department of Pathology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Yiqun G. Shellman
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Aik-Choon Tan
- Division of Medical Oncology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| | - Craig Ceol
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado
| |
Collapse
|
30
|
Cypris O, Eipel M, Franzen J, Rösseler C, Tharmapalan V, Kuo CC, Vieri M, Nikolić M, Kirschner M, Brümmendorf TH, Zenke M, Lampert A, Beier F, Wagner W. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. Clin Epigenetics 2020; 12:125. [PMID: 32819411 PMCID: PMC7439574 DOI: 10.1186/s13148-020-00914-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Dyskeratosis congenita (DKC) and idiopathic aplastic anemia (AA) are bone marrow failure syndromes that share characteristics of premature aging with severe telomere attrition. Aging is also reflected by DNA methylation changes, which can be utilized to predict donor age. There is evidence that such epigenetic age predictions are accelerated in premature aging syndromes, but it is yet unclear how this is related to telomere length. DNA methylation analysis may support diagnosis of DKC and AA, which still remains a challenge for these rare diseases. RESULTS In this study, we analyzed blood samples of 70 AA and 18 DKC patients to demonstrate that their epigenetic age predictions are overall increased, albeit not directly correlated with telomere length. Aberrant DNA methylation was observed in the gene PRDM8 in DKC and AA as well as in other diseases with premature aging phenotype, such as Down syndrome and Hutchinson-Gilford-Progeria syndrome. Aberrant DNA methylation patterns were particularly found within subsets of cell populations in DKC and AA samples as measured with barcoded bisulfite amplicon sequencing (BBA-seq). To gain insight into the functional relevance of PRDM8, we used CRISPR/Cas9 technology to generate induced pluripotent stem cells (iPSCs) with heterozygous and homozygous knockout. Loss of PRDM8 impaired hematopoietic and neuronal differentiation of iPSCs, even in the heterozygous knockout clone, but it did not impact on epigenetic age. CONCLUSION Taken together, our results demonstrate that epigenetic aging is accelerated in DKC and AA, independent from telomere attrition. Furthermore, aberrant DNA methylation in PRDM8 provides another biomarker for bone marrow failure syndromes and modulation of this gene in cellular subsets may be related to the hematopoietic and neuronal phenotypes observed in premature aging syndromes.
Collapse
Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Corinna Rösseler
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Vithurithra Tharmapalan
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Tim H. Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| |
Collapse
|
31
|
Global translation during early development depends on the essential transcription factor PRDM10. Nat Commun 2020; 11:3603. [PMID: 32681107 PMCID: PMC7368010 DOI: 10.1038/s41467-020-17304-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/21/2020] [Indexed: 01/08/2023] Open
Abstract
Members of the PR/SET domain-containing (PRDM) family of zinc finger transcriptional regulators play diverse developmental roles. PRDM10 is a yet uncharacterized family member, and its function in vivo is unknown. Here, we report an essential requirement for PRDM10 in pre-implantation embryos and embryonic stem cells (mESCs), where loss of PRDM10 results in severe cell growth inhibition. Detailed genomic and biochemical analyses reveal that PRDM10 functions as a sequence-specific transcription factor. We identify Eif3b, which encodes a core component of the eukaryotic translation initiation factor 3 (eIF3) complex, as a key downstream target, and demonstrate that growth inhibition in PRDM10-deficient mESCs is in part mediated through EIF3B-dependent effects on global translation. Our work elucidates the molecular function of PRDM10 in maintaining global translation, establishes its essential role in early embryonic development and mESC homeostasis, and offers insights into the functional repertoire of PRDMs as well as the transcriptional mechanisms regulating translation.
Collapse
|
32
|
Mzoughi S, Fong JY, Papadopoli D, Koh CM, Hulea L, Pigini P, Di Tullio F, Andreacchio G, Hoppe MM, Wollmann H, Low D, Caldez MJ, Peng Y, Torre D, Zhao JN, Uchenunu O, Varano G, Motofeanu CM, Lakshmanan M, Teo SX, Wun CM, Perini G, Tan SY, Ong CB, Al-Haddawi M, Rajarethinam R, Hue SSS, Lim ST, Ong CK, Huang D, Ng SB, Bernstein E, Hasson D, Wee KB, Kaldis P, Jeyasekharan A, Dominguez-Sola D, Topisirovic I, Guccione E. PRDM15 is a key regulator of metabolism critical to sustain B-cell lymphomagenesis. Nat Commun 2020; 11:3520. [PMID: 32665551 PMCID: PMC7360777 DOI: 10.1038/s41467-020-17064-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/01/2020] [Indexed: 01/22/2023] Open
Abstract
PRDM (PRDI-BF1 and RIZ homology domain containing) family members are sequence-specific transcriptional regulators involved in cell identity and fate determination, often dysregulated in cancer. The PRDM15 gene is of particular interest, given its low expression in adult tissues and its overexpression in B-cell lymphomas. Despite its well characterized role in stem cell biology and during early development, the role of PRDM15 in cancer remains obscure. Herein, we demonstrate that while PRDM15 is largely dispensable for mouse adult somatic cell homeostasis in vivo, it plays a critical role in B-cell lymphomagenesis. Mechanistically, PRDM15 regulates a transcriptional program that sustains the activity of the PI3K/AKT/mTOR pathway and glycolysis in B-cell lymphomas. Abrogation of PRDM15 induces a metabolic crisis and selective death of lymphoma cells. Collectively, our data demonstrate that PRDM15 fuels the metabolic requirement of B-cell lymphomas and validate it as an attractive and previously unrecognized target in oncology.
Collapse
Affiliation(s)
- Slim Mzoughi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Yi Fong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - David Papadopoli
- Lady Davis Institute, SMBD JGH, McGill University, Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Cheryl M Koh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Laura Hulea
- Lady Davis Institute, SMBD JGH, McGill University, Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, H3T 1E2, Canada
- Maisonneuve-Rosemont Hospital Research Centre, 5415 Assumption Blvd, Montreal, QC, H1T 2M4, Canada
- Département de Médecine, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Paolo Pigini
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pharmacy and Biotechnology, University of Bologna, Via F. Selmi 3, 40126, Bologna, Italy
| | - Federico Di Tullio
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Giuseppe Andreacchio
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pharmacy and Biotechnology, University of Bologna, Via F. Selmi 3, 40126, Bologna, Italy
| | - Michal Marek Hoppe
- Cancer Science Institute (CSI), National University of Singapore, Singapore, Singapore
| | - Heike Wollmann
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Diana Low
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Matias J Caldez
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Frontiers Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Yanfen Peng
- Cancer Science Institute (CSI), National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julia N Zhao
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oro Uchenunu
- Lady Davis Institute, SMBD JGH, McGill University, Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Gabriele Varano
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Immunology Institute and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corina-Mihaela Motofeanu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shun Xie Teo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Cheng Mun Wun
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Via F. Selmi 3, 40126, Bologna, Italy
| | - Soo Yong Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Advanced Molecular Pathology Laboratory, IMCB, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chee Bing Ong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Advanced Molecular Pathology Laboratory, IMCB, Singapore, Singapore
| | - Muthafar Al-Haddawi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Advanced Molecular Pathology Laboratory, IMCB, Singapore, Singapore
| | - Ravisankar Rajarethinam
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Advanced Molecular Pathology Laboratory, IMCB, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National University Hospital (NUH), Singapore, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Choon Kiat Ong
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dachuan Huang
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute (CSI), National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Emily Bernstein
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keng Boon Wee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anand Jeyasekharan
- Cancer Science Institute (CSI), National University of Singapore, Singapore, Singapore
| | - David Dominguez-Sola
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Immunology Institute and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD JGH, McGill University, Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, H3T 1E2, Canada.
- Lady Davis Institute, SMBD JGH, McGill University, Departments of Experimental Medicine and Biochemistry, McGill University, Montreal, QC, H3T 1E2, Canada.
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological and Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
33
|
Batista-Gomes JA, Mello FAR, de Oliveira EHC, de Souza MPC, Wanderley AV, da Costa Pantoja L, dos Santos NPC, Khayat BCM, Khayat AS. Identifying novel genetic alterations in pediatric acute lymphoblastic leukemia based on copy number analysis. Mol Cytogenet 2020; 13:25. [PMID: 32607130 PMCID: PMC7320540 DOI: 10.1186/s13039-020-00491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/08/2020] [Indexed: 11/12/2022] Open
Abstract
Copy number variations (CNVs) analysis may reveal molecular biomarkers and provide information on the pathogenesis of acute lymphoblastic leukemia (ALL). We investigated the gene copy number in childhood ALL by microarray and select three new recurrent CNVs to evaluate by real-time PCR assay: DMBT1, KIAA0125 and PRDM16 were selected due to high frequency of CNVs in ALL samples and based on their potential biological functions in carcinogenesis described in the literature. DBMT1 deletion was associated with patients with chromosomal translocations and is a potential tumor suppressor; KIAA0125 and PRDM16 may act as an oncogene despite having a paradoxical behavior in carcinogenesis. This study reinforces that microarrays/aCGH is it is a powerful tool for detection of genomic aberrations, which may be used in the risk stratification.
Collapse
|
34
|
Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
Collapse
Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| |
Collapse
|
35
|
Wei D, Yiyuan C, Qian L, Jianhua L, Yazhuo Z, Hua G. The absence of PRDM2 involved the tumorigenesis of somatotroph adenomas through regulating c-Myc. Gene 2020; 737:144456. [PMID: 32044406 DOI: 10.1016/j.gene.2020.144456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023]
Abstract
Somatotroph adenoma is the main cause of acromegaly which have peripheral signs with growth of soft tissues and multiple comorbidities. Surgery and adjuvant therapy with somatostatin analogs (SSA) fail in more than 25% of patients. PRDM2, a tumor suppressor, plays an important role in cancer and obesity, including pituitary adenomas. In this study, we analyze the correlation of PRDM2 and oncogene c-Myc in 70 somatotroph adenomas according immunohistochemical staining, furthermore, we probed that whether PRDM2 participates in c-Myc signaling pathway in vitro experiment. 70 somatotroph adenomas patients were divided into low patients and high patients according to median of H-score of PRDM2 or c-Myc. Low PRDM2 patients had higher risk of invasive behavior, larger tumor volume and recurrence chance than high PRDM2 group (P = 0.015, P = 0.031, P = 0.017). High c-Myc patients had higher risk of invasive behavior, larger tumor volume and recurrence chance than low c-Myc group (P = 0.012, P = 0.002, P = 0.015). It was a negative correlation between H-score of PRDM2 and c-Myc (PRDM2 = -0.163 × c-Myc + 67.11, r = -0.407). The ability of cell proliferation was declined in a time dependent manner after overexpression of PRDM2 (PRDM2 group) compared to that in control GH3 cells (P < 0.05). Through flow cytometry assay, PRDM2 could induce the apoptosis and G2/M arrest in GH3 cell (both p < 0.05). Transwell experiment proved less trans-membrane cells in PRDM2 group than those in control group (415 ± 76 vs 145 ± 37, P < 0.01). RT-PCR and western blot both proved PRDM2 could inhibit the level c-Myc and elevate the levels of CDKN1A and CDKN1B. Combined with c-Myc inhibitor 10058-F4, PRDM2 further inhibited cell proliferation and induced more apoptosis in GH3 cell. Taken together, we found that PRDM2 negatively regulated the expression of c-Myc in somatotroph adenomas, and testified the synergism between PRDM2 gene therapy and c-Myc inhibitor in vitro experiment.
Collapse
Affiliation(s)
- Dong Wei
- Department of Neurosurgery, Tangshan People's Hospital, Tangshan, Hebei, China; Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Chen Yiyuan
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Liu Qian
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Li Jianhua
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China; Department of Neurosurgery, Binzhou People's Hospital, Binzhou, Shandong 256610, China
| | - Zhang Yazhuo
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China
| | - Gao Hua
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Capital Medical University, 119# Southwest 4rd, Beijing 100050, China.
| |
Collapse
|
36
|
Allali-Hassani A, Szewczyk MM, Ivanochko D, Organ SL, Bok J, Ho JSY, Gay FPH, Li F, Blazer L, Eram MS, Halabelian L, Dilworth D, Luciani GM, Lima-Fernandes E, Wu Q, Loppnau P, Palmer N, Talib SZA, Brown PJ, Schapira M, Kaldis P, O'Hagan RC, Guccione E, Barsyte-Lovejoy D, Arrowsmith CH, Sanders JM, Kattar SD, Bennett DJ, Nicholson B, Vedadi M. Discovery of a chemical probe for PRDM9. Nat Commun 2019; 10:5759. [PMID: 31848333 PMCID: PMC6917776 DOI: 10.1038/s41467-019-13652-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
Collapse
Affiliation(s)
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Shawna L Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Qin Wu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore (NUS), Department of Biochemistry, 117597, Singapore, Singapore
| | - Ronan C O'Hagan
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Nature Research Center, Vilnius, Akademijos, 2, Lithuania
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - John M Sanders
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Solomon D Kattar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | | | - Benjamin Nicholson
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
37
|
Prajapati RS, Hintze M, Streit A. PRDM1 controls the sequential activation of neural, neural crest and sensory progenitor determinants. Development 2019; 146:dev.181107. [PMID: 31806661 DOI: 10.1242/dev.181107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 11/27/2019] [Indexed: 12/25/2022]
Abstract
During early embryogenesis, the ectoderm is rapidly subdivided into neural, neural crest and sensory progenitors. How the onset of lineage determinants and the loss of pluripotency markers are temporally and spatially coordinated in vivo is still debated. Here, we identify a crucial role for the transcription factor PRDM1 in the orderly transition from epiblast to defined neural lineages in chick. PRDM1 is initially expressed broadly in the entire epiblast, but becomes gradually restricted as cell fates are specified. We find that PRDM1 is required for the loss of some pluripotency markers and the onset of neural, neural crest and sensory progenitor specifier genes. PRDM1 directly activates their expression by binding to their promoter regions and recruiting the histone demethylase Kdm4a to remove repressive histone marks. However, once neural lineage determinants become expressed, they in turn repress PRDM1, whereas prolonged PRDM1 expression inhibits neural, neural crest and sensory progenitor genes, suggesting that its downregulation is necessary for cells to maintain their identity. Therefore, PRDM1 plays multiple roles during ectodermal cell fate allocation.
Collapse
Affiliation(s)
- Ravindra S Prajapati
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| |
Collapse
|
38
|
Hofvander J, Puls F, Pillay N, Steele CD, Flanagan AM, Magnusson L, Nilsson J, Mertens F. Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile. J Pathol 2019; 249:425-434. [PMID: 31313299 DOI: 10.1002/path.5326] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022]
Abstract
Undifferentiated pleomorphic sarcoma (UPS) is a highly aggressive soft tissue tumor. A subset of UPS is characterized by a CITED2-PRDM10 or a MED12-PRDM10 gene fusion. Preliminary data suggest that these so-called PRDM10-rearranged tumors (PRT) are clinically more indolent than classical high-grade UPS, and hence important to recognize. Here, we assessed the spectrum of accompanying mutations and the gene expression profile in PRT using genomic arrays and sequencing of the genome (WGS) and transcriptome (RNA-seq). The fusion protein's function was further investigated by conditional expression of the CITED2-PRDM10 fusion in a fibroblast cell line, followed by RNA-seq and an assay for transposase-accessible chromatin (ATAC-seq). The CADM3 gene was found to be differentially up-regulated in PRT and cell lines and was also evaluated for expression at the protein level using immunohistochemistry (IHC). The genomic analyses identified few and nonrecurrent mutations in addition to the structural variants giving rise to the gene fusions, strongly indicating that the PRDM10-fusions represent the critical driver mutations. RNA-seq of tumors showed a distinct gene expression profile, separating PRT from high-grade UPS and other soft tissue tumors. CADM3 was among the genes that was consistently and highly expressed in both PRT and fibroblasts expressing CITED2-PRDM10, suggesting that it is a direct target of the PRDM10 transcription factor. This conclusion is in line with sequencing data from ATAC-seq, showing enrichment of PRDM10 binding sites, suggesting that the amino-terminal fusion partner contributes by making the DNA more accessible to PRDM10 binding. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Florian Puls
- Department of Pathology and Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nischalan Pillay
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | | | - Adrienne M Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
- UCL Cancer Institute, London, UK
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund University, Lund, Sweden
| |
Collapse
|
39
|
Silencing PRDM14 via Oligonucleotide Therapeutics Suppresses Tumorigenicity and Metastasis of Breast Cancer. Methods Mol Biol 2019; 1974:233-243. [PMID: 31099008 DOI: 10.1007/978-1-4939-9220-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PRDI-BF1 and RIZ (PR) domain zinc finger protein 14 (PRDM14) is upregulated in approximately 60% of breast cancers, some of which exhibit gene amplification. In contrast, PRDM14 is not expressed in normal, and differentiated tissues. PRDM14+ breast cancer cells are resistant to chemotherapy drugs, are tumorigenic, and metastasize to the lungs. It is commonly assumed that genes that are overexpressed in cancers, such as PRDM14, are effective targets for new therapies that specifically abrogate the expression of these genes. RNA interference of PRDM14, a gene expressed by breast cancer cells, reduced the size of tumors and lung metastases in nude mice. In this chapter, we introduce the concept and methods to develop and apply systematically injected small interfering RNA therapy for breast cancer models in vivo.
Collapse
|
40
|
[Chemical targeting of DNA and histone methylation in cancer: Novelties, hopes and promises]. Bull Cancer 2019; 106:823-833. [PMID: 31522746 DOI: 10.1016/j.bulcan.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 01/10/2023]
|
41
|
Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH. Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex. Nucleic Acids Res 2019; 47:1225-1238. [PMID: 30462309 PMCID: PMC6379669 DOI: 10.1093/nar/gky1192] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (ΔPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and ΔPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the ΔPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 μM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex.
Collapse
Affiliation(s)
- Danton Ivanochko
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Elizabeth Henderson
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Pavel Savitsky
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Edyta Marcon
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Evelyne Lima-Fernandes
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| |
Collapse
|
42
|
Tracey LJ, Justice MJ. Off to a Bad Start: Cancer Initiation by Pluripotency Regulator PRDM14. Trends Genet 2019; 35:489-500. [PMID: 31130394 DOI: 10.1016/j.tig.2019.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 04/23/2019] [Indexed: 12/16/2022]
Abstract
Despite advances in chemotherapies that improve cancer survival, most patients who relapse succumb to the disease due to the presence of cancer stem cells (CSCs), which are highly chemoresistant. The pluripotency factor PR domain 14 (PRDM14) has a key role in initiating many types of cancer. Normally, PRDM14 uses epigenetic mechanisms to establish and maintain the pluripotency of embryonic cells, and its role in cancer is similar. This important link between cancer and induced pluripotency is a key revelation for how CSCs may form: pluripotency genes, such as PRDM14, can expand stem-like cells as they promote ongoing DNA damage. PRDM14 and its protein-binding partners, the ETO/CBFA2T family, are ideal candidates for eliminating CSCs from relevant cancers, preventing relapse and improving long-term survival.
Collapse
Affiliation(s)
- Lauren J Tracey
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ONT, M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ONT, M5S 1A8, Canada
| | - Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ONT, M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ONT, M5S 1A8, Canada.
| |
Collapse
|
43
|
Chen N, Hu T, Gui Y, Gao J, Li Z, Huang S. Transcriptional regulation of Bcl-2 gene by the PR/SET domain family member PRDM10. PeerJ 2019; 7:e6941. [PMID: 31143550 PMCID: PMC6525587 DOI: 10.7717/peerj.6941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022] Open
Abstract
Bcl-2 (B-cell lymphoma 2) protein is localized in the outer membrane of mitochondria, where it plays an important role in promoting cellular survival and inhibiting the actions of pro-apoptotic proteins. PRDM10 is a member of the PR/SET family of epigenetic regulators and may play a role in development and cell differentiation. Here we show that human PRDM10 contributes to the transcriptional regulation of human Bcl-2 gene. We found that PRDM10-depletion in human cells reduced the expression of Bcl-2 protein and over-expression of PRDM10 promoted Bcl-2 protein expression. Furthermore, luciferase reporter activity of Bcl-2 gene P1 promoter was significantly increased in cells co-transfected with PRDM10, and PRDM10 was able to bind to the Bcl-2 P1 promoter in vivo. Using The Cancer Genome Atlas (TCGA) data set, we found weak positive correlation between PRDM10 and Bcl-2 in several cancer types including cancers of the breast, colon, and lung tissues. These data identify a novel function for PRDM10 protein and provide insights on the transcriptional control of Bcl-2 expression.
Collapse
Affiliation(s)
- Na Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Taobo Hu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuanyuan Gui
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jieying Gao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shi Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|
44
|
PRDM1 levels are associated with clinical diseases in chronic HBV infection and survival of patients with HBV-related hepatocellular carcinoma. Int Immunopharmacol 2019; 73:156-162. [PMID: 31100710 DOI: 10.1016/j.intimp.2019.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022]
Abstract
PR domain zinc finger protein 1 (PRDM1)/B lymphocyte-induced maturation protein 1 (BLIMP1) is a transcriptional repressor involved in B and T cell responses which are implicated in chronic hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC). This study investigated the association of PRDM1 with clinical diseases of chronic HBV infection and prognosis of HBV -related HCC patients. Serum PRDM1 levels were determined in 403 patients with chronic HBV infection (171 chronic hepatitis, 119 cirrhosis and 113 HCC), 70 HBV infection resolvers and 96 healthy control individuals. The PRDM1 levels were analyzed with regard to clinical diseases and overall survival of HCC patients. Serum PRDM1 concentrations in patients with chronic HBV infection were significantly elevated compared with infection resolvers and healthy controls. HBV-related HCC patients had the most significantly elevated PRDM1 levels. PRDM1 levels could considerably differentiate HCC from chronic hepatitis [area under receiver operating characteristic curve (AUC) 0.889, p < 0.001] or cirrhosis (AUC 0.910, p < 0.001). HCC patients with high PRDM1 levels had a poor prognosis (>300 pg/mL vs. ≤300 pg/mL, p = 0.001). High PRDM1 levels were independently associated with increased mortality in HCC patients (hazard ratio 2.997, 95% confidence interval 1.103-4.722, p = 0.003). Overall, this study demonstrated that PRDM1 levels are associated with the clinical diseases of chronic HBV infection. Highly elevated PRDM1 levels are discriminative of HCC from other clinical diseases and indicative of a poor prognosis of HCC patients. The potential association of PRDM1 levels with disease progression and treatment response warrants further investigation.
Collapse
|
45
|
Puls F, Pillay N, Fagman H, Palin-Masreliez A, Amary F, Hansson M, Kindblom LG, McCulloch TA, Meligonis G, Muc R, Rissler P, Sumathi VP, Tirabosco R, Hofvander J, Magnusson L, Nilsson J, Flanagan AM, Mertens F. PRDM10-rearranged Soft Tissue Tumor: A Clinicopathologic Study of 9 Cases. Am J Surg Pathol 2019; 43:504-513. [PMID: 30570551 DOI: 10.1097/pas.0000000000001207] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene fusion transcripts containing PRDM10 were recently identified in low-grade undifferentiated pleomorphic sarcomas (UPS). Here, we describe the morphologic and clinical features of 9 such tumors from 5 men and 4 women (age: 20 to 61 y). Three cases had previously been diagnosed as UPS, 3 as superficial CD34-positive fibroblastic tumor (SCD34FT), 2 as pleomorphic liposarcoma, and 1 as pleomorphic hyalinizing angiectatic tumor. The tumors were located in the superficial and deep soft tissues of the thigh/knee region (4 cases), shoulder (2 cases), foot, trunk, and perineum (1 case each) ranging in size from 1 to 6 cm. All showed poorly defined cellular fascicles of pleomorphic cells within a fibrous stroma with frequent myxoid change and a prominent inflammatory infiltrate. All displayed highly pleomorphic nuclear features, but a low mitotic count. Most tumors were well circumscribed. One of 9 tumors recurred locally, but none metastasized. Immunohistochemically, all were CD34 and showed nuclear positivity for PRDM10; focal positivity for cytokeratins was seen in 5/6 cases. PRDM10 immunoreactivity was evaluated in 50 soft tissue tumors that could mimic PRDM10-rearranged tumors, including 4 cases exhibiting histologic features within the spectrum of SCD34FT. Except for 2/6 pleomorphic liposarcomas and 1/4 myxofibrosarcomas, other tumors did not show nuclear positivity but displayed weak to moderate cytoplasmic immunoreactivity. In conclusion, PRDM10-rearranged soft tissue tumor is characterized by pleomorphic morphology and a low mitotic count. Its morphologic spectrum overlaps with SCD34FT. Clinical features of this small series suggest an indolent behavior, justifying its distinction from UPS and other sarcomas.
Collapse
Affiliation(s)
- Florian Puls
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg
| | - Nischalan Pillay
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore
- Research Department of Pathology, University College London Cancer Institute, London
| | - Henrik Fagman
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg
| | - Anne Palin-Masreliez
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg
| | - Fernanda Amary
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore
| | - Magnus Hansson
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg
| | - Lars-Gunnar Kindblom
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg
| | - Tom A McCulloch
- Department of Histopathology, Nottingham City Hospital, Nottingham
| | | | - Ronald Muc
- Department of Histopathology, Heartlands Hospital, Birmingham
| | - Pehr Rissler
- Department of Clinical Genetics and Pathology, University and Regional Laboratories, Skåne University Hospital, Lund University
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Birmingham, UK
| | - Roberto Tirabosco
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore
| | - Jakob Hofvander
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Adrienne M Flanagan
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore
- Research Department of Pathology, University College London Cancer Institute, London
| | - Fredrik Mertens
- Department of Clinical Genetics and Pathology, University and Regional Laboratories, Skåne University Hospital, Lund University
- Department of Clinical Genetics, Lund University, Lund, Sweden
| |
Collapse
|
46
|
Prdm12 Directs Nociceptive Sensory Neuron Development by Regulating the Expression of the NGF Receptor TrkA. Cell Rep 2019; 26:3522-3536.e5. [DOI: 10.1016/j.celrep.2019.02.097] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
|
47
|
Functional relevance of genes predicted to be affected by epigenetic alterations in atypical teratoid/rhabdoid tumors. J Neurooncol 2018; 141:43-55. [DOI: 10.1007/s11060-018-03018-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/28/2018] [Indexed: 02/01/2023]
|
48
|
Sorrentino A, Federico A, Rienzo M, Gazzerro P, Bifulco M, Ciccodicola A, Casamassimi A, Abbondanza C. PR/SET Domain Family and Cancer: Novel Insights from the Cancer Genome Atlas. Int J Mol Sci 2018; 19:ijms19103250. [PMID: 30347759 PMCID: PMC6214140 DOI: 10.3390/ijms19103250] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
The PR/SET domain gene family (PRDM) encodes 19 different transcription factors that share a subtype of the SET domain [Su(var)3-9, enhancer-of-zeste and trithorax] known as the PRDF1-RIZ (PR) homology domain. This domain, with its potential methyltransferase activity, is followed by a variable number of zinc-finger motifs, which likely mediate protein⁻protein, protein⁻RNA, or protein⁻DNA interactions. Intriguingly, almost all PRDM family members express different isoforms, which likely play opposite roles in oncogenesis. Remarkably, several studies have described alterations in most of the family members in malignancies. Here, to obtain a pan-cancer overview of the genomic and transcriptomic alterations of PRDM genes, we reanalyzed the Exome- and RNA-Seq public datasets available at The Cancer Genome Atlas portal. Overall, PRDM2, PRDM3/MECOM, PRDM9, PRDM16 and ZFPM2/FOG2 were the most mutated genes with pan-cancer frequencies of protein-affecting mutations higher than 1%. Moreover, we observed heterogeneity in the mutation frequencies of these genes across tumors, with cancer types also reaching a value of about 20% of mutated samples for a specific PRDM gene. Of note, ZFPM1/FOG1 mutations occurred in 50% of adrenocortical carcinoma patients and were localized in a hotspot region. These findings, together with OncodriveCLUST results, suggest it could be putatively considered a cancer driver gene in this malignancy. Finally, transcriptome analysis from RNA-Seq data of paired samples revealed that transcription of PRDMs was significantly altered in several tumors. Specifically, PRDM12 and PRDM13 were largely overexpressed in many cancers whereas PRDM16 and ZFPM2/FOG2 were often downregulated. Some of these findings were also confirmed by real-time-PCR on primary tumors.
Collapse
Affiliation(s)
- Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
| | - Antonio Federico
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Salerno, Italy.
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Alfredo Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
| |
Collapse
|
49
|
Chen Z, Gao W, Pu L, Zhang L, Han G, Zuo X, Zhang Y, Li X, Shen H, Wu J, Wang X. PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1. Hepatology 2018; 68:994-1009. [PMID: 29572888 DOI: 10.1002/hep.29890] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/01/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major leading cause of cancer mortality worldwide. PRDI-BF1 and RIZ homology domain containing 8 (PRDM8) is a key regulator in neural development and testis steroidogenesis; however, its role in liver carcinogenesis remains to be investigated. In this study, PRDM8 was found to be down-regulated in HCC, which was linked with shorter recurrence-free survival. Lentiviral-based overexpression and knockdown approaches showed that PRDM8 inhibited HCC cell proliferation, migration, and invasion. PRDM8 caused G1/S cell cycle arrest and induced apoptosis. An in vivo tumor model confirmed the antitumor role of PRDM8 in HCC growth and metastasis. Mechanistic study showed that PRDM8 suppressed the PI3K/AKT/mTOR signaling cascade through the regulation of nucleosome assembly protein 1-like 1 (NAP1L1). Conclusion: PRDM8 as a functional tumor suppressor is frequently down-regulated in HCC. Through regulating NAP1L1, PRDM8 inhibits PI3K/AKT/mTOR signaling in HCC. PRDM8 is a potential target for therapies of HCC. (Hepatology 2018).
Collapse
Affiliation(s)
- Zhiqiang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liyong Pu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Long Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Guoyong Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xueliang Zuo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Yao Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xiangcheng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jindao Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| |
Collapse
|
50
|
PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility. Genes (Basel) 2018; 9:genes9080391. [PMID: 30071651 PMCID: PMC6116052 DOI: 10.3390/genes9080391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/16/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
There is a correlation between cryptorchidism and an increased risk of testicular cancer and infertility. During orchidopexy, testicular biopsies are performed to confirm the presence of type A dark (Ad) spermatogonia, which are a marker for low infertility risk (LIR). The Ad spermatogonia are absent in high infertility risk (HIR) patients, who are treated with a gonadotropin-releasing hormone agonist (GnRHa) to significantly lower the risk of infertility. Despite its prevalence, little is known about the molecular events involved in cryptorchidism. Previously, we compared the transcriptomes of LIR versus HIR patients treated with and without hormones. Here, we interpreted data regarding members of the positive regulatory domain-containing (PRDM) family; some of which encoded histone methyltransferases that are important for reproduction. We found there were lower levels of PRDM1, PRDM6, PRDM9, PRDM13, and PRDM14 mRNA in the testes of HIR patients compared with LIR patients, and that PRDM7, PRDM9, PRDM12, and PRDM16 were significantly induced after GnRHa treatment. Furthermore, we observed PRDM9 protein staining in the cytoplasm of germ cells in the testes from LIR and HIR patients, indicating that the mRNA and protein levels corresponded. This result indicated that the curative hormonal therapy for cryptorchidism involved conserved chromatin modification enzymes.
Collapse
|