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Yue B, Chen J, Bao T, Zhang Y, Yang L, Zhang Z, Wang Z, Zhu C. Chromosomal copy number amplification-driven Linc01711 contributes to gastric cancer progression through histone modification-mediated reprogramming of cholesterol metabolism. Gastric Cancer 2024; 27:308-323. [PMID: 38270815 DOI: 10.1007/s10120-023-01464-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Chromosome gains or localized amplifications are frequently observed in human gastric cancer (GC) and are major causes of aberrant oncogene activation. However, the significance of long non-coding RNAs (LncRNAs) in the above process is largely unknown. METHODS The copy number aberrations (CNAs) data of GC samples were downloaded and analyzed from the TCGA database. qRT-PCR and fluorescence in situ hybridization were used to evaluate the expression of Linc01711 in GC. The effects of Linc01711 on GC progression were investigated through in vitro and in vivo assays. The mechanism of Linc01711 action was explored through transcriptome sequencing, chromatin immunoprecipitation sequencing, RNA immunoprecipitation, RNA pull-down and chromatin isolation by RNA purification (ChIRP) assays. RESULTS We report for the first time a novel DNA copy number amplification-driven LncRNA on chromosome 20q13, designated Linc01711 in human GC, which is highly associated with malignant features. Functionally, Linc01711 significantly accelerates the proliferation and metastasis of GC. Mechanistically, Linc01711 acts as a modular scaffold to promote the binding of histone acetyltransferase HBO1 and histone demethylase KDM9. By coordinating the localization of the HBO1/KDM9 complex, Linc01711 specifies the histone modification pattern on the target genes, such as LPCAT1, and consequently facilitates the cholesterol synthesis, thereby contributing to tumor progression. CONCLUSIONS Our findings suggest that copy number amplification-driven Linc01711 may serve as a promising prognostic predictor for GC patients and targeting Linc01711-related cholesterol metabolism pathway may be meaningful in anticancer strategies.
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Affiliation(s)
- Ben Yue
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Jianjun Chen
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Tianshang Bao
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Yuanruohan Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Linxi Yang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
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Lee SHT, Kim JY, Kim P, Dong Z, Su CY, Ahn EH. Changes of Mutations and Copy-Number and Enhanced Cell Migration during Breast Tumorigenesis. Adv Biol (Weinh) 2023; 7:e2200072. [PMID: 36449747 PMCID: PMC10836759 DOI: 10.1002/adbi.202200072] [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: 03/16/2022] [Revised: 11/14/2022] [Indexed: 12/02/2022]
Abstract
Although cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost in in vitro cell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
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Affiliation(s)
- Seung Hyuk T. Lee
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Joon Yup Kim
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Peter Kim
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, USA
| | - Zhipeng Dong
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Chia-Yi Su
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Eun Hyun Ahn
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
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3
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Oncogene addiction to GNAS in GNAS R201 mutant tumors. Oncogene 2022; 41:4159-4168. [PMID: 35879396 DOI: 10.1038/s41388-022-02388-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/28/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
The GNASR201 gain-of-function mutation is the single most frequent cancer-causing mutation across all heterotrimeric G proteins, driving oncogenesis in various low-grade/benign gastrointestinal and pancreatic tumors. In this study, we investigated the role of GNAS and its product Gαs in tumor progression using peritoneal models of colorectal cancer (CRC). GNAS was knocked out in multiple CRC cell lines harboring GNASR201C/H mutations (KM12, SNU175, SKCO1), leading to decreased cell-growth in 2D and 3D organoid models. Nude mice were peritoneally injected with GNAS-knockout KM12 cells, leading to a decrease in tumor growth and drastically improved survival at 7 weeks. Supporting these findings, GNAS overexpression in LS174T cells led to increased cell-growth in 2D and 3D organoid models, and increased tumor growth in PDX mouse models. GNAS knockout decreased levels of cyclic AMP in KM12 cells, and molecular profiling identified phosphorylation of β-catenin and activation of its targets as critical downstream effects of mutant GNAS signaling. Supporting these findings, chemical inhibition of both PKA and β-catenin reduced growth of GNAS mutant organoids. Our findings demonstrate oncogene addiction to GNAS in peritoneal models of GNASR201C/H tumors, which signal through the cAMP/PKA and Wnt/β-catenin pathways. Thus, GNAS and its downstream mediators are promising therapeutic targets for GNAS mutant tumors.
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4
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Larasati Y, Boudou C, Koval A, Katanaev VL. Unlocking the Wnt pathway: Therapeutic potential of selective targeting FZD 7 in cancer. Drug Discov Today 2021; 27:777-792. [PMID: 34915171 DOI: 10.1016/j.drudis.2021.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/09/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
Abstract
The Wnt signaling is of paramount pathophysiological importance. Despite showing promising anticancer activities in pre-clinical studies, current Wnt pathway inhibitors face complications in clinical trials resulting from on-target toxicity. Hence, the targeting of pathway component(s) that are essential for cancer but dispensable for normal physiology is key to the development of a safe Wnt signaling inhibitor. Frizzled7 (FZD7) is a Wnt pathway receptor that is redundant in healthy tissues but crucial in various cancers. FZD7 modulates diverse aspects of carcinogenesis, including cancer growth, metastasis, maintenance of cancer stem cells, and chemoresistance. In this review, we describe state-of-the-art knowledge of the functions of FZD7 in carcinogenesis and adult tissue homeostasis. Next, we overview the development of small molecules and biomolecules that target FZD7. Finally, we discuss challenges and possibilities in developing FZD7-selective antagonists.
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Affiliation(s)
- Yonika Larasati
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Cédric Boudou
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia.
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5
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Verigos J, Kordias D, Papadaki S, Magklara A. Transcriptional Profiling of Tumorspheres Reveals TRPM4 as a Novel Stemness Regulator in Breast Cancer. Biomedicines 2021; 9:biomedicines9101368. [PMID: 34680485 PMCID: PMC8533210 DOI: 10.3390/biomedicines9101368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) have been implicated in the development of chemoresistance, tumor recurrence and metastasis in breast cancer, thus emerging as a promising target for novel therapies. To identify novel stemness regulators that could potentially be targeted in luminal ER+ tumors, we performed RNA-sequencing (RNA-seq) in MCF-7 adherent monolayer cells and tumorspheres enriched in breast CSCs (bCSCs). We identified 1421 differentially expressed genes (DEGs), with 923 of them being upregulated and 498 downregulated in tumorspheres. Gene ontology and pathway enrichment analyses revealed that distinct gene networks underlie the biology of the two cell systems. We selected the transient receptor potential cation channel subfamily M member 4 (TRPM4) gene that had not been associated with cancer stemness before for further investigation. We confirmed that TRPM4 was overexpressed in tumorspheres and showed that its knock-down affected the stemness properties of bCSCs in vitro. TRPM4 inhibition revealed potential anti-tumor effects by directly targeting the bCSC subpopulation. We suggest that TRPM4 plays a key role in stemness mediation, and its inhibition may represent a novel therapeutic modality against bCSCs contributing in the improvement of breast cancer treatments.
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Affiliation(s)
- John Verigos
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology, 45110 Ioannina, Greece; (J.V.); (D.K.)
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece;
| | - Dimitris Kordias
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology, 45110 Ioannina, Greece; (J.V.); (D.K.)
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece;
| | - Styliani Papadaki
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece;
| | - Angeliki Magklara
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology, 45110 Ioannina, Greece; (J.V.); (D.K.)
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece;
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
- Correspondence:
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Gong P, Xu Y, Liu M, Shen X, Mao Y, Li Y, Zhang K, Yu S, Fan H. Upregulation of LINC00659 expression predicts a poor prognosis and promotes migration and invasion of gastric cancer cells. Oncol Lett 2021; 22:557. [PMID: 34084224 PMCID: PMC8161466 DOI: 10.3892/ol.2021.12818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) serve an important role in the progression of cancer. LINC00659 was recently identified as a novel oncogenic lncRNA involved in colon cancer cell proliferation via modulating the cell cycle. However, the function of LINC00659 in other types of cancer, especially in gastric cancer (GC), remains unknown. In the present study, bioinformatics analysis combined with cell experiments were performed to explore the function of LINC00659 in GC. It was revealed that LINC00659 expression was significantly upregulated in GC tissues and cell lines. Increased levels of LINC00659 were associated with advanced tumor stage and unfavorable prognosis of patients with GC. Additionally, upregulated LINC00659 expression promoted the migration and invasion of GC cells. Further analysis using a bioinformatics method revealed that matrix metalloproteinase 15 and IQ motif-containing GTPase activating protein 3 were potential downstream targets of LINC00659 involved in tumor metastasis, although the precise underlying mechanism requires further exploration.
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Affiliation(s)
- Pihai Gong
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China.,School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Ying Xu
- School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Min Liu
- School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Xiaohui Shen
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yuhang Mao
- School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Yiping Li
- Department of Pathology, Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Kun Zhang
- Department of Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 154000, P.R. China
| | - Shenling Yu
- School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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7
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Nuñez FJ, Johnstone TB, Corpuz ML, Kazarian AG, Mohajer NN, Tliba O, Panettieri RA, Koziol-White C, Roosan MR, Ostrom RS. Glucocorticoids rapidly activate cAMP production via G αs to initiate non-genomic signaling that contributes to one-third of their canonical genomic effects. FASEB J 2019; 34:2882-2895. [PMID: 31908022 PMCID: PMC7027561 DOI: 10.1096/fj.201902521r] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/27/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
Abstract
Glucocorticoids are widely used for the suppression of inflammation, but evidence is growing that they can have rapid, non-genomic actions that have been unappreciated. Diverse cell signaling effects have been reported for glucocorticoids, leading us to hypothesize that glucocorticoids alone can swiftly increase the 3',5'-cyclic adenosine monophosphate (cAMP) production. We found that prednisone, fluticasone, budesonide, and progesterone each increased cAMP levels within 3 minutes without phosphodiesterase inhibitors by measuring real-time cAMP dynamics using the cAMP difference detector in situ assay in a variety of immortalized cell lines and primary human airway smooth muscle (HASM) cells. A membrane- impermeable glucocorticoid showed similarly rapid stimulation of cAMP, implying that responses are initiated at the cell surface. siRNA knockdown of Gαs virtually eliminated glucocorticoid-stimulated cAMP responses, suggesting that these drugs activate the cAMP production via a G protein-coupled receptor. Estradiol had small effects on cAMP levels but G protein estrogen receptor antagonists had little effect on responses to any of the glucocorticoids tested. The genomic and non-genomic actions of budesonide were analyzed by RNA-Seq analysis of 24 hours treated HASM, with and without knockdown of Gαs . A 140-gene budesonide signature was identified, of which 48 genes represent a non-genomic signature that requires Gαs signaling. Collectively, this non-genomic cAMP signaling modality contributes to one-third of the gene expression changes induced by glucocorticoid treatment and shifts the view of how this important class of drugs exerts its effects.
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Affiliation(s)
- Francisco J Nuñez
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Timothy B Johnstone
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Maia L Corpuz
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Austin G Kazarian
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Nicole N Mohajer
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Omar Tliba
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, USA
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Cynthia Koziol-White
- Rutgers Institute for Translational Medicine and Science, Child Health Institute, Rutgers University, New Brunswick, NJ, USA
| | - Moom R Roosan
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Rennolds S Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
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8
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Park S, Brugiolo M, Akerman M, Das S, Urbanski L, Geier A, Kesarwani AK, Fan M, Leclair N, Lin KT, Hu L, Hua I, George J, Muthuswamy SK, Krainer AR, Anczuków O. Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep 2019; 29:2672-2688.e7. [PMID: 31775037 PMCID: PMC6936330 DOI: 10.1016/j.celrep.2019.10.110] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Misregulation of alternative splicing is a hallmark of human tumors, yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer and uncover differences and redundancies in their targets and biological functions. We identify splicing factors frequently altered in human breast tumors and assay their oncogenic functions using breast organoid models. We demonstrate that not all splicing factors affect mammary tumorigenesis in MCF-10A cells. Specifically, the upregulation of SRSF4, SRSF6, or TRA2β disrupts acinar morphogenesis and promotes cell proliferation and invasion in MCF-10A cells. By characterizing the targets of these oncogenic splicing factors, we identify shared spliced isoforms associated with well-established cancer hallmarks. Finally, we demonstrate that TRA2β is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo, and its levels correlate with breast cancer patient survival.
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Affiliation(s)
- SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Mattia Brugiolo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Envisagenics Inc., New York, NY, USA,These authors contributed equally
| | - Shipra Das
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,These authors contributed equally
| | - Laura Urbanski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | | | | | - Martin Fan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nathan Leclair
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Leo Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ian Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Senthil K. Muthuswamy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Correspondence: (O.A.), (A.R.K.)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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9
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Metabolic Regulation of Glycolysis and AMP Activated Protein Kinase Pathways during Black Raspberry-Mediated Oral Cancer Chemoprevention. Metabolites 2019; 9:metabo9070140. [PMID: 31336728 PMCID: PMC6680978 DOI: 10.3390/metabo9070140] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/15/2019] [Accepted: 07/08/2019] [Indexed: 12/26/2022] Open
Abstract
Oral cancer is a public health problem with an incidence of almost 50,000 and a mortality of 10,000 each year in the USA alone. Black raspberries (BRBs) have been shown to inhibit oral carcinogenesis in several preclinical models, but our understanding of how BRB phytochemicals affect the metabolic pathways during oral carcinogenesis remains incomplete. We used a well-established rat oral cancer model to determine potential metabolic pathways impacted by BRBs during oral carcinogenesis. F344 rats were exposed to the oral carcinogen 4-nitroquinoline-1-oxide in drinking water for 14 weeks, then regular drinking water for six weeks. Carcinogen exposed rats were fed a 5% or 10% BRB supplemented diet or control diet for six weeks after carcinogen exposure. RNA-Seq transcriptome analysis on rat tongue, and mass spectrometry and NMR metabolomics analysis on rat urine were performed. We tentatively identified 57 differentially or uniquely expressed metabolites and over 662 modulated genes in rats being fed with BRB. Glycolysis and AMPK pathways were modulated during BRB-mediated oral cancer chemoprevention. Glycolytic enzymes Aldoa, Hk2, Tpi1, Pgam2, Pfkl, and Pkm2 as well as the PKA-AMPK pathway genes Prkaa2, Pde4a, Pde10a, Ywhag, and Crebbp were downregulated by BRBs during oral cancer chemoprevention. Furthermore, the glycolysis metabolite glucose-6-phosphate decreased in BRB-administered rats. Our data reveal the novel metabolic pathways modulated by BRB phytochemicals that can be targeted during the chemoprevention of oral cancer.
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10
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Möhlendick B, Schmid KW, Siffert W. The GNAS SNP c.393C>T (rs7121) as a marker for disease progression and survival in cancer. Pharmacogenomics 2019; 20:553-562. [PMID: 31124412 DOI: 10.2217/pgs-2018-0199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G-protein receptor signaling plays a key role in multiple signal transduction pathways. Aberrant activity of the stimulatory Gsα subunit has been frequently associated with cancer. GNAS sequence alterations and conformational changes of Gsα can both enhance or diminish its function and change downstream effects of G-protein receptor signaling. In this review and meta-analysis, we focus on the synonymous SNP rs7121 (FokI, c.393C>T), which is associated with either tumor progression or prolonged survival in cancer patients (overall hazard ratio = 2.256; p < 0.001). We finally point out the relevance of GNAS rs7121 as a promising biomarker and a prediction tool for therapy response and the need of further experiments to implement it into routine clinical diagnostics.
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Affiliation(s)
- Birte Möhlendick
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Kurt W Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany
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11
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Kim SY, Jeong HH, Kim J, Moon JH, Sohn KA. Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies. Biol Direct 2019; 14:8. [PMID: 31036036 PMCID: PMC6489180 DOI: 10.1186/s13062-019-0239-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/10/2019] [Indexed: 01/15/2023] Open
Abstract
Background Integrating the rich information from multi-omics data has been a popular approach to survival prediction and bio-marker identification for several cancer studies. To facilitate the integrative analysis of multiple genomic profiles, several studies have suggested utilizing pathway information rather than using individual genomic profiles. Methods We have recently proposed an integrative directed random walk-based method utilizing pathway information (iDRW) for more robust and effective genomic feature extraction. In this study, we applied iDRW to multiple genomic profiles for two different cancers, and designed a directed gene-gene graph which reflects the interaction between gene expression and copy number data. In the experiments, the performances of the iDRW method and four state-of-the-art pathway-based methods were compared using a survival prediction model which classifies samples into two survival groups. Results The results show that the integrative analysis guided by pathway information not only improves prediction performance, but also provides better biological insights into the top pathways and genes prioritized by the model in both the neuroblastoma and the breast cancer datasets. The pathways and genes selected by the iDRW method were shown to be related to the corresponding cancers. Conclusions In this study, we demonstrated the effectiveness of a directed random walk-based multi-omics data integration method applied to gene expression and copy number data for both breast cancer and neuroblastoma datasets. We revamped a directed gene-gene graph considering the impact of copy number variation on gene expression and redefined the weight initialization and gene-scoring method. The benchmark result for iDRW with four pathway-based methods demonstrated that the iDRW method improved survival prediction performance and jointly identified cancer-related pathways and genes for two different cancer datasets. Reviewers This article was reviewed by Helena Molina-Abril and Marta Hidalgo.
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Affiliation(s)
- So Yeon Kim
- Department of Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Hyun-Hwan Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Jaesik Kim
- Department of Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Jeong-Hyeon Moon
- Department of Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Kyung-Ah Sohn
- Department of Computer Engineering, Ajou University, Suwon, 16499, South Korea.
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12
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Elevated expression of GNAS promotes breast cancer cell proliferation and migration via the PI3K/AKT/Snail1/E-cadherin axis. Clin Transl Oncol 2019; 21:1207-1219. [PMID: 30767161 DOI: 10.1007/s12094-019-02042-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/14/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Although it has been well established that G protein plays pivotal roles in physiologic or pathologic conditions, including cancer formation, its role in breast cancer, especially specific subunits, remains largely unknown. Our work aimed to evaluate the correlation of the G protein alpha subunit (GNAS) with breast cancer and to investigate the underlying molecular mechanism. METHODS The expression of GNAS was determined by breast tumor tissue microarray of 150 patients with complete follow-up information. The correlation between GNAS expression and clinical features was assessed. CCK8, EdU incorporation, flow cytometry, wound healing, transwell, western blot and tumor formation assays were carried out in nude mice to study the biological function of GNAS and the underlying molecular mechanism in breast cancer by silencing GNAS using a specific siRNA. RESULTS High GNAS expression showed a close correlation with a reduced overall survival (p = 0.021), frequent distal metastasis (p = 0.026), advanced clinical stage (p = 0.001), stronger cell proliferation (ki67+ positive cell rate, p = 0.0351) and enhanced cancer cell migration, which was further confirmed by in vitro and in vivo assays and might be dependent on the PI3K/AKT/Snail1/E-cadherin axis. CONCLUSION The data suggested that GNAS promoted breast cancer cell proliferation and migration (EMT) through the PI3K/AKT/Snail1/E-cadherin signaling pathway. These findings also indicate that GNAS can serve as a potential prognostic indicator and novel therapeutic target in breast cancer.
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Kechavarzi BD, Wu H, Doman TN. Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA. PLoS One 2019; 14:e0210910. [PMID: 30653567 PMCID: PMC6336338 DOI: 10.1371/journal.pone.0210910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022] Open
Abstract
The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions.
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Affiliation(s)
- Bobak D. Kechavarzi
- Indiana University Purdue University Indianapolis, School of Informatics and Computing, Indianapolis, IN, United States of America
- Eli Lilly, Indianapolis, IN, United States of America
- * E-mail:
| | - Huanmei Wu
- Indiana University Purdue University Indianapolis, School of Informatics and Computing, Indianapolis, IN, United States of America
| | - Thompson N. Doman
- Indiana University Purdue University Indianapolis, School of Informatics and Computing, Indianapolis, IN, United States of America
- Eli Lilly, Indianapolis, IN, United States of America
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14
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Teng H, Gao R, Qin N, Jiang X, Ren M, Wang Y, Wu S, Li N, Zhao J, Qin H. Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China. Mol Med Rep 2018; 18:5361-5370. [PMID: 30365144 PMCID: PMC6236297 DOI: 10.3892/mmr.2018.9563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.
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Affiliation(s)
- Hongfei Teng
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Renyuan Gao
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Nan Qin
- Department of Gut Microbiota Diagnosis and Treatment, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Xun Jiang
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Min Ren
- Department of Medicine, Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201204, P.R. China
| | - Yu Wang
- Department of Medicine, Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201204, P.R. China
| | - Shouxin Wu
- Department of Medicine, Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201204, P.R. China
| | - Ning Li
- Department of Gut Microbiota Diagnosis and Treatment, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Jiangman Zhao
- Department of Medicine, Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201204, P.R. China
| | - Huanlong Qin
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
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15
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Ma L, Liang Z, Zhou H, Qu L. Applications of RNA Indexes for Precision Oncology in Breast Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:108-119. [PMID: 29753129 PMCID: PMC6112337 DOI: 10.1016/j.gpb.2018.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/25/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
Precision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In this review, we take breast cancer as an example to demonstrate the applications of these rich RNA resources in precision medicine exploration. These include the use of mRNA profiles in triple-negative breast cancer (TNBC) subtyping to inform corresponding candidate targeted therapies; current advancements and achievements of high-throughput RNA interference (RNAi) screening technologies in breast cancer; and microRNAs as functional signatures for defining cell identities and regulating the biological activities of breast cancer cells. We summarize the benefits of transcriptomic analyses in breast cancer management and propose that unscrambling the core signaling networks of cancer may be an important task of multiple-omic data integration for precision oncology.
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Affiliation(s)
- Liming Ma
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zirui Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Lianghu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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16
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Chen YC, Gotea V, Margolin G, Elnitski L. Significant associations between driver gene mutations and DNA methylation alterations across many cancer types. PLoS Comput Biol 2017; 13:e1005840. [PMID: 29125844 PMCID: PMC5709060 DOI: 10.1371/journal.pcbi.1005840] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/30/2017] [Accepted: 10/23/2017] [Indexed: 12/15/2022] Open
Abstract
Recent evidence shows that mutations in several driver genes can cause aberrant methylation patterns, a hallmark of cancer. In light of these findings, we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected. We measured this relationship using principal component analyses and methylation-mutation associations applied at the nucleotide level and with respect to genome-wide trends. We found that a few mutated driver genes were associated with genome-wide patterns of aberrant hypomethylation or CpG island hypermethylation in specific cancer types. In addition, we identified associations between 737 mutated driver genes and site-specific methylation changes. Moreover, using these mutation-methylation associations, we were able to distinguish between two uterine and two thyroid cancer subtypes. The driver gene mutation–associated methylation differences between the thyroid cancer subtypes were linked to differential gene expression in JAK-STAT signaling, NADPH oxidation, and other cancer-related pathways. These results establish that driver gene mutations are associated with methylation alterations capable of shaping regulatory network functions. In addition, the methodology presented here can be used to subdivide tumors into more homogeneous subsets corresponding to underlying molecular characteristics, which could improve treatment efficacy. Mutations that alter the function of driver genes by changing DNA nucleotides have been recognized as key players in cancer progression. However, recent evidence has shown that DNA methylation, which can control gene expression, is also highly dysregulated in cancer and contributes to carcinogenesis. Whether methylation alterations correspond to mutated driver genes in cancer remains unclear. In this study, we analyzed 4,302 tumors from 18 cancer types and demonstrated that driver gene mutations are inherently connected with the aberrant DNA methylation landscape in cancer. We showed that driver gene–associated methylation patterns can classify heterogeneous tumors within a cancer type into homogeneous subtypes and have the potential to influence genes that contribute to tumor growth. This finding could help us better understand the fundamental connection between driver gene mutations and DNA methylation alterations in cancer, and to further improve cancer treatment.
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Affiliation(s)
- Yun-Ching Chen
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Valer Gotea
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Gennady Margolin
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Laura Elnitski
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States
- * E-mail:
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17
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Large G protein α-subunit XLαs limits clathrin-mediated endocytosis and regulates tissue iron levels in vivo. Proc Natl Acad Sci U S A 2017; 114:E9559-E9568. [PMID: 29078380 DOI: 10.1073/pnas.1712670114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Alterations in the activity/levels of the extralarge G protein α-subunit (XLαs) are implicated in various human disorders, such as perinatal growth retardation. Encoded by GNAS, XLαs is partly identical to the α-subunit of the stimulatory G protein (Gsα), but the cellular actions of XLαs remain poorly defined. Following an initial proteomic screen, we identified sorting nexin-9 (SNX9) and dynamins, key components of clathrin-mediated endocytosis, as binding partners of XLαs. Overexpression of XLαs in HEK293 cells inhibited internalization of transferrin, a process that depends on clathrin-mediated endocytosis, while its ablation by CRISPR/Cas9 in an osteocyte-like cell line (Ocy454) enhanced it. Similarly, primary cardiomyocytes derived from XLαs knockout (XLKO) pups showed enhanced transferrin internalization. Early postnatal XLKO mice showed a significantly higher degree of cardiac iron uptake than wild-type littermates following iron dextran injection. In XLKO neonates, iron and ferritin levels were elevated in heart and skeletal muscle, where XLαs is normally expressed abundantly. XLKO heart and skeletal muscle, as well as XLKO Ocy454 cells, showed elevated SNX9 protein levels, and siRNA-mediated knockdown of SNX9 in XLKO Ocy454 cells prevented enhanced transferrin internalization. In transfected cells, XLαs also inhibited internalization of the parathyroid hormone and type 2 vasopressin receptors. Internalization of transferrin and these G protein-coupled receptors was also inhibited in cells expressing an XLαs mutant missing the Gα portion, but not Gsα or an N-terminally truncated XLαs mutant unable to interact with SNX9 or dynamin. Thus, XLαs restricts clathrin-mediated endocytosis and plays a critical role in iron/transferrin uptake in vivo.
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18
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Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z. Reconstructing cancer drug response networks using multitask learning. BMC SYSTEMS BIOLOGY 2017; 11:96. [PMID: 29017547 PMCID: PMC5635550 DOI: 10.1186/s12918-017-0471-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to reconstruct drug specific response networks in cancer. RESULTS The reconstructed networks correctly identify several shared key proteins and pathways while simultaneously highlighting many cell type specific proteins. We used top proteins from each drug network to predict survival for patients prescribed the drug. CONCLUSIONS Predictions based on proteins from the in-vitro derived networks significantly outperformed predictions based on known cancer genes indicating that Multi-Task learning can indeed identify accurate drug response networks.
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Affiliation(s)
- Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Petar Stojanov
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Venkata Krishna Pillutla
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rohan Varma
- Electrical and Computer Engineering, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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19
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Bastepe M, Turan S, He Q. Heterotrimeric G proteins in the control of parathyroid hormone actions. J Mol Endocrinol 2017; 58:R203-R224. [PMID: 28363951 PMCID: PMC5650080 DOI: 10.1530/jme-16-0221] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/17/2017] [Indexed: 12/17/2022]
Abstract
Parathyroid hormone (PTH) is a key regulator of skeletal physiology and calcium and phosphate homeostasis. It acts on bone and kidney to stimulate bone turnover, increase the circulating levels of 1,25 dihydroxyvitamin D and calcium and inhibit the reabsorption of phosphate from the glomerular filtrate. Dysregulated PTH actions contribute to or are the cause of several endocrine disorders. This calciotropic hormone exerts its actions via binding to the PTH/PTH-related peptide receptor (PTH1R), which couples to multiple heterotrimeric G proteins, including Gs and Gq/11 Genetic mutations affecting the activity or expression of the alpha-subunit of Gs, encoded by the GNAS complex locus, are responsible for several human diseases for which the clinical findings result, at least partly, from aberrant PTH signaling. Here, we review the bone and renal actions of PTH with respect to the different signaling pathways downstream of these G proteins, as well as the disorders caused by GNAS mutations.
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Affiliation(s)
- Murat Bastepe
- Endocrine UnitDepartment of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Serap Turan
- Department of Pediatric EndocrinologyMarmara University School of Medicine, Istanbul, Turkey
| | - Qing He
- Endocrine UnitDepartment of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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20
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Benza RL, Gomberg-Maitland M, Demarco T, Frost AE, Torbicki A, Langleben D, Pulido T, Correa-Jaque P, Passineau MJ, Wiener HW, Tamari M, Hirota T, Kubo M, Tiwari HK. Endothelin-1 Pathway Polymorphisms and Outcomes in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2016; 192:1345-54. [PMID: 26252367 DOI: 10.1164/rccm.201501-0196oc] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RATIONALE Pulmonary arterial hypertension (PAH) is a progressive fatal disease. Variable response and tolerability to PAH therapeutics suggests that genetic differences may influence outcomes. The endothelin pathway is central to pulmonary vascular function, and several polymorphisms and/or mutations in the genes coding for endothelin (ET)-1 and its receptors correlate with the clinical manifestations of other diseases. OBJECTIVES To examine the interaction of ET-1 pathway polymorphisms and treatment responses of patients with PAH treated with ET receptor antagonists (ERAs). METHODS A total of 1,198 patients with PAH were prospectively enrolled from 45 U.S. and Canadian pulmonary hypertension centers or retrospectively from global sites participating in the STRIDE (Sitaxsentan To Relieve Impaired Exercise) trials. Comprehensive objective measures including a 6-minute-walk test, Borg dyspnea score, functional class, and laboratory studies were completed at baseline, before the initiation of ERAs, and repeated serially. Single-nucleotide polymorphisms from ET-1 pathway candidate genes were selected from a completed genome-wide association study performed on the study cohort. MEASUREMENTS AND MAIN RESULTS Patient efficacy outcomes were analyzed for a relationship between ET-1 pathway polymorphisms and clinical efficacy using predefined, composite positive and negative outcome measures in 715 European descent samples. A single-nucleotide polymorphism (rs11157866) in the G-protein alpha and gamma subunits gene was significantly associated, accounting for multiple testing, with a combined improvement in functional class and 6-minute-walk distance at 12 and 18 months and marginally significant at 24 months. CONCLUSIONS ET-1 pathway associated polymorphisms may influence the clinical efficacy of ERA therapy for PAH. Further prospective studies are needed.
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Affiliation(s)
- Raymond L Benza
- 1 Division of Cardiovascular Disease, Department of Medicine, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | - Mardi Gomberg-Maitland
- 2 Division of Cardiovascular Disease, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Teresa Demarco
- 3 Division of Cardiovascular Disease, Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Adam Torbicki
- 5 Department of Pulmonary Circulation and Thromboembolic Diseases, Centre of Postgraduate Medical Education, ECZ, Otwock, Poland
| | - David Langleben
- 6 Department of Medicine, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, Canada
| | - Tomas Pulido
- 7 Cardiopulmonary Department, National Heart Institute, Mexico City, Mexico
| | - Priscilla Correa-Jaque
- 1 Division of Cardiovascular Disease, Department of Medicine, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | - Michael J Passineau
- 1 Division of Cardiovascular Disease, Department of Medicine, Allegheny General Hospital, Pittsburgh, Pennsylvania
| | | | - Mayumi Tamari
- 9 Institute of Physical and Chemical Research (RIKEN), Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomomitsu Hirota
- 9 Institute of Physical and Chemical Research (RIKEN), Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- 9 Institute of Physical and Chemical Research (RIKEN), Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hemant K Tiwari
- 10 Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama; and
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21
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Copy number analysis of ductal carcinoma in situ with and without recurrence. Mod Pathol 2015; 28:1174-84. [PMID: 26321097 DOI: 10.1038/modpathol.2015.75] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 11/08/2022]
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer and a frequent mammographic finding requiring treatment. Up to 25% of DCIS can recur and half of recurrences are invasive, but there are no reliable biomarkers for recurrence. We hypothesised that copy number aberrations could predict likelihood of recurrence. We analysed a cohort of pure DCIS cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan MIP arrays. Cases included those without recurrence within 7 years (n = 25) and with recurrence between 1 and 5 years after diagnosis (n = 15). Pure DCIS were broadly similar in copy number changes compared with invasive breast cancer, with the consistent exception of a greater frequency of ERBB2 amplification in DCIS. There were no significant differences in age or ER status between the cases with a recurrence vs those without. Overall, the DCIS cases with recurrence had more copy number events than the DCIS without recurrence. The increased copy number appeared non-random with several genomic regions showing an increase in frequency in recurrent cases, including 20 q gain, ERBB2 amplification and 15q loss. Copy number changes may provide prognostic information for DCIS recurrence, but validation in additional cohorts is required.
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He Q, Zhu Y, Corbin BA, Plagge A, Bastepe M. The G protein α subunit variant XLαs promotes inositol 1,4,5-trisphosphate signaling and mediates the renal actions of parathyroid hormone in vivo. Sci Signal 2015; 8:ra84. [PMID: 26307011 DOI: 10.1126/scisignal.aaa9953] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
GNAS, which encodes the stimulatory G protein (heterotrimeric guanine nucleotide-binding protein) α subunit (Gαs), also encodes a large variant of Gαs termed extra-large α subunit (XLαs), and alterations in XLαs abundance or activity are implicated in various human disorders. Although XLαs, like Gαs, stimulates generation of the second messenger cyclic adenosine monophosphate (cAMP), evidence suggests that XLαs and Gαs have opposing effects in vivo. We investigated the role of XLαs in mediating signaling by parathyroid hormone (PTH), which activates a G protein-coupled receptor (GPCR) that stimulates both Gαs and Gαq/11 in renal proximal tubules to maintain phosphate and vitamin D homeostasis. At postnatal day 2 (P2), XLαs knockout (XLKO) mice exhibited hyperphosphatemia, hypocalcemia, and increased serum concentrations of PTH and 1,25-dihydroxyvitamin D. The ability of PTH to reduce serum phosphate concentrations was impaired, and the abundance of the sodium phosphate cotransporter Npt2a in renal brush border membranes was reduced in XLKO mice, whereas PTH-induced cAMP excretion in the urine was modestly increased. Basal and PTH-stimulated production of inositol 1,4,5-trisphosphate (IP3), which is the second messenger produced by Gαq/11 signaling, was repressed in renal proximal tubules from XLKO mice. Crossing of XLKO mice with mice overexpressing XLαs specifically in renal proximal tubules rescued the phenotype of the XLKO mice. Overexpression of XLαs in HEK 293 cells enhanced IP3 generation in unstimulated cells and in cells stimulated with PTH or thrombin, which acts through a Gq/11-coupled receptor. Together, our findings suggest that XLαs enhances Gq/11 signaling to mediate the renal actions of PTH during early postnatal development.
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Affiliation(s)
- Qing He
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yan Zhu
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Braden A Corbin
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Antonius Plagge
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine University of Liverpool, Liverpool L69 3BX, UK
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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Abstract
The GNAS complex locus encodes the alpha-subunit of the stimulatory G protein (Gsα), a ubiquitous signaling protein mediating the actions of many hormones, neurotransmitters, and paracrine/autocrine factors via generation of the second messenger cAMP. GNAS gives rise to other gene products, most of which exhibit exclusively monoallelic expression. In contrast, Gsα is expressed biallelically in most tissues; however, paternal Gsα expression is silenced in a small number of tissues through as-yet-poorly understood mechanisms that involve differential methylation within GNAS. Gsα-coding GNAS mutations that lead to diminished Gsα expression and/or function result in Albright's hereditary osteodystrophy (AHO) with or without hormone resistance, i.e., pseudohypoparathyroidism type-Ia/Ic and pseudo-pseudohypoparathyroidism, respectively. Microdeletions that alter GNAS methylation and, thereby, diminish Gsα expression in tissues in which the paternal Gsα allele is normally silenced also cause hormone resistance, which occurs typically in the absence of AHO, a disorder termed pseudohypoparathyroidism type-Ib. Mutations of GNAS that cause constitutive Gsα signaling are found in patients with McCune-Albright syndrome, fibrous dysplasia of bone, and different endocrine and non-endocrine tumors. Clinical features of these diseases depend significantly on the parental allelic origin of the GNAS mutation, reflecting the tissue-specific paternal Gsα silencing. In this article, we review the pathogenesis and the phenotypes of these human diseases.
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Affiliation(s)
- Serap Turan
- Pediatric Endocrinology, Marmara University School of Medicine Hospital, Istanbul, Turkey;
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114;
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Guest ST, Kratche ZR, Bollig-Fischer A, Haddad R, Ethier SP. Two members of the TRiC chaperonin complex, CCT2 and TCP1 are essential for survival of breast cancer cells and are linked to driving oncogenes. Exp Cell Res 2015; 332:223-35. [DOI: 10.1016/j.yexcr.2015.02.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/02/2015] [Accepted: 02/07/2015] [Indexed: 11/26/2022]
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25
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Kougioumtzi A, Tsaparas P, Magklara A. Deep sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells. PLoS One 2014; 9:e98404. [PMID: 24897521 PMCID: PMC4045674 DOI: 10.1371/journal.pone.0098404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Despite the pleiotropic effects of the progesterone receptor in breast cancer, the molecular mechanisms in play remain largely unknown. To gain a global view of the PR-orchestrated networks, we used next-generation sequencing to determine the progestin-regulated transcriptome in T47D breast cancer cells. We identify a large number of PR target genes involved in critical cellular programs, such as regulation of transcription, apoptosis, cell motion and angiogenesis. Integration of the transcriptomic data with the PR-binding profiling of hormonally treated cells identifies numerous components of the small-GTPases signaling pathways as direct PR targets. Progestin-induced deregulation of the small GTPases may contribute to the PR's role in mammary tumorigenesis. Transcript expression analysis reveals significant expression changes of specific transcript variants in response to the extracellular hormonal stimulus. Using the NET1 gene as an example, we show that the PR can dictate alternative promoter usage leading to the upregulation of an isoform that may play a role in metastatic breast cancer. Future studies should aim to characterize these selectively regulated variants and evaluate their clinical utility in prognosis and targeted therapy of hormonally responsive breast tumors.
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Affiliation(s)
- Anastasia Kougioumtzi
- Department of Biological Applications and Technologies, University of Ioannina, Ioannina, Greece
| | - Panayiotis Tsaparas
- Department of Computer Science and Engineering, University of Ioannina, Ioannina, Greece
| | - Angeliki Magklara
- Laboratory of Clinical Chemistry, School of Medicine, University of Ioannina, Ioannina, Greece
- Foundation of Research and Technology-Hellas, Institute of Molecular Biology & Biotechnology, Department of Biomedical Research, Ioannina, Greece
- * E-mail:
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