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Liu W, Liu Y, Chen S, Hui J, He S. AURKB promotes immunogenicity and immune infiltration in clear cell renal cell carcinoma. Discov Oncol 2024; 15:286. [PMID: 39014265 PMCID: PMC11252114 DOI: 10.1007/s12672-024-01141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Chromatin regulators (CRs) are capable of causing epigenetic alterations, which are significant features of cancer. However, the function of CRs in controlling Clear Cell Renal Cell Carcinoma (ccRCC) is not well understood. This research aims to discover a CRs prognostic signature in ccRCC and to elucidate the roles of CRs-related genes in tumor microenvironment (TME). METHODS Expression profiles and relevant clinical annotations were retrieved from the Cancer Genome Atlas (TCGA) and UCSC Xena platform for progression-free survival (PFS) data. The R package "limma" was used to identify differentially expressed CRs. A predictive model based on five CRs was developed using LASSO-Cox analysis. The model's predictive power and applicability were validated using K-M curves, ROC curves, nomograms, comparisons with other models, stratified survival analyses, and validation with the ICGC cohort. GO and GSEA analyses were performed to investigate mechanisms differentiating low and high riskScore groups. Immunogenicity was assessed using Tumor Mutational Burden (TMB), immune cell infiltrations were inferred, and immunotherapy was evaluated using immunophenogram analysis and the expression patterns of human leukocyte antigen (HLA) and checkpoint genes. Differentially expressed CRs (DECRs) between low and high riskScore groups were identified using log2|FC|> 1 and FDR < 0.05. AURKB, one of the high-risk DECRs and a component of our prognostic model, was selected for further analysis. RESULTS We constructed a 5 CRs signature, which demonstrated a strong capacity to predict survival and greater applicability in ccRCC. Elevated immunogenicity and immune infiltration in the high riskScore group were associated with poor prognosis. Immunotherapy was more effective in the high riskScore group, and certain chemotherapy medications, including cisplatin, docetaxel, bleomycin, and axitinib, had lower IC50 values. Our research shows that AURKB is critical for the immunogenicity and immune infiltration of the high riskScore group. CONCLUSION Our study produced a reliable prognostic prediction model using only 5 CRs. We found that AURKB promotes immunogenicity and immune infiltration. This research provides crucial support for the development of prognostic biomarkers and treatment strategies for ccRCC.
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Affiliation(s)
- Weihao Liu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ying Liu
- Department of Oncology, Huadu District People's Hospital of Guangzhou, Guangzhou, 510810, Guangdong, China
| | - Shisheng Chen
- Department of Urology, Dongguan Tungwah Hospital, Dongguan, 523110, Guangdong, China
| | - Jialiang Hui
- Department of Organ Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Shuhua He
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Hoang PM, Torre D, Jaynes P, Ho J, Mohammed K, Alvstad E, Lam WY, Khanchandani V, Lee JM, Toh CMC, Lee RX, Anbuselvan A, Lee S, Sebra RP, Martin J Walsh, Marazzi I, Kappei D, Guccione E, Jeyasekharan AD. A PRMT5-ZNF326 axis mediates innate immune activation upon replication stress. SCIENCE ADVANCES 2024; 10:eadm9589. [PMID: 38838142 DOI: 10.1126/sciadv.adm9589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
DNA replication stress (RS) is a widespread phenomenon in carcinogenesis, causing genomic instability and extensive chromatin alterations. DNA damage leads to activation of innate immune signaling, but little is known about transcriptional regulators mediating such signaling upon RS. Using a chemical screen, we identified protein arginine methyltransferase 5 (PRMT5) as a key mediator of RS-dependent induction of interferon-stimulated genes (ISGs). This response is also associated with reactivation of endogenous retroviruses (ERVs). Using quantitative mass spectrometry, we identify proteins with PRMT5-dependent symmetric dimethylarginine (SDMA) modification induced upon RS. Among these, we show that PRMT5 targets and modulates the activity of ZNF326, a zinc finger protein essential for ISG response. Our data demonstrate a role for PRMT5-mediated SDMA in the context of RS-induced transcriptional induction, affecting physiological homeostasis and cancer therapy.
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Affiliation(s)
- Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jessica Ho
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Alvstad
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Wan Yee Lam
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jie Min Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chin Min Clarissa Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akshaya Anbuselvan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Robert P Sebra
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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3
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Mao J, Song F, Zhang Y, Li Y, Inchingolo R, Chauhan A, Midorikawa Y, Chen Z, Tang W. Development and validation of a chromatin regulator signature for predicting prognosis hepatocellular carcinoma patient. J Gastrointest Oncol 2024; 15:397-414. [PMID: 38482221 PMCID: PMC10932653 DOI: 10.21037/jgo-23-996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/01/2024] [Indexed: 12/11/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a malignancy with a bleak prognosis. Although emerging research increasingly supports the involvement of chromatin regulators (CRs) in cancer development, CRs in HCC patients have not received proportionate attention. This study aimed to investigate the role and prognostic significance of CRs in HCC patients, providing new insights for clinical diagnosis and treatment strategies. METHODS We analyzed 424 samples in The Cancer Genome Atlas-Liver hepatocellular carcinoma (TCGA-LIHC) data to identify key CR genes associated with HCC prognosis by differential expression and univariate Cox regression analyses. LASSO-multivariate Cox regression method was used for construction of a prognostic signature and development of a CR-related prognosis model. The prognosis capacity of the model was evaluated via Kaplan-Meier method. Relationship between the model and tumor microenvironment (TME) was evaluated. Additionally, clinical variables and the model were incorporated to create a nomogram. The role of the prognostic gene MRG-binding protein (MRGBP) in HCC was elucidated by immunohistochemistry and semiquantitative analysis. RESULTS A risk score model, comprising B-lymphoma Mo-MLV insertion region 1 (BMI1), chromobox 2 (CBX2), and MRGBP, was constructed. The area under the curve (AUC) of the CR-based signature is 0.698 (P<0.05), exhibiting robust predictive power. Functional and pathway analyses illuminated the biological relevance of these genes. Immune microenvironment analysis suggested potential implications for immunotherapy. Drug sensitivity analysis identified agents for targeted treatment. Clinical samples show that MRGBP is highly expressed in HCC tissues. CONCLUSIONS This CR-based signature shows promise as a valuable prognostic tool for HCC patients. It demonstrates predictive capabilities, independence from other clinical factors, and potential clinical applicability. In addition, we need more experiments to validate our findings. These findings offer insights into HCC prognosis and treatment, with implications for personalized medicine and improved patient outcomes.
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Affiliation(s)
- Jiazhen Mao
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Fei Song
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yu Zhang
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yifan Li
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Riccardo Inchingolo
- Interventional Radiology Unit, “F. Miulli” Regional General Hospital, Bari, Italy
| | - Aman Chauhan
- Division of Medical Oncology, Department of Internal Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Yutaka Midorikawa
- Department of Surgery, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Zhong Chen
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Weidong Tang
- Department of Hepatobiliary Pancreatic Splenic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of General Surgery, Nantong Elderly Rehabilitation Hospital, Nantong, China
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Liu YS, Wang JX, Jin GY, Hu MH, Wang XD. Combination Therapy with a TLR7 Agonist and a BRD4 Inhibitor Suppresses Tumor Growth via Enhanced Immunomodulation. Int J Mol Sci 2024; 25:663. [PMID: 38203835 PMCID: PMC10779224 DOI: 10.3390/ijms25010663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
JQ-1 is a typical BRD4 inhibitor with the ability to directly fight tumor cells and evoke antitumor immunity via reducing the expression of PD-L1. However, problems arise with the development of JQ-1 in clinical trials, such as marked lymphoid and hematopoietic toxicity, leading to the investigation of combination therapy. SZU-101 is a TLR7 agonist designed and synthesized by our group with potent immunostimulatory activity. Therefore, we hypothesized that combination therapy of SZU-101 and JQ-1 would target innate immunity and adaptive immunity simultaneously, to achieve a better antitumor efficacy than monotherapy. In this study, the repressive effects of the combination administration on tumor growth and metastasis were demonstrated in both murine breast cancer and melanoma models. In 4T1 tumor-bearing mice, i.t. treatment with SZU-101 in combination with i.p. treatment with JQ-1 suppressed the growth of tumors at both injected and uninjected sites. Combination therapy increased M1/M2 ratio in TAMs, decreased PD-L1 expression and promoted the recruitment of activated CD8+ T cells in the TME. In summary, the improved therapeutic efficacy of the novel combination therapy appears to be feasible for the treatment of a diversity of cancers.
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Affiliation(s)
| | | | | | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China; (Y.-S.L.); (J.-X.W.); (G.-Y.J.)
| | - Xiao-Dong Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China; (Y.-S.L.); (J.-X.W.); (G.-Y.J.)
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5
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Wang B, Feng Y, Li Z, Zhou F, Luo J, Yang B, Long S, Li X, Liu Z, Li X, Chen J, Wang L, Wei W. Identification and validation of chromatin regulator-related signatures as a novel prognostic model for low-grade gliomas using translational bioinformatics. Life Sci 2024; 336:122312. [PMID: 38042284 DOI: 10.1016/j.lfs.2023.122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
AIMS The purpose of this study is to explore the potential biological role and prognostic significance of chromatin regulators (CRs) in low-grade gliomas (LGGs). MAIN METHODS CRs were obtained from the FACER database. Transcription profiles of LGG patients were collected from the TCGA and CGGA databases. Differentially expressed CRs (DECRs) between LGGs and normal controls were identified using DESeq2. The consensus clustering algorithm was employed to distinguish subtypes of LGGs based on prognosis-related DECRs. The differences in clinical and molecular characteristics between different subtypes were explored. R packages, GSVA, ssGSEA, and ESTIMATE were utilized to elucidate the tumor microenvironment and activated pathways in different subtypes. Subsequently, a CRs-related signature was developed using LASSO Cox regression. Its performance was evaluated by Kaplan-Meier curve and ROC curve analyses. In vitro experiments were performed to explore the function of JADE3 in LGGs, which predominantly expressed in glioma cells. KEY FINDINGS We identified 43 DECRs and two CRs-related subtypes of LGGs. The subtype characterized by shorter survival displayed significant enrichment for pathways associated with DNA damage response and repair, along with heightened immune cell infiltration. Furthermore, the CRs-based signature exhibited excellent prognostic performance in both the TCGA and CGGA databases. Knockdown of JADE3 significantly increased the invasion, migration, and proliferation abilities of Hs683. SIGNIFICANCE Our study reveals the aberrant expression and prognostic value of CRs in LGGs. It emphasizes the potential regulatory role of CRs in the microenvironment and DNA damage repair in LGGs. JADE3 could be a possible therapeutic target for LGGs.
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Affiliation(s)
- Bo Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Feng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Fan Zhou
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China
| | - Jie Luo
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China
| | - Bin Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shengrong Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinyi Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Zhenyuan Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Lei Wang
- Huanggang Central Hospital of Yangtze University, Hubei 438000, China.
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China; Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Santorsola M, Capuozzo M, Savarese G, Ianniello M, Petrillo N, Casillo M, Sabbatino F, Perri F, Ferrara F, Zovi A, Berretta M, Granata V, Nasti G, Ottaiano A. Oligo-Metastatic Disease in Oncology: Exploring the Limits and the Potential of Genetic Assessment. Genes (Basel) 2023; 14:2131. [PMID: 38136953 PMCID: PMC10742616 DOI: 10.3390/genes14122131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Oligo-metastatic disease (OMD) in the field of oncology denotes a distinct subset of metastatic tumors characterized by less aggressive biological behavior and extended survival times in comparison to their widely metastatic counterparts. While there is a general consensus regarding the existence of OMD, there remains a lack of widely accepted criteria for its a priori identification at the time of presentation. This review delves into the concept of OMD, placing a particular emphasis on the significance of understanding the limitations and potential of genetic assessments. It explores how these aspects are crucial in advancing our comprehension of this phenomenon. In a rapidly advancing era of precision medicine, understanding the intricacies of OMD opens up exciting possibilities for tailored treatment approaches. By elucidating the genetic underpinnings and dynamic nature of this condition, we stand to improve patient outcomes and potentially shift the paradigm of metastatic cancer management.
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Affiliation(s)
- Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via Mariano Semmola, 80131 Napoli, Italy; (M.S.); (F.P.); (V.G.); (G.N.)
| | | | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (M.I.); (N.P.); (M.C.)
| | - Monica Ianniello
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (M.I.); (N.P.); (M.C.)
| | - Nadia Petrillo
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (M.I.); (N.P.); (M.C.)
| | - Marika Casillo
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (M.I.); (N.P.); (M.C.)
| | - Francesco Sabbatino
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Baronissi, Italy;
| | - Francesco Perri
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via Mariano Semmola, 80131 Napoli, Italy; (M.S.); (F.P.); (V.G.); (G.N.)
| | - Francesco Ferrara
- Hospital Pharmacist Manager, Pharmaceutical Department, Asl Napoli 3 Sud, Via Dell’amicizia 22, 80035 Nola, Italy;
| | - Andrea Zovi
- Hospital Pharmacist, Ministry of Health, Viale Giorgio Ribotta 5, 00144 Rome, Italy;
| | - Massimiliano Berretta
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy;
| | - Vincenza Granata
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via Mariano Semmola, 80131 Napoli, Italy; (M.S.); (F.P.); (V.G.); (G.N.)
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via Mariano Semmola, 80131 Napoli, Italy; (M.S.); (F.P.); (V.G.); (G.N.)
| | - Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via Mariano Semmola, 80131 Napoli, Italy; (M.S.); (F.P.); (V.G.); (G.N.)
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Cheng MW, Mitra M, Coller HA. Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Commun Biol 2023; 6:1138. [PMID: 37973839 PMCID: PMC10654613 DOI: 10.1038/s42003-023-05459-w] [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: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.
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Affiliation(s)
- Michael W Cheng
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hilary A Coller
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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Haan D, Bergamaschi A, Friedl V, Guler GD, Ning Y, Reggiardo R, Kesling M, Collins M, Gibb B, Hazen K, Bates S, Antoine M, Fraire C, Lopez V, Malta R, Nabiyouni M, Nguyen A, Phillips T, Riviere M, Leighton A, Ellison C, McCarthy E, Scott A, Gigliotti L, Nilson E, Sheard J, Peters M, Bethel K, Chowdhury S, Volkmuth W, Levy S. Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA. Clin Gastroenterol Hepatol 2023; 21:1802-1809.e6. [PMID: 36967102 DOI: 10.1016/j.cgh.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/05/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND & AIMS Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bill Gibb
- ClearNote Health, San Mateo, California
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Li Y, Xiong C, Wu LL, Zhang BY, Wu S, Chen YF, Xu QH, Liao HF. Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma. Pathol Oncol Res 2023; 29:1610980. [PMID: 37362244 PMCID: PMC10287976 DOI: 10.3389/pore.2023.1610980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.
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Affiliation(s)
- Yue Li
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Chao Xiong
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Li Li Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Bo Yuan Zhang
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Sha Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Yu Fen Chen
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Qi Hua Xu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Hong Fei Liao
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
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10
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Zhang J, Hu Z, Chung HH, Tian Y, Lau KW, Ser Z, Lim YT, Sobota RM, Leong HF, Chen BJ, Yeo CJ, Tan SYX, Kang J, Tan DEK, Sou IF, McClurg UL, Lakshmanan M, Vaiyapuri TS, Raju A, Wong ESM, Tergaonkar V, Rajarethinam R, Pathak E, Tam WL, Tan EY, Tee WW. Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis. Nat Commun 2023; 14:2439. [PMID: 37117180 PMCID: PMC10147683 DOI: 10.1038/s41467-023-38132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
Cancer cells undergo transcriptional reprogramming to drive tumor progression and metastasis. Using cancer cell lines and patient-derived tumor organoids, we demonstrate that loss of the negative elongation factor (NELF) complex inhibits breast cancer development through downregulating epithelial-mesenchymal transition (EMT) and stemness-associated genes. Quantitative multiplexed Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins (qPLEX-RIME) further reveals a significant rewiring of NELF-E-associated chromatin partners as a function of EMT and a co-option of NELF-E with the key EMT transcription factor SLUG. Accordingly, loss of NELF-E leads to impaired SLUG binding on chromatin. Through integrative transcriptomic and genomic analyses, we identify the histone acetyltransferase, KAT2B, as a key functional target of NELF-E-SLUG. Genetic and pharmacological inactivation of KAT2B ameliorate the expression of EMT markers, phenocopying NELF ablation. Elevated expression of NELF-E and KAT2B is associated with poorer prognosis in breast cancer patients, highlighting the clinical relevance of our findings. Taken together, we uncover a crucial role of the NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis.
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Affiliation(s)
- Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore
| | - Zhenhua Hu
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwa Hwa Chung
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yun Tian
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, 210004, Nanjing, People's Republic of China
| | - Kah Weng Lau
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Benjamin Jieming Chen
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Clarisse Jingyi Yeo
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jian Kang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Dennis Eng Kiat Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Ieng Fong Sou
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Urszula Lucja McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Anandhkumar Raju
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Esther Sook Miin Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Vinay Tergaonkar
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Ravisankar Rajarethinam
- Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Elina Pathak
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
| | - Wai Leong Tam
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Ern Yu Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Republic of Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
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11
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Duan W, Yu M, Chen J. BRD4: New Hope in the Battle Against Glioblastoma. Pharmacol Res 2023; 191:106767. [PMID: 37061146 DOI: 10.1016/j.phrs.2023.106767] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
The BET family proteins, comprising BRD2, BRD3 and BRD4, represent epigenetic readers of acetylated histone marks that play pleiotropic roles in the tumorigenesis and growth of multiple human malignancies, including glioblastoma (GBM). A growing body of investigation has proven BET proteins as valuable therapeutic targets for cancer treatment. Recently, several BRD4 inhibitors and degraders have been reported to successfully suppress GBM in preclinical and clinical studies. However, the precise role and mechanism of BRD4 in the pathogenesis of GBM have not been fully elucidated or summarized. This review focuses on summarizing the roles and mechanisms of BRD4 in the context of the initiation and development of GBM. In addition, several BRD4 inhibitors have been evaluated for therapeutic purposes as monotherapy or in combination with chemotherapy, radiotherapy, and immune therapies. Here, we provide a critical appraisal of studies evaluating various BRD4 inhibitors and degraders as novel treatment strategies against GBM.
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Affiliation(s)
- Weichen Duan
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Miao Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jiajia Chen
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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12
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Ottaiano A, Santorsola M, Circelli L, Trotta AM, Izzo F, Perri F, Cascella M, Sabbatino F, Granata V, Correra M, Tarotto L, Stilo S, Fiore F, Martucci N, Rocca AL, Picone C, Muto P, Borzillo V, Belli A, Patrone R, Mercadante E, Tatangelo F, Ferrara G, Di Mauro A, Scognamiglio G, Berretta M, Capuozzo M, Lombardi A, Galon J, Gualillo O, Pace U, Delrio P, Savarese G, Scala S, Nasti G, Caraglia M. Oligo-Metastatic Cancers: Putative Biomarkers, Emerging Challenges and New Perspectives. Cancers (Basel) 2023; 15:cancers15061827. [PMID: 36980713 PMCID: PMC10047282 DOI: 10.3390/cancers15061827] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Some cancer patients display a less aggressive form of metastatic disease, characterized by a low tumor burden and involving a smaller number of sites, which is referred to as "oligometastatic disease" (OMD). This review discusses new biomarkers, as well as methodological challenges and perspectives characterizing OMD. Recent studies have revealed that specific microRNA profiles, chromosome patterns, driver gene mutations (ERBB2, PBRM1, SETD2, KRAS, PIK3CA, SMAD4), polymorphisms (TCF7L2), and levels of immune cell infiltration into metastases, depending on the tumor type, are associated with an oligometastatic behavior. This suggests that OMD could be a distinct disease with specific biological and molecular characteristics. Therefore, the heterogeneity of initial tumor burden and inclusion of OMD patients in clinical trials pose a crucial methodological question that requires responses in the near future. Additionally, a solid understanding of the molecular and biological features of OMD will be necessary to support and complete the clinical staging systems, enabling a better distinction of metastatic behavior and tailored treatments.
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Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Luisa Circelli
- AMES, Centro Polidiagnostico Strumentale SRL, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy
| | - Anna Maria Trotta
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Francesco Izzo
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Francesco Perri
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Marco Cascella
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Francesco Sabbatino
- Oncology Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Baronissi, Italy
| | - Vincenza Granata
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Marco Correra
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Luca Tarotto
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Salvatore Stilo
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Francesco Fiore
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Nicola Martucci
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Antonello La Rocca
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Carmine Picone
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Paolo Muto
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Valentina Borzillo
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Andrea Belli
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Renato Patrone
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Edoardo Mercadante
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Fabiana Tatangelo
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Gerardo Ferrara
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Annabella Di Mauro
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Giosué Scognamiglio
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Massimiliano Berretta
- Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | | | - Angela Lombardi
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75006 Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Oreste Gualillo
- SERGAS (Servizo Galego de Saude) and NEIRID Lab (Neuroendocrine Interactions in Rheumatology and Inflammatory Diseases), Research Laboratory 9, IDIS (Instituto de Investigación Sanitaria de Santiago), Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Ugo Pace
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Paolo Delrio
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale SRL, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy
| | - Stefania Scala
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via Mariano Semmola, 80131 Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio 7, 80138 Naples, Italy
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13
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Wu Q, Tian R, Liu J, Ou C, Li Y, Fu X. Deciphering comprehensive features of tumor microenvironment controlled by chromatin regulators to predict prognosis and guide therapies in uterine corpus endometrial carcinoma. Front Immunol 2023; 14:1139126. [PMID: 36936912 PMCID: PMC10022674 DOI: 10.3389/fimmu.2023.1139126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Dysregulation of chromatin regulators (CRs) can perturb the tumor immune microenvironment, but the underlying mechanism remains unclear. We focused on uterine corpus endometrial carcinoma (UCEC) and used gene expression data from TCGA-UCEC to investigate this mechanism. Methods We used weighted gene co-expression network analysis (WGCNA) and consensus clustering algorithm to classify UCEC patients into Cluster_L and Cluster_H. TME-associated CRs were identified using WGCNA and differential gene expression analysis. A CR risk score (CRRS) was constructed using univariate Cox and LASSO-Cox regression analyses. A nomogram was developed based on CRRS and clinicopathologic factors to predict patients' prognosis. Results Lower CRRS was associated with lower grade, more benign molecular subtypes, and improved survival. Patients with low CRRS showed abundant immune infiltration, a higher mutation burden, fewer CNVs, and better response to immunotherapy. Moreover, low CRRS patients were more sensitive to 24 chemotherapeutic agents. Conclusion A comprehensive assessment of CRRS could identify immune activation and improve the efficacy of UCEC treatments.
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Affiliation(s)
- Qihui Wu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Ruotong Tian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaxin Liu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Chunlin Ou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
| | - Yimin Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
| | - Xiaodan Fu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Yimin Li, ; Chunlin Ou,
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14
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Xie J, Xiao X, Dong Z, Wang Q. The Systemic Inflammation Score is Associated with the Survival of Patients with Prostate Cancer. J Inflamm Res 2023; 16:963-975. [PMID: 36915616 PMCID: PMC10007981 DOI: 10.2147/jir.s385308] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/02/2023] [Indexed: 03/09/2023] Open
Abstract
Background The systemic inflammation score (SIS) based on the albumin (Alb) level and lymphocyte-to-monocyte ratio (LMR), has been associated with survival in some cancers. However, its prognostic role in prostate cancer (PCa) remains unclear. Methods The associations between the SIS and the clinicopathological features of PCa were evaluated. The correlations between the SIS and overall survival (OS) and progression-free survival (PFS) were assessed using Kaplan-Meier analysis and the Log rank test. Univariate and multivariate Cox analyses were conducted to determine the prognostic factors for PCa. Hazard ratios and 95% confidence intervals were calculated. Results A total of 253 patients with PCa were included in this study. The Kaplan-Meier analysis and Log rank test suggested that patients with a higher Alb level, higher LMR, or a lower SIS had better 5-year OS and PFS compared with patients with a lower Alb level or lower LMR or higher SIS. Univariate and multivariate Cox analyses showed that drinking, prostate-specific antigen level >100 ng/mL, and neutrophil-to-lymphocyte ratio >2.09 were significant prognostic factors for OS and PFS in patients with PCa. Nomograms for 5-year OS and PFS were established with concordance index values of 0.888 and 0.824, respectively. The calibration curve was consistent between the actual observations and the prediction nomogram for OS and PFS probability at 5 years. Conclusion A high SIS is associated with unfavorable survival in patients with PCa. The SIS serves as a novel independent prognostic factor for OS in patients with PCa.
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Affiliation(s)
- Jie Xie
- Department of Urology, the Fifth People's Hospital of Huai'an, Huai'an City, People's Republic of China
| | - Xu Xiao
- Department of Urology, the Fifth People's Hospital of Huai'an, Huai'an City, People's Republic of China
| | - Zhenjia Dong
- Department of Urology, the Fifth People's Hospital of Huai'an, Huai'an City, People's Republic of China
| | - Qiangdong Wang
- Department of Urology, the Fifth People's Hospital of Huai'an, Huai'an City, People's Republic of China
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15
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Li X, Huo X, Zhao C, Chen Z, Xu Z, Yu J, Sun X. A novel chromatin regulator signature predicts the prognosis, clinical features and immunotherapy of colon cancer. Epigenomics 2022; 14:1325-1341. [PMID: 36545887 DOI: 10.2217/epi-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To elucidate the potential function and prognostic value of chromatin regulators (CRs) in colon cancer. Materials & methods: A comprehensive analysis of CR RNA expression data from public databases was conducted. Results: The authors successfully established and validated a 17 CR-based signature using public databases. Ten CRs of the signature were eventually verified at the protein level using the Human Protein Atlas database. Functional enrichment showed that CRs were significantly enriched in cancer-related pathways. This signature was remarkably relevant to immune cell infiltration, immune checkpoints, tumor immune dysfunction and exclusion (TIDE) score and drug sensitivity. Conclusion: The authors identified a novel, reliable prognostic signature for colon cancer. The study provided new insights into the function of CRs and has important clinical implications for immunotherapy for colon cancer.
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Affiliation(s)
- Xiaopeng Li
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiongwei Huo
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Chenye Zhao
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zilu Chen
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhengshui Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, China
| | - Junhui Yu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xuejun Sun
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
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16
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Liu Z, Yang H, Chen Z, Jing C. A novel chromatin regulator-related immune checkpoint related gene prognostic signature and potential candidate drugs for endometrial cancer patients. Hereditas 2022; 159:40. [PMID: 36253800 PMCID: PMC9578220 DOI: 10.1186/s41065-022-00253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/22/2022] [Indexed: 11/14/2022] Open
Abstract
Background Endometrial cancer (EC) is the most common gynecologic malignancy in developed countries and its prevalence is increasing. As an emerging therapy with a promising efficacy, immunotherapy has been extensively applied in the treatment of solid tumors. In addition, chromatin regulators (CRs), as essential upstream regulators of epigenetics, play a significant role in tumorigenesis and cancer development. Methods CRs and immune checkpoint-related genes (ICRGs) were obtained from the previous top research. The Genome Cancer Atlas (TCGA) was utilized to acquire the mRNA expression and clinical information of patients with EC. Correlation analysis was utilized for screen CRs-related ICRGs (CRRICRGs). By Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, prognosis related CRRICRGs were screened out and risk model was constructed. The Kaplan–Meier curve was used to estimate the prognosis between high- and low-risk group. By comparing the IC50 value, the drugs sensitivity difference was explored. We obtained small molecule drugs for the treatment of UCEC patients based on CAMP dataset. Results We successfully constructed a 9 CRRICRs-based prognostic signature for patients with UCEC and found the riskscore was an independent prognostic factor. The results of functional analysis suggested that CRRICRGs may be involved in immune processes associated with cancer. Immune characteristics analysis provided further evidence that the CRRICRGs-based model was correlated with immune cells infiltration and immune checkpoint. Eight small molecule drugs that may be effective for the treatment of UCEC patients were screened. Effective drugs identified by drug sensitivity profiling in high- and low-risk groups. Conclusion In summary, our study provided novel insights into the function of CRRICRGs in UCEC. We also developed a reliable prognostic panel for the survival of patients with UCEC. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00253-w.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Hongxia Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Ziyu Chen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Chunli Jing
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China.
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17
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Dai YW, Chen HB, Pan YT, Lv LX, Wang WM, Chen XH, Zhou X. Characterization of chromatin regulators identified prognosis and heterogeneity in hepatocellular carcinoma. Front Oncol 2022; 12:1002781. [PMID: 36158697 PMCID: PMC9505021 DOI: 10.3389/fonc.2022.1002781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Liver carcinogenesis is a multiprocess that involves complicated interactions between genetics, epigenetics, and transcriptomic alterations. Aberrant chromatin regulator (CR) expressions, which are vital regulatory epigenetics, have been found to be associated with multiple biological processes. Nevertheless, the impression of CRs on tumor microenvironment remodeling and hepatocellular carcinoma (HCC) prognosis remains obscure. Thus, this study aimed to systematically analyze CR-related patterns and their correlation with genomic features, metabolism, cuproptosis activity, and clinicopathological features of patients with HCC in The Cancer Genome Atlas, International Cancer Genome Consortium-LIRI-JP cohort, and GSE14520 that utilized unsupervised consensus clustering. Three CR-related patterns were recognized, and the CRs phenotype-related gene signature (CRsscore) was developed using the least absolute shrinkage and selection operator-Cox regression and multivariate Cox algorithms to represent the individual CR-related pattern. Additionally, the CRsscore was an independent prognostic index that served as a fine predictor for energy metabolism and cuproptosis activity in HCC. Accordingly, describing a wide landscape of CR characteristics may assist us to illustrate the sealed association between epigenetics, energy metabolism, and cuproptosis activity. This study may discern new tumor therapeutic targets and exploit personalized therapy for patients.
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Affiliation(s)
- Yin-wei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Han-bin Chen
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ya-ting Pan
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lin-xi Lv
- Wenzhou Medical University, Wenzhou, China
| | - Wei-ming Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-Hu Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Hu Chen, ; Xiang Zhou,
| | - Xiang Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Hu Chen, ; Xiang Zhou,
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18
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Li J, Jia Y, Tang L, Zhang R, Zhang Y. Identification of a chromatin regulator signature and potential prognostic ability for adrenocortical carcinoma. Front Genet 2022; 13:948353. [PMID: 36092868 PMCID: PMC9459121 DOI: 10.3389/fgene.2022.948353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Adrenocortical carcinoma (ACC) is a rare malignant tumor. Chromatin regulators (CRs) can drive epigenetic changes, which have been considered as one of the most vital hallmarks of tumors. This study aimed to explore the CR signature for ACC in order to clarify the molecular basis of ACC’s pathogenic mechanism and provide novel methods to diagnose and treat ACC clinically.Methods: This study obtained transcriptome sequencing datasets of ACC patients and sequencing data on normal adrenal tissues in TCGA and GTEx databases, respectively. Meanwhile, prognostic genes were selected through Lasso and Cox regression analyses. Using the transcriptome sequencing datasets of ACC patients downloaded from the GEO database to finish validation, we performed Kaplan–Meier (KM) analysis for evaluating the differential survival between low- and high-risk groups. Then, this work constructed the risk model for predicting ACC prognosis. TIMER 2.0 was employed to assess the differences in immune infiltration between the two groups. Furthermore, this work adopted the R package “pRRophetic” for exploring and estimating the sensitivity of patients to different chemotherapeutic agents.Results: A 5-CR model was established to predict ACC survival, and the CR signature was confirmed as a factor in order to independently predict ACC patient prognosis. In addition, a nomogram composed of the risk score and clinical T stage performed well in the prediction of patients’ prognosis. Differentially expressed CRs (DECRs) were mostly associated with the cell cycle, base excision repair, colon cancer, gene duplication, homologous recombination, and other signaling pathways for the high-risk group. As for the low-risk group, DECRs were mainly enriched in allograft rejection, drug metabolism of cytochrome P450, metabolism of xenogeneic organisms by cytochrome P450, retinol metabolism, and other signaling pathways. According to TIMER analysis, the immune infiltration degrees of endothelial cells, M2 macrophages, myeloid dendritic cells, CD4+ Th1 cells, NKT cells, and M0 macrophages showed significant statistical differences between the high- and low-risk groups, and high infiltration levels of M0 and M2 macrophages were more pronounced in higher T stage (T3 and T4), N stage (N1), and clinical stages (III and IV). In addition, high-risk cases exhibited higher sensitivity to etoposide and doxorubicin. Additionally, low-risk patients had significantly decreased expression of RRM1 compared with high-risk cases, suggesting the better effect of mitotane treatment.Conclusion: This study identified the DECRs, which might be related to ACC genesis and progression. The pathways enriched by these DECRs were screened, and these DECRs were verified with excellent significance for estimating ACC survival. Drug sensitivity analysis also supported the current clinical treatment plan. Moreover, this study will provide reliable ideas and evidence for diagnosing and treating ACC in the clinic.
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Affiliation(s)
- Junwu Li
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuanzhen Jia
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ronggui Zhang
- Department of Urology, Chongqing Emergency Medical Center, Chongqing, China
| | - Yuanfeng Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Yuanfeng Zhang,
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19
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Jia X, Zhang G. Characterization of chromatin regulators in hepatocellular carcinoma to guide clinical therapy. Front Genet 2022; 13:961018. [PMID: 36092923 PMCID: PMC9452841 DOI: 10.3389/fgene.2022.961018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is notorious for its high mortality and incidence. Accumulating evidence confirms that chromatin regulators (CRs) have a significant impact on cancer. Therefore, exploring the mode of action and prognostic value of CRs is imminent for the treatment of hepatocellular carcinoma. Method: Transcriptome and clinical data for this study have been downloaded from TCGA (https://portal.gdc.cancer.gov/) and ICGC (https://dcc.icgc.org/). Univariate analysis was used to screen CRs with prognostic value, and our prognostic risk score signature was developed using least absolute shrinkage along with selection operator (lasso) Cox regression analysis. The CRs-based prognostic model was constructed in the TCGA dataset, and low-risk HCC patients had a better prognosis, which was finally validated in the ICGC dataset. We used the receiver operating characteristic curve to identify the accuracy of the prediction model and establish a line chart to prove the clinical effectiveness of the model. We also discussed the differences in drug sensitivity via CellMiner database, tumor immune microenvironment via ssGSEA algorithm, and clinical characteristics among different risk groups. Results: A prognostic model consisting of seven CRs was constructed and verified in HCC patients. Furthermore, we found that this risk score prognostic signature could independently predict the prognosis of HCC patients. Functional enrichment analysis revealed that CRs are mainly associated with cancer-related signaling pathways and metabolic pathways. In addition, immune cell abundance correlates with risk score levels Conclusion: In brief, we systematically explored the mode of action of CRs in HCC patients and established a reliable prognostic prediction model.
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Affiliation(s)
- Xiangen Jia
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
| | - Guozhi Zhang
- North China University of Science and Technology Affiliated Hospital, Tangshan, China
- North China University of Science and Technology, Tangshan, China
- *Correspondence: Guozhi Zhang,
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20
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Liu C, Zhou Y, Zhao D, Yu L, Zhou Y, Xu M, Tang L. Identification and validation of differentially expressed chromatin regulators for diagnosis of aortic dissection using integrated bioinformatics analysis and machine-learning algorithms. Front Genet 2022; 13:950613. [PMID: 36035141 PMCID: PMC9403720 DOI: 10.3389/fgene.2022.950613] [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: 05/23/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Aortic dissection (AD) is a life-threatening disease. Chromatin regulators (CRs) are indispensable epigenetic regulators. We aimed to identify differentially expressed chromatin regulators (DECRs) for AD diagnosis. Methods: We downloaded the GSE52093 and GSE190635 datasets from the Gene Expression Omnibus database. Following the merging and processing of datasets, bioinformatics analysis was applied to select candidate DECRs for AD diagnosis: CRs exertion; DECR identification using the “Limma” package; analyses of enrichment of function and signaling pathways; construction of protein–protein interaction (PPI) networks; application of machine-learning algorithms; evaluation of receiver operating characteristic (ROC) curves. GSE98770 served as the validation dataset to filter DECRs. Moreover, we collected peripheral-blood samples to further validate expression of DECRs by real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Finally, a nomogram was built for clinical use. Results: A total of 841 CRs were extracted from the merged dataset. Analyses of functional enrichment of 23 DECRs identified using Limma showed that DECRs were enriched mainly in epigenetic-regulation processes. From the PPI network, 17 DECRs were selected as node DECRs. After machine-learning calculations, eight DECRs were chosen from the intersection of 13 DECRs identified using support vector machine recursive feature elimination (SVM-RFE) and the top-10 DECRs selected using random forest. DECR expression between the control group and AD group were considerably different. Moreover, the area under the ROC curve (AUC) of each DECR was >0.75, and four DECRs (tumor protein 53 (TP53), chromobox protein homolog 7 (CBX7), Janus kinase 2 (JAK2) and cyclin-dependent kinase 5 (CDK5)) were selected as candidate biomarkers after validation using the external dataset and clinical samples. Furthermore, a nomogram with robust diagnostic value was established (AUC = 0.960). Conclusion: TP53, CBX7, JAK2, and CDK5 might serve as diagnostic DECRs for AD diagnosis. These DECRs were enriched predominantly in regulating epigenetic processes.
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Affiliation(s)
- Chunjiang Liu
- Department of General Surgery, Vascular Surgery Division, Shaoxing People’s Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, China
| | - Yufei Zhou
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Di Zhao
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Luchen Yu
- Case Western Reserve University, Cleveland, OH, United States
| | - Yue Zhou
- Department of General Surgery, Vascular Surgery Division, Shaoxing People’s Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, China
| | - Miaojun Xu
- Department of General Surgery, Vascular Surgery Division, Shaoxing People’s Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, China
| | - Liming Tang
- Department of General Surgery, Vascular Surgery Division, Shaoxing People’s Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, China
- *Correspondence: Liming Tang,
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21
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Zhu K, Wang Y, Sarlus H, Geng K, Nutma E, Sun J, Kung SY, Bay C, Han J, Min JH, Benito-Cuesta I, Lund H, Amor S, Wang J, Zhang XM, Kutter C, Guerreiro-Cacais AO, Högberg B, Harris RA. Myeloid cell-specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation. EMBO Rep 2022; 23:e54499. [PMID: 35593064 PMCID: PMC9253741 DOI: 10.15252/embr.202154499] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Targeting myeloid cells, especially microglia, for the treatment of neuroinflammatory diseases such as multiple sclerosis (MS), is underappreciated. Our in silico drug screening reveals topoisomerase 1 (TOP1) inhibitors as promising drug candidates for microglial modulation. We show that TOP1 is highly expressed in neuroinflammatory conditions, and TOP1 inhibition using camptothecin (CPT) and its FDA-approved analog topotecan (TPT) reduces inflammatory responses in microglia/macrophages and ameliorates neuroinflammation in vivo. Transcriptomic analyses of sorted microglia from LPS-challenged mice reveal an altered transcriptional phenotype following TPT treatment. To target myeloid cells, we design a nanosystem using β-glucan-coated DNA origami (MyloGami) loaded with TPT (TopoGami). MyloGami shows enhanced specificity to myeloid cells while preventing the degradation of the DNA origami scaffold. Myeloid-specific TOP1 inhibition using TopoGami significantly suppresses the inflammatory response in microglia and mitigates MS-like disease progression. Our findings suggest that TOP1 inhibition in myeloid cells represents a therapeutic strategy for neuroinflammatory diseases and that the myeloid-specific nanosystems we designed may also benefit the treatment of other diseases with dysfunctional myeloid cells.
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Affiliation(s)
- Keying Zhu
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Heela Sarlus
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Erik Nutma
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jingxian Sun
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai, China.,Shanghai Medical College, Fudan University, Shanghai, China
| | - Shin-Yu Kung
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Cindy Bay
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jinming Han
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jin-Hong Min
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Irene Benito-Cuesta
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Harald Lund
- Department of Physiology and Pharmacology, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Sandra Amor
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jun Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai, China.,Shanghai Medical College, Fudan University, Shanghai, China
| | - Xing-Mei Zhang
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - André Ortlieb Guerreiro-Cacais
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert A Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
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22
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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23
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Lou X, Gao H, Xu X, Ye Z, Zhang W, Wang F, Chen J, Zhang Y, Chen X, Qin Y, Yu X, Ji S. The Interplay of Four Main Pathways Recomposes Immune Landscape in Primary and Metastatic Gastroenteropancreatic Neuroendocrine Tumors. Front Oncol 2022; 12:808448. [PMID: 35664743 PMCID: PMC9158120 DOI: 10.3389/fonc.2022.808448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Background The four major pathways in gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) including chromatin remodeling, DNA damage repair, activation of mTOR signaling, and telomere maintenance were mediated by some critical molecules and constituted critical processes of regulation in cancer-causing processes. However, the interplay and potential role of these pathway-related molecules in the tumor microenvironment of the primary and metastatic site remained unknown. Methods We systematically evaluated the mRNA expression of 34 molecules associated with the four pathways in 227 GEP−NEN samples from 5 datasets. We assigned the samples into two expression patterns of pathway-related molecules by an unsupervised clustering method. Subsequently, we explored the specific cell-related molecules, especially immune and stromal cells using the WGCNA method, based on differentially expressed genes (DEGs) responsible for the different patterns of pathway-related molecules, which provided a new method to qualify the pathway-related subtypes of individual tumors, then the PC_Score and PI_Score scoring systems were also constructed using obtained specific cell-related molecules. Furthermore, we performed the association of pathway-related subtypes with characteristics of immune landscape in primary and metastatic GEP-NENs. Results We demonstrated that the specific pathway-related molecules (SMARCA4, MLH1, TSC1, ATRX, and ATR) were associated with cytolytic activity. Then we identified the two distinct patterns of pathway-related molecules, which were characteristic with a significantly distinct immune landscape. Using WGCNA, we also identified the fibroblast-related molecules, including ASPN, COL10A1, COL3A1, EDNRA, MYL9, PRELP, RAB31, SPARC, and THBS2, and immune-related molecules including CASP1, CCL5, CTSS, CYBRD1, PMP22, and TFEC. Based on these specific markers, we identified four distinct pathway-related subtypes, characterized by immune and fibrotic enriched (I/FE), immune enriched (IE), fibrotic enriched (FE), and immune and fibrotic desert (I/FD), of which I/FE was characteristic with the highest PC_Score and PI_Score whereas I/FD presents the opposite trend. I/FE was positively correlated with immune landscape of T-cell activation and immunosuppression. Furthermore, the I/FE marked GEP-NENs with increased immune activation scores (T-cell costimulation, MHC I presentation, and APC costimulation). Importantly, the four distinct pathway-related subtypes were not conserved in different tumor sites, because I/FE was lacking in the liver metastatic site even though IE, FE, and I/FD also could be observed in the metastatic site. Conclusions This study was the first to perform a comprehensive analysis of the four major pathways in GEP-NENs. We demonstrated the potential function of these pathway-related molecules in immune landscapes. Our findings indicated that the primary and metastatic GEP-NENs had distinct antitumor phenotypes. This work highlighted the interplay and potential clinical utility of these pathway-related molecules in GEP-NENs.
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Affiliation(s)
- Xin Lou
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Heli Gao
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xiaowu Xu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Zeng Ye
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wuhu Zhang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Fei Wang
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jie Chen
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yue Zhang
- Department of Hepatopancreatobiliary Surgery, the Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xuemin Chen
- Department of Hepatopancreatobiliary Surgery, the Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yi Qin
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Shunrong Ji
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
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Vaasjo LO. LncRNAs and Chromatin Modifications Pattern m6A Methylation at the Untranslated Regions of mRNAs. Front Genet 2022; 13:866772. [PMID: 35368653 PMCID: PMC8968631 DOI: 10.3389/fgene.2022.866772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
New roles for RNA in mediating gene expression are being discovered at an alarming rate. A broad array of pathways control patterning of N6-methyladenosine (m6A) methylation on RNA transcripts. This review comprehensively discusses long non-coding RNAs (lncRNAs) as an additional dynamic regulator of m6A methylation, with a focus on the untranslated regions (UTRs) of mRNAs. Although there is extensive literature describing m6A modification of lncRNA, the function of lncRNA in guiding m6A writers has not been thoroughly explored. The independent control of lncRNA expression, its heterogeneous roles in RNA metabolism, and its interactions with epigenetic machinery, alludes to their potential in dynamic patterning of m6A methylation. While epigenetic regulation by histone modification of H3K36me3 has been demonstrated to pattern RNA m6A methylation, these modifications were specific to the coding and 3′UTR regions. However, there are observations that 5′UTR m6A is distinct from that of the coding and 3′UTR regions, and substantial evidence supports the active regulation of 5′UTR m6A methylation. Consequently, two potential mechanisms in patterning the UTRs m6A methylation are discussed; (1) Anti-sense lncRNA (AS-lncRNA) can either bind directly to the UTR, or (2) act indirectly via recruitment of chromatin-modifying complexes to pattern m6A. Both pathways can guide the m6A writer complex, facilitate m6A methylation and modulate protein translation. Findings in the lncRNA-histone-m6A axis could potentially contribute to the discovery of new functions of lncRNAs and clarify lncRNA-m6A findings in translational medicine.
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Affiliation(s)
- Lee O. Vaasjo
- Cellular and Molecular Biology, Tulane University, New Orleans, LA, United States
- Neuroscience Program, Brain Institute, Tulane University, New Orleans, LA, United States
- *Correspondence: Lee O. Vaasjo,
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Cai M, Dong J, Li H, Qin JJ. Recent Developments in Targeting Bromodomain and Extra Terminal Domain Proteins for Cancer Therapeutics. Curr Med Chem 2022; 29:4391-4409. [PMID: 35152859 DOI: 10.2174/0929867329666220211091806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Bromodomain and extra-terminal domain (BET) proteins are a well-studied family of proteins associated with a variety of diseases including malignancy and chronic inflammation. Currently, numerous pan BET inhibitors have exhibited potent efficacy in several in vivo preclinical models and entered clinical trials, but have largely stalled due to their adverse events. Therefore, the development of new selective inhibitors and PROTACs (Proteolysis Targeting Chimeras) targeting BET is urgently needed. In the present review, we summarize the BET protein structure, the recent development of BET inhibitors, focusing mainly on BRD4-selective inhibitors and PROTAC degraders.
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Affiliation(s)
- Maohua Cai
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jinyun Dong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Haobin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jiang-Jiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
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Zhu K, Liu X, Deng W, Wang G, Fu B. Identification of a chromatin regulator signature and potential candidate drugs for bladder cancer. Hereditas 2022; 159:13. [PMID: 35125116 PMCID: PMC8819906 DOI: 10.1186/s41065-021-00212-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
Bladder cancer (BLCA) is a malignant tumor with a dismay outcome. Increasing evidence has confirmed that chromatin regulators (CRs) are involved in cancer progression. Therefore, we aimed to explore the function and prognostic value of CRs in BLCA patients.
Methods
Chromatin regulators (CRs) were acquired from the previous top research. The mRNA expression and clinical information were downloaded from TCGA and GEO datasets. Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed to select the prognostic gene and construct the risk model for predicting outcome in BLCA. The Kaplan-Meier analysis was used to assess the prognosis between high- and low-risk groups. We also investigated the drug sensitivity difference between high- and low-risk groups. CMAP dataset was performed to screen the small molecule drugs for treatment.
Results
We successfully constructed and validated an 11 CRs-based model for predicting the prognosis of patients with BLCA. Moreover, we also found 11 CRs-based model was an independent prognostic factor. Functional analysis suggested that CRs were mainly enriched in cancer-related signaling pathways. The CR-based model was also correlated with immune cells infiltration and immune checkpoint. Patients in the high-risk group were more sensitive to several drugs, such as mitomycin C, gemcitabine, cisplatin. Eight small molecule drugs could be beneficial to treatment for BLCA patients.
Conclusion:
In conclusion, our study provided novel insights into the function of CRs in BLCA. We identified a reliable prognostic biomarker for the survival of patients with BLCA.
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Gong ZG, Zhao Y, Wang ZY, Fan RF, Liu ZP, Wang L. Epigenetic regulator BRD4 is involved in cadmium-induced acute kidney injury via contributing to lysosomal dysfunction, autophagy blockade and oxidative stress. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127110. [PMID: 34523489 DOI: 10.1016/j.jhazmat.2021.127110] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) is a known nephrotoxic heavy metal and proximal tubules are the major target of Cd-induced acute kidney injury (AKI). We previously demonstrated that lysosomal dysfunction and dysregulated autophagy contribute to Cd-induced AKI. Recent studies have revealed that bromodomain-containing protein 4 (BRD4) is a transcriptional repressor of autophagy and lysosomal function. Hence, in vivo and in vitro studies were performed to clarify the role of BRD4 in Cd-induced AKI. Firstly, Cd has no effect on BRD4 expression levels, but increases H4K16 acetylation. Resultantly, Cd promotes the recruitment of BRD4 to lysosomal gene promoter regions to make it as a transcriptional regulator. Pharmacological and genetic inhibition of BRD4 alleviates Cd-inhibited lysosomal gene transcript levels and lysosomal function, leading to the alleviation of Cd-induced autophagy inhibition. Moreover, inhibition of BRD4 relieves Cd-induced oxidative stress and concurrent cytotoxicity, which is counteracted by the inhibition of autophagy via Atg5 knockdown, indicating that alleviation of oxidative stress by BRD4 inhibition is ascribed to its restoration of autophagic flux. Collectively, these results demonstrate that BRD4 acts as a transcriptional repressor to mediate lysosomal dysfunction, autophagy blockade and oxidative stress during Cd exposure, which may be a potential therapeutic target for Cd-induced AKI.
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Affiliation(s)
- Zhong-Gui Gong
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu Province 225009, People's Republic of China
| | - Yuan Zhao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Zhen-Yong Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Rui-Feng Fan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Zong-Ping Liu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu Province 225009, People's Republic of China.
| | - Lin Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China.
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Meier-Soelch J, Mayr-Buro C, Juli J, Leib L, Linne U, Dreute J, Papantonis A, Schmitz ML, Kracht M. Monitoring the Levels of Cellular NF-κB Activation States. Cancers (Basel) 2021; 13:5351. [PMID: 34771516 PMCID: PMC8582385 DOI: 10.3390/cancers13215351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The NF-κB signaling system plays an important regulatory role in the control of many biological processes. The activities of NF-κB signaling networks and the expression of their target genes are frequently elevated in pathophysiological situations including inflammation, infection, and cancer. In these conditions, the outcome of NF-κB activity can vary according to (i) differential activation states, (ii) the pattern of genomic recruitment of the NF-κB subunits, and (iii) cellular heterogeneity. Additionally, the cytosolic NF-κB activation steps leading to the liberation of DNA-binding dimers need to be distinguished from the less understood nuclear pathways that are ultimately responsible for NF-κB target gene specificity. This raises the need to more precisely determine the NF-κB activation status not only for the purpose of basic research, but also in (future) clinical applications. Here we review a compendium of different methods that have been developed to assess the NF-κB activation status in vitro and in vivo. We also discuss recent advances that allow the assessment of several NF-κB features simultaneously at the single cell level.
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Affiliation(s)
- Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Christin Mayr-Buro
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Jana Juli
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Lisa Leib
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany;
| | - Jan Dreute
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
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Chen Z, Huang Y, Yu C, Liu Q, Qiu C, Wan G. Cochlear Sox2 + Glial Cells Are Potent Progenitors for Spiral Ganglion Neuron Reprogramming Induced by Small Molecules. Front Cell Dev Biol 2021; 9:728352. [PMID: 34621745 PMCID: PMC8490772 DOI: 10.3389/fcell.2021.728352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
In the mammalian cochlea, spiral ganglion neurons (SGNs) relay the acoustic information to the central auditory circuits. Degeneration of SGNs is a major cause of sensorineural hearing loss and severely affects the effectiveness of cochlear implant therapy. Cochlear glial cells are able to form spheres and differentiate into neurons in vitro. However, the identity of these progenitor cells is elusive, and it is unclear how to differentiate these cells toward functional SGNs. In this study, we found that Sox2+ subpopulation of cochlear glial cells preserves high potency of neuronal differentiation. Interestingly, Sox2 expression was downregulated during neuronal differentiation and Sox2 overexpression paradoxically inhibited neuronal differentiation. Our data suggest that Sox2+ glial cells are potent SGN progenitor cells, a phenotype independent of Sox2 expression. Furthermore, we identified a combination of small molecules that not only promoted neuronal differentiation of Sox2– glial cells, but also removed glial cell identity and promoted the maturation of the induced neurons (iNs) toward SGN fate. In summary, we identified Sox2+ glial subpopulation with high neuronal potency and small molecules inducing neuronal differentiation toward SGNs.
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Affiliation(s)
- Zhen Chen
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China
| | - Yuhang Huang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China
| | - Chaorong Yu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China
| | - Qing Liu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China
| | - Cui Qiu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China
| | - Guoqiang Wan
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, China.,Research Institute of Otolaryngology, Nanjing, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Institute for Brain Sciences, Nanjing University, Nanjing, China
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30
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Niu H, Song F, Wei H, Li Y, Huang H, Wu C. Inhibition of BRD4 Suppresses the Growth of Esophageal Squamous Cell Carcinoma. Cancer Invest 2021; 39:826-841. [PMID: 34519605 DOI: 10.1080/07357907.2021.1975736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Bromodomain-containing protein 4 (BRD4) binds acetylated lysine residues on histones to facilitate the epigenetic regulation of many genes, and it plays a key role in many cancer types. Despite many prior reports that have explored the importance of BRD4 in oncogenesis and the regulation of epigenetic memory, its role in esophageal squamous cell carcinoma (ESCC) progression is poorly understood. Here, we investigated BRD4 expression in human ESCC tissues to understand how it regulates the biology of these tumor cells. METHODS BRD4 expression in ESCC tissues was measured via immunohistochemical staining. BRD4 inhibition in the Eca-109 and KYSE-150 ESCC cell lines was conducted to explore its functional role in these tumor cells. RESULTS BRD4 overexpression was observed in ESCC tissues and cells, and inhibiting the function of the gene impaired the proliferative, invasive, and migratory activity of these cells while promoting their apoptosis. Cyclin D1 and c-Myc expression were also suppressed by BRD4 inhibition, and the expression of key epithelial-mesenchymal transition markers including E-cadherin and Vimentin was markedly altered by such inhibition. CONCLUSIONS BRD4 plays key functional roles in the biology of ESCC, proposing that it could be a viable therapeutic target for treating this cancer type.
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Affiliation(s)
- Haiyu Niu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Department of Oncology, Lanzhou University Second Hospital, Lanzhou, China.,Institute of Cell Therapy, Soochow University, Changzhou, China
| | - Feixue Song
- Department of Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Hanwen Wei
- Department of Cardiology, The First People's Hospital of Lanzhou, Lanzhou, China
| | - Yuan Li
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Institute of Cell Therapy, Soochow University, Changzhou, China
| | - Hao Huang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Institute of Cell Therapy, Soochow University, Changzhou, China
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Institute of Cell Therapy, Soochow University, Changzhou, China.,Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
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Gong Z, Liu G, Liu W, Zou H, Song R, Zhao H, Yuan Y, Gu J, Bian J, Zhu J, Liu Z. The epigenetic regulator BRD4 is involved in cadmium-triggered inflammatory response in rat kidney. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112620. [PMID: 34392152 DOI: 10.1016/j.ecoenv.2021.112620] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) has been described as a potential inflammatory inducer, while increasing evidence shows that inappropriate inflammation is a contributing factor to kidney injury. Hence, research on Cd-triggered inflammatory response is of great significance for elucidating the mechanism of Cd-induced nephrotoxicity. Bromodomain-containing 4 (BRD4) is an important epigenetic regulator involved in the development of many inflammatory diseases, but its regulatory roles in Cd-triggered inflammatory response remain to be clarified. Here, we found that treatment with Cd in Sprague-Dawley rats (2 mg/kg bw, i.p., 5 consecutive days) and in rat kidney cell line (NRK-52E, 0-10 μM, 12 h) induced the transcription of inflammatory cytokines, which could be reduced by JQ1 (BRD4 inhibitor, 25 mg/kg bw, i.p., 3 consecutive days in vivo; 0.5 μM, 12 h in vitro) or BRD4 small interfering RNA (siRNA, in vitro), suggesting that BRD4 participates in Cd-triggered inflammatory response. Next, our study clarified the roles of BRD4 in Cd-triggered inflammatory response. The inhibition of BRD4 decreased Cd-promoted NF-κB nuclear translocation and activation in vivo and in vitro. Cd increased the acetylation level of RelA K310 and enhanced BRD4 binding to acetylated NF-κB RelA in vivo and in vitro, which were abrogated by inhibiting BRD4. In summary, our study suggests that BRD4 is involved in Cd-triggered transcription of inflammatory cytokines by mediating the activation of NF-κB signaling pathway and increasing itself binding to acetylated NF-κB RelA in rat kidney, therefore, BRD4 could be a potential therapeutic target for Cd-induced renal diseases.
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Affiliation(s)
- Zhonggui Gong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Gang Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Wenjing Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Hui Zou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Ruilong Song
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Hongyan Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Yan Yuan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Jianhong Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Jianchun Bian
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China
| | - Jiaqiao Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China.
| | - Zongping Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Key Laboratory of Zoonosis, Yangzhou, PR China.
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Ottaiano A, Santorsola M, Caraglia M, Circelli L, Gigantino V, Botti G, Nasti G. Genetic regressive trajectories in colorectal cancer: A new hallmark of oligo-metastatic disease? Transl Oncol 2021; 14:101131. [PMID: 34034007 PMCID: PMC8144733 DOI: 10.1016/j.tranon.2021.101131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) originates as consequence of multiple genetic alterations. Some of the involved genes have been extensively studied (APC, TP53, KRAS, SMAD4, PIK3CA, MMR genes) in highly heterogeneous and poly-metastatic cohorts. However, about 10% of metastatic CRC patients presents with an indolent oligo-metastatic disease differently from other patients with poly-metastatic and aggressive clinical course. Which are the genetic dynamics underlying the differences between oligo- and poly-metastatic CRC? The understanding of the genetic trajectories (primary→metastatic) of CRC, in patients selected to represent homogenous clinical models, is crucial to make genotype/phenotype correlations and to identify the molecular events pushing the disease towards an increasing malignant phenotype. This information is crucial to plan innovative therapeutic strategies aimed to reverse or inhibit these phenomena. In the present study, we review the genetic evolution of CRC with the intent to give a developmental perspective on the border line between oligo- and poly-metastatic diseases.
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Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy.
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio, 7 80138, Naples, Italy; Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031, Ariano Irpino, Italy
| | - Luisa Circelli
- AMES-Centro Polidiagnostico Strumentale, 80013, Casalnuovo di Napoli, Italy
| | - Valerio Gigantino
- Innovalab scarl, Molecular Biology, Centro Direzionale, isola A2, 80143, Naples, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
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Holloman BL, Nagarkatti M, Nagarkatti P. Epigenetic Regulation of Cannabinoid-Mediated Attenuation of Inflammation and Its Impact on the Use of Cannabinoids to Treat Autoimmune Diseases. Int J Mol Sci 2021; 22:ijms22147302. [PMID: 34298921 PMCID: PMC8307988 DOI: 10.3390/ijms22147302] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic inflammation is considered to be a silent killer because it is the underlying cause of a wide range of clinical disorders, from cardiovascular to neurological diseases, and from cancer to obesity. In addition, there are over 80 different types of debilitating autoimmune diseases for which there are no cure. Currently, the drugs that are available to suppress chronic inflammation are either ineffective or overtly suppress the inflammation, thereby causing increased susceptibility to infections and cancer. Thus, the development of a new class of drugs that can suppress chronic inflammation is imperative. Cannabinoids are a group of compounds produced in the body (endocannabinoids) or found in cannabis (phytocannabinoids) that act through cannabinoid receptors and various other receptors expressed widely in the brain and immune system. In the last decade, cannabinoids have been well established experimentally to mediate anti-inflammatory properties. Research has shown that they suppress inflammation through multiple pathways, including apoptosis and inducing immunosuppressive T regulatory cells (Tregs) and myeloid-derived suppressor cells (MDSCs). Interestingly, cannabinoids also mediate epigenetic alterations in genes that regulate inflammation. In the current review, we highlight how the epigenetic modulations caused by cannabinoids lead to the suppression of inflammation and help identify novel pathways that can be used to target autoimmune diseases.
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Ho JSY, Mok BWY, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Zhang AJ, Lee ACY, Liu WC, Jangra S, Escalera A, Aydillo T, Melo BS, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Miraldi ER, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell 2021; 184:2618-2632.e17. [PMID: 33836156 PMCID: PMC8008343 DOI: 10.1016/j.cell.2021.03.051] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 12/29/2022]
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro, and in vivo analyses, we report that topoisomerase 1 (TOP1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of topotecan (TPT), an FDA-approved TOP1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as 4 days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of TOP1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing TOP1 inhibitors for severe coronavirus disease 2019 (COVID-19) in humans.
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Affiliation(s)
- Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bobo Wing-Yee Mok
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tristan Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joseph A Wayman
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
| | - Natasha N Gaudreault
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - David A Meekins
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Sabarish V Indran
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Igor Morozov
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Jessie D Trujillo
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeyu Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Helen Ray-Jones
- MRC London Institute of Medical Sciences, London W12 0NN, UK
| | | | | | - Siu-Ying Lau
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Honglian Liu
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Anna Junxia Zhang
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Andrew Chak-Yiu Lee
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Betsaida Salom Melo
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Sema4, a Mount Sinai venture, Stamford, CT, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elaine Shum
- Division of Medical Oncology and Hematology, NYU Langone Perlmutter Cancer Center, New York, NY 10016, USA
| | - Jan Bakker
- Pontificia Universidad Católica de Chile, Santiago, Chile; Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Editor in Chief, Journal of Critical Care, NYU School of Medicine, Columbia University College of Physicians & Surgeons, New York, NY, USA
| | - David A Kaufman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Minji Byun
- Department of Medicine, Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 10029, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Emily R Miraldi
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
| | - Anand D Jeyasekharan
- Department of Haematology-Oncology, National University Hospital and Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
| | - Benjamin R TenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sven Heinz
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92092, USA
| | - Honglin Chen
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine (HKUMed), The University of Hong Kong, Hong Kong
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92092, USA
| | - Juergen A Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), Kansas State University, Manhattan, KS, USA; Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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BET bromodomain inhibitors regulate keratinocyte plasticity. Nat Chem Biol 2021; 17:280-290. [PMID: 33462494 DOI: 10.1038/s41589-020-00716-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/23/2020] [Indexed: 01/29/2023]
Abstract
Although most acute skin wounds heal rapidly, non-healing skin ulcers represent an increasing and substantial unmet medical need that urgently requires effective therapeutics. Keratinocytes resurface wounds to re-establish the epidermal barrier by transitioning to an activated, migratory state, but this ability is lost in dysfunctional chronic wounds. Small-molecule regulators of keratinocyte plasticity with the potential to reverse keratinocyte malfunction in situ could offer a novel therapeutic approach in skin wound healing. Utilizing high-throughput phenotypic screening of primary keratinocytes, we identify such small molecules, including bromodomain and extra-terminal domain (BET) protein family inhibitors (BETi). BETi induce a sustained activated, migratory state in keratinocytes in vitro, increase activation markers in human epidermis ex vivo and enhance skin wound healing in vivo. Our findings suggest potential clinical utility of BETi in promoting keratinocyte re-epithelialization of skin wounds. Importantly, this novel property of BETi is exclusively observed after transient low-dose exposure, revealing new potential for this compound class.
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Yuin Ho JS, Wing-Yee Mok B, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Junxia Zhang A, Chak-Yiu Lee A, Liu WC, Aydillo T, Salom Melo B, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Miraldi ER, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I. Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33299999 DOI: 10.1101/2020.12.01.404483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we report that Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of Topotecan (TPT), a FDA-approved Top1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as four days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of Top1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing Top1 inhibitors for COVID-19 in humans.
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37
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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Yang Y, Wang C, Wei N, Hong T, Sun Z, Xiao J, Yao J, Li Z, Liu T. Identification of prognostic chromatin-remodeling genes in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:25614-25642. [PMID: 33232269 PMCID: PMC7803503 DOI: 10.18632/aging.104170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
The aim of this study was to investigate the effects of chromatin-remodeling genes on the prognosis of patients with clear cell renal cell carcinoma (ccRCC). In TCGA-KIRC patients, two subgroups based on 86 chromatin-remodeling genes were established. The random forest algorithm was used for feature selection to identify BPTF, SIN3A and CNOT1 as characterized chromatin remodelers in ccRCC with good prognostic value. YY1 was indicated to be a transcription factor of genes highly related to BPTF, SIN3A and CNOT1. Functional annotations indicated that BPTF, SIN3A, CNOT1 and YY1 are all involved in the ubiquitin-mediated proteolysis process and that high expression of any of the five associated E3 ubiquitin ligases found in the pathway suggests a good prognosis. Protein network analysis indicated that BPTF has a targeted regulatory effect on YY1. Another independent dataset from International Cancer Genome Consortium (ICGC) showed a strong consistency with results in TCGA. In conclusion, we demonstrate that BPTF, SIN3A and CNOT1 are novel prognostic factors that predict good survival in ccRCC. We predicted that the good prognostic value of chromatin-remodeling genes BPTF and SIN3A is related to the regulation of YY1 and that YY1 regulates E3 ubiquitin ligases for further degradation of oncoproteins in ccRCC.
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Affiliation(s)
- Yujing Yang
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Chengyuan Wang
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ningde Wei
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ting Hong
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zuyu Sun
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Tiexi District, Shenyang 110001, P.R. China
| | - Jiaxi Yao
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zhi Li
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Tao Liu
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
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Ottaiano A, Caraglia M, Di Mauro A, Botti G, Lombardi A, Galon J, Luce A, D’Amore L, Perri F, Santorsola M, Hermitte F, Savarese G, Tatangelo F, Granata V, Izzo F, Belli A, Scala S, Delrio P, Circelli L, Nasti G. Evolution of Mutational Landscape and Tumor Immune-Microenvironment in Liver Oligo-Metastatic Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12103073. [PMID: 33096795 PMCID: PMC7589866 DOI: 10.3390/cancers12103073] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary About 10% of colorectal cancer patients presents with oligo-metastatic disease. The aim of our study was to assess genetic and immunologic dynamics underlying the oligo-metastatic status, evaluating genotype-phenotype correlations in a clean and homogeneous clinical model of liver-limited metastatic colorectal cancer. We show that loss of KRAS and SMAD4 mutations characterizes the oligo-metastatic disease while a progressive mutational evolution (gain in KRAS, PI3KCA, BRAF and SMAD4) is observed in poly-metastatic evolving disease. Furthermore, high granzyme-B+ T-cells infiltration is found in oligo-metastatic lesions. This study can support innovative strategies to monitor clinical evolution and to induce regressive genetic trajectories in cancer. Abstract Genetic dynamics underlying cancer progression are largely unknown and several genes involved in highly prevalent illnesses (e.g., hypertension, obesity, and diabetes) strongly concur to cancer phenotype heterogeneity. To study genotype-phenotype relationships contributing to the mutational evolution of colorectal cancer (CRC) with a focus on liver metastases, we performed genome profiling on tumor tissues of CRC patients with liver metastatic disease and no co-morbidities. We studied 523 cancer-related genes and tumor-immune microenvironment characteristics in primary and matched metastatic tissues. We observed a loss of KRAS and SMAD4 alterations and a high granzyme-B+ T-cell infiltration when the disease did not progress. Conversely, gain in KRAS, PIK3CA and SMAD4 alterations and scarce granzyme-B+ T-cells infiltration were observed when the tumor evolved towards a poly-metastatic spread. These findings provide novel insights into the identification of tumor oligo-metastatic status, indicating that some genes are on a boundary line between these two clinical settings (oligo- vs. poly-metastatic CRC). We speculate that the identification of these genes and modification of their evolution could be a new approach for anti-cancer therapeutic strategies.
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Affiliation(s)
- Alessandro Ottaiano
- Department of Abdominal Oncology, SSD-Innovative Therapies for Abdominal Cancers, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (G.N.)
- Correspondence: ; Tel.: +39-081-590-3510; Fax: +39-081-771-4224
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (M.C.); (A.L.); (A.L.)
- Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031 Ariano Irpino, Italy
| | - Annabella Di Mauro
- Department of Pathology, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (A.D.M.); (G.B.); (F.T.)
| | - Gerardo Botti
- Department of Pathology, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (A.D.M.); (G.B.); (F.T.)
| | - Angela Lombardi
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (M.C.); (A.L.); (A.L.)
- Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031 Ariano Irpino, Italy
| | - Jerome Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Université Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, F-75006 Paris, France;
| | - Amalia Luce
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (M.C.); (A.L.); (A.L.)
- Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031 Ariano Irpino, Italy
| | - Luigi D’Amore
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (L.D.); (G.S.); (L.C.)
| | - Francesco Perri
- Head and Neck Cancer Medical Oncology Unit, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy;
| | - Mariachiara Santorsola
- Department of Abdominal Oncology, SSD-Innovative Therapies for Abdominal Cancers, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (G.N.)
| | | | - Giovanni Savarese
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (L.D.); (G.S.); (L.C.)
| | - Fabiana Tatangelo
- Department of Pathology, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (A.D.M.); (G.B.); (F.T.)
| | - Vincenza Granata
- Department of Radiology, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy;
| | - Francesco Izzo
- Hepatic Surgery Unit, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (F.I.); (A.B.)
| | - Andrea Belli
- Hepatic Surgery Unit, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (F.I.); (A.B.)
| | - Stefania Scala
- Functional Genomics, Istituto Nazionale Tumori, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy;
| | - Paolo Delrio
- Colorectal Abdominal Surgery Division, Istituto Nazionale Tumori, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy;
| | - Luisa Circelli
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (L.D.); (G.S.); (L.C.)
| | - Guglielmo Nasti
- Department of Abdominal Oncology, SSD-Innovative Therapies for Abdominal Cancers, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (G.N.)
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Guler GD, Ning Y, Ku CJ, Phillips T, McCarthy E, Ellison CK, Bergamaschi A, Collin F, Lloyd P, Scott A, Antoine M, Wang W, Chau K, Ashworth A, Quake SR, Levy S. Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA. Nat Commun 2020; 11:5270. [PMID: 33077732 PMCID: PMC7572413 DOI: 10.1038/s41467-020-18965-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 09/18/2020] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is often detected late, when curative therapies are no longer possible. Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5-hydroxymethylcytosine (5hmC) changes in circulating cell free DNA from a PDAC cohort (n = 64) in comparison with a non-cancer cohort (n = 243). Differential hydroxymethylation is found in thousands of genes, most significantly in genes related to pancreas development or function (GATA4, GATA6, PROX1, ONECUT1, MEIS2), and cancer pathogenesis (YAP1, TEAD1, PROX1, IGF1). cfDNA hydroxymethylome in PDAC cohort is differentially enriched for genes that are commonly de-regulated in PDAC tumors upon activation of KRAS and inactivation of TP53. Regularized regression models built using 5hmC densities in genes perform with AUC of 0.92 (discovery dataset, n = 79) and 0.92-0.94 (two independent test sets, n = 228). Furthermore, tissue-derived 5hmC features can be used to classify PDAC cfDNA (AUC = 0.88). These findings suggest that 5hmC changes enable classification of PDAC even during early stage disease.
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Affiliation(s)
- Gulfem D Guler
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Yuhong Ning
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Chin-Jen Ku
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Tierney Phillips
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Erin McCarthy
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | | | - Anna Bergamaschi
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Francois Collin
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Paul Lloyd
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Aaron Scott
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Michael Antoine
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Wendy Wang
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Kim Chau
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, 94304, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Samuel Levy
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA.
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA.
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41
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Wang X, Yu B, Cao B, Zhou J, Deng Y, Wang Z, Jin G. A chemical conjugation of JQ-1 and a TLR7 agonist induces tumoricidal effects in a murine model of melanoma via enhanced immunomodulation. Int J Cancer 2020; 148:437-447. [PMID: 32683685 DOI: 10.1002/ijc.33222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/29/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022]
Abstract
In recent years, inhibitors of the BET bromodomain proteins, such as BRD4 inhibitors, have demonstrated robust antitumor activity. JQ-1, a representative small molecular BRD4 inhibitor, is also effective to block PD-1/PD-L1 signaling by significantly decreasing the PD-L1 expression on tumor cells. However, toxicity of BRD4 inhibitors on lymphoid and hematopoietic tissues limits their clinical usage. In this research, we designed and studied an immunogenic BRD4 inhibitor, SZU-119, by coupling JQ-1 with a TLR7 agonist, SZU-101. In vitro, SZU-119 stimulated the production of cytokines in mouse BMDCs and spleen lymphocytes, and inhibited the expression of PD-L1 in mouse B16 tumor cells. In vivo, SZU-119 suppressed the B16 tumor growth at both injected and uninjected sites, and prolonged the survival time of mice. SZU-119 elevated the number of total CD8+ and IFN-γ+ CD8+ T cells in spleens, with greater CTL cytotoxicity to B16 tumor cells. It was also observed that the infiltration of CD8+ T cells was increased in tumors at both local and distant sites, and the PD-L1 expression was decreased in tumor cells at the primary site. In conclusion, we have demonstrated that SZU-119 activated the innate immune cells, kept efficacy of PD-L1 blockade and abrogated immune toxicity, showing more potent antitumor effects than the simple mixture of SZU-101 and JQ-1 in a mouse melanoma model. Our work provides new insights for the development of anti-melanoma drugs that concurrently target innate and adaptive immunity.
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Affiliation(s)
- Xiaodong Wang
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Bingying Yu
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Birong Cao
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Ji Zhou
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Yongqiang Deng
- Department of Oral and Maxillofacial Surgery, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Zhulin Wang
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Guangyi Jin
- School of Pharmaceutical Sciences, National-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
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42
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Wu C, Chen W, He J, Jin S, Liu Y, Yi Y, Gao Z, Yang J, Yang J, Cui J, Zhao W. Interplay of m 6A and H3K27 trimethylation restrains inflammation during bacterial infection. SCIENCE ADVANCES 2020; 6:eaba0647. [PMID: 32875102 PMCID: PMC7438091 DOI: 10.1126/sciadv.aba0647] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/02/2020] [Indexed: 05/07/2023]
Abstract
While N 6-methyladenosine (m6A) is the most prevalent modification of eukaryotic messenger RNA (mRNA) involved in various cellular responses, its role in modulating bacteria-induced inflammatory response remains elusive. Here, we showed that loss of the m6A reader YTH-domain family 2 (YTHDF2) promoted demethylation of histone H3 lysine-27 trimethylation (H3K27me3), which led to enhanced production of proinflammatory cytokines and facilitated the deposition of m6A cotranscriptionally. Mechanistically, the mRNA of lysine demethylase 6B (KDM6B) was m6A-modified and its decay mediated by YTHDF2. YTHDF2 deficiency stabilized KDM6B to promote H3K27me3 demethylation of multiple proinflammatory cytokines and subsequently enhanced their transcription. Furthermore, we identified H3K27me3 as a barrier for m6A modification during transcription. KDM6B recruits the m6A methyltransferase complex to facilitate the methylation of m6A in transcribing mRNA by removing adjacent H3K27me3 barriers. These results revealed cross-talk between m6A and H3K27me3 during bacterial infection, which has broader implications for deciphering epitranscriptomics in immune homeostasis.
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Affiliation(s)
- Chenglei Wu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Weixin Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jincan He
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Shouheng Jin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Yukun Liu
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Yang Yi
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Zhuoxing Gao
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jiayan Yang
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
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43
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Liu M, Zhou J, Liu X, Feng Y, Yang W, Wu F, Cheung OKW, Sun H, Zeng X, Tang W, Mok MTS, Wong J, Yeung PC, Lai PBS, Chen Z, Jin H, Chen J, Chan SL, Chan AWH, To KF, Sung JJY, Chen M, Cheng ASL. Targeting monocyte-intrinsic enhancer reprogramming improves immunotherapy efficacy in hepatocellular carcinoma. Gut 2020; 69:365-379. [PMID: 31076403 DOI: 10.1136/gutjnl-2018-317257] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/01/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC), mostly developed in fibrotic/cirrhotic liver, exhibits relatively low responsiveness to immune checkpoint blockade (ICB) therapy. As myeloid-derived suppressor cell (MDSC) is pivotal for immunosuppression, we investigated its role and regulation in the fibrotic microenvironment with an aim of developing mechanism-based combination immunotherapy. DESIGN Functional significance of MDSCs was evaluated by flow cytometry using two orthotopic HCC models in fibrotic liver setting via carbon tetrachloride or high-fat high-carbohydrate diet and verified by clinical specimens. Mechanistic studies were conducted in human hepatic stellate cell (HSC)-peripheral blood mononuclear cell culture systems and fibrotic-HCC patient-derived MDSCs. The efficacy of single or combined therapy with anti-programmed death-1-ligand-1 (anti-PD-L1) and a clinically trialled BET bromodomain inhibitor i-BET762 was determined. RESULTS Accumulation of monocytic MDSCs (M-MDSCs), but not polymorphonuclear MDSCs, in fibrotic livers significantly correlated with reduced tumour-infiltrating lymphocytes (TILs) and increased tumorigenicity in both mouse models. In human HCCs, the tumour-surrounding fibrotic livers were markedly enriched with M-MDSC, with its surrogate marker CD33 significantly associated with aggressive tumour phenotypes and poor survival rates. Mechanistically, activated HSCs induced monocyte-intrinsic p38 MAPK signalling to trigger enhancer reprogramming for M-MDSC development and immunosuppression. Treatment with p38 MAPK inhibitor abrogated HSC-M-MDSC crosstalk to prevent HCC growth. Concomitant with patient-derived M-MDSC suppression by i-BET762, combined treatment with anti-PD-L1 synergistically enhanced TILs, resulting in tumour eradication and prolonged survival in the fibrotic-HCC mouse model. CONCLUSION Our results signify how non-tumour-intrinsic properties in the desmoplastic microenvironment can be exploited to reinstate immunosurveillance, providing readily translatable combination strategies to empower HCC immunotherapy.
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Affiliation(s)
- Man Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingying Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyu Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Feng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Otto Ka-Wing Cheung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hanyong Sun
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China, Shanghai, China
| | - Xuezhen Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenshu Tang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Myth T S Mok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Philip Chun Yeung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul Bo San Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiwei Chen
- AIDS Institute, Department of Microbiology and Research Center for Infection and Immunity, The University of Hong Kong, Hong Kong, China
| | - Hongchuan Jin
- Labortaory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Runrun Shaw hospital, Medical School of Zhejiang University, Hang Zhou, China
| | - Jie Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Stephen Lam Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Anthony W H Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
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44
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Göndör A. WNT-mediated gene gating: a novel principle connecting oncogenic super-enhancers with the nuclear pore to drive pathological expression of MYC. Mol Cell Oncol 2020; 7:1710992. [PMID: 32158925 PMCID: PMC7051154 DOI: 10.1080/23723556.2019.1710992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 11/27/2022]
Abstract
WNT signaling enhances MYC expression in cancer cells to increase the rate of cell proliferation. We have recently found that this principle involves the gating of MYC to nuclear pores mediated by an oncogenic super-enhancer in a ß-catenin-dependent manner in colon cancer cells. This phenomenon, which is absent in normal cells, leads to pathological levels of MYC expression.
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Affiliation(s)
- Anita Göndör
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Bioclinicum, Solna, Sweden
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45
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Michalak EM, Burr ML, Bannister AJ, Dawson MA. The roles of DNA, RNA and histone methylation in ageing and cancer. Nat Rev Mol Cell Biol 2019; 20:573-589. [PMID: 31270442 DOI: 10.1038/s41580-019-0143-1] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2019] [Indexed: 12/17/2022]
Abstract
Chromatin is a macromolecular complex predominantly comprising DNA, histone proteins and RNA. The methylation of chromatin components is highly conserved as it helps coordinate the regulation of gene expression, DNA repair and DNA replication. Dynamic changes in chromatin methylation are essential for cell-fate determination and development. Consequently, inherited or acquired mutations in the major factors that regulate the methylation of DNA, RNA and/or histones are commonly observed in developmental disorders, ageing and cancer. This has provided the impetus for the clinical development of epigenetic therapies aimed at resetting the methylation imbalance observed in these disorders. In this Review, we discuss the cellular functions of chromatin methylation and focus on how this fundamental biological process is corrupted in cancer. We discuss methylation-based cancer therapies and provide a perspective on the emerging data from early-phase clinical trial therapies that target regulators of DNA and histone methylation. We also highlight promising therapeutic strategies, including monitoring chromatin methylation for diagnostic purposes and combination epigenetic therapy strategies that may improve immune surveillance in cancer and increase the efficacy of conventional and targeted anticancer drugs.
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Affiliation(s)
- Ewa M Michalak
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.
- Centre for Cancer Research, The University of Melbourne, Melbourne, Australia.
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46
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Interferon-inducible cytoplasmic lncLrrc55-AS promotes antiviral innate responses by strengthening IRF3 phosphorylation. Cell Res 2019; 29:641-654. [PMID: 31213650 DOI: 10.1038/s41422-019-0193-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/30/2019] [Indexed: 01/12/2023] Open
Abstract
Type I interferon (IFN-I) production is efficiently induced to ensure a potent innate immune response to viral infection. How this response can be enhanced, however, remains to be explored. Here, we identify a new cytoplasmic long non-coding RNA (lncRNA), lncLrrc55-AS, that drives a positive feedback loop to promote interferon regulatory factor 3 (IRF3) signaling and IFN-I production. We show that lncLrrc55-AS is virus-induced in multiple cell types via the IFN-JAK-STAT pathway. LncLrrc55-AS-deficient mice display a weakened antiviral immune response and are more susceptible to viral challenge. Mechanistically, lncLrrc55-AS binds phosphatase methylesterase 1 (PME-1), and promotes the interaction between PME-1 and the phosphatase PP2A, an inhibitor of IRF3 signaling. LncLrrc55-AS supports PME-1-mediated demethylation and inactivation of PP2A, thereby enhancing IRF3 phosphorylation and signaling. Loss of PME-1 phenocopies lncLrrc55-AS deficiency, leading to diminished IRF3 phosphorylation and IFN-I production. We have identified an IFN-induced lncRNA as a positive regulator of IFN-I production, adding mechanistic insight into lncRNA-mediated regulation of signaling in innate immunity and inflammation.
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47
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Liu H, Zhao YR, Chen B, Ge Z, Huang JS. High expression of SMARCE1 predicts poor prognosis and promotes cell growth and metastasis in gastric cancer. Cancer Manag Res 2019; 11:3493-3509. [PMID: 31118775 PMCID: PMC6498956 DOI: 10.2147/cmar.s195137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Gastric cancer (GC) is one of the most lethal cancers worldwide with a high risk for recurrence and metastasis. Therefore, further understanding of the metastatic mechanism and the development of treatment strategies are required. Although increasing evidence suggests that SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin, Subfamily E, Member 1 (SMARCE1) promotes cancer metastasis, its role in GC remains unclear. Materials and methods: GC samples (n=122) were used to investigate the association between SMARCE1 expression, patient clinicopathological features, and prognosis. The expression of SMARCE1 in GC tissues was measured using real-time polymerase chain reaction, western blotting, and immunohistochemistry. MGC-803 and AGS cells were transfected with lentivirus to upregulate or downregulate SMARCE1 expression. The roles of SMARCE1 in GC cell proliferation, migration, and invasion were determined using Cell Counting Kit-8 assay, colony formation assay, wound healing, transwell migration, and invasion assay. Nude mice models were established to observe tumorigenesis. The specific mitogen-activated protein kinase (MAPK) inhibitor U0126 was utilized to verify the involved pathway. Results: SMARCE1 was highly expressed in GC tissues and cell lines. High expression of SMARCE1 was correlated with the malignant clinicopathological characteristics of GC patients, including tumor size, depth of invasion, degree of differentiation, lymph node involvement, and TNM stage (all P<0.05). Kaplan–Meier survival analysis revealed that high SMARCE1 expression predicted poor prognosis in GC patients (P<0.01). Moreover, SMARCE1 was an independent risk factor of poor prognosis (P<0.01). Functional study revealed that overexpression of SMARCE1 markedly promoted the proliferation, migration, and invasion of GC cells in vitro and tumorigenesis in vivo. Furthermore, SMARCE1 activated the MAPK/ERK signaling pathway. U0126 significantly inhibited the SMARCE1-induced proliferation and mobility of GC cells. Conclusion: SMARCE1 promoted growth and metastasis of GC, indicating its potential usefulness as a prognostic biomarker and target for therapeutic intervention against this disease.
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Affiliation(s)
- Hao Liu
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Yan-Rong Zhao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Bo Chen
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zheng Ge
- Department of General Surgery, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Jiang-Sheng Huang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
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48
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Lee Y, Yoon E, Cho S, Schmähling S, Müller J, Song JJ. Structural Basis of MRG15-Mediated Activation of the ASH1L Histone Methyltransferase by Releasing an Autoinhibitory Loop. Structure 2019; 27:846-852.e3. [PMID: 30827841 DOI: 10.1016/j.str.2019.01.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/23/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Abstract
Human ASH1L is the catalytic subunit of the conserved histone methyltransferase (HMTase) complex AMC that dimethylates lysine 36 in histone H3 (H3K36me2) to promote gene transcription in mammals and flies. Unlike AMC, ASH1L alone shows poor catalytic activity, because access to its substrate binding pocket is blocked by an autoinhibitory loop (AI loop) from the postSET domain. We report the crystal structure of the minimal catalytic active AMC complex containing ASH1L and its partner subunit MRG15. The structure reveals how binding of the MRG domain of MRG15 to a conserved FxLP motif in ASH1L results in the displacement of the AI loop to permit substrates to access the catalytic pocket of the ASH1L SET domain. Together, ASH1L activation by MRG15 therefore represents a delicate regulatory mechanism for how a cofactor activates an SET domain HMTase by releasing autoinhibition.
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Affiliation(s)
- Yoonjung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea; Center for Bioanalysis, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Eojin Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Saehyun Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Sigrun Schmähling
- MPI of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürg Müller
- MPI of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea.
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49
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Emerging roles of and therapeutic strategies targeting BRD4 in cancer. Cell Immunol 2019; 337:48-53. [PMID: 30832981 DOI: 10.1016/j.cellimm.2019.02.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/27/2019] [Accepted: 02/02/2019] [Indexed: 12/12/2022]
Abstract
The Bromodomain and Extra-terminal (BET) family of proteins were first recognized as important epigenetic regulators in inflammatory processes; however, there is increasing evidence to support the notion that BET proteins also play a critical role in 'reading' chromatin and recruiting chromatin-regulating enzymes to control gene expression in a number of pathologic processes, including cancer. To this end, the mechanisms by which BET proteins regulate chromatin remodeling and promote tumor-associated inflammation have been heavily studied over the past decade. This article to review the biology of BET protein dysfunction in promoting tumor-associated inflammation and cancer progression and the application of small molecule inhibitors that target specific BET proteins, alone or in combination with immunomodulatory agents as a novel therapeutic strategy for cancer patients.
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50
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Targeting Cancer through the Epigenetic Features of Telomeric Regions. Trends Cell Biol 2019; 29:281-290. [PMID: 30660503 DOI: 10.1016/j.tcb.2018.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022]
Abstract
The integrity of the chromatin associated with telomeric regions, which include telomeres and subtelomeres, is essential for telomeres function and cell viability. Whereas human subtelomeres are heterochromatic, telomeres are labeled with euchromatic marks like H4K20me1 and H3K27ac in most commonly studied human cell lines. The epigenetic marks of human telomeric regions influence oncogenic processes. Indeed, different drugs that decrease their genome-wide levels are currently being used or tested in specific cancer therapies. These drugs can challenge cancer by altering the function of key cellular proteins. However, they should also compromise oncogenic processes by modifying the epigenetic landscape of telomeric regions. We believe that studies of telomeric chromatin structure and telomeres dysfunction should help to design epigenetic therapies for cancer treatment.
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