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Chen J, Wang S, Yang Q, Zhang Y, Shen J, Chai K. Identification of Biomarkers for Lung Adenocarcinoma With Qi Deficiency and Phlegm Dampness. THE CLINICAL RESPIRATORY JOURNAL 2024; 18:e13812. [PMID: 39107932 PMCID: PMC11303266 DOI: 10.1111/crj.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/04/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Qi deficiency and phlegm dampness (QPD) is one of the most common traditional Chinese medicine (TCM) syndromes in lung adenocarcinoma (LUAD). This study aimed to identify syndrome-specific biomarkers for LUAD with QPD syndrome. METHODS Peripheral blood mononuclear cells (PBMCs) from LUAD patients with QPD, LUAD patients with non-QPD (N-QPD), and healthy control (H) were collected and analyzed with RNA-seq to identify differentially expressed genes (DEGs). The area under the receiver operator characteristic curve (AUC) of each DEG was calculated, and the top 10 highest AUC DEGs were validated by qRT-PCR. Logistic regression analysis was used to develop a diagnostic model evaluated with AUC. RESULTS A total of 135 individuals were enrolled in this study (training set: 15 QPD, 15 N-QPD, 15 H; validation set: 30 QPD, 30 N-QPD, 30 H). A total of 1480 DEGs were identified between QPD and N-QPD. The qRT-PCR results showed that the expression of DDR2 was downregulated, and PPARG was upregulated, which was in line with the finding of the training set. We developed a diagnostic model with these two genes. The AUC of the diagnostic model in the training cohort and validation cohort was 0.891 and 0.777, respectively. CONCLUSIONS We identified the two genes (DDR2 and PPARG) as syndrome-specific biomarkers for LUAD with QPD syndrome and developed a novel diagnostic model, which may help to improve the accuracy and sensibility of clinical diagnosis and provide a new target for natural drug treatment of LUAD.
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Affiliation(s)
- Jiabin Chen
- Department of OncologyTongde Hospital of Zhejiang, affiliated to Zhejiang Chinese Medicine UniversityHangzhouChina
| | - Sheng Wang
- Department of RespiratoryJinhua Guangfu HospitalJinhuaChina
| | - Qiaolei Yang
- Institute of Pharmaceutical Biotechnology, Faculty of MedicineZhejiang UniversityHangzhouChina
| | - Yongjun Zhang
- Department of Integrated Chinese and Western MedicineCancer Hospital of University of Chinese Academy of SciencesHangzhouChina
| | - Jianfei Shen
- Department of Thoracic SurgeryTaizhou HospitalTaizhouChina
| | - Kequn Chai
- Department of OncologyTongde Hospital of Zhejiang, affiliated to Zhejiang Chinese Medicine UniversityHangzhouChina
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2
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Roberts BS, Anderson AG, Partridge EC, Cooper GM, Myers RM. Probabilistic association of differentially expressed genes with cis-regulatory elements. Genome Res 2024; 34:620-632. [PMID: 38631728 PMCID: PMC11146588 DOI: 10.1101/gr.278598.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements (CREs) with their target genes is a challenging task that is essential to address many biological and mechanistic questions. Many current approaches rely on chromatin conformation capture techniques or single-cell correlational methods to establish CRE-to-gene associations. These methods can be effective but have limitations, including resolution, gaps in detectable association distances, and cost. As an alternative, we have developed DegCre, a nonparametric method that evaluates correlations between measurements of perturbation-induced differential gene expression and differential regulatory signal at CREs to score possible CRE-to-gene associations. It has several unique features, including the ability to use any type of CRE activity measurement, yield probabilistic scores for CRE-to-gene pairs, and assess CRE-to-gene pairings across a wide range of sequence distances. We apply DegCre to six data sets, each using different perturbations and containing a variety of regulatory signal measurements, including chromatin openness, histone modifications, and TF occupancy. To test their efficacy, we compare DegCre associations to Hi-C loop calls and CRISPR-validated CRE-to-gene associations, establishing good performance by DegCre that is comparable or superior to competing methods. DegCre is a novel approach to the association of CREs to genes from a perturbation-differential perspective, with strengths that are complementary to existing approaches and allow for new insights into gene regulation.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
| | - Ashlyn G Anderson
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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3
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Wang Y, Yu Y, Li L, Zheng M, Zhou J, Gong H, Feng B, Wang X, Meng X, Cui Y, Xia Y, Chu S, Lin L, Chang H, Zhou R, Ma M, Li Z, Ji R, Lu M, Yang X, Zuo X, Li S, Li Y. Bile acid-dependent transcription factors and chromatin accessibility determine regional heterogeneity of intestinal antimicrobial peptides. Nat Commun 2023; 14:5093. [PMID: 37607912 PMCID: PMC10444805 DOI: 10.1038/s41467-023-40565-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Antimicrobial peptides (AMPs) are important mediators of intestinal immune surveillance. However, the regional heterogeneity of AMPs and its regulatory mechanisms remain obscure. Here, we clarified the regional heterogeneity of intestinal AMPs at the single-cell level, and revealed a cross-lineages AMP regulation mechanism that bile acid dependent transcription factors (BATFs), NR1H4, NR1H3 and VDR, regulate AMPs through a ligand-independent manner. Bile acids regulate AMPs by perturbing cell differentiation rather than activating BATFs signaling. Chromatin accessibility determines the potential of BATFs to regulate AMPs at the pre-transcriptional level, thus shaping the regional heterogeneity of AMPs. The BATFs-AMPs axis also participates in the establishment of intestinal antimicrobial barriers of fetuses and the defects of antibacterial ability during Crohn's disease. Overall, BATFs and chromatin accessibility play essential roles in shaping the regional heterogeneity of AMPs at pre- and postnatal stages, as well as in maintenance of antimicrobial immunity during homeostasis and disease.
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Affiliation(s)
- Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Jiawei Zhou
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Haifan Gong
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Bingcheng Feng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Wang
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Xuanlin Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Cui
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Yanan Xia
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuzheng Chu
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Lin Lin
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Ruchen Zhou
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Mingjun Ma
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhen Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Rui Ji
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Ming Lu
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaoyun Yang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, China.
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China.
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4
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de la Aleja AG, Herrero C, Torres-Torresano M, Schiaffino MT, Del Castillo A, Alonso B, Vega MA, Puig-Kröger A, Castrillo A, Corbí ÁL. Inhibition of LXR controls the polarization of human inflammatory macrophages through upregulation of MAFB. Cell Mol Life Sci 2023; 80:96. [PMID: 36930354 PMCID: PMC10020776 DOI: 10.1007/s00018-023-04745-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Monocyte-derived macrophages contribute to pathogenesis in inflammatory diseases and their effector functions greatly depend on the prevailing extracellular milieu. Whereas M-CSF primes macrophages for acquisition of an anti-inflammatory profile, GM-CSF drives the generation of T cell-stimulatory and pro-inflammatory macrophages. Liver X Receptors (LXRα and LXRβ) are nuclear receptors that control cholesterol metabolism and regulate differentiation of tissue-resident macrophages. Macrophages from rheumatoid arthritis and other inflammatory pathologies exhibit an enriched LXR pathway, and recent reports have shown that LXR activation raises pro-inflammatory effects and impairs the acquisition of the anti-Inflammatory profile of M-CSF-dependent monocyte-derived macrophages (M-MØ). We now report that LXR inhibition prompts the acquisition of an anti-inflammatory gene and functional profile of macrophages generated within a pathological environment (synovial fluid from Rheumatoid Arthritis patients) as well as during the GM-CSF-dependent differentiation of human monocyte-derived macrophages (GM-MØ). Mechanistically, inhibition of LXR results in macrophages with higher expression of the v-Maf Avian Musculoaponeurotic Fibrosarcoma Oncogene Homolog B (MAFB) transcription factor, which governs the macrophage anti-inflammatory profile, as well as over-expression of MAFB-regulated genes. Indeed, gene silencing experiments on human macrophages evidenced that MAFB is required for the LXR inhibitor to enhance the anti-inflammatory nature of human macrophages. As a whole, our results demonstrate that LXR inhibition prompts the acquisition of an anti-inflammatory transcriptional and functional profile of human macrophages in a MAFB-dependent manner, and propose the use of LXR antagonists as potential therapeutic alternatives in macrophage re-programming strategies during inflammatory responses.
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Affiliation(s)
- Arturo González de la Aleja
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Cristina Herrero
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Mónica Torres-Torresano
- Unidad de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Teresa Schiaffino
- Unidad de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alejandro Del Castillo
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Bárbara Alonso
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Miguel A Vega
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Amaya Puig-Kröger
- Unidad de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Antonio Castrillo
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
- Instituto Investigaciones Biomédicas "Alberto Sols" (IIBM), Centro Mixto Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Ángel L Corbí
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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5
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Ishtiaq SM, Arshad MI, Khan JA. PPARγ signaling in hepatocarcinogenesis: Mechanistic insights for cellular reprogramming and therapeutic implications. Pharmacol Ther 2022; 240:108298. [PMID: 36243148 DOI: 10.1016/j.pharmthera.2022.108298] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022]
Abstract
Liver cancer or hepatocellular carcinoma (HCC) is leading cause of cancer-related mortalities globally. The therapeutic approaches for chronic liver diseases-associated liver cancers aimed at modulating immune check-points and peroxisome proliferator-activated receptor gamma (PPARγ) signaling pathway during multistep process of hepatocarcinogenesis that played a dispensable role in immunopathogenesis and outcomes of disease. Herein, the review highlights PPARγ-induced effects in balancing inflammatory (tumor necrosis factor alpha (TNF-α), interleukin (IL)-6, IL-1) and anti-inflammatory cytokines (IL-10, transforming growth factor beta (TGF-β), and interplay of PPARγ, hepatic stellate cells and fibrogenic niche in cell-intrinsic and -extrinsic crosstalk of hepatocarcinogenesis. PPARγ-mediated effects in pre-malignant microenvironment promote growth arrest, cell senescence and cell clearance in liver cancer pathophysiology. Furthermore, PPARγ-immune cell axis of liver microenvironment exhibits an immunomodulation strategy of resident immune cells of the liver (macrophages, natural killer cells, and dendritic cells) in concomitance with current clinical guidelines of the European Association for Study of Liver Diseases (EASL) for several liver diseases. Thus, mechanistic insights of PPARγ-associated high value targets and canonical signaling suggest PPARγ as a possible therapeutic target in reprogramming of hepatocarcinogenesis to decrease burden of liver cancers, worldwide.
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Affiliation(s)
- Syeda Momna Ishtiaq
- Institute of Physiology and Pharmacology, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Junaid Ali Khan
- Department of Pharmacology and Physiology, MNS University of Agriculture, Multan 60000, Pakistan.
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6
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Bergeron BP, Diedrich JD, Zhang Y, Barnett KR, Dong Q, Ferguson DC, Autry RJ, Yang W, Hansen BS, Smith C, Crews KR, Fan Y, Pui CH, Pruett-Miller SM, Relling MV, Yang JJ, Li C, Evans WE, Savic D. Epigenomic profiling of glucocorticoid responses identifies cis-regulatory disruptions impacting steroid resistance in childhood acute lymphoblastic leukemia. Leukemia 2022; 36:2374-2383. [PMID: 36028659 PMCID: PMC9522591 DOI: 10.1038/s41375-022-01685-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/03/2022]
Abstract
Glucocorticoids (GCs) are a mainstay of contemporary, multidrug chemotherapy in the treatment of childhood acute lymphoblastic leukemia (ALL), and resistance to GCs remains a major clinical concern. Resistance to GCs is predictive of ALL relapse and poor clinical outcome, and therefore represents a major hurdle limiting further improvements in survival rates. While advances have been made in identifying genes implicated in GC resistance, there remains an insufficient understanding of the impact of cis-regulatory disruptions in resistance. To address this, we mapped the gene regulatory response to GCs in two ALL cell lines using functional genomics and high-throughput reporter assays and identified thousands of GC-responsive changes to chromatin state, including the formation of over 250 GC-responsive super-enhancers and a depletion of AP-1 bound cis-regulatory elements implicated in cell proliferation and anti-apoptotic processes. By integrating our GC response maps with genetic and epigenetic datasets in primary ALL cells from patients, we further uncovered cis-regulatory disruptions at GC-responsive genes that impact GC resistance in childhood ALL. Overall, these data indicate that GCs initiate pervasive effects on the leukemia epigenome, and that alterations to the GC gene regulatory network contribute to GC resistance.
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Affiliation(s)
- Brennan P Bergeron
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kelly R Barnett
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baranda S Hansen
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Chunliang Li
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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7
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Feng T, Wu T, Zhang Y, Zhou L, Liu S, Li L, Li M, Hu E, Wang Q, Fu X, Zhan L, Xie Z, Xie W, Huang X, Shang X, Yu G. Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells. Front Oncol 2022; 12:912694. [PMID: 35957896 PMCID: PMC9361019 DOI: 10.3389/fonc.2022.912694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) stem cells are regarded as an important part of individualized HCC treatment and sorafenib resistance. However, there is lacking systematic assessment of stem-like indices and associations with a response of sorafenib in HCC. Our study thus aimed to evaluate the status of tumor dedifferentiation for HCC and further identify the regulatory mechanisms under the condition of resistance to sorafenib. Datasets of HCC, including messenger RNAs (mRNAs) expression, somatic mutation, and clinical information were collected. The mRNA expression-based stemness index (mRNAsi), which can represent degrees of dedifferentiation of HCC samples, was calculated to predict drug response of sorafenib therapy and prognosis. Next, unsupervised cluster analysis was conducted to distinguish mRNAsi-based subgroups, and gene/geneset functional enrichment analysis was employed to identify key sorafenib resistance-related pathways. In addition, we analyzed and confirmed the regulation of key genes discovered in this study by combining other omics data. Finally, Luciferase reporter assays were performed to validate their regulation. Our study demonstrated that the stemness index obtained from transcriptomic is a promising biomarker to predict the response of sorafenib therapy and the prognosis in HCC. We revealed the peroxisome proliferator-activated receptor signaling pathway (the PPAR signaling pathway), related to fatty acid biosynthesis, that was a potential sorafenib resistance pathway that had not been reported before. By analyzing the core regulatory genes of the PPAR signaling pathway, we identified four candidate target genes, retinoid X receptor beta (RXRB), nuclear receptor subfamily 1 group H member 3 (NR1H3), cytochrome P450 family 8 subfamily B member 1 (CYP8B1) and stearoyl-CoA desaturase (SCD), as a signature to distinguish the response of sorafenib. We proposed and validated that the RXRB and NR1H3 could directly regulate NR1H3 and SCD, respectively. Our results suggest that the combined use of SCD inhibitors and sorafenib may be a promising therapeutic approach.
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Affiliation(s)
- Tingze Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tianzhi Wu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yanxia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lang Zhou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shanshan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Country Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ming Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Erqiang Hu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qianwen Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaocong Fu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Li Zhan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenqin Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xianying Huang
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Xianying Huang, ; Xuan Shang, ; Guangchuang Yu,
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Xianying Huang, ; Xuan Shang, ; Guangchuang Yu,
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Xianying Huang, ; Xuan Shang, ; Guangchuang Yu,
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8
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González de la Aleja A, Herrero C, Torres-Torresano M, de la Rosa JV, Alonso B, Capa-Sardón E, Muller IB, Jansen G, Puig-Kröger A, Vega MA, Castrillo A, Corbí ÁL. Activation of LXR Nuclear Receptors Impairs the Anti-Inflammatory Gene and Functional Profile of M-CSF-Dependent Human Monocyte-Derived Macrophages. Front Immunol 2022; 13:835478. [PMID: 35280993 PMCID: PMC8907538 DOI: 10.3389/fimmu.2022.835478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/07/2022] [Indexed: 12/30/2022] Open
Abstract
Liver X Receptors (LXR) control cholesterol metabolism and exert anti-inflammatory actions but their contribution to human macrophage polarization remains unclear. The LXR pathway is enriched in pro-inflammatory macrophages from rheumatoid arthritis as well as in tumors-associated macrophages from human tumors. We now report that LXR activation inhibits the anti-inflammatory gene and functional profile of M-CSF-dependent human macrophages, and prompts the acquisition of a pro-inflammatory gene signature, with both effects being blocked by an LXR inverse agonist. Mechanistically, the LXR-stimulated macrophage polarization shift correlates with diminished expression of MAFB and MAF, which govern the macrophage anti-inflammatory profile, and with enhanced release of activin A. Indeed, LXR activation impaired macrophage polarization in response to tumor-derived ascitic fluids, as well as the expression of MAF- and MAFB-dependent genes. Our results demonstrate that LXR activation limits the anti-inflammatory human macrophage polarization and prompts the acquisition of an inflammatory transcriptional and functional profile.
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Affiliation(s)
- Arturo González de la Aleja
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Cristina Herrero
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mónica Torres-Torresano
- Unidad de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Juan Vladimir de la Rosa
- Unidad de Biomedicina (Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC)), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Bárbara Alonso
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Enrique Capa-Sardón
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ittai B. Muller
- Department of Clinical Chemistry, Amsterdam University Medical Center, Location VUmc, Amsterdam, Netherlands
| | - Gerrit Jansen
- Department of Rheumatology and Clinical Immunology, Amsterdam University Medical Center, Location VUmc, Amsterdam, Netherlands
| | - Amaya Puig-Kröger
- Unidad de Inmuno-Metabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Miguel A. Vega
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Antonio Castrillo
- Unidad de Biomedicina (Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC)), Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
- Instituto Investigaciones Biomédicas “Alberto Sols” (IIBM), and Centro Mixto Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid (Consejo Superior de Investigaciones Científicas (ICSIC)-UAM), Madrid, Spain
| | - Ángel L. Corbí
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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9
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Diedrich JD, Dong Q, Ferguson DC, Bergeron BP, Autry RJ, Qian M, Yang W, Smith C, Papizan JB, Connelly JP, Hagiwara K, Crews KR, Pruett-Miller SM, Pui CH, Yang JJ, Relling MV, Evans WE, Savic D. Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks. Leukemia 2021; 35:3078-3091. [PMID: 33714976 PMCID: PMC8435544 DOI: 10.1038/s41375-021-01209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematopoietic malignancy comprised of molecular subtypes largely characterized by aneuploidy or recurring chromosomal rearrangements. Despite extensive information on the ALL transcriptome and methylome, there is limited understanding of the ALL chromatin landscape. We therefore mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital. Our findings highlight extensive chromatin reprogramming in ALL, including the identification ALL subtype-specific chromatin landscapes that are additionally modulated by genetic variation. Chromatin accessibility differences between ALL and normal B-cells implicate the activation of B-cell repressed chromatin domains and detail the disruption of normal B-cell development in ALL. Among ALL subtypes, we uncovered roles for basic helix-loop-helix, homeodomain and activator protein 1 transcription factors in promoting subtype-specific chromatin accessibility and distinct gene regulatory networks. In addition to chromatin subtype-specificity, we further identified over 3500 DNA sequence variants that alter the ALL chromatin landscape and contribute to inter-individual variability in chromatin accessibility. Collectively, our data suggest that subtype-specific chromatin landscapes and gene regulatory networks impact ALL biology and contribute to transcriptomic differences among ALL subtypes.
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Affiliation(s)
- Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Maoxiang Qian
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James B Papizan
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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10
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Muzio G, Barrera G, Pizzimenti S. Peroxisome Proliferator-Activated Receptors (PPARs) and Oxidative Stress in Physiological Conditions and in Cancer. Antioxidants (Basel) 2021; 10:antiox10111734. [PMID: 34829605 PMCID: PMC8614822 DOI: 10.3390/antiox10111734] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/18/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor superfamily. Originally described as “orphan nuclear receptors”, they can bind both natural and synthetic ligands acting as agonists or antagonists. In humans three subtypes, PPARα, β/δ, γ, are encoded by different genes, show tissue-specific expression patterns, and contribute to the regulation of lipid and carbohydrate metabolisms, of different cell functions, including proliferation, death, differentiation, and of processes, as inflammation, angiogenesis, immune response. The PPAR ability in increasing the expression of various antioxidant genes and decreasing the synthesis of pro-inflammatory mediators, makes them be considered among the most important regulators of the cellular response to oxidative stress conditions. Based on the multiplicity of physiological effects, PPAR involvement in cancer development and progression has attracted great scientific interest with the aim to describe changes occurring in their expression in cancer cells, and to investigate the correlation with some characteristics of cancer phenotype, including increased proliferation, decreased susceptibility to apoptosis, malignancy degree and onset of resistance to anticancer drugs. This review focuses on mechanisms underlying the antioxidant and anti-inflammatory properties of PPARs in physiological conditions, and on the reported beneficial effects of PPAR activation in cancer.
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11
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Shen Y, Su Y, Silva FJ, Weller AH, Sostre-Colón J, Titchenell PM, Steger DJ, Seale P, Soccio RE. Shared PPARα/γ Target Genes Regulate Brown Adipocyte Thermogenic Function. Cell Rep 2021; 30:3079-3091.e5. [PMID: 32130908 DOI: 10.1016/j.celrep.2020.02.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/10/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Brown adipose tissue (BAT) generates heat to maintain body temperature and suppress obesity. Agonists for nuclear receptors PPARα and PPARγ both affect brown adipocyte function, yet the interplay between these factors in BAT is uncertain. Here, we report that PPARα shares most genomic binding sites with PPARγ, and these common binding sites are more related to BAT function than PPARγ-selective sites without PPARα. Integrating PPARα and PPARγ genomic occupancy with cold-responsive BAT transcriptomes identifies a subset of 16 genes with potential relevance to BAT function. Among these, we focused on the lysosomal protease cathepsin Z (CTSZ) and showed it is necessary for mitochondrial respiration in both mouse and human brown adipocytes. Thus, CTSZ is a shared PPARα/γ target gene in BAT and a regulator of brown adipocyte thermogenic function.
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Affiliation(s)
- Yachen Shen
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yvonne Su
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francisco J Silva
- Research and Development BioRestorative Therapies, New York, NY 11747, USA
| | - Angela H Weller
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jaimarie Sostre-Colón
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Titchenell
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David J Steger
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Seale
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond E Soccio
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Zhang X, Zhu J, Yan J, Xiao Y, Yang R, Huang R, Zhou J, Wang Z, Xiao W, Zheng C, Wang Y. Systems pharmacology unravels the synergic target space and therapeutic potential of Rhodiola rosea L. for non-small cell lung cancer. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2020; 79:153326. [PMID: 32992083 DOI: 10.1016/j.phymed.2020.153326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/13/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Lung cancer is the most common and mortal cancer worldwide. Rhodiola rosea L. (RR), a well-known traditional Chinese medicine (TCM), has been turned out to be effective in anti-lung cancer therapy, but its molecular mechanism of action has not been clearly understood. PURPOSE In this study, we aimed to elucidate the possible molecular mechanism underlying the effect of RR against non-small cell lung cancer (NSCLC) by systems pharmacology. METHODS The effects of RR on NSCLC were examined in Lewis lung carcinoma (LLC) tumor-bearing mice models. The possible molecular mechanism was unraveled by systems pharmacology, which includes pharmacokinetics evaluation, active compounds screening, target prediction and network analysis. Cell proliferation was examined by cell counting kit-8 (CCK-8) assay; cell apoptosis was detected by flow cytometry; protein and proinflammatory cytokines expression were evaluated by Western blot and qRT-PCR. RESULTS In vivo, RR significantly inhibited the tumor growth and prolonged the survival of the tumor bearing mice. In silico, we identified 19 potential active molecules (e.g., salidroside and rhodiosin), 112 targets (e.g., COX-2 and AKT) and 27 pathways (e.g., PI3K/AKT signaling pathway and NF-κB signaling pathway) for RR. Additionally, targets analysis and networks construction further revealed that RR exerted anti-cancer effects by regulating apoptosis, angiogenesis and inflammation. In vitro, salidroside could significantly decrease expression of pro-angiogenic factors (e.g., VEGF and eNOS) and proinflammatory cytokines (e.g., COX-2, iNOS and TNF-α). Also, Bcl-2, an anti-apoptotic protein was decreased whereas Bax, a pro-apoptotic protein, was increased. Further flow cytometry analysis showed that salidroside could induce apoptosis in H1975 cells. CONCLUSIONS Mechanistically, the antitumor effect of RR on NSCLC was responsible for the synergy among anti-inflammatory, anti-angiogenic and pro-apoptotic.
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MESH Headings
- Animals
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/pharmacokinetics
- Antineoplastic Agents, Phytogenic/pharmacology
- Apoptosis/drug effects
- Biological Availability
- Carcinoma, Lewis Lung/drug therapy
- Carcinoma, Lewis Lung/pathology
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Cell Proliferation/drug effects
- Drug Screening Assays, Antitumor/methods
- Flavonoids/pharmacology
- Gene Expression Regulation, Neoplastic/drug effects
- Glucosides/pharmacology
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Mice
- Mice, Inbred C57BL
- Monosaccharides/pharmacology
- Phenols/pharmacology
- Phosphatidylinositol 3-Kinases/metabolism
- Proto-Oncogene Proteins c-bcl-2/metabolism
- RAW 264.7 Cells
- Rhodiola/chemistry
- Signal Transduction/drug effects
- Transcription Factor RelA
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Jinglin Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Jiangna Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Yue Xiao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Ruijie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Ruifei Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Jun Zhou
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang, China
| | - Zhenzhong Wang
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang, China
| | - Wei Xiao
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang, China.
| | - Chunli Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China.
| | - Yonghua Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China.
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13
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Piccinin E, Cariello M, Moschetta A. Lipid metabolism in colon cancer: Role of Liver X Receptor (LXR) and Stearoyl-CoA Desaturase 1 (SCD1). Mol Aspects Med 2020; 78:100933. [PMID: 33218679 DOI: 10.1016/j.mam.2020.100933] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most commonly occurring cancers worldwide. Although several genetic alterations have been associated with CRC onset and progression, nowadays the reprogramming of cellular metabolism has been recognized as a fundamental step of the carcinogenic process. Intestinal tumor cells frequently display an aberrant activation of lipid metabolism. Indeed, to satisfy the growing needs of a continuous proliferation, cancer cells can either increase the uptake of exogenous lipids or upregulate the endogenous lipogenesis and cholesterol synthesis. Therefore, strategies aimed at limiting lipid accumulation are now under development in order to counteract malignancies. Two major players of lipids metabolism have been so far identified for their contribution to CRC development: the nuclear receptor Liver X Receptor (LXRs) and the enzyme Stearoyl-CoA Desaturase 1 (SCD1). Whereas LXR is mainly recognized for its role as a cholesterol sensor, finally promoting the loss of cellular cholesterol and whole-body homeostasis, SCD1 acts as the major regulator of new fatty acids, finely tuning the monounsaturated fatty acids (MUFA) to saturated fatty acids (SFA) ratio. Intriguingly, SCD1 is directly regulated by LXRs. Despite LXRs agonists have elicited great interest as a promising therapeutic target for cancer, LXR's ability to induce SCD1 and new fatty acids synthesis represent a major obstacle in the development of new effective treatments. Thus, further investigations are required to fully dissect the concomitant modulation of both players, to develop specific therapies aimed at blocking intestinal cancer cells proliferation, eventually counteracting CRC progression.
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Affiliation(s)
- Elena Piccinin
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy; Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - Marica Cariello
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy; INBB, National Institute for Biostructures and Biosystems, Rome, Italy
| | - Antonio Moschetta
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy; INBB, National Institute for Biostructures and Biosystems, Rome, Italy; National Cancer Center, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy.
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14
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Liver X receptor agonist T0901317 inhibits the migration and invasion of non-small-cell lung cancer cells in vivo and in vitro. Anticancer Drugs 2020; 30:495-500. [PMID: 30724772 PMCID: PMC6485493 DOI: 10.1097/cad.0000000000000758] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liver X receptors are recognized as important regulators of cholesterol, fatty acid metabolism, inflammatory responses, and glucose homeostasis. The antineoplastic properties of synthetic liver X receptor (LXR) agonists (T0901317 and GW3965) have been reported in human carcinomas. Epidermal growth factor tyrosine kinase inhibitor (EGFR-TKI) is a first-line treatment for non-small-cell lung cancer patients with EGFR mutations. We used scratch and transwell assays to analyze cell migration and invasion. We evaluated tumor migration and invasion in vitro using a fluorescent orthotopic lung cancer model. An MMP9 (mouse) enzyme-linked immunosorbent assay kit was used to measure serum MMP9 concentrations. Protein expression was identified by western blot assays. In this study, we determined the effects of T0901317 and/or an EGFR-TKI on the lung cancer cell lines A549 and HCC827-8-1 in vitro and in vivo. We confirmed that the combination of the LXR agonist T0901317 and gefitinib can inhibit the migration and invasion of lung cancer both in vivo and in vitro, and this effect was possibly achieved by the inhibition of the ERK/MAPK signaling pathway. Our study showed that the combination of the LXR agonist T0901317 and gefitinib can inhibit the migration and invasion of lung cancer both in vivo and in vitro.
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15
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Pontini L, Marinozzi M. Shedding light on the roles of liver X receptors in cancer by using chemical probes. Br J Pharmacol 2020; 178:3261-3276. [PMID: 32673401 DOI: 10.1111/bph.15200] [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: 04/30/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear receptors, liver X receptor-α (LXRα; NR1H3) and liver X receptor-β (LXRβ; NR1H2), are considered master regulators of lipid homeostasis. During the last couple of decades, their pivotal roles in several physiological and pathological processes ranging from energy supply, immunity, cardiovascular, neurodegenerative disorders and cancer have been highlighted. In this review, the main results achieved during more recent years about our understanding of the LXR involvement in cancer has been mainly obtained using small-molecule chemical probes. Remarkably, all these probes, albeit having different structure and biological properties, have a well demonstrated anti-tumoral activity arising from LXR modulation, indicating a high potential of LXR targeting for the treatment of cancer. LINKED ARTICLES: This article is part of a themed issue on Oxysterols, Lifelong Health and Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.16/issuetoc.
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Affiliation(s)
- Lorenzo Pontini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Maura Marinozzi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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16
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Slavish PJ, Chi L, Yun MK, Tsurkan L, Martinez NE, Jonchere B, Chai SC, Connelly M, Waddell MB, Das S, Neale G, Li Z, Shadrick WR, Olsen RR, Freeman KW, Low JA, Price JE, Young BM, Bharatham N, Boyd VA, Yang J, Lee RE, Morfouace M, Roussel MF, Chen T, Savic D, Guy RK, White SW, Shelat AA, Potter PM. Bromodomain-Selective BET Inhibitors Are Potent Antitumor Agents against MYC-Driven Pediatric Cancer. Cancer Res 2020; 80:3507-3518. [PMID: 32651255 DOI: 10.1158/0008-5472.can-19-3934] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/27/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022]
Abstract
Inhibition of members of the bromodomain and extraterminal (BET) family of proteins has proven a valid strategy for cancer chemotherapy. All BET identified to date contain two bromodomains (BD; BD1 and BD2) that are necessary for recognition of acetylated lysine residues in the N-terminal regions of histones. Chemical matter that targets BET (BETi) also interact via these domains. Molecular and cellular data indicate that BD1 and BD2 have different biological roles depending upon their cellular context, with BD2 particularly associated with cancer. We have therefore pursued the development of BD2-selective molecules both as chemical probes and as potential leads for drug development. Here we report the structure-based generation of a novel series of tetrahydroquinoline analogs that exhibit >50-fold selectivity for BD2 versus BD1. This selective targeting resulted in engagement with BD-containing proteins in cells, resulting in modulation of MYC proteins and downstream targets. These compounds were potent cytotoxins toward numerous pediatric cancer cell lines and were minimally toxic to nontumorigenic cells. In addition, unlike the pan BETi (+)-JQ1, these BD2-selective inhibitors demonstrated no rebound expression effects. Finally, we report a pharmacokinetic-optimized, metabolically stable derivative that induced growth delay in a neuroblastoma xenograft model with minimal toxicity. We conclude that BD2-selective agents are valid candidates for antitumor drug design for pediatric malignancies driven by the MYC oncogene. SIGNIFICANCE: This study presents bromodomain-selective BET inhibitors that act as antitumor agents and demonstrates that these molecules have in vivo activity towards neuroblastoma, with essentially no toxicity.
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Affiliation(s)
- P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liying Chi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lyudmila Tsurkan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nancy E Martinez
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Barbara Jonchere
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michele Connelly
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Geoffrey Neale
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William R Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rachelle R Olsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kevin W Freeman
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan A Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeanine E Price
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brandon M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nagakumar Bharatham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Vincent A Boyd
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marie Morfouace
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel Savic
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee.
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17
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Seiler CL, Song JUM, Kotandeniya D, Chen J, Kono TJY, Han Q, Colwell M, Auch B, Sarver AL, Upadhyaya P, Ren Y, Faulk C, De Flora S, La Maestra S, Chen Y, Kassie F, Tretyakova NY. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung. Sci Rep 2020; 10:11290. [PMID: 32647312 PMCID: PMC7347915 DOI: 10.1038/s41598-020-67502-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/09/2020] [Indexed: 01/05/2023] Open
Abstract
Smoking-related lung tumors are characterized by profound epigenetic changes including scrambled patterns of DNA methylation, deregulated histone acetylation, altered gene expression levels, distorted microRNA profiles, and a global loss of cytosine hydroxymethylation marks. Here, we employed an enhanced version of bisulfite sequencing (RRBS/oxRRBS) followed by next generation sequencing to separately map DNA epigenetic marks 5-methyl-dC and 5-hydroxymethyl-dC in genomic DNA isolated from lungs of A/J mice exposed whole-body to environmental cigarette smoke for 10 weeks. Exposure to cigarette smoke significantly affected the patterns of cytosine methylation and hydroxymethylation in the lungs. Differentially hydroxymethylated regions were associated with inflammatory response/disease, organismal injury, and respiratory diseases and were involved in regulation of cellular development, function, growth, and proliferation. To identify epigenetic changes in the lung associated with exposure to tobacco carcinogens and inflammation, A/J mice were intranasally treated with the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), the inflammatory agent lipopolysaccharide (LPS), or both. NNK alone caused minimal epigenetic alterations, while exposure either to LPS or NNK/LPS in combination led to increased levels of global cytosine methylation and formylation, reduced cytosine hydroxymethylation, decreased histone acetylation, and altered expression levels of multiple genes. Our results suggest that inflammatory processes are responsible for epigenetic changes contributing to lung cancer development.
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Affiliation(s)
- Christopher L Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - J Ung Min Song
- Department of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Jianji Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mathia Colwell
- Department of Animal Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Benjamin Auch
- Genomics Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Aaron L Sarver
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Pramod Upadhyaya
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Yanan Ren
- Biostatistics Core, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvio De Flora
- Department of Health Sciences, University of Genoa, 16132, Genoa, Italy
| | | | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fekadu Kassie
- Department of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA.
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18
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Unraveling the Hierarchy of cis and trans Factors That Determine the DNA Binding by Peroxisome Proliferator-Activated Receptor γ. Mol Cell Biol 2020; 40:MCB.00547-19. [PMID: 31932484 DOI: 10.1128/mcb.00547-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor essential for adipocyte development and the maintenance of the alternatively polarized macrophage phenotype. Biochemical studies have established that as an obligate heterodimer with retinoid X receptor (RXR), PPARγ binds directly repeated nuclear receptor half sites spaced by one nucleotide (direct repeat 1 [DR1]). However, it has not been analyzed systematically and genome-wide how cis factors such as the sequences of DR1s and adjacent sequences and trans factors such as cobinding lineage-determining transcription factors (LDTFs) contribute to the direct binding of PPARγ in different cellular contexts. We developed a novel motif optimization approach using sequence composition and chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) densities from macrophages and adipocytes to complement de novo motif enrichment analysis and to define and classify high-affinity binding sites. We found that approximately half of the PPARγ cistrome represents direct DNA binding; both half sites can be extended upstream, and these are typically not of equal strength within a DR1. Strategically positioned LDTFs have greater impact on PPARγ binding than the quality of DR1, and the presence of the extension of DR1 provides a remarkable synergy with LDTFs. This approach of considering not only nucleotide frequencies but also their contribution to protein binding in a cellular context is applicable to other transcription factors.
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19
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Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, Lau CE, Bonten EJ, Yang W, McCorkle JR, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Khatamian A, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, Paietta EM, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui CH, Cheng C, Savic D, Yu J, Gawad C, Relling MV, Yang JJ, Evans WE. Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. NATURE CANCER 2020; 1:329-344. [PMID: 32885175 PMCID: PMC7467080 DOI: 10.1038/s43018-020-0037-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022]
Abstract
Identification of genomic and epigenomic determinants of drug resistance provides important insights for improving cancer treatment. Using agnostic genome-wide interrogation of mRNA and miRNA expression, DNA methylation, SNPs, CNAs and SNVs/Indels in primary human acute lymphoblastic leukemia cells, we identified 463 genomic features associated with glucocorticoid resistance. Gene-level aggregation identified 118 overlapping genes, 15 of which were confirmed by genome-wide CRISPR screen. Collectively, this identified 30 of 38 (79%) known glucocorticoid-resistance genes/miRNAs and all 38 known resistance pathways, while revealing 14 genes not previously associated with glucocorticoid-resistance. Single cell RNAseq and network-based transcriptomic modelling corroborated the top previously undiscovered gene, CELSR2. Manipulation of CELSR2 recapitulated glucocorticoid resistance in human leukemia cell lines and revealed a synergistic drug combination (prednisolone and venetoclax) that mitigated resistance in mouse xenograft models. These findings illustrate the power of an integrative genomic strategy for elucidating genes and pathways conferring drug resistance in cancer cells.
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Affiliation(s)
- Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steven W Paugh
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert Carter
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Calvin E Lau
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Pediatric Oncology Education Program, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik J Bonten
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Robert McCorkle
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jordan A Beard
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John C Panetta
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Coke
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alireza Khatamian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seth E Karol
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elixabet Lopez-Lopez
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Barthelemy Diouf
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoshihiro Gocho
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steven M Kornblau
- Department of Leukemia, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Hematopoiesis and Hematological Malignancies Program, University of Chicago, Chicago, IL, USA
| | - Elisabeth M Paietta
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, North Division, Bronx, NY, USA
| | - Mark R Litzow
- Division of Hematology and Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Hiroto Inaba
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles Gawad
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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20
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Wang Y, Lv K, Zhao M, Chen H, Ji G, Zhang Y, Wang T, Cao H, Li Y, Qu L. Analysis of miRNA expression profiles in the liver of Clock Δ19 mutant mice. PeerJ 2019; 7:e8119. [PMID: 31799078 PMCID: PMC6885354 DOI: 10.7717/peerj.8119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/29/2019] [Indexed: 12/31/2022] Open
Abstract
The circadian clock controls the physiological functions of many tissues including the liver via an autoregulatory transcriptional−translational feedback loop, of which CLOCK is a core positive component. In addition, many studies have indicated that microRNAs (miRNAs) regulate liver function. However, how CLOCK-regulated miRNAs are linked to liver function remains largely unknown. In this study, miRNAs expression profiles were performed in the liver of ClockΔ19 mutant mice. Compared to wild type mice, totals of 61 and 57 putative CLOCK-regulated miRNAs were differentially expressed (fold change absolute value ≥2) at zeitgeber time 2 and zeitgeber time 14, respectively. According to the pathway analyses, the target genes of differentially expressed miRNAs were mainly involved in pathways in cancer, the PI3K-Akt signaling pathway and the MAPK signaling pathway. Protein−protein interaction analyses revealed that the hub genes were primarily associated with pathway in cancer and circadian rhythms. Expression validation showed that while the expression levels of miR-195 and miR-340 were up-regulated, the rhythms of these two miRNAs were always maintained. The expression level of nr1d2 mRNA was down-regulated. We identified a number of prospective CLOCK-regulated miRNAs that play roles in the various physiological processes of the liver, providing a reference to better understanding the potential regulatory mechanisms in the liver.
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Affiliation(s)
- Yanli Wang
- School of Life Sciences, Northwestern Polytechnical University, Xian, Shaanxi, China
| | - Ke Lv
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Mei Zhao
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Hailong Chen
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Guohua Ji
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yongliang Zhang
- School of Life Sciences, Northwestern Polytechnical University, Xian, Shaanxi, China
| | - Tingmei Wang
- School of Life Sciences, Northwestern Polytechnical University, Xian, Shaanxi, China
| | - Hongqing Cao
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Yinghui Li
- School of Life Sciences, Northwestern Polytechnical University, Xian, Shaanxi, China.,State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Lina Qu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
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21
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ER-Negative Breast Cancer Is Highly Responsive to Cholesterol Metabolite Signalling. Nutrients 2019; 11:nu11112618. [PMID: 31683867 PMCID: PMC6893441 DOI: 10.3390/nu11112618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 12/29/2022] Open
Abstract
Interventions that alter cholesterol have differential impacts on hormone receptor positive- and negative-breast cancer risk and prognosis. This implies differential regulation or response to cholesterol within different breast cancer subtypes. We evaluated differences in side-chain hydroxycholesterol and liver X nuclear receptor signalling between Oestrogen Receptor (ER)-positive and ER-negative breast cancers and cell lines. Cell line models of ER-positive and ER-negative disease were treated with Liver X Receptor (LXR) ligands and transcriptional activity assessed using luciferase reporters, qPCR and MTT. Publicly available datasets were mined to identify differences between ER-negative and ER-positive tumours and siRNA was used to suppress candidate regulators. Compared to ER-positive breast cancer, ER-negative breast cancer cells were highly responsive to LXR agonists. In primary disease and cell lines LXRA expression was strongly correlated with its target genes in ER-negative but not ER-positive disease. Expression of LXR’s corepressors (NCOR1, NCOR2 and LCOR) was significantly higher in ER-positive disease relative to ER-negative, and their knock-down equalized sensitivity to ligand between subtypes in reporter, gene expression and viability assays. Our data support further evaluation of dietary and pharmacological targeting of cholesterol metabolism as an adjunct to existing therapies for ER-negative and ER-positive breast cancer patients.
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22
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System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells. PLoS One 2019; 14:e0220894. [PMID: 31437187 PMCID: PMC6705839 DOI: 10.1371/journal.pone.0220894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022] Open
Abstract
Transcriptional regulations exert a critical control of metabolic homeostasis. In particular, the nuclear receptors (NRs) are involved in regulating numerous pathways of the intermediate metabolism. The purpose of the present study was to explore in liver cells the interconnectedness between three of them, LXR, FXR, and PPARα, all three known to act on lipid and glucose metabolism, and also on inflammation. The human cell line HepaRG was selected for its best proximity to human primary hepatocytes. Global gene expression of differentiated HepaRG cells was assessed after 4 hours and 24 hours of exposure to GW3965 (LXR agonist), GW7647 (PPARα agonist), and GW4064 and CDCA (FXR synthetic and natural agonist, respectively). Our work revealed that, contrary to our expectations, NR specificity is largely present at the level of target genes, with a smaller than expected overlap of the set of genes targeted by the different NRs. It also highlighted the much broader activity of the synthetic FXR ligand compared to CDCA. More importantly, our results revealed that activation of FXR has a pro-proliferative effect and decreases the number of tetraploid (or binucleated) hepatocytes, while LXR inhibits the cell cycle progression, inducing hepatocyte differentiation and an increase in tetraploidism. Conclusion: these results highlight the importance of analyzing the different NR activities in a context allowing a direct confrontation of each receptor outcome, and reveals the opposite role of FXR and LXR in hepatocyte cells division and maturation.
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23
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Penvose A, Keenan JL, Bray D, Ramlall V, Siggers T. Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. Nat Commun 2019; 10:2514. [PMID: 31175293 PMCID: PMC6555819 DOI: 10.1038/s41467-019-10264-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 05/02/2019] [Indexed: 01/06/2023] Open
Abstract
The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for understanding NR regulatory specificity and will facilitate more accurate analyses of genomic datasets. The type II nuclear receptors (NRs) and the retinoid X receptor (RXR) form heterodimeric transcription factors to regulate development, metabolism, and inflammation. Here the authors employ protein-binding microarrays to comprehensively analyze the DNA binding of 12 NR:RXRα heterodimers, and report promiscuous NR-DNA binding.
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Affiliation(s)
- Ashley Penvose
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Jessica L Keenan
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - David Bray
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Vijendra Ramlall
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
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24
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Furth PA. Peroxisome proliferator-activated receptor gamma and BRCA1. Endocr Relat Cancer 2019; 26:R73-R79. [PMID: 30444720 PMCID: PMC6494719 DOI: 10.1530/erc-18-0449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 01/02/2023]
Abstract
Peroxisome proliferator-activated receptor gamma agonists have been proposed as breast cancer preventives. Individuals who carry a mutated copy of BRCA1, DNA repair-associated gene, are at increased risk for development of breast cancer. Published data in the field suggest there could be interactions between peroxisome proliferator-activated receptor gamma and BRCA1 that could influence the activity of peroxisome proliferator-activated receptor gamma agonists for prevention. This review explores these possible interactions between peroxisome proliferator-activated receptor gamma, peroxisome proliferator-activated receptor gamma agonists and BRCA1 and discusses feasible experimental directions to provide more definitive information on the potential connections.
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Affiliation(s)
- Priscilla A Furth
- Departments of Oncology and Medicine, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
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25
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Kovač U, Skubic C, Bohinc L, Rozman D, Režen T. Oxysterols and Gastrointestinal Cancers Around the Clock. Front Endocrinol (Lausanne) 2019; 10:483. [PMID: 31379749 PMCID: PMC6653998 DOI: 10.3389/fendo.2019.00483] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
This review focuses on the role of oxidized sterols in three major gastrointestinal cancers (hepatocellular carcinoma, pancreatic, and colon cancer) and how the circadian clock affects the carcinogenesis by regulating the lipid metabolism and beyond. While each field of research (cancer, oxysterols, and circadian clock) is well-studied within their specialty, little is known about the intertwining mechanisms and how these influence the disease etiology in each cancer type. Oxysterols are involved in pathology of these cancers, but final conclusions about their protective or damaging effects are elusive, since the effect depends on the type of oxysterol, concentration, and the cell type. Oxysterol concentrations, the expression of key regulators liver X receptors (LXR), farnesoid X receptor (FXR), and oxysterol-binding proteins (OSBP) family are modulated in tumors and plasma of cancer patients, exposing these proteins and selected oxysterols as new potential biomarkers and drug targets. Evidence about how cholesterol/oxysterol pathways are intertwined with circadian clock is building. Identified key contact points are different forms of retinoic acid receptor related orphan receptors (ROR) and LXRs. RORs and LXRs are both regulated by sterols/oxysterols and the circadian clock and in return also regulate the same pathways, representing a complex interplay between sterol metabolism and the clock. With this in mind, in addition to classical therapies to modulate cholesterol in gastrointestinal cancers, such as the statin therapy, the time is ripe also for therapies where time and duration of the drug application is taken as an important factor for successful therapies. The final goal is the personalized approach with chronotherapy for disease management and treatment in order to increase the positive drug effects.
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26
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Yang H, Li Q, Wang C, Wang J, Lv J, Wang L, Zhang ZS, Yao Z, Wang Q. Cytotoxic Necrotizing Factor 1 Downregulates CD36 Transcription in Macrophages to Induce Inflammation During Acute Urinary Tract Infections. Front Immunol 2018; 9:1987. [PMID: 30233583 PMCID: PMC6128224 DOI: 10.3389/fimmu.2018.01987] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) induce cystitis, pyelonephritis, and can cause kidney scarring and failure if inflammation is not under control. The detailed effects of cytotoxic necrotizing factor 1 (CNF1), the key UPEC toxin, on the pathogenicity of UPEC remain unclear. CD36 is an important scavenger receptor, responsible for pathogen and apoptotic cell clearance, and plays an essential role in host immune defense and homeostasis. Regulation of CD36 by bacterial toxins has not been reported. In this study, using a pyelonephritis mouse model, CNF1 was observed to contribute to increasing neutrophils and bacterial titers in infected bladder and kidney tissues, resulting in severe inflammation and tissue damage. CD36 expression in macrophages was found to be decreased by CNF1 in vitro and in vivo. We demonstrated that CNF1 attenuated CD36 transcription by decreasing expressions of its upstream transcription factors LXRβ and C/EBPα and their recruitment to the CD36 promotor. In addition, Cdc42 was found to be involved in CNF1-mediated downregulation of LXRβ. Our study investigated the pathogenesis of cnf1-carrying UPEC, which affected host innate immune defenses and homeostasis through regulation of CD36 in macrophages during acute UTIs.
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Affiliation(s)
- Huan Yang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qianqian Li
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Changying Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingyu Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junqiang Lv
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lei Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Collaborative Innovation Center for Biotherapy, College of Pharmacy, Nankai University, Tianjin, China
| | - Zhi-Song Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Collaborative Innovation Center for Biotherapy, College of Pharmacy, Nankai University, Tianjin, China
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Quan Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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27
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Babeu JP, Jones C, Geha S, Carrier JC, Boudreau F. P1 promoter-driven HNF4α isoforms are specifically repressed by β-catenin signaling in colorectal cancer cells. J Cell Sci 2018; 131:jcs.214734. [PMID: 29898915 DOI: 10.1242/jcs.214734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/31/2018] [Indexed: 01/19/2023] Open
Abstract
HNF4α is a key nuclear receptor for regulating gene expression in the gut. Although both P1 and P2 isoform classes of HNF4α are expressed in colonic epithelium, specific inhibition of P1 isoforms is commonly found in colorectal cancer. Previous studies have suggested that P1 and P2 isoforms might regulate different cellular functions. Despite these advances, it remains unclear whether these isoform classes are functionally divergent in the context of human biology. Here, the consequences of specific inhibition of P1 or P2 isoform expression was measured in a human colorectal cancer cell transcriptome. Results indicate that P1 isoforms were specifically associated with the control of cell metabolism, whereas P2 isoforms globally supported aberrant oncogenic signalization, promoting cancer cell survival and progression. P1 promoter-driven isoform expression was found to be repressed by β-catenin, one of the earliest oncogenic pathways to be activated during colon tumorigenesis. These findings identify a novel cascade by which the expression of P1 isoforms is rapidly shut down in the early stages of colon tumorigenesis, allowing a change in HNF4α-dependent transcriptome, thereby promoting colorectal cancer progression.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jean-Philippe Babeu
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1E4K8
| | - Christine Jones
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1E4K8
| | - Sameh Geha
- Department of Pathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1E4K8
| | - Julie C Carrier
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada, J1E4K8
| | - François Boudreau
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1E4K8.
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28
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Dhiman VK, Bolt MJ, White KP. Nuclear receptors in cancer — uncovering new and evolving roles through genomic analysis. Nat Rev Genet 2017; 19:160-174. [DOI: 10.1038/nrg.2017.102] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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29
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Dendrogenin A drives LXR to trigger lethal autophagy in cancers. Nat Commun 2017; 8:1903. [PMID: 29199269 PMCID: PMC5712521 DOI: 10.1038/s41467-017-01948-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023] Open
Abstract
Dendrogenin A (DDA) is a newly discovered cholesterol metabolite with tumor suppressor properties. Here, we explored its efficacy and mechanism of cell death in melanoma and acute myeloid leukemia (AML). We found that DDA induced lethal autophagy in vitro and in vivo, including primary AML patient samples, independently of melanoma Braf status or AML molecular and cytogenetic classifications. DDA is a partial agonist on liver-X-receptor (LXR) increasing Nur77, Nor1, and LC3 expression leading to autolysosome formation. Moreover, DDA inhibited the cholesterol biosynthesizing enzyme 3β-hydroxysterol-Δ8,7-isomerase (D8D7I) leading to sterol accumulation and cooperating in autophagy induction. This mechanism of death was not observed with other LXR ligands or D8D7I inhibitors establishing DDA selectivity. The potent anti-tumor activity of DDA, its original mechanism of action and its low toxicity support its clinical evaluation. More generally, this study reveals that DDA can direct control a nuclear receptor to trigger lethal autophagy in cancers.
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30
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Ramaker RC, Savic D, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ. A genome-wide interactome of DNA-associated proteins in the human liver. Genome Res 2017; 27:1950-1960. [PMID: 29021291 PMCID: PMC5668951 DOI: 10.1101/gr.222083.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here, we identify and analyze more than 440,000 binding sites using ChIP-seq data for 20 DAPs in two human liver tissue samples. We integrated binding data with transcriptome and phased WGS data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. Our tissue-based data set exhibits binding patterns more consistent with liver biology than cell lines, and we describe uses of these data to better prioritize impactful noncoding variation. Collectively, our rich data set offers novel insights into genome function in human liver tissue and provides a valuable resource for assessing disease-related disruptions.
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Affiliation(s)
- Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Kimberly Newberry
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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31
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Wang L, Nanayakkara G, Yang Q, Tan H, Drummer C, Sun Y, Shao Y, Fu H, Cueto R, Shan H, Bottiglieri T, Li YF, Johnson C, Yang WY, Yang F, Xu Y, Xi H, Liu W, Yu J, Choi ET, Cheng X, Wang H, Yang X. A comprehensive data mining study shows that most nuclear receptors act as newly proposed homeostasis-associated molecular pattern receptors. J Hematol Oncol 2017; 10:168. [PMID: 29065888 PMCID: PMC5655880 DOI: 10.1186/s13045-017-0526-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/19/2017] [Indexed: 12/16/2022] Open
Abstract
Background Nuclear receptors (NRs) can regulate gene expression; therefore, they are classified as transcription factors. Despite the extensive research carried out on NRs, still several issues including (1) the expression profile of NRs in human tissues, (2) how the NR expression is modulated during atherosclerosis and metabolic diseases, and (3) the overview of the role of NRs in inflammatory conditions are not fully understood. Methods To determine whether and how the expression of NRs are regulated in physiological/pathological conditions, we took an experimental database analysis to determine expression of all 48 known NRs in 21 human and 17 murine tissues as well as in pathological conditions. Results We made the following significant findings: (1) NRs are differentially expressed in tissues, which may be under regulation by oxygen sensors, angiogenesis pathway, stem cell master regulators, inflammasomes, and tissue hypo-/hypermethylation indexes; (2) NR sequence mutations are associated with increased risks for development of cancers and metabolic, cardiovascular, and autoimmune diseases; (3) NRs have less tendency to be upregulated than downregulated in cancers, and autoimmune and metabolic diseases, which may be regulated by inflammation pathways and mitochondrial energy enzymes; and (4) the innate immune sensor inflammasome/caspase-1 pathway regulates the expression of most NRs. Conclusions Based on our findings, we propose a new paradigm that most nuclear receptors are anti-inflammatory homeostasis-associated molecular pattern receptors (HAMPRs). Our results have provided a novel insight on NRs as therapeutic targets in metabolic diseases, inflammations, and malignancies. Electronic supplementary material The online version of this article (10.1186/s13045-017-0526-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luqiao Wang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China.,Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Cardiovascular Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Gayani Nanayakkara
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Qian Yang
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Ultrasound, Xijing Hospital and Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Hongmei Tan
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Charles Drummer
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yu Sun
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ying Shao
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Hangfei Fu
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ramon Cueto
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Huimin Shan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Teodoro Bottiglieri
- Institute of Metabolic Disease, Baylor Research Institute, 3500 Gaston Avenue, Dallas, TX, 75246, USA
| | - Ya-Feng Li
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Candice Johnson
- Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - William Y Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Fan Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yanjie Xu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Hang Xi
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Weiqing Liu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Jun Yu
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Eric T Choi
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiaoshu Cheng
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Hong Wang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA. .,Centers for Cardiovascular Research and Thrombosis Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA. .,Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
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32
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Wu J, Wan F, Sheng H, Shi G, Shen Y, Lin G, Dai B, Zhu Y, Ye D. NR1H3 Expression is a Prognostic Factor of Overall Survival for Patients with Muscle-Invasive Bladder Cancer. J Cancer 2017; 8:852-860. [PMID: 28382148 PMCID: PMC5381174 DOI: 10.7150/jca.17845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Background: Nuclear receptors (NRs) are a class of transcription factors that regulate many cellular functions through manipulation of gene expression and also play important roles in tumorigenesis, proliferation, progression and prognosis in various kinds of cancers according to recent studies. This work aimed to determine the predictive ability of NRs in muscle-invasive bladder cancer (MIBC). Patients and methods: A total of 308 MIBC patients with complete clinicopathological and RNASeq data from The Cancer Genome Atlas (TCGA) cohort were collected for filtration. Genes showed clear correlations with overall survival (OS) and recurrence free survival (RFS) were further validated in 123 MIBC patients recruited consecutively from 2008 to 2012 in Fudan University Shanghai Cancer Center (FUSCC) cohort. Cox proportional hazards regression model and Kaplan-Meier plot were used to assess the relative factors. Results: In TCGA cohort, we found that high NR1H3 (HR=0.779, 95% CI: 0.634 - 0.957), NR2C1 (HR=0.673, 95% CI: 0.458 - 0.989) and NR2F6 (HR=0.750, 95% CI: 0.574 - 0.980) expressions were independent factors of favorable OS, while only low NR1H3 (log-rank test, P=0.0076) and NR2F6 (log-rank test, P=0.0395) expressions had the ability to predict poor prognosis for RFS. Further, in FUSCC validating cohort, we confirmed that low NR1H3 expression level was independent factor of poor OS (HR=1.295, 95% CI: 1.064 - 1.576) and it had the ability to predict poor RFS (log-rank test, P=0.0059). Conclusions: Low NR1H3 expression level is an independent prognostic factor of poor OS, and can also predict worse RFS in MIBC patients. Our “TCGA filtrating and local database validating” model can help reveal more prognostic biomarkers and cast a new light in understanding certain gene function in MIBC.
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Affiliation(s)
- Junlong Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoyue Sheng
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijun Shen
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guowen Lin
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiping Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China;; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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