1
|
Lu Y, Ma WB, Ren GM, Li YT, Wang T, Zhan YQ, Xiang SS, Chen H, Gao HY, Zhao K, Yu M, Li CY, Yang XM, Yin RH. GPS2 promotes erythroid differentiation in K562 erythroleukemia cells primarily via NCOR1. Int J Hematol 2024:10.1007/s12185-024-03797-x. [PMID: 38814500 DOI: 10.1007/s12185-024-03797-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
G protein pathway suppressor 2 (GPS2) has been shown to play a pivotal role in human and mouse definitive erythropoiesis in an EKLF-dependent manner. However, whether GPS2 affects human primitive erythropoiesis is still unknown. This study demonstrated that GPS2 positively regulates erythroid differentiation in K562 cells, which have a primitive erythroid phenotype. Overexpression of GPS2 promoted hemin-induced hemoglobin synthesis in K562 cells as assessed by the increased percentage of benzidine-positive cells and the deeper red coloration of the cell pellets. In contrast, knockdown of GPS2 inhibited hemin-induced erythroid differentiation of K562 cells. GPS2 overexpression also enhanced erythroid differentiation of K562 cells induced by cytosine arabinoside (Ara-C). GPS2 induced hemoglobin synthesis by increasing the expression of globin and ALAS2 genes, either under steady state or upon hemin treatment. Promotion of erythroid differentiation of K562 cells by GPS2 mainly relies on NCOR1, as knockdown of NCOR1 or lack of the NCOR1-binding domain of GPS2 potently diminished the promotive effect. Thus, our study revealed a previously unknown role of GPS2 in regulating human primitive erythropoiesis in K562 cells.
Collapse
Affiliation(s)
- Ying Lu
- College of Life Science and Bioengineering, Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen-Bing Ma
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Guang-Ming Ren
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ya-Ting Li
- College of Life Science and Bioengineering, Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ting Wang
- College of Life Science and Bioengineering, Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yi-Qun Zhan
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Shen-Si Xiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hui Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ke Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Miao Yu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chang-Yan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiao-Ming Yang
- College of Life Science and Bioengineering, Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China.
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Rong-Hua Yin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| |
Collapse
|
2
|
Hussain S, Yates C, Campbell MJ. Vitamin D and Systems Biology. Nutrients 2022; 14:nu14245197. [PMID: 36558356 PMCID: PMC9782494 DOI: 10.3390/nu14245197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The biological actions of the vitamin D receptor (VDR) have been investigated intensively for over 100 years and has led to the identification of significant insights into the repertoire of its biological actions. These were initially established to be centered on the regulation of calcium transport in the colon and deposition in bone. Beyond these well-known calcemic roles, other roles have emerged in the regulation of cell differentiation processes and have an impact on metabolism. The purpose of the current review is to consider where applying systems biology (SB) approaches may begin to generate a more precise understanding of where the VDR is, and is not, biologically impactful. Two SB approaches have been developed and begun to reveal insight into VDR biological functions. In a top-down SB approach genome-wide scale data are statistically analyzed, and from which a role for the VDR emerges in terms of being a hub in a biological network. Such approaches have confirmed significant roles, for example, in myeloid differentiation and the control of inflammation and innate immunity. In a bottom-up SB approach, current biological understanding is built into a kinetic model which is then applied to existing biological data to explain the function and identify unknown behavior. To date, this has not been applied to the VDR, but has to the related ERα and identified previously unknown mechanisms of control. One arena where applying top-down and bottom-up SB approaches may be informative is in the setting of prostate cancer health disparities.
Collapse
Affiliation(s)
- Shahid Hussain
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Moray J. Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
| |
Collapse
|
3
|
Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
Collapse
Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
4
|
Genomic Insights into Non-steroidal Nuclear Receptors in Prostate and Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:227-239. [DOI: 10.1007/978-3-031-11836-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer. Cell Rep 2021; 37:110109. [PMID: 34910907 PMCID: PMC8889623 DOI: 10.1016/j.celrep.2021.110109] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 01/27/2023] Open
Abstract
This study addresses the roles of nuclear receptor corepressor 2 (NCOR2) in prostate cancer (PC) progression in response to androgen deprivation therapy (ADT). Reduced NCOR2 expression significantly associates with shorter disease-free survival in patients with PC receiving adjuvant ADT. Utilizing the CWR22 xenograft model, we demonstrate that stably reduced NCOR2 expression accelerates disease recurrence following ADT, associates with gene expression patterns that include neuroendocrine features, and induces DNA hypermethylation. Stably reduced NCOR2 expression in isogenic LNCaP (androgen-sensitive) and LNCaP-C4–2 (androgen-independent) cells revealed that NCOR2 reduction phenocopies the impact of androgen treatment and induces global DNA hypermethylation patterns. NCOR2 genomic binding is greatest in LNCaP-C4–2 cells and most clearly associates with forkhead box (FOX) transcription factor FOXA1 binding. NCOR2 binding significantly associates with transcriptional regulation most when in active enhancer regions. These studies reveal robust roles for NCOR2 in regulating the PC transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PC disease progression. Long et al. show that reduced levels of NCOR2 lead to accelerated prostate cancer recurrence during androgen withdrawal in a patient-derived xenograft model. NCOR2 reduction is characterized by incomplete response to androgen withdrawal, and recurrent tumors show increased neuroendocrine traits. These phenotypic changes are associated with hypermethylated enhancers.
Collapse
|
6
|
GPS2 promotes erythroid differentiation by control of the stability of EKLF protein. Blood 2021; 135:2302-2315. [PMID: 32384137 DOI: 10.1182/blood.2019003867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
Erythropoiesis is a complex multistage process that involves differentiation of early erythroid progenitors to enucleated mature red blood cells, in which lineage-specific transcription factors play essential roles. Erythroid Krüppel-like factor (EKLF/KLF1) is a pleiotropic erythroid transcription factor that is required for the proper maturation of the erythroid cells, whose expression and activation are tightly controlled in a temporal and differentiation stage-specific manner. Here, we uncover a novel role of G-protein pathway suppressor 2 (GPS2), a subunit of the nuclear receptor corepressor/silencing mediator of retinoic acid and thyroid hormone receptor corepressor complex, in erythrocyte differentiation. Our study demonstrates that knockdown of GPS2 significantly suppresses erythroid differentiation of human CD34+ cells cultured in vitro and xenotransplanted in nonobese diabetic/severe combined immunodeficiency/interleukin-2 receptor γ-chain null mice. Moreover, global deletion of GPS2 in mice causes impaired erythropoiesis in the fetal liver and leads to severe anemia. Flow cytometric analysis and Wright-Giemsa staining show a defective differentiation at late stages of erythropoiesis in Gps2-/- embryos. Mechanistically, GPS2 interacts with EKLF and prevents proteasome-mediated degradation of EKLF, thereby increasing EKLF stability and transcriptional activity. Moreover, we identify the amino acids 191-230 region in EKLF protein, responsible for GPS2 binding, that is highly conserved in mammals and essential for EKLF protein stability. Collectively, our study uncovers a previously unknown role of GPS2 as a posttranslational regulator that enhances the stability of EKLF protein and thereby promotes erythroid differentiation.
Collapse
|
7
|
SIRT1 induces the adipogenic differentiation of mouse embryonic stem cells by regulating RA-induced RAR expression via NCOR1 acetylation. Stem Cell Res 2020; 44:101771. [DOI: 10.1016/j.scr.2020.101771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/11/2020] [Indexed: 01/12/2023] Open
|
8
|
The nuclear receptor corepressor NCoR1 regulates hematopoiesis and leukemogenesis in vivo. Blood Adv 2020; 3:644-657. [PMID: 30804018 DOI: 10.1182/bloodadvances.2018022756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 01/18/2019] [Indexed: 12/19/2022] Open
Abstract
Enhanced understanding of normal and malignant hematopoiesis pathways should facilitate the development of effective clinical treatment strategies for hematopoietic malignancies. Nuclear receptor corepressor 1 (NCoR1) has been implicated in transcriptional repression and embryonic organ development, but its role in hematopoiesis is yet to be fully elucidated. Here, we showed that hematopoietic-specific loss of NCoR1 leads to expansion of the hematopoietic stem cell (HSC) pool due to aberrant cell cycle entry of long-term HSCs under steady-state conditions. Moreover, NCoR1-deficient HSCs exhibited normal self-renewal capacity but severely impaired lymphoid-differentiation potential in competitive hematopoietic-reconstitution assays. Transcriptome analysis further revealed that several hematopoiesis-associated genes are regulated by NCoR1. In addition, NCoR1 deficiency in hematopoietic cells delayed the course of leukemia and promoted leukemia cell differentiation in an MLL-AF9-induced mouse model. NCoR1 and its partner, histone deacetylase 3, can modulate histone acetylation and gene transcription through binding the promoter regions of myeloid-differentiation genes. Our collective results support the critical involvement of NCoR1 in normal and malignant hematopoiesis in vivo.
Collapse
|
9
|
Wei C, Dong X, Lu H, Tong F, Chen L, Zhang R, Dong J, Hu Y, Wu G, Dong X. LPCAT1 promotes brain metastasis of lung adenocarcinoma by up-regulating PI3K/AKT/MYC pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:95. [PMID: 30791942 PMCID: PMC6385475 DOI: 10.1186/s13046-019-1092-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/06/2019] [Indexed: 12/15/2022]
Abstract
Background Brain metastasis (BM) is associated with poor prognosis, recurrence, and death in patients with non-small cell lung cancer (NSCLC). Lysophosphatidylcholine acyltransferase 1 (LPCAT1) has been reported to be involved in the progression, metastasis and recurrence of malignancies. However, the potential role of LPCAT1 in NSCLC remains poorly understood. This study was aimed to identify genes involved in lung adenocarcinoma (LUAD) brain metastasis, and look into the role of LPCAT1 in LUAD progression. Methods We used integrative genomic analysis to identify genes involved in lung adenocarcinomas. LPCAT1 expression was evaluated in tumor tissues from LUAD patients and LUAD cell lines. The role of LPCAT1 was subsequently investigated both in vitro and in vivo. The mechanism underlying the involvement of LPCAT1 in LUAD progression was explored with the activator of PI3K/AKT pathway. RNA sequencing was performed to confirm the involvement of LPCAT1 and associated pathway in LUAD brain metastasis. Results LPCAT1 was up-regulated in LUAD tissues and cell lines. shRNA-mediated depletion of LPCAT1 not only abrogated cell proliferation, migration and invasion in vitro, but also arrested tumor growth and brain metastases in vivo. Notably, LPCAT1 at least partially influenced LUAD progression through PI3K/AKT signal pathway by targeting MYC transcription. Moreover, expression of LPCAT1 was higher in tissues of LUAD patients with BM than those without BM as revealed by IHC staining, RNA-Sequencing and qPCR analysis. Finally, elevated LPCAT1 expression in patients with lung adenocarcinomas was associated with a poor clinical outcome. Conclusions This study showed that LPCAT1 works as a regulator of cell metastasis and may serve as a novel therapeutic target for BM in lung adenocarcinoma. Electronic supplementary material The online version of this article (10.1186/s13046-019-1092-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chunhua Wei
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaomin Dong
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Hui Lu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fan Tong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lingjuan Chen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ruiguang Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jihua Dong
- Medical Research Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| |
Collapse
|
10
|
Long MD, Singh PK, Russell JR, Llimos G, Rosario S, Rizvi A, van den Berg PR, Kirk J, Sucheston-Campbell LE, Smiraglia DJ, Campbell MJ. The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression. Oncogene 2019; 38:421-444. [PMID: 30120411 PMCID: PMC6336686 DOI: 10.1038/s41388-018-0450-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/25/2018] [Accepted: 06/26/2018] [Indexed: 01/22/2023]
Abstract
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARγ) are commonly reduced in prostate cancer (PCa). Therefore, we sought to establish the cellular and gene regulatory consequences of reduced RARγ expression, and determine RARγ regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARγ levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARγ cistrome, which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARγ to regulate androgen signaling, RARγ knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARγ downregulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARγ expression and function. Capture of the miR-96 targetome by biotin-miR-96 identified that RARγ and a number of RARγ interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARγ target genes (e.g., SOX15) that significantly associated with worse disease-free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p = 0.015). In summary, miR-96 targets a RARγ network to govern AR signaling, PCa progression and disease outcome.
Collapse
MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/mortality
- Adenocarcinoma/pathology
- Androgens
- Animals
- Cell Line, Tumor
- Disease Progression
- Enhancer Elements, Genetic
- Fetal Proteins/metabolism
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Kaplan-Meier Estimate
- Male
- Mice
- MicroRNAs/physiology
- Microtubule-Associated Proteins/metabolism
- Neoplasm Proteins/physiology
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Neoplasms, Hormone-Dependent/mortality
- Neoplasms, Hormone-Dependent/pathology
- Nuclear Proteins/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/mortality
- Prostatic Neoplasms/pathology
- RNA Interference
- RNA, Neoplasm/physiology
- RNA, Small Interfering/genetics
- Receptors, Androgen/metabolism
- Receptors, Retinoic Acid/physiology
- Signal Transduction
- Retinoic Acid Receptor gamma
Collapse
Affiliation(s)
- Mark D Long
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Prashant K Singh
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - James R Russell
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Gerard Llimos
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Spencer Rosario
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R van den Berg
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
- Leiden institute of Physics, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Jason Kirk
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Lara E Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Dominic J Smiraglia
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 536 Parks Hall, Columbus, OH, 43210, USA.
| |
Collapse
|
11
|
Hanson C, Cairns J, Wang L, Sinha S. Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Res 2018; 28:1207-1216. [PMID: 29898900 PMCID: PMC6071639 DOI: 10.1101/gr.227066.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/31/2018] [Indexed: 12/12/2022]
Abstract
Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to reveal cis-regulatory mechanisms underlying phenotypic differences. In this study, we develop a new probabilistic model, called pGENMi, that integrates multi-omic data to investigate the transcriptional regulatory mechanisms underlying interindividual variation of a specific phenotype—that of cell line response to cytotoxic treatment. In particular, pGENMi simultaneously analyzes genotype, DNA methylation, gene expression, and transcription factor (TF)-DNA binding data, along with phenotypic measurements, to identify TFs regulating the phenotype. It does so by combining statistical information about expression quantitative trait loci (eQTLs) and expression-correlated methylation marks (eQTMs) located within TF binding sites, as well as observed correlations between gene expression and phenotype variation. Application of pGENMi to data from a panel of lymphoblastoid cell lines treated with 24 drugs, in conjunction with ENCODE TF ChIP data, yielded a number of known as well as novel (TF, Drug) associations. Experimental validations by TF knockdown confirmed 41% of the predicted and tested associations, compared to a 12% confirmation rate of tested nonassociations (controls). An extensive literature survey also corroborated 62% of the predicted associations above a stringent threshold. Moreover, associations predicted only when combining eQTL and eQTM data showed higher precision compared to an eQTL-only or eQTM-only analysis using pGENMi, further demonstrating the value of multi-omic integrative analysis.
Collapse
Affiliation(s)
- Casey Hanson
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Saurabh Sinha
- Department of Computer Science and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
12
|
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]
|
13
|
Abstract
The vitamin D receptor (VDR) binds the secosteroid hormone 1,25(OH)2D3 with high affinity and regulates gene programs that control a serum calcium levels, as well as cell proliferation and differentiation. A significant focus has been to exploit the VDR in cancer settings. Although preclinical studies have been strongly encouraging, to date clinical trials have delivered equivocal findings that have paused the clinical translation of these compounds. However, it is entirely possible that mining of genomic data will help to refine precisely what are the key anticancer actions of vitamin D compounds and where these can be used most effectively.
Collapse
Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 536 Parks Hall, Columbus, OH 43210, USA.
| | - Donald L Trump
- Department of Medicine, Inova Schar Cancer Institute, Virginia Commonwealth University, 3221 Gallows Road, Fairfax, VA 22031, USA
| |
Collapse
|
14
|
Avilés-Vázquez S, Chávez-González A, Hidalgo-Miranda A, Moreno-Lorenzana D, Arriaga-Pizano L, Sandoval-Esquivel MÁ, Ayala-Sánchez M, Aguilar R, Alfaro-Ruiz L, Mayani H. Global gene expression profiles of hematopoietic stem and progenitor cells from patients with chronic myeloid leukemia: the effect of in vitro culture with or without imatinib. Cancer Med 2017; 6:2942-2956. [PMID: 29030909 PMCID: PMC5727298 DOI: 10.1002/cam4.1187] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 01/04/2023] Open
Abstract
In this study, we determined the gene expression profiles of bone marrow‐derived cell fractions, obtained from normal subjects and Chronic Myeloid Leukemia (CML) patients, that were highly enriched for hematopoietic stem (HSCs) and progenitor (HPCs) cells. Our results indicate that the profiles of CML HSCs and HPCs were closer to that of normal progenitors, whereas normal HSCs showed the most different expression profile of all. We found that the expression profiles of HSCs and HPCs from CML marrow were closer to each other than those of HSCs and HPCs from normal marrow. The major biologic processes dysregulated in CML cells included DNA repair, cell cycle, chromosome condensation, cell adhesion, and the immune response. We also determined the genomic changes in both normal and CML progenitor cells under culture conditions, and found that several genes involved in cell cycle, steroid biosynthesis, and chromosome segregation were upregulated, whereas genes involved in transcription regulation and apoptosis were downregulated. Interestingly, these changes were the same, regardless of the addition of Imatinib (IM) to the culture. Finally, we identified three genes—PIEZO2, RXFP1, and MAMDC2‐ that are preferentially expressed by CML primitive cells and that encode for cell membrane proteins; thus, they could be used as biomarkers for CML stem cells.
Collapse
Affiliation(s)
- Sócrates Avilés-Vázquez
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Antonieta Chávez-González
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Dafne Moreno-Lorenzana
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Lourdes Arriaga-Pizano
- Immunochemistry Research Unit, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Miguel Á Sandoval-Esquivel
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Manuel Ayala-Sánchez
- Department of Hematology, La Raza Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Rafael Aguilar
- Department of Hip Surgery, Villa Coapa General Hospital, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Hector Mayani
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| |
Collapse
|
15
|
Campbell MJ. Bioinformatic approaches to interrogating vitamin D receptor signaling. Mol Cell Endocrinol 2017; 453:3-13. [PMID: 28288905 DOI: 10.1016/j.mce.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity. Integrative approaches can combine VDR ChIP-Seq in cell systems where significant volumes of publically available data are available. For example, VDR ChIP-Seq studies can be combined with genome-wide association studies to reveal significant associations to immune phenotypes. Similarly, VDR ChIP-Seq can be combined with data from Cancer Genome Atlas (TCGA) to infer the impact of VDR target genes in cancer progression. Therefore, bioinformatic approaches can reveal what aspects of VDR downstream networks are significantly related to disease or phenotype.
Collapse
Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, 536 Parks Hall, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
16
|
Maneix L, Catic A. Touch and go: nuclear proteolysis in the regulation of metabolic genes and cancer. FEBS Lett 2016; 590:908-23. [PMID: 26832397 PMCID: PMC4833644 DOI: 10.1002/1873-3468.12087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/15/2016] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The recruitment of transcription factors to promoters and enhancers is a critical step in gene regulation. Many of these proteins are quickly removed from DNA after they completed their function. Metabolic genes in particular are dynamically regulated and continuously adjusted to cellular requirements. Transcription factors controlling metabolism are therefore under constant surveillance by the ubiquitin–proteasome system, which can degrade DNA‐bound proteins in a site‐specific manner. Several of these metabolic transcription factors are critical to cancer cells, as they promote uncontrolled growth and proliferation. This review highlights recent findings in the emerging field of nuclear proteolysis and outlines novel paradigms for cancer treatment, with an emphasis on multiple myeloma.
Collapse
Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
17
|
Abstract
Nuclear receptors (NR) act as an integrated conduit for environmental and hormonal signals to govern genomic responses, which relate to cell fate decisions. We review how their integrated actions with each other, shared co-factors and other transcription factors are disrupted in cancer. Steroid hormone nuclear receptors are oncogenic drivers in breast and prostate cancer and blockade of signaling is a major therapeutic goal. By contrast to blockade of receptors, in other cancers enhanced receptor function is attractive, as illustrated initially with targeting of retinoic acid receptors in leukemia. In the post-genomic era large consortia, such as The Cancer Genome Atlas, have developed a remarkable volume of genomic data with which to examine multiple aspects of nuclear receptor status in a pan-cancer manner. Therefore to extend the review of NR function we have also undertaken bioinformatics analyses of NR expression in over 3000 tumors, spread across six different tumor types (bladder, breast, colon, head and neck, liver and prostate). Specifically, to ask how the NR expression was distorted (altered expression, mutation and CNV) we have applied bootstrapping approaches to simulate data for comparison, and also compared these NR findings to 12 other transcription factor families. Nuclear receptors were uniquely and uniformly downregulated across all six tumor types, more than predicted by chance. These approaches also revealed that each tumor type had a specific NR expression profile but these were most similar between breast and prostate cancer. Some NRs were down-regulated in at least five tumor types (e.g. NR3C2/MR and NR5A2/LRH-1)) whereas others were uniquely down-regulated in one tumor (e.g. NR1B3/RARG). The downregulation was not driven by copy number variation or mutation and epigenetic mechanisms maybe responsible for the altered nuclear receptor expression.
Collapse
Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| |
Collapse
|