1
|
Xiong A, Xiong R, Luo F. Ski ameliorates synovial cell inflammation in monosodium iodoacetate-induced knee osteoarthritis. Heliyon 2024; 10:e24471. [PMID: 38298665 PMCID: PMC10827772 DOI: 10.1016/j.heliyon.2024.e24471] [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: 09/23/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Knee osteoarthritis (KOA) is one of the most common degenerative diseases and is characterized by cartilage degeneration, synovial inflammation, joint stiffness and even loss of motor function. In the clinical treatment of arthritis, conventional analgesic and anti-inflammatory drugs have great side effects. We have evaluated the possibility of the endogenous transcription regulator Ski as an anti-inflammatory alternative in OA through experimental studies in animal models and in vivo and in vitro. Male Sprague‒Dawley rats were injected with monosodium iodoacetate (MIA) into the knee joints to induce symptoms identical to those of human OA. We isolated knee synovial tissue under sterile conditions and cultured primary synovial cells. In vitro, Ski inhibits the proinflammatory factors IL-1β, IL-6 and TNF-α mRNA and protein expression in lipopolysaccharide (LPS)-stimulated fibroblast-like synoviocytes (FLSs) and U-937 cells. In addition, Ski attenuates or inhibits OA-induced synovial inflammation by upregulating the protein expression of the anti-inflammatory factor IL-4 and downregulating the protein expression of downstream molecules related to the NF-κB inflammatory signaling pathway. In vivo, Ski downregulated proinflammatory factors and p-NF-κB p65 in KOA synovial tissue and alleviated pain-related behaviors in KOA rats. These experimental data show that Ski has strong anti-inflammatory activity. Ski is an endogenous factor, and if used in the clinical treatment of OA, the side effects are small. However, the anti-inflammatory mechanism of Ski must be further studied.
Collapse
Affiliation(s)
- Ao Xiong
- Department of Orthopaedics, First Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
- Research Institute of Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Renping Xiong
- Research Institute of Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Fei Luo
- Department of Orthopaedics, First Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| |
Collapse
|
2
|
Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir K, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. Structural variants drive context-dependent oncogene activation in cancer. Nature 2022; 612:564-572. [PMID: 36477537 PMCID: PMC9810360 DOI: 10.1038/s41586-022-05504-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Higher-order chromatin structure is important for the regulation of genes by distal regulatory sequences1,2. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer3. However, only a small minority of SVs are associated with altered gene expression4,5, and it remains unclear why certain SVs lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analysing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT and CCND1. By using CRISPR-Cas9 genome engineering to generate de novo SVs, we show that oncogene activity can be predicted by using 'activity-by-contact' models that consider partner region chromatin contacts and enhancer activity. However, activity-by-contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that SVs that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of SVs on oncogene activation.
Collapse
Affiliation(s)
- Zhichao Xu
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,These authors contributed equally
| | - Dong-Sung Lee
- Department of Life Sciences, University of Seoul, Seoul, South Korea,These authors contributed equally
| | - Sahaana Chandran
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Victoria T. Le
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Rosalind Bump
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jean Yasis
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Sofia Dallarda
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Samantha Marcotte
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Benjamin Clock
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Nicholas Haghani
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Chae Yun Cho
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Kadir Akdemir
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Selene Tyndale
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - P. Andrew Futreal
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Graham McVicker
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Geoffrey M. Wahl
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jesse R. Dixon
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,Correspondence:
| |
Collapse
|
3
|
Chelladurai P, Kuenne C, Bourgeois A, Günther S, Valasarajan C, Cherian AV, Rottier RJ, Romanet C, Weigert A, Boucherat O, Eichstaedt CA, Ruppert C, Guenther A, Braun T, Looso M, Savai R, Seeger W, Bauer UM, Bonnet S, Pullamsetti SS. Epigenetic reactivation of transcriptional programs orchestrating fetal lung development in human pulmonary hypertension. Sci Transl Med 2022; 14:eabe5407. [PMID: 35675437 DOI: 10.1126/scitranslmed.abe5407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Phenotypic alterations in resident vascular cells contribute to the vascular remodeling process in diseases such as pulmonary (arterial) hypertension [P(A)H]. How the molecular interplay between transcriptional coactivators, transcription factors (TFs), and chromatin state alterations facilitate the maintenance of persistently activated cellular phenotypes that consequently aggravate vascular remodeling processes in PAH remains poorly explored. RNA sequencing (RNA-seq) in pulmonary artery fibroblasts (FBs) from adult human PAH and control lungs revealed 2460 differentially transcribed genes. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed extensive differential distribution of transcriptionally accessible chromatin signatures, with 4152 active enhancers altered in PAH-FBs. Integrative analysis of RNA-seq and ChIP-seq data revealed that the transcriptional signatures for lung morphogenesis were epigenetically derepressed in PAH-FBs, including coexpression of T-box TF 4 (TBX4), TBX5, and SRY-box TF 9 (SOX9), which are involved in the early stages of lung development. These TFs were expressed in mouse fetuses and then repressed postnatally but were maintained in persistent PH of the newborn and reexpressed in adult PAH. Silencing of TBX4, TBX5, SOX9, or E1A-associated protein P300 (EP300) by RNA interference or small-molecule compounds regressed PAH phenotypes and mesenchymal signatures in arterial FBs and smooth muscle cells. Pharmacological inhibition of the P300/CREB-binding protein complex reduced the remodeling of distal pulmonary vessels, improved hemodynamics, and reversed established PAH in three rodent models in vivo, as well as reduced vascular remodeling in precision-cut tissue slices from human PAH lungs ex vivo. Epigenetic reactivation of TFs associated with lung development therefore underlies PAH pathogenesis, offering therapeutic opportunities.
Collapse
Affiliation(s)
- Prakash Chelladurai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Carsten Kuenne
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Alice Bourgeois
- Department of Medicine Laval University, Pulmonary Hypertension and Vascular Biology Research Group of Quebec Heart and Lung Institute, G1V 4G5 Quebec, Canada
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Chanil Valasarajan
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Anoop V Cherian
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, 3015CN Rotterdam, Netherlands.,Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Charlotte Romanet
- Department of Medicine Laval University, Pulmonary Hypertension and Vascular Biology Research Group of Quebec Heart and Lung Institute, G1V 4G5 Quebec, Canada
| | - Andreas Weigert
- Institute of Biochemistry I, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Olivier Boucherat
- Department of Medicine Laval University, Pulmonary Hypertension and Vascular Biology Research Group of Quebec Heart and Lung Institute, G1V 4G5 Quebec, Canada
| | - Christina A Eichstaedt
- Centre for Pulmonary Hypertension, Thoraxklinik Heidelberg GmbH, Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Laboratory for Molecular Diagnostics, Institute of Human Genetics, Heidelberg University, 69126 Heidelberg, Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen 35392, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen 35392, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Mario Looso
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany.,Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen 35392, Germany.,Institute for Lung Health (ILH), Member of the DZL, Justus Liebig University, Giessen 35392, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany.,Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen 35392, Germany.,Institute for Lung Health (ILH), Member of the DZL, Justus Liebig University, Giessen 35392, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, 35043 Marburg, Germany
| | - Sébastien Bonnet
- Department of Medicine Laval University, Pulmonary Hypertension and Vascular Biology Research Group of Quebec Heart and Lung Institute, G1V 4G5 Quebec, Canada
| | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany.,Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen 35392, Germany
| |
Collapse
|
4
|
Li CC, Zhang G, Du J, Liu D, Li Z, Ni Y, Zhou J, Li Y, Hou S, Zheng X, Lan Y, Liu B, He A. Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos. Nat Commun 2022; 13:346. [PMID: 35039499 PMCID: PMC8764075 DOI: 10.1038/s41467-022-28018-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.
Collapse
Affiliation(s)
- Chen C Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Junjie Du
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Di Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yunqiao Li
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaona Zheng
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| |
Collapse
|
5
|
Liao HY, Da CM, Wu ZL, Zhang HH. Ski: Double roles in cancers. Clin Biochem 2020; 87:1-12. [PMID: 33188772 DOI: 10.1016/j.clinbiochem.2020.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 02/07/2023]
Abstract
The Ski (Sloan-Kettering Institute) is an evolutionarily conserved protein that plays a dual role as an oncoprotein and tumor suppressor gene in the development of human cancer. The Ski oncogene was first identified as a transforming protein of the avian Sloan-Kettering retrovirus in 1986. Since its discovery, Ski has been identified as a carcinogenic regulator in a variety of malignant tumors. Later, it was reported that Ski regulates the occurrence and development of some cancers by acting as an oncogene. Ski mediates the proliferation, differentiation, metastasis, and invasion of numerous cancer cells through various mechanisms. Several studies have shown that Ski expression is correlated with the clinical characteristics of cancer patients and is a promising biomarker and therapeutic target for cancer. In this review, we summarize the mechanisms and potential clinical implications of Ski in dimorphism, cancer occurrence, and progression in various types of cancer.
Collapse
Affiliation(s)
- Hai-Yang Liao
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Chao-Ming Da
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Zuo-Long Wu
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Hai-Hong Zhang
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China.
| |
Collapse
|
6
|
Lu J, Wu X, Wang L, Li T, Sun L. Long noncoding RNA LINC00467 facilitates the progression of acute myeloid leukemia by targeting the miR-339/SKI pathway. Leuk Lymphoma 2020; 62:428-437. [PMID: 33054480 DOI: 10.1080/10428194.2020.1832667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A growing body of evidence indicates that long non-coding RNA (lncRNA) is involved in the development and progression of many diseases. It has been reported that lncRNA LINC00467 is disregulated in multiple tumors, while its role in acute myeloid leukemia (AML) is still unknown. Here, we find that LINC00467 expression is significantly increased in AML specimens and cell lines. Further investigations show that knockdown of LINC00467 inhibits the malignant phenotypes of AML cells. Consistently, LINC00467 knockdown slows AML progression in immunodeficient mice. Interestingly, microRNA-339 (miR-339) is upregulated and its target gene SKI, an oncogene, is downregulated in AML cells after LINC00467 knockdown. More importantly, inhibition of miR-339 can largely abolish the effect of LINC00467 knockdown on AML cells. Collectively, our data demonstrate that LINC00467 plays an important role in the pathogenesis of AML by targeting the miR-339/SKI pathway, which provides a new sight for the subsequent treatment of AML.
Collapse
Affiliation(s)
- Jun Lu
- Department of Hematology, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan City People's Hospital, Jinan, China
| | - Xifeng Wu
- Department of Hematology, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan City People's Hospital, Jinan, China
| | - Lijuan Wang
- Department of Hematology, Qingdao Binhai University Affiliated Hospital, Qingdao, China
| | - Tantan Li
- Department of Hematology, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan City People's Hospital, Jinan, China
| | - Ling Sun
- Department of Hematology, Jinan People's Hospital Affiliated to Shandong First Medical University, Jinan City People's Hospital, Jinan, China
| |
Collapse
|
7
|
Ponath V, Frech M, Bittermann M, Al Khayer R, Neubauer A, Brendel C, Pogge von Strandmann E. The Oncoprotein SKI Acts as A Suppressor of NK Cell-Mediated Immunosurveillance in PDAC. Cancers (Basel) 2020; 12:cancers12102857. [PMID: 33023028 PMCID: PMC7601115 DOI: 10.3390/cancers12102857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/23/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Pancreatic ductal adeno carcinoma is one of the most lethal solid tumors and the survival rate has not improved significantly over the past decades. The disease is characterized by an immune-suppressive tumor microenvironment, which promotes the limited response to novel immunotherapies. The aim of our study was to contribute to a better understanding of the diminished Natural Killer (NK) cell-activity in pancreatic cancer. We showed that oncoprotein SKI, which is involved in CBP/p300-mediated acetylation, diminished the expression of activating ligands for the cytotoxicity receptor NKG2D on tumor cells, thereby counteracting NK cell-dependent cytotoxicity. Treatment of tumor cells with histone deacetylase inhibitors (HDACi) induced the expression of these ligands and improved NK cell-dependent killing. Thus, we unraveled a so far unknown role of SKI in NK cell-mediated immunosurveillance. Our results suggest that the combination of HDACi with NK cell-based immunotherapies may be beneficial for pancreatic cancer patients. Abstract Drugs targeting epigenetic mechanisms such as histone deacetylase inhibitors (HDACi) suppress tumor growth. HDACi also induce the expression of ligands for the cytotoxicity receptor NKG2D rendering tumors more susceptible to natural killer (NK) cell-dependent killing. The major acetylases responsible for the expression of NKG2D ligands (NKG2D-L) are CBP and p300. The role of the oncogene and transcriptional repressor SKI, an essential part of an HDAC-recruiting co-repressor complex, which competes with CBP/p300 for binding to SMAD3 in TGFβ signaling, is unknown. Here we show that the siRNA-mediated downregulation of SKI in the pancreatic cancer cell lines Panc-1 and Patu8988t leads to an increased target cell killing by primary NK cells. However, the higher cytotoxicity of NK cells did not correlate with the induction of NKG2D-L. Of note, the expression of NKG2D-L and consequently NK cell-dependent killing could be induced upon LBH589 (LBH, panobinostat) or valproic acid (VPA) treatment irrespective of the SKI expression level but was significantly higher in pancreatic cancer cells upon genetic ablation of SKI. These data suggest that SKI represses the inducible expression of NKG2D-L. The combination of HDACi with NK cell-based immunotherapy is an attractive treatment option for pancreatic tumors, specifically for patients with high SKI protein levels.
Collapse
Affiliation(s)
- Viviane Ponath
- Institute for Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University of Marburg, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany; (V.P.); (M.B.); (R.A.K.)
| | - Miriam Frech
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, Baldingerstrasse, 35037 Marburg, Germany; (M.F.); (A.N.); (C.B.)
| | - Mathis Bittermann
- Institute for Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University of Marburg, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany; (V.P.); (M.B.); (R.A.K.)
| | - Reem Al Khayer
- Institute for Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University of Marburg, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany; (V.P.); (M.B.); (R.A.K.)
| | - Andreas Neubauer
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, Baldingerstrasse, 35037 Marburg, Germany; (M.F.); (A.N.); (C.B.)
| | - Cornelia Brendel
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, Baldingerstrasse, 35037 Marburg, Germany; (M.F.); (A.N.); (C.B.)
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Philipps University of Marburg, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany; (V.P.); (M.B.); (R.A.K.)
- Correspondence: or ; Tel.: +49-6421-2821640; Fax: +49-64212868923
| |
Collapse
|
8
|
Leonards K, Almosailleakh M, Tauchmann S, Bagger FO, Thirant C, Juge S, Bock T, Méreau H, Bezerra MF, Tzankov A, Ivanek R, Losson R, Peters AHFM, Mercher T, Schwaller J. Nuclear interacting SET domain protein 1 inactivation impairs GATA1-regulated erythroid differentiation and causes erythroleukemia. Nat Commun 2020; 11:2807. [PMID: 32533074 PMCID: PMC7293310 DOI: 10.1038/s41467-020-16179-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The nuclear receptor binding SET domain protein 1 (NSD1) is recurrently mutated in human cancers including acute leukemia. We show that NSD1 knockdown alters erythroid clonogenic growth of human CD34+ hematopoietic cells. Ablation of Nsd1 in the hematopoietic system of mice induces a transplantable erythroleukemia. In vitro differentiation of Nsd1−/− erythroblasts is majorly impaired despite abundant expression of GATA1, the transcriptional master regulator of erythropoiesis, and associated with an impaired activation of GATA1-induced targets. Retroviral expression of wildtype NSD1, but not a catalytically-inactive NSD1N1918Q SET-domain mutant induces terminal maturation of Nsd1−/− erythroblasts. Despite similar GATA1 protein levels, exogenous NSD1 but not NSDN1918Q significantly increases the occupancy of GATA1 at target genes and their expression. Notably, exogenous NSD1 reduces the association of GATA1 with the co-repressor SKI, and knockdown of SKI induces differentiation of Nsd1−/− erythroblasts. Collectively, we identify the NSD1 methyltransferase as a regulator of GATA1-controlled erythroid differentiation and leukemogenesis. Loss of function mutations of NSD1 occur in blood cancers. Here, the authors report that NSD1 loss blocks erythroid differentiation which leads to an erythroleukemia-like disease in mice by impairing GATA1-induced target gene activation.
Collapse
Affiliation(s)
- Katharina Leonards
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Marwa Almosailleakh
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Samantha Tauchmann
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Frederik Otzen Bagger
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Swiss Institute of Bioinfomatics, 4031, Basel, Switzerland.,Genomic Medicine, Righospitalet, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Cécile Thirant
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif, 94800, France
| | - Sabine Juge
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Thomas Bock
- Proteomics Core Facility, Biozentrum University of Basel, Basel, Switzerland
| | - Hélène Méreau
- Department of Biomedicine, University of Basel, 4031, Basel, Switzerland
| | - Matheus F Bezerra
- University Children's Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Alexandar Tzankov
- Institute for Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Robert Ivanek
- Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.,Swiss Institute of Bioinfomatics, 4031, Basel, Switzerland
| | - Régine Losson
- Institute de Génétique et de Biologie Moléculaire et Cellulaire (I.G.B.M.C.), CNRS/INSERM Université de Strasbourg, BP10142, 67404, Illkirch Cedex, France
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.,Faculty of Sciences, University of Basel, 4056, Basel, Switzerland
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, Université Paris Diderot, Université Paris-Sud, Villejuif, 94800, France
| | - Juerg Schwaller
- University Children's Hospital Basel, Basel, Switzerland. .,Department of Biomedicine, University of Basel, 4031, Basel, Switzerland.
| |
Collapse
|
9
|
Cappelli C, Sepulveda H, Rivas S, Pola V, Urzúa U, Donoso G, Sagredo E, Carrero D, Casanova-Ortiz E, Sagredo A, González M, Manterola M, Nardocci G, Armisén R, Montecino M, Marcelain K. Ski Is Required for Tri-Methylation of H3K9 in Major Satellite and for Repression of Pericentromeric Genes: Mmp3, Mmp10 and Mmp13, in Mouse Fibroblasts. J Mol Biol 2020; 432:3222-3238. [PMID: 32198114 DOI: 10.1016/j.jmb.2020.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 11/27/2022]
Abstract
Several mechanisms directing a rapid transcriptional reactivation of genes immediately after mitosis have been described. However, little is known about the maintenance of repressive signals during mitosis. In this work, we address the role of Ski in the repression of gene expression during M/G1 transition in mouse embryonic fibroblasts (MEFs). We found that Ski localises as a distinct pair of dots at the pericentromeric region of mitotic chromosomes, and the absence of the protein is related to high acetylation and low tri-methylation of H3K9 in pericentromeric major satellite. Moreover, differential expression assays in early G1 cells showed that the presence of Ski is significantly associated with repression of genes localised nearby to pericentromeric DNA. In mitotic cells, chromatin immunoprecipitation assays confirmed the association of Ski to major satellite and the promoters of the most repressed genes: Mmp3, Mmp10 and Mmp13. These genes are at pericentromeric region of chromosome 9. In these promoters, the presence of Ski resulted in increased H3K9 tri-methylation levels. This Ski-dependent regulation is also observed during interphase. Consequently, Mmp activity is augmented in Ski-/- MEFs. Altogether, these data indicate that association of Ski with the pericentromeric region of chromosomes during mitosis is required to maintain the silencing bookmarks of underlying chromatin.
Collapse
Affiliation(s)
- Claudio Cappelli
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Bioquimica y Microbiologia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Hugo Sepulveda
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Solange Rivas
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Pola
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gerardo Donoso
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eduardo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - David Carrero
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Emmanuel Casanova-Ortiz
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alfredo Sagredo
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marisel González
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcia Manterola
- Instituto de Ciencias Biomédicas. Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gino Nardocci
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ricardo Armisén
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile; Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Martin Montecino
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínica. Facultad de Medicina, Universidad de Chile, Santiago, Chile.
| |
Collapse
|
10
|
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol 2019; 37:1458-1465. [PMID: 31792411 DOI: 10.1038/s41587-019-0332-7] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022]
Abstract
Identifying the causes of human diseases requires deconvolution of abnormal molecular phenotypes spanning DNA accessibility, gene expression and protein abundance1-3. We present a single-cell framework that integrates highly multiplexed protein quantification, transcriptome profiling and analysis of chromatin accessibility. Using this approach, we establish a normal epigenetic baseline for healthy blood development, which we then use to deconvolve aberrant molecular features within blood from patients with mixed-phenotype acute leukemia4,5. Despite widespread epigenetic heterogeneity within the patient cohort, we observe common malignant signatures across patients as well as patient-specific regulatory features that are shared across phenotypic compartments of individual patients. Integrative analysis of transcriptomic and chromatin-accessibility maps identified 91,601 putative peak-to-gene linkages and transcription factors that regulate leukemia-specific genes, such as RUNX1-linked regulatory elements proximal to the marker gene CD69. These results demonstrate how integrative, multiomic analysis of single cells within the framework of normal development can reveal both distinct and shared molecular mechanisms of disease from patient samples.
Collapse
|
11
|
Abstract
Next-generation sequencing (NGS) data have been central to the development of targeted therapy and immunotherapy for precision oncology. In targeted therapy, drugs directly attack cancer, by altering the expression of critical cancer genes identified with cancer genome profiling. Immunotherapy drugs indirectly attack cancer, by inducing the immune system to attack and treat cancer. Harnessing genomic data for deployment and development of immunotherapy comprises the field of immunogenomics. The discovery of a link between cancer cells escaping immune destruction and cancer progression, led to extensive research into this mechanism and drug development. In the past few years, FDA has granted accelerated approval to several immunotherapy cancer treatment drugs, pembrolizumab, nivolumab, and atezolizumab, belonging to the class of checkpoint inhibitors. Utilization of pretreatment genomic cancer screening to identify patients most likely to respond to immunotherapy and to customize immunotherapy for a given patient, promises to improve cancer treatment outcomes. Recent advances in molecular profiling, high-throughput sequencing, and computational efficiency has made immunogenomics the major tenet of precision medicine in cancer treatment. This review provides a brief overview on the state of art of immunogenomics in precision cancer medicine.
Collapse
|
12
|
Rakow S, Pullamsetti SS, Bauer UM, Bouchard C. Assaying epigenome functions of PRMTs and their substrates. Methods 2019; 175:53-65. [PMID: 31542509 DOI: 10.1016/j.ymeth.2019.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Among the widespread and increasing number of identified post-translational modifications (PTMs), arginine methylation is catalyzed by the protein arginine methyltransferases (PRMTs) and regulates fundamental processes in cells, such as gene regulation, RNA processing, translation, and signal transduction. As epigenetic regulators, PRMTs play key roles in pluripotency, differentiation, proliferation, survival, and apoptosis, which are essential biological programs leading to development, adult homeostasis but also pathological conditions including cancer. A full understanding of the molecular mechanisms that underlie PRMT-mediated gene regulation requires the genome wide mapping of each player, i.e., PRMTs, their substrates and epigenetic marks, methyl-marks readers as well as interaction partners, in a thorough and unambiguous manner. However, despite the tremendous advances in high throughput sequencing technologies and the numerous efforts from the scientific community, the epigenomic profiling of PRMTs as well as their histone and non-histone substrates still remains a big challenge owing to obvious limitations in tools and methodologies. This review will summarize the present knowledge about the genome wide mapping of PRMTs and their substrates as well as the technical approaches currently in use. The limitations and pitfalls of the technical tools along with conventional approaches will be then discussed in detail. Finally, potential new strategies for chromatin profiling of PRMTs and histone substrates will be proposed and described.
Collapse
Affiliation(s)
- Sinja Rakow
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Soni Savai Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany.
| |
Collapse
|